Jithesh Kottur
@iav.kerala.gov.in
Scientist C, Department of Antiviral Drug Research
Institute of Advanced Virology, Trivandrum
RESEARCH, TEACHING, or OTHER INTERESTS
Molecular Biology, Structural Biology, Biophysics, Biochemistry
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Xufen Yu, Dongxu Li, Jithesh Kottur, Huen Suk Kim, Laura E. Herring, Yao Yu, Ling Xie, Xiaoping Hu, Xian Chen, Ling Cai,et al.
American Chemical Society (ACS)
As a core chromatin-regulatory scaffolding protein, WDR5 mediates numerous protein-protein interactions (PPIs) with other partner oncoproteins. However, small-molecule inhibitors that block these PPIs exert limited cell-killing effects. Here, we report structure-activity relationship studies in pancreatic ductal adenocarcinoma (PDAC) cells that led to the discovery of several WDR5 proteolysis-targeting chimer (PROTAC) degraders, including 11 (MS132), a highly potent and selective von Hippel-Lindau (VHL)-recruiting WDR5 degrader, which displayed positive binding cooperativity between WDR5 and VHL, effectively inhibited proliferation in PDAC cells, and was bioavailable in mice and 25, a cereblon (CRBN)-recruiting WDR5 degrader, which selectively degraded WDR5 over the CRBN neo-substrate IKZF1. Furthermore, by conducting site-directed mutagenesis studies, we determined that WDR5 K296, but not K32, was involved in the PROTAC-induced WDR5 degradation. Collectively, these studies resulted in a highly effective WDR5 degrader, which could be a potential therapeutic for pancreatic cancer and several potentially useful tool compounds.
Jithesh Kottur, Kris M. White, M. Luis Rodriguez, Olga Rechkoblit, Richard Quintana-Feliciano, Ahana Nayar, Adolfo García-Sastre, and Aneel K. Aggarwal
Public Library of Science (PLoS)
The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2’s nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5’ end of the SARS-CoV-2 mRNA and generates S-adenosyl homocysteine (SAH) as the reaction byproduct. Due to the central role of histone MTases in cancer, many SAM/SAH analogs with properties of cell permeability have recently been developed for the inhibition of these MTases. We have succeeded in identifying two such compounds (SGC0946 and SGC8158) that display significant antiviral activity and bind to the SARS-CoV-2 nsp14 N7-MTase core. Unexpectedly, crystal structures of SGC0946 and SGC8158 with the SARS-CoV-2 nsp14 N7-MTase core identify them as bi-substrate inhibitors of the viral MTase, co-occupying both the SAM and RNA binding sites; positing novel features that can be derivatized for increased potency and selectivity for SARS-CoV-2 nsp14. Taken together, the high-resolution structures and the accompanying biophysical and viral replication data provide a new avenue for developing analogs of SGC0946 and SGC8158 as antivirals.
Jithesh Kottur, Olga Rechkoblit, Richard Quintana-Feliciano, Daniela Sciaky, and Aneel K. Aggarwal
Springer Science and Business Media LLC
Dongxu Li, Xufen Yu, Jithesh Kottur, Weida Gong, Zhao Zhang, Aaron J. Storey, Yi-Hsuan Tsai, Hidetaka Uryu, Yudao Shen, Stephanie D. Byrum,et al.
Springer Science and Business Media LLC
Xufen Yu, Dongxu Li, Jithesh Kottur, Yudao Shen, Huen Suk Kim, Kwang-Su Park, Yi-Hsuan Tsai, Weida Gong, Jun Wang, Kyogo Suzuki,et al.
American Association for the Advancement of Science (AAAS)
WDR5-degrader-E3 ligase ternary complex structure–based design led to a highly effective WDR5 degrader with robust in vivo antitumor activities.
Mary K Johnson, Jithesh Kottur, and Deepak T Nair
Oxford University Press (OUP)
Abstract The presence of ribonucleotides in DNA can lead to genomic instability and cellular lethality. To prevent adventitious rNTP incorporation, the majority of the DNA polymerases (dPols) possess a steric filter. The dPol named MsDpo4 (Mycobacterium smegmatis) naturally lacks this steric filter and hence is capable of rNTP addition. The introduction of the steric filter in MsDpo4 did not result in complete abrogation of the ability of this enzyme to incorporate ribonucleotides. In comparison, DNA polymerase IV (PolIV) from Escherichia coli exhibited stringent selection for deoxyribonucleotides. A comparison of MsDpo4 and PolIV led to the discovery of an additional polar filter responsible for sugar selectivity. Thr43 represents the filter in PolIV and this residue forms interactions with the incoming nucleotide to draw it closer to the enzyme surface. As a result, the 2’-OH in rNTPs will clash with the enzyme surface, and therefore ribonucleotides cannot be accommodated in the active site in a conformation compatible with productive catalysis. The substitution of the equivalent residue in MsDpo4–Cys47, with Thr led to a drastic reduction in the ability of the mycobacterial enzyme to incorporate rNTPs. Overall, our studies evince that the polar filter serves to prevent ribonucleotide incorporation by dPols.
Jithesh Kottur and Deepak T Nair
Oxford University Press (OUP)
Abstract DNA synthesis by DNA polymerases (dPols) is central to duplication and maintenance of the genome in all living organisms. dPols catalyze the formation of a phosphodiester bond between the incoming deoxynucleoside triphosphate and the terminal primer nucleotide with the release of a pyrophosphate (PPi) group. It is believed that formation of the phosphodiester bond is an endergonic reaction and PPi has to be hydrolyzed by accompanying pyrophosphatase enzymes to ensure that the free energy change of the DNA synthesis reaction is negative and it can proceed in the forward direction. The fact that DNA synthesis proceeds in vitro in the absence of pyrophosphatases represents a long-standing conundrum regarding the thermodynamics of the DNA synthesis reaction. Using time-resolved crystallography, we show that hydrolysis of PPi is an intrinsic and critical step of the DNA synthesis reaction catalyzed by dPols. The hydrolysis of PPi occurs after the formation of the phosphodiester bond and ensures that the DNA synthesis reaction is energetically favorable without the need for additional enzymes. Also, we observe that DNA synthesis is a two Mg2+ ion assisted stepwise associative SN2 reaction. Overall, this study provides deep temporal insight regarding the primary enzymatic reaction responsible for genome duplication.
Jithesh Kottur and Deepak T. Nair
Wiley
AbstractRecent studies posit that reactive oxygen species (ROS) contribute to the cell lethality of bactericidal antibiotics. However, this conjecture has been challenged and remains controversial. To resolve this controversy, we adopted a strategy that involves DNA polymerase IV (PolIV). The nucleotide pool of the cell gets oxidized by ROS and PolIV incorporates the damaged nucleotides (especially 8oxodGTP) into the genome, which results in death of the bacteria. By using a combination of structural and biochemical tools coupled with growth assays, it was shown that selective perturbation of the 8oxodGTP incorporation activity of PolIV results in considerable enhancement of the survival of bacteria in the presence of the norfloxacin antibiotic. Our studies therefore indicate that ROS induced in bacteria by the presence of antibiotics in the environment contribute significantly to cell lethality.
Pratibha P. Ghodke, Kiran R. Gore, S. Harikrishna, Biswajit Samanta, Jithesh Kottur, Deepak T. Nair, and P. I. Pradeepkumar
American Chemical Society (ACS)
N(2)-Furfuryl-deoxyguanosine (fdG) is carcinogenic DNA adduct that originates from furfuryl alcohol. It is also a stable structural mimic of the damage induced by the nitrofurazone family of antibiotics. For the structural and functional studies of this model N(2)-dG adduct, reliable and rapid access to fdG-modified DNAs are warranted. Toward this end, here we report the synthesis of fdG-modified DNAs using phosphoramidite chemistry involving only three steps. The functional integrity of the modified DNA has been verified by primer extension studies with DNA polymerases I and IV from E. coli. Introduction of fdG into a DNA duplex decreases the Tm by ∼1.6 °C/modification. Molecular dynamics simulations of a DNA duplex bearing the fdG adduct revealed that though the overall B-DNA structure is maintained, this lesion can disrupt W-C H-bonding, stacking interactions, and minor groove hydrations to some extent at the modified site, and these effects lead to slight variations in the local base pair parameters. Overall, our studies show that fdG is tolerated at the minor groove of the DNA to a better extent compared with other bulky DNA damages, and this property will make it difficult for the DNA repair pathways to detect this adduct.
Deepak T. Nair, Jithesh Kottur, and Rahul Sharma
Wiley
AbstractGenomic DNA is continually subjected to a number of chemical insults that result in the formation of modified nucleotides—termed as DNA lesions. The N2‐atom of deoxyguanosine is particularly reactive and a number of chemicals react at this site to form different kinds of DNA adducts. The N2‐deoxyguanosine adducts perturb different genomic processes and are particularly deleterious for DNA replication as they have a strong tendency to inhibit replicative DNA polymerases. Many organisms possess specialized dPols—generally classified in the Y‐family—that serves to rescue replication stalled at N2‐dG and other adducts. A review of minor groove N2‐adducts and the known strategies utilized by Y‐family dPols to replicate past these lesions will be presented here. © 2015 IUBMB Life, 67(7):564–574, 2015
Tobias Weinert, Vincent Olieric, Sandro Waltersperger, Ezequiel Panepucci, Lirong Chen, Hua Zhang, Dayong Zhou, John Rose, Akio Ebihara, Seiki Kuramitsu,et al.
Springer Science and Business Media LLC
Jithesh Kottur, Amit Sharma, Kiran R. Gore, Naveen Narayanan, Biswajit Samanta, Pushpangadan I. Pradeepkumar, and Deepak T. Nair
Elsevier BV
Tobias Weinert, Vincent Olieric, Sandro Waltersperger, Ezequiel Panepucci, Lirong Chen, Hua Zhang, Dayong Zhou, John Rose, Akio Ebihara, Seiki Kuramitsu,et al.
Springer Science and Business Media LLC
Amit Sharma, Jithesh Kottur, Naveen Narayanan, and Deepak T. Nair
Oxford University Press (OUP)
The Y-family DNA polymerase IV or PolIV (Escherichia coli) is the founding member of the DinB family and is known to play an important role in stress-induced mutagenesis. We have determined four crystal structures of this enzyme in its pre-catalytic state in complex with substrate DNA presenting the four possible template nucleotides that are paired with the corresponding incoming nucleotide triphosphates. In all four structures, the Ser42 residue in the active site forms interactions with the base moieties of the incipient Watson–Crick base pair. This residue is located close to the centre of the nascent base pair towards the minor groove. In vitro and in vivo assays show that the fidelity of the PolIV enzyme increases drastically when this Ser residue was mutated to Ala. In addition, the structure of PolIV with the mismatch A:C in the active site shows that the Ser42 residue plays an important role in stabilizing dCTP in a conformation compatible with catalysis. Overall, the structural, biochemical and functional data presented here show that the Ser42 residue is present at a strategic location to stabilize mismatches in the PolIV active site, and thus facilitate the appearance of transition and transversion mutations.