DNA Base Excision Repair (BER)
DNA repair and recombination are essential processes for an organism.
J. Biol. Chem.280, 30273-30281, 2005;
Nucleic Acids Res. 33, 7090-7101, 2005;
PROTEINS:69, 97-111, 2007;
Organic & Biomolecular Chemistry, 13, 5475-5487, 2015;
Nucleic Acids Research. 48, 4325-4343, 2020
Our work on important mycobacterial components from the DNA Base Excision Repair (BER) pathway has demonstrated the existence of large multimolecular assemblies (BERosomes) that function in this pathway. We showed that XthA, an exonuclease, exhibits DNA regulated modes of interaction with the β-clamp, and also that it is possible to specifically disrupt the interactions using small molecules and peptides.
Mol. Microbiol. 98, 46-68, 2015
Our studies have led to the identification of new classes of inhibitors that exhibit anti-bacterial specificity and distinguish the human enzyme several fold, both in vitro and in LigA-deficient strains.
Nucleic Acids Research. 48, 4325-4343, 2020
Importantly, we have shown that XthA engages with LigA to counter futile cleavage and ligation cycles in DNA Base Excision Repair (BER).
Feast/ Famine regulation
Feast/ famine regulatory proteins (FFRPs) apparently help bacteria to switch/ adapt from 'Feast' to 'Famine' state. We showed that the rarely observed ‘open’ quaternary structure is important for the proteins to bind to non-symmetric target DNA sites.
Nucleic Acids Res. 35, 7324-7335, 2007;
J. Mol. Biol.392, 1007-1019, 2009;
J. Biol. Chem. 291, 11967-11980, 2016
We also suggested how mycobacterial FFRP can form nucleosome-like particles, and how effector-binding events can trigger specific regulatory outcomes. First-in-class small-molecule inhibitors have been identified by our group against an FFRP
Host-pathogen interactions involving Mtb SerB2
We identified new functions for an essential mycobacterial HAD phosphatase, SerB2. Using Broncho Alveolar Lavage (BAL) samples from TB patients, we showed that it is secreted and mediates host-pathogen interactions.
PLoS ONE. 9(12): e115409. doi: 10.1371/journal.pone.0115409, 2014
Cell. Mol. Life Sci. 73, 3401-3417, 2016
Subsequently we identified several small-molecule inhibitors for it, including Clofazimine that is being evaluated in clinical trials against drug resistant TB by the Global TB alliance. The results excitingly demonstrate that SerB2 is a target for riminophenazines being evaluated clinically. A translational output in this context is that an agreement with the 'Global TB Alliance' was signed by our group/ CSIR-CDRI for evaluating such compounds. Our group is presently evaluating the implications of interactions of SerB2 with host proteins in detail.
Glutamate ‘switch’ mechanism in aminotransferases
Another important contribution from my group involves identification of direct evidence for a glutamate ‘switch’ mechanism to operate in a sub-class of aminotransferases, and structure-function studies on mycobacterial factors like Lysine ε-aminotansferase (MtbLAT) and L-Alanine dehydrogenase (MtbALD) that are thought to be important for adaptation/maintenance of tuberculosis persistence/latency [25, 35].
J. Mol. Biol. 362, 877-886, 2006
They were incidentally ranked among the top-3 targets against tuberculosis persistence by the TB-Structural-Genomics Consortium [PLOS Comp. Biol. 2, 539-550, 2006]. The results were exploited to identify the very first inhibitors of MtbLAT using structure-based approaches (Biochem Biophys Res Commun 463, 154-160, 2015).
Type VII/ Esx secretion pathway
EccA-type proteins are essential for secretion of the virulence factors through Esx/ Type VII secretion pathways.
Adapted from J. Biol. Chem.,283, 36532-36541, 2008
Our work suggests how EccA proteins transfer energy to other secretion system components and blocking the activity of these proteins can prevent the export of critical virulence factors. Our characterization showed that EccA1-like proteins are novel members of a previously uncharacterised CbbX/CfqX family of AAA-ATPases (Biochim.Biophys. Acta 1834, 1181-1186).
Sigma and anti-sigma factors
Our work on sigma factors and associated proteins like UsfX, SigF and RsfA demonstrates that these mycobacterial factors are exquisitely regulated. We showed that RsfA's binding to UsfX is triggered by reduction of an intra-chain disulphide bond and also that the complex has an unusual 2:1 stoichiometry in mycobacteria. These novel properties form a framework for new therapy development.
Host pathogen interactions involving Viruses:
Viruses hijack the hosts’s replication system and also modulate the host pathways to elicit various effects including immune modulation.
⦁ HIV-1 Nef is known to play a pivotal role in HIV pathogenesis and binds to different protein partners in lower and higher oligomeric states respectively.
PLoS ONE 6(11): e26629. doi:10.1371/journal.pone.0026629, 2011
Our work on HIV-1 Nef derived from patient samples, identified the only known instance of a structural transition from a dimer to a tetramer with 4-fold symmetry. The functional implications of this unique transition are in an elegant mechanism where HIV-1 Nef in the dimeric state binds to a set of protein partners that are subsequently excluded from associating with the protein at higher oligomeric states due to the change in the subunit association. Subsequently, we rationally identified inhibitors with a new mode of action that work by disrupting specific HIV-1 Nef–co-protein interactions [PCT patent granted].
⦁ Work on viruses like SARS COV2 & Japanese Encephalitis has been initiated.
Drug repurposing studies:
Drug repurposing often offers quick and rapid therapeutic intervention where existing drugs have problems like resistance issues or where no drug is available against a disease condition.
⦁ My group, as part of team-CDRI, has been involved in repurposing of a drug against Chronic Myeloid Leukemia (CML). This has several advantages over existing Bcr-abl tyrosine kinase inhibitors (TKI) like Dasatinib, Imatinib, etc. It eliminates drug resistance arising from Leukemia stem cells (LSC) when used in combination with TKI. Filing for Phase-2 clinical trials is underway [Patent filed].
⦁ Other studies are ongoing to repurpose drugs against SARS COV2