Dr. Shubhendu Palei – Chemistry, IIT Kharagpur

Profile

spalei@chem.iitkgp.ac.in

Dr. Shubhendu Palei Assistant Professor & Ramalingaswami Fellow Room HP-204, High Pressure Building Department of Chemistry Indian Institute of Technology (IIT) Kharagpur Kharagpur-721302 West Bengal, India

Education

Ph.D in Chemical Biology, University of Muenster, Germany (magna cum laude plus) (10/2012 – 08/2017)
M.Sc in Chemistry, IIT Kanpur, India (07/2010 – 06/2012)
Integrated B.Sc B.Ed (4 year), Regional Institute of Education (RIE) (Affiliated to NCERT, New Delhi), Utkal University, Bhubaneswar (07/2006 – 06/2010)
+2 Science, Council of Higher Secondary Education (CHSE), Odisha (2003 - 2005)
10th, Board of Secondary Education, Odisha (2003)

Experience

Assistant Professor (Grade-I), Indian Institute of Technology (IIT) Kharagpur (04/2024 – present)
Senior Scientist, Athebio AG (Biotech Start-up Company), Zurich, Switzerland (01/2023 – 10/2023)
Post-doctoral researcher (Chemical Biology and Genetic code expansion), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zürich, Switzerland (10/2021 – 12/2022) Supervisor: Prof. Dr. Kathrin Lang
Post-doctoral researcher (Epigenetics Chemical Biology of TET enzymes), Chemistry and Chemical Biology (CCB), TU Dortmund, Germany (01/2018 – 05/2021) Supervisor: Prof. Dr. Daniel Summerer
Bridging Post-doc (Cyclic peptides, Bacterial display, Inteins), Institute of Biochemistry, University of Muenster, Germany (09/2017 – 12/2017) Supervisor: Prof. Dr. Henning. D. Mootz
Ph.D. in Chemical Biology (Cyclic peptides, Bacterial display, Inteins), Institute of Biochemistry, University of Muenster, Germany (10/2012 – 08/2017) Supervisor: Prof. Dr. Henning. D. Mootz.
MSc Dissertation (Amyloid peptide aggregation), Department of Chemistry & Department of Bioscience and Bioengineering, IIT Kanpur, India (12/2011– 04/2012) Supervisor: Prof. Dr. Sandeep Verma (Dept. of Chemistry), Co-supervisor: Prof. Dr. Ashwani Kumar Thakur (Dept. of Biological Science and Bioengineering)

Research Statement

Our research focuses on developing chemical and synthetic biology tools for molecular level understanding of the histone code with implications in fundamental science and drug discovery. My group will develop cyclic peptide-based ligands to modulate specific epigenetic PTM states of histones both in vitro and in vivo. We aim to mimic the epigenetic modifications of histones e.g. methylation, acetylation, ubiquitination using genetic code expansion technique to understand the molecular basis of crosstalks and their roles in controlling the chromatin landscape. We aim to rescue the loss-of-function effect of oncohistone mutations by site specifically introducing specific PTM by genetic code expansion. We want to incorporate photocrosslinker AA in histones to study PTM readers and erasers.

1. Developing chemical biology and therapeutics toolbox to understand the molecular basis of the histone code

Publications

Books & Chapters

S. Palei, J. Jose, H. D. Mootz, "Preparation of Cell-Surface Displayed Semisynthetic Cyclic Peptides" Methods in Molecular Biology, 2022

S. Palei, H. D. Mootz, "Preparation of semisynthetic macrocycle using split inteins" Methods in Molecular Biology, 2017

Journal Publications

S. Banerjee, Z. V. Cakil, K. Gallant, J. van den Boom, S. Palei, H. Meyer, M. Gersch, D. Summerer, "Light-Activatable Ubiquitin for Studying Linkage-Specific Ubiquitin Chain Formation Kinetics" Advanced Science, 2025

, "Synthesis, SAR, and application of JQ1 analogs as PROTACs for cancer therapy" Bioorg. Med. Chem., 2024

S. Palei, J. Weisner, M. Vogt, R. Gontala, B. Buchmuller, C. Ehrt, T. Grabe, S. Kleinbölting, M. Müller, G. H. Clever, D. Rauh, D. Summerer, "Correction: A high-throughput effector screen identifies a novel small molecule scaffold for inhibition of ten-eleven translocation dioxygenase 2" RSC Med. Chem., 2024

3. B. Buchmuller, J. Dröden, H. Singh, S. Palei, M. Drescher, R. Linser, D. Summerer, "Evolved DNA Duplex Readers for Strand-Asymmetrically Modified 5-Hydroxymethylcytosine/5-Methylcytosine CpG Dyads." J. Am. Chem. Soc., 2022

T-C Lin, S. Palei, D. Summerer, "Optochemical Studies Enable Kinetic Insights into the Domain-Dependent Interplay of TET1 and MBD1 while Reading and Oxidizing 5-Methylcytosine" ACS Chem. Bio., 2022

1. S. Palei*, J. Weisner*, M. Vogt, R. Gontala, B. Buchmuller, C. Ehrt, T. Grabe, S. Kleinbölting, M. Müller, G. H. Clever, D. Rauh, D. Summerer, "A high-throughput effector screen identifies a novel small molecule scaffold for inhibition of ten-eleven translocation dioxygenase 2" RSC Med. Chem., 2022

S. Palei, H. D. Mootz, "Semisynthetic head-to-tail cyclized peptides obtained by combining protein trans-splicing and intramolecular expressed protein ligation" Chem. Commun., 2021

5. J. Wolffgramm, B. Buchmuller, S. Palei, A. Munoz-Lopez, J. Kane, P. Janning, M. Schweiger, Daniel Summerer, "Light-Activation of DNA-Methyltransferases" Angew. Chem. Int. Ed., 2021

7. S. Palei, B. Buchmuller, J. Wolffgramm, Á. Muñoz-Lopez, S. Jung, P. Czodrowski, D. Summerer, "Light-Activatable TET-Dioxygenases Reveal Dynamics of 5-Methylcytosine Oxidation and Transcriptome Reorganization" J. Am. Chem. Soc., 2020

S. Palei*, K-S Becher*, C. Nienberg, J. Jose, H.D. Mootz, "Bacterial cell surface display of semisynthetic cyclic peptide." ChemBioChem, 2019

S. Palei, H. D. Mootz, "Cyclic peptides made from synthetic and genetically encoded fragments" ChemBioChem, 2016

Projects

Developing chemical biology and therapeutics toolbox to understand the molecular basis of the histone code
Client: DBT
PI: PI | Co-Consultant(s):

A phage display platform for discovery of semisynthetic cyclic peptide inhibitors of readers, writers and erasers of histone post-translational modifications.
Client: SRIC, IIT Kharagpur
PI: PI | Co-Consultant(s):

A ribosomal display platform for directed evolution of semisynthetic cyclic peptide inhibitors of readers, writers and erasers of histone post-translational modifications.
Client: ANRF
PI: PI | Co-Consultant(s):

Directed Evolution of Enzyme in the Crowded Confinement of DNA Synthetic Cells
Client: DBT
PI: PI | Co-Consultant(s): Prof. Avik Samanta

Engineering allosteric regulation in an intein enzyme and its application for the synthesis and purification of linear and cyclic therapeutic peptides from bacteria
Client:
PI: Co-PI | Co-Consultant(s): Prof. Soumya De

Awards and Recognition

1. Ramalingaswami Re-entry Fellowship 2023 from DBT, India

Awarded Ramalingaswami Re-entry Fellowship 2022-23 worth 83 lakhs INR by DBT, India for three years or up to five years (1.37 crores INR) to establish own research lab

2. ERC post-doctoral fellowship

ERC post-doctoral fellowship (1/2018-5/2021) at TU Dortmund and (10/2021-12/2022) at ETH Zürich.

3. EMBL Advanced Training Centre Corporate Partnership Programme Fellowship

Awarded EMBL Advanced Training Centre Corporate Partnership Programme Fellowship to attend EMBO Chemical Biology 2016 conference in Heidelberg, Germany

4. Best poster award

Best poster award in Muenster Conference for Biomolecule Analysis-2014 from Springer Nature

5. International Graduate School of Chemistry (GSC-MS), Muenster fellowship

Awarded prestigious International Graduate School of Chemistry (GSC-MS), Muenster fellowship 2012-2014 from Ministry of Science and Education of the federal state of Northrhine Westphalia (NRW)

6. Best Poster award

Best Poster award in Summer Undergraduate Research Grant for Excellence (SURGE), 2011, IIT Kanpur

7. Summer Undergraduate Research Grant for Excellence (SURGE) Fellowship

Awarded prestigious Summer Undergraduate Research Grant for Excellence (SURGE), 2011 Fellowship, IIT Kanpur

8. CSIR NET-2011 (JRF)

Qualified CSIR NET-2011 in Junior Research Fellowship (JRF) category with all India rank 10 conducted by Council of Scientific and Industrial Research (CSIR), India

9. Graduate Aptitude Test for Engineering (GATE) 2012

Qualified Graduate Aptitude Test for Engineering (GATE) 2012 conducted by IIT Delhi with all India rank 20 (percentile: 99.78)

10. JAM-2010

Placed within top 3% (AIR 104) in Joint Admission Test to M.Sc.(JAM-2010) conducted by Indian Institute of Technology (IITs)

11. Best Student Award

Awarded Best Student Award at P.S. College, Barsahi during 2004-2005

12. National Rural Talent Search Scholarship (NRTS)

Awarded the Prestigious National Rural Talent Search Scholarship (NRTS) by State Government of Odisha from 1999 to 2003