@article {96619, title = {Antiviral therapeutics directed against RNA dependent RNA polymerases from positive-sense viruses.}, journal = {Mol Aspects Med}, year = {2021}, month = {2021 Jul 24}, pages = {101005}, abstract = {

Viruses with positive-sense single stranded RNA (+ssRNA) genomes are responsible for different diseases and represent a global health problem. In addition to developing new vaccines that protect against severe illness on infection, it is imperative to identify new antiviral molecules to treat infected patients. The genome of these RNA viruses generally codes for an enzyme with RNA dependent RNA polymerase (RdRP) activity. This molecule is centrally involved in the duplication of the RNA genome. Inhibition of this enzyme by small molecules will prevent duplication of the RNA genome and thus reduce the viral titer. An overview of the different therapeutic strategies used to inhibit RdRPs from +ssRNA viruses is provided, along with an analysis of these enzymes to highlight new binding sites for inhibitors.

}, issn = {1872-9452}, doi = {10.1016/j.mam.2021.101005}, author = {Bhatia, Sonam and Narayanan, Naveen and Nagpal, Shilpi and Nair, Deepak T} } @article {3559, title = {Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators.}, journal = {J Biol Chem}, volume = {291}, year = {2016}, month = {2016 Jan 15}, pages = {1235-42}, abstract = {

Transcription factor-DNA interactions are central to gene regulation. Many transcription factors regulate multiple target genes and can bind sequences that do not conform strictly to the consensus. To understand the structural mechanism utilized by the transcription regulators to bind diverse target sequences, we have employed the repressor AraR from Bacillus subtilis as a model system. AraR is known to bind to eight different operator sites in the bacterial genome. Although there are differences in the sequences of four of these operators, ORE1, ORX1, ORA1, and ORR3, the AraR-DNA binding domain (AraR-DBD) as well as full-length AraR unexpectedly binds to each of these sequences with similar affinities as measured by fluorescence anisotropy experiments. We have determined crystal structures of AraR-DBD in complex with two different natural operators ORE1 and ORX1 up to 2.07 and 1.97 {\r A} resolution, respectively. These structures were compared with the previously reported structures of AraR-DBD bound to two other natural operators (ORA1 and ORR3). Interactions of two molecules of AraR-DBD with the symmetric operator, ORE1, are identical, but their interaction with the non-symmetric operator ORX1 results in breakdown of the symmetry in protein-DNA interactions. The novel interactions observed are accompanied by local conformational change in the DNA. ChIP-sequencing (ChIP-Seq) data on other transcription factors has shown that they can bind to diverse targets, and hence the plasticity exhibited by AraR may be a general phenomenon. The ability of transcription factors to form alternate interactions may be important for employment in new functions and evolution of novel regulatory circuits.

}, issn = {1083-351X}, doi = {10.1074/jbc.M115.689695}, author = {Jain, Deepti and Narayanan, Naveen and Nair, Deepak T} } @article {856, title = {Unique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic.}, journal = {Structure}, volume = {23}, year = {2015}, month = {2015 Jan 6}, pages = {56-67}, abstract = {

The reduction in the efficacy of therapeutic antibiotics represents a global problem of increasing intensity and concern. Nitrofuran antibiotics act primarily through the formation of covalent adducts at the N(2) atom of the deoxyguanosine nucleotide in genomic DNA. These adducts inhibit replicative DNA polymerases (dPols), leading to the death of the prokaryote. N(2)-furfuryl-deoxyguanosine (fdG) represents a stable structural analog of the nitrofuran-induced adducts. Unlike other known dPols, DNA polymerase IV (PolIV) from E.\ coli can bypass the fdG adduct accurately with high catalytic efficiency. This property of PolIV is central to its role in reducing the sensitivity of E.\ coli toward nitrofuran antibiotics such as nitrofurazone (NFZ). We present the mechanism used by PolIV to bypass NFZ-induced adducts and thus improve viability of E.\ coli in the presence of NFZ. Our results can be used to develop specific inhibitors of PolIV that may potentiate the activity of nitrofuran antibiotics.

}, keywords = {Anti-Bacterial Agents, Crystallography, X-Ray, DNA Adducts, DNA Polymerase beta, Drug Resistance, Bacterial, Escherichia coli, Escherichia coli Proteins, Models, Molecular, Nitrofurazone, Nitrogen Compounds, Protein Structure, Tertiary, Reactive Nitrogen Species}, issn = {1878-4186}, doi = {10.1016/j.str.2014.10.019}, author = {Kottur, Jithesh and Sharma, Amit and Gore, Kiran R and Narayanan, Naveen and Samanta, Biswajit and Pradeepkumar, Pushpangadan I and Nair, Deepak T} }