Principal Investigator – NCN Sonatina project: Specificity in detection of PTCs in mRNA by NMD and its network, insights from cancer perspective and cross-linking (XL-MS)
Main research focus: structural biology, biophysics, proteomics, protein-protein/RNA/DNA interactions, drug / vaccine discovery
Dr inż. Umesh Kalathiya is currently a principal investigator at ICCVS, University of Gdansk. He obtained his PhD degree in 2018 in chemical sciences from the Faculty of Chemistry, Gdansk University of Technology, and graduated in bioinformatics from Wroclaw University of Technology. In addition, he received training in bioinformatics field from Indian Institute of Technology (IIT), New Delhi. His current projects are funded by National Science Centre, Poland (SONATINA and OPUS NCN grants), and PhD was funded by Polish National Agency for Academic Exchange (NAWA). In May/2022, dr Kalathiya has submitted his application for obtaining the habilitation degree from Rada Doskonałości Naukowej, Poland. He has expertise in working with proteomics and transcriptomics large datasets, along with identification or characterizing of proteins/peptides from mass spectrometry / immunopeptidomics datasets. He believes that the network between the protein-RNA or protein-protein or RNA-RNA components could be traced using the structural computational biology methods, with the use of mass spectrometry (MS)-based structural techniques (cross-linking; XL-MS). He has knowledge of different molecular dynamics algorithms and programming languages such as Python, Tcl, and C++. Applying computational and theoretical methods (molecular modelling/docking/dynamics, quantum calculations, protein-protein/drug interactions, ligand- and structure- based in silico virtual screening) to understand biomolecular systems is his area of expertise. He also has experience in database development and data mining. Moreover, he is always active to take opportunities in learning new skills/methods in the field of bioinformatics. His scientific work includes publication of 37 research papers and appearance in several conferences’ symposium/workshop.
Premature termination codons readthrough in mRNAs
- Kalathiya have been working on generating translation readthrough thus creating neoantigen by virtue of the amino acid, which is added at a stop codon, in a sense stimulates the tumour cell to make its own neoantigen vaccine. This strategy is applied by blocking the nonsense-mediated mRNA decay (NMD) components as an initial target the hUPF1 protein activity is inhibited with a small molecule. The NMD is a translation-coupled quality control system that recognizes and degrades aberrant mRNAs with truncated open reading frames due to the presence of a premature termination codon (PTC). It has been estimated that up to 30% of all mutations resulting in human genetic disorders result in PTCs, and this PTCs represent a unique constellation of diseases which afflict over 30 million people worldwide, accounting for 10-15% of all genetic diseases. Applying molecular dynamics and machine learning platform with structural mass spectrometry they investigated druggable proteins from the NMD set, that could modulate the mRNA binding and postulate theory behind stop codon read through. In such case, they build efforts to design self-derived vaccine (mutant peptide) candidates in cancer cells. The advantage of NMD inhibition over standard vaccine approaches is that this chemical tool that inhibits UPF1 can be used in a wide range of patients without the need to use the current vaccine pipeline-the current vaccine pipeline is sequencing patients’ genomic DNA; creating the vaccine based on mutated proteins that dock into MHC Class I; and injecting the vaccine into the patient. Moreover, most cancer vaccines in clinical trials exploit mutated proteins; these vaccines include peptide synthesis, viral assembly of genomic encoded mutated peptides, or mRNA synthesis that encodes mutated peptides in a patient specific manner. However, their approach to stimulate PTC readthrough with a small molecule that drives the tumour to synthesize its own novel mutated peptides, is itself a novel approach for developing neoantigen vaccines.
(https://doi.org/10.3390/biomedicines10112981, https://doi.org/10.1038/s41598-022-21393-z, https://doi.org/10.3390/ijms222312744, https://doi.org/10.3390/biom11030382, https://doi.org/10.3390/ijms20225644, https://doi.org/10.3390/cancers12030765 )
In addition, investigating the mutational effect on the stability and binding or protein-protein, protein-RNA, and RNA-RNA over the NMD components can provide new insights into the molecular mechanisms of this complex process and assist in development of novel therapeutic approaches. Applying molecular dynamics simulations and cross-linking mass spectrometry (XL-MS) they are working on characterizing the dynamics and molecular properties of the NMD, EJC, and eRFs complexes. Together, these approaches aim to develop biochemical and in vivo data to establish the potential of the NMD system as a cancer drug target for use in tumour rejection.
Understanding structural properties SARS-CoV-2 proteins
Most of the current efforts are focused on the viral spike protein used by SARS-CoV-2 to infect cells, with a strategy to disrupt virus entry. Since SARS-CoV-2 binds to ACE2 receptors (via spike protein) with high affinity, molecules preventing this binding will be of great importance in the treatment. They have evaluated the druggability of the SARS-CoV-2 spike protein using in vitro viral replication assays as a potential target to find novel small molecule hits that might lead to novel chemically engineered inhibitors. Their findings from different rounds/repeats of SARS-CoV-2 infect cells and treating them by our in silico identified compounds, suggest hit molecules reducing the replication of infected cells. In addition, the conformational dynamics of the simulated protein complexes revealed several interaction sites that mirrored the interactions. Self-derived peptides (vaccine candidates) from the SARS-CoV-2 spike glycoprotein were extracted and investigated with the proposition that it could disrupt shaping and stability of the homotrimer unit. (https://doi.org/10.1016/j.biopha.2022.113190, https://doi.org/10.1016/j.bpc.2022.106909, https://doi.org/10.1080/07391102.2021.1977698, https://doi.org/10.3390/jcm9051473, https://doi.org/10.3390/biom11020297 )
Molecular evolution and binding pattern of p53-mdm2
They investigated the molecular evolution of the p53–MDM2 system by combining molecular dynamics and in vitro assays to explore structural and functional aspects of p53 isoforms retaining the MDM2 interaction, whereas forming distinct pools of cell signaling. The dynamics and influence of distinct elephant p53 isoforms binding mdm2 in different temperature coupling will be studied. Using free energy-based molecular dynamics technique we make efforts to understand the ribosome translation elongation and concentration of tRNAs required for this rate of translation. In addition, using next-generation sequencing of a combinatorial peptide phage library were screened against ubiquitin that identified peptide aptamers that can inhibit the in vitro ubiquitin transfer cascade. Ubiquitin-binding peptides were identified that inhibit both E3 ubiquitin ligases MDM2 and CHIP. (https://doi.org/10.3389/fmicb.2022.875556, https://doi.org/10.1093/molbev/msac149 )
The peptide-loading complex
Making orthogonal validation of a cohort of novel interferon-induced protein networks formed by the HLA-A protein using co-immunoprecipitation assay, they investigated them by molecular dynamics simulation. In direction to develop vaccine candidate, they studied the peptide loading complex (PLC) as well as peptide transporters; and from a series of datasets containing the structural and numerical details, and postulated the selectivity of peptides by different MHC molecules and TCR receptors. The PLC can provide a large pool of MHC-I allomorphs, and thus, fulfills an essential function in the differentiation and priming of T lymphocytes as well as in controlling viral infections and tumour development. However, the compositional heterogeneity and the intrinsic dynamic nature of PLC have limited the detailed structural studies. Moreover, several haplotypes/alleles of HLA molecules are identified, whereas other components (e.g. β2m, Calreticulin, ERp57, Tapasin, TAP1 and TAP2) of the PLC has only one or two isoforms, and how these functional proteins behaves as a complex or how they change the dynamics of the complex when bound with different HLA alleles are being studied. They modeled the entire PLC and all available HLA alleles from different sources, as well as build viral protein structures (e.g. US2, US3, US6, E3/19K, ICP47, UL18, BNLF2a, CPXV012, UL49.5, etc) with PLC. In addition, immunopeptidome derived dataset of peptides from cancer cells (e.g. melanoma A375; with/without IFN treatment or viral infection), will also be used to understand the PLC dynamics. We believe understanding structural dynamics of the PLC complex with different alleles or haplotypes and change in dynamics upon viral protein binding will advance the knowledge in the field of antigen recognition and presentation. (https://doi.org/10.1016/j.csbj.2021.09.006, https://doi.org/10.1098/rsob.200348, https://doi.org/10.3390/cancers12030737 )
Projects and Awards
- Principal Investigator: Specificity in detection of PTCs in mRNA by NMD and its network, insights from cancer perspective and cross-linking (XL-MS). SONATINA, National Science Center, Poland (grant agreement no. 2020/36/C/NZ2/00108).
- Principal Investigator: Targeted inhibition of SARS-CoV-2 Spike Glycoprotein by novel medicinal compounds, reduced the replication of virus infected cells, UGrants-START (grant agreement no. 1220.6010.37.2022).
- Co-author of the grant application / Scientific leader; The impact of UPF1 ATP mimetics on the mutant immunopeptidome. OPUS, National Science Center, Poland (grant agreement no. 2020/39/B/NZ7/02677).
- Collaborative Investigator: Examination of drug leads for binding to a novel homotrimer cavity formed by the SARS-CoV-2 spike glycoprotein. Medical Research Scotland. (08/2020-04/2021).
- Co-investigator: New compounds with anticancer activity that disrupt telomere functions. The National Centre for Research and Development, Poland (TARGETTELO; grant agreement no. STRATEGMED3/306853/9/NCBR/2017).
- Co-investigator: New inhibitors of catalytic subunit of telomerase. OPUS, National Science Center, Poland (grant agreement no. 2014/13/B/NZ7/02207).
- III Degree Award of Rector of University of Gdansk, for your scientific work in 2021.
- D. funded by the Polish National Agency for Academic Exchange (NAWA), Poland under the program the Ignacy Łukasiewicz Scholarship, (2013-2016).
- PZ/8885/RW/PCT, Inhibitors of interactions between TRF1-TIN2 or TRF2-TIN2 telomeric proteins for use in anticancer therapy. Visegrad Patent Institute (ISA/XV), 2022 (patent application).