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Name : Surajit Sinha

Department : School of Applied & Interdisciplinary Sciences
Designation : School Chair & Senior Professor
Contact : +91 33 2473 4971 (Ext: 1400)
Email : ocss5@iacs.res.in
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Find out more on https://www.themorpholinogroup.in/

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Our Mission: 

We are actively engaged in the field of macromolecular drug delivery through the development of peptidic/non-peptidic delivery agents which undergo endocytosis spontaneously. These delivery agents are being utilized for the intracellular availability of Phosphorodiamidate Morpholino Oligonucleotides (PMOs), which have huge application in the treatment of genetic disorders, most importantly in Duchenne Muscular Dystrophy (DMD). Innovative synthetic methodologies are being dedicatedly pursued for scaling up the production of PMOs along with simultaneous modifications in PMO backbone for enhanced activity. Self-penetrating PMOs are also being developed for the treatment of cancer by downregulating the stemness genes responsible for recurrence as well as by modulating the immunogenic pathways which are responsible for immune evasion in cancer both in vitro and in vivo.  
 

Research interests: Organic Synthesis, Chemical Biology, Drug discovery and delivery

  • Synthesis of biologically important natural products and their analogues.
  • Studies of small molecule modulation of Hedgehog signaling pathway in tissue culture and studies of Hedgehog dependent physiology using “zebrafish (Danio rerio) as a model organism.
  • Synthesis of artificial amino acids and nucleic acids for biological probes.
  • Synthesis and evaluation of antisense properties of cell-penetrating morpholino oligonucleotides in cancers targeting hedgehog signaling pathway.
  • Non-peptide-based molecular transporter used for drug, peptide and biomolecules delivery.
  • Antisense-based therapy for the treatment of Duchenne muscular dystrophy (DMD).

 


Group News

Looking for a 5′→3′ Phosphoramidite Approach for PMO synthesis? The Morpholino Group delivers!!

 

 
The Chemistry just got accepted in
 @J_A_C_S Congrats
 @ATG_Oligo
 @arpanbanerjee_ and @Shalini_IACS for the efforts 👏


Academic Profile

Education:

Int. PhD (M.S. and PhD) (2000): Indian Institute of Science (IISc), Bangalore, (Under Professor S. Chandrasekaran, Department of Organic Chemistry).

Professional:

  • Postdoctoral Fellow (2000-2003): Department of Chemistry, University of California, Riverside, in NASA Astrobiology Program (Advisor: Professor Christopher Switzer).
  • Postdoctoral Fellow (2003-2006 March): Chemical and Systems Biology, School of Medicine, Stanford University, (Advisor: Professor James K. Chen).
  • Assistant Professor (April 2006 – January2012): Indian Association for the Cultivation of Science, Kolkata, India.
  • Associate Professor (January 2012 – January 2017): Indian Association for the Cultivation of Science, Kolkata, India. 
  • Professor (Jan 2017 to 2020)
  • Senior Professor(2020 to till date)


Team

Dr. Senjuti Sen

RA-1(TRC Project)
Development of Anticancer Therapeutics Using Morpholino Antisense.
NPDF, IICB, Kolkata
Ph.D. Bose Institute
M.Sc Calcutta University
B.Sc Calcutta University
Date of joining: July 2023
Dr. Shalini Gupta

RA-1
Synthesis of non-peptide-based delivery agents, ideally non-toxic, and their biological efficacy.
Ph.D. IACS
M.Sc. IACS (Int. Ph.D.)
B.Sc. Lady Brabourne College
An OCD patient with respect to cleanliness and organized things.
Date of joining: June 2018
intsg2@iacs.res.in
Abhishek Gupta

RA 1
Development of Azaproline-based peptides and delivery agents.
M. Sc. IACS (Int. Ph.D.)
B. Sc. Scottish Church College
Four C’s of his life: Chemistry, Chicken, Carrom and Cricket (never plays though). Standardizes reactions slowly, steadily and with resilience.
Date of joining: June, 2018
intag@iacs.res.in
Atanu Ghosh

Senior Research Fellow(CSIR)
Synthesis of Functionalized Morpholino Oligonucleotides.
M. Sc. IACS (Int. Ph.D.)
B. Sc. City College
Loves cricket. On the pitch, an all-rounder. Off the pitch, he loves to take clean NMR spectra.
Date of joining: July 2019
intag3@iacs.res.in
Arnab Das

Senior Research Fellow(CSIR)
Synthesis of Functionalized and Self-Transfecting Morpholino Oligonucleotides .
M. Sc. IACS (Int. Ph.D.)
B. Sc. Vivekananda College
Mimicry artist of the group. DCM runs through his veins instead of blood.
Date of joining: July 2019
intad2@iacs.res.in
Swrajit Nath Sharma

Senior Research Fellow
Synthesis of IGT and evaluation of biological efficacy.
M.Sc IACS (Int. Ph.D.)
Bsc. Dibrugarh University
Focused, humble, and witty, with a keen interest in Chemistry and a passion for dancing.
Date of joining: September 2021
swrajitn@gmail.com
Sudipta Sarkar

Senior Research Fellow(CSIR)
Oncoimmunotherapy.
M.Sc, Rajabazar Science College, University of Calcutta
B.Sc.: Hooghly Mohsin College.
Serious Biologist. She isn't in any way shape or form what you think she is.
Date of joining: February 2022
sudiptasarkar903@gmail.com
Md Qasim

Senior Research Fellow(UGC)
Development of Internal Oligo-guanidinium Transporter (IGT).
M. Sc. IACS (Int. Ph.D.)
B. Sc. Maulana Azad College
Funny and serious. Calm and mischievous. He is not at all what you think he is.
Date of Joining: August 2022
mdq789@gmail.com
Subhamoy Pratihar

Senior Research Fellow
Synthesis of Antisense Morpholino Oligonucleotides.
M.Sc. IACS (Int. Ph.D.)
B. Sc. Bankura Sammilani College.
Vivacious manager and go-to person of the group. Also a night owl and a comic.
Date of Joining: August 2022
subhamoypratihar@gmail.com
Sharmeen Naaz

Junior Research Fellow (UGC)
Therapeutic Evaluation of Antisense Oligonucleotide.
M.Sc & B.Sc Rammohan College
Date of Joining: August 2023
sharmeenaaz@gmail.com


Publications

2024

Ghosh, A.; Banerjee, A.; Gupta, S. Sinha, S. A Unified Phosphoramidite Platform for the Synthesis of Morpholino Oligonucleotides and Diverse Chimeric Backbones. J. Am. Chem. Soc. 2024, 146, 32989-33001. https://doi.org/10.1021/jacs.4c09510

                                                                                                   

Choudhary, N. K.; Gupta, S.; Das, G.; Sahoo, A.; Harikrishna, S.; Sinha, S. and Gore, K. R. Selective Recognition of the Dimeric NG16 Parallel G‑Quadruplex Structure Using Synthetic Turn-On Red Fluorescent Protein Chromophore. Biochemisry 2024, https://doi.org/10.1021/acs.biochem.4c00407


Pratihar, S.; Qasim, Md.; Sinha, S. Synthesis of Phosphorodiamidate Morpholino Oligonucleotides (PMOs) Using Staudinger Reduction as a Deblocking Condition and its Usefulness for Orthogonal Conjugation in Bi- and Tri-functionalized PMOs. Synlett 2024. 10.1055/a-2384-7323

Auddy, S. S.; Gupta, S.; Mandi, S.; Sharma, H.; Sinha, S.* and Goswami, R. K.* Total Synthesis of Lipopeptide Bacilotetrin C: Discovery of Potent Anticancer Congeners Promoting Autophagy. ACS Med. Chem. Lett. 2024, 15, 1340-1350.

 

Sahoo, A.; Gupta, S.; Das, G.; Ghosh, A.; Bagale, S. S.; Sinha, S. and Gore, K. R. 2′‑O‑Alkyl‑N3‑Methyluridine Functionalized Passenger Strand Improves RNAi Activity by Modulating the Thermal Stability. ACS Med. Chem. Lett. 2024, 15, 1250-1259. 

Bhattacharya, T.; Gupta, A.; Gupta, S.; Saha, S.; Ghosh, S.; Shireen, Z.; Dey, S.* and Sinha, S.* Benzofuran Iboga-analogs Modulate Nociception in an Acute Mouse Pain Model. ChemBioChem 2024  DOI:10.1002/cbic.202400162

                            


Qasim, M.; Ghosh, A.; Das, A.; Sinha, S. Evaluation of Transiently O-6 Protected Guanosine Morpholino Nucleosides in PMO Synthesis. Synlett 2024, 35, 1315 - 1320 DOI: 10.1055/a-2322-3741 (Special Issue to Celebrate the Centenary Year of Prof. Har Gobind Khorana and qualified for the best paper award competition).

Masid, A.; Das, O.; Roy, D.; Dutta, A.; Sikdar, S.; Ghosh, A.; Banerjee, A.; Ghosh, U.; Chowdhury, S. A.; Majumder, S.; Yahya, M.; Sinha, S.; Bhaumik, M.* (2024). Butyrate ameliorates inflammation in colon biopsy samples of IBD patients and experimental colitis in mice involving RNA binding protein, AUF1-IL-27 axis and accelerating B1a to B10 polarization. bioRxiv doi: https://doi.org/10.1101/2024.05.24.595646

Ghosh, A.; Banerjee, A.; Das, B. and Sinha, S. A 5′→3′ Phosphoramidite Approach for the Synthesis of Phosphorodiamidate and Thiophosphoramidate Morpholino Oligonucleotides and Their Chimera. 10.26434/chemrxiv-2024-213qg (2024).

                                        

Gangopadhyay, S.; Das, G.; Gupta, S.; Ghosh, A.; Bagale, S. S.; Roy, P. K.; Mandal, M.;  Harikrishna, S.; Sinha, S. and Gore, K. R. 4′‑C‑Acetamidomethyl-2′‑O‑methoxyethyl Nucleic Acid Modifications Improve Thermal Stability, Nuclease Resistance, Potency, and hAgo2 Binding of Small Interfering RNAs. J. Org. Chem. 2024, https://doi.org/10.1021/acs.joc.3c02506.

Sahoo, A.; Das, G.; Ghosh, A.; Bagale, S. S.; Choudhary, N. K.; Harikrishna, S.; Sinha, S.; Gore, K. R. N3-Methyluridine and 2′-O-Alkyl/2′-Fluoro-N3-Methyluridine Functionalized Nucleic Acids Improve Nuclease Resistance While Maintaining Duplex Geometry. Bioorg. Med. Chem. 2024, 100, 117616. DOI:10.1016/j.bmc.2024.117616 

Das, A.; Gupta, S.; Shaw, P. and Sinha, S. Synthesis of Self Permeable Antisense PMO using C5-guanidino-functionalized-pyrimidines at the 5ʹ-end Enables Sox2 Downregulation in Triple Negative Breast Cancer Cells. Mol. Pharmaceutics 2024, 21, 3, 1256–1271. https://doi.org/10.1021/acs.molpharmaceut.3c00924

Goswami, K.*; Chakraborty, A.; Sinha, S.* and Jana, A.* Recent Advances in the Pd-Catalyzed Synthesis of Unnatural Tryptophans. Eur. J. Org. 2024, 27, e202301028(1 of 13) DOI: 10.1002/adsc.202

Banerjee, A.; Das, A.; Ghosh, A.; Gupta, A.; Sinha, S. Synthesis and Biophysical Properties of Triazole-Incorporated PMOs (TzPMOs): A Convergent, Click Ligation Approach. J. Org. Chem. 2024, 89, 5, 2895-2903; ChemRxiv 2023, 10.26434/chemrxiv-2023-l9zmx

2023

Gupta, S.; Sharma, S. N.; Kundu, J.; Pattanayak, S.; and Sinha, S. Morpholino oligonucleotide-mediated exon skipping for DMD treatment: Past insights, present challenges and future perspectives. J. BioSci. 2023, 48:38 https://doi.org/10.1007/s12038-023-00365-z

 

Das, A.; Ghosh, A.; Kundu, J.; Egli, M.; Manoharan, M. and Sinha, S. Synthesis and Biophysical Studies of High-Affinity Morpholino Oligomers Containing G-clamp Analogs. J. Org. Chem. 2023, 88, 21, 15168–15175, https://doi.org/10.1021/acs.joc.3c01658

 

Sarkar, S.; Kar, A.; Shaw, P.; DasGupta, B.; Keithellakpam, O. J.; Mukherjee, P. K.; Bhardwaj, P. K.; Sharma, N.; Haldar, P. K. and Sinha. S. Hydroalcoholic root extracts of Houttuynia cordata (Thunb.) standardized by UPLC-Q-TOF-MS/MS promotes apoptosis in human hepatocarcinoma cell HepG2 via GSK-3β/β-catenin/PDL-1 axis. Fitoterapia 2023,171,105684 (https://doi.org/10.1016/j.fitote.2023.105684)

 

Self-transfecting GMO-PMO antisense chimera targeting Nanog enable gene silencing in vitro and suppresses tumor growth in 4T1 allografts in mouse. Das, Ujjal.; Kundu, J.; Shaw, P.; Bose, C.; Ghosh, A.; Gupta, S.; Sarkar, S.; Bhadra, J.; and Sinha, S. Mol. Ther. Nucleic Acids 2023. https://doi.org/10.1016/j.omtn.2023.03.011

 

Synthesis and Biophysical Properties of Phosphorodiamidate Piperidino Oligomers (PPOs). Ghosh, A.; Akabane-Nakata, M.; Kundu, J.; Harp, J. M.; Madaoui, M.; Egli, M.; Manoharan, M.;  and Sinha, S.

Org. Lett. 2023, 25, 6, 901–906, https://doi.org/10.1021/acs.orglett.2c04067

 

Synthesis of Chlorophosphoramidate Monomer Morpholinos and PMOs. Kundu, J.; Ghosh, U.; Ghosh, A.; Pattanayak, S.; Das, A. and Sinha, S.  

Current Protocols in Nucl. Acid Chem,  2023,3, 1-25, https://doi.org/10.1002/cpz1.686

 

 

C5-Pyrimidine-Functionalized Morpholino Oligonucleotides Exhibit Differential Binding Affinity, Target Specificity and Lipophilicity. Das, A.; Ghosh, A.; Sinha, S. Org. Biomol. Chem. 2023, 21, 1242 - 1253 https://doi.org/10.1039/D2OB01759H

 

Synthesis of 5ʹ-Thiol Functionalized Morpholino Oligo-nucleotide and Subsequent Conjugation with IGT to Improve Delivery and Antisense Efficacy In Vitro. Ghosh, U.; Gupta, S. and Sinha, S. Bioconjugate Chem. 2023, 34, 174–180, https://doi.org/10.1021/acs.bioconjchem.2c00587


 
 

2022

IGT mediated Nanog siRNA delivery in prostate cancer cells improves chemosensitization of Epirubicin in vitro. Gupta, S.; Das, U.; Sinha, S. Bioorg. Med. Chem. Lett. 2022, https://doi.org/10.1016/j.bmcl.2022.129017.

 

AUF-1 knock down in mice overarches butyrate driven hypo-cholesteraemia by conjuring 1 AUF-1-Dicer-1-miR122 hierarchy

Das, O.; Kundu, J.; Ghosh, A.; Gautam, A.; Ghosh, S.; Chakraborty, M.; Masid, A.; Gauri, S. S.; Mitra, D.; Dutta, M.; Mukherjee, B.; Sinha, S.; Bhaumik, M.

bioRxiv 2022, https://doi.org/10.1101/2022.06.13.496022, Published in Frontiers Cellular and Infection Microbiology 2022, 1-20 (doi: 10.3389/fcimb.2022.1011386).

 
 

Guanidinium Functionalized Flexible Azaproline Transporter for Efficient Intracellular Delivery of Proapoptotic Peptide and PDL1 Antisense Morpholino Oligo in Human Carcinoma Cells In Vitro. Gupta, A.; Gupta, S.; Das, U. and Sinha, S. Bioconjugate Chem. 2022, 33, 907-917 https://doi.org/10.1021/acs.bioconjchem.2c00129
 

J. Kundu, A. Ghosh, U. Ghosh, A. Das, D. Nagar, S. Pattanayak, A. Ghose and S. Sinha: Synthesis of Phosphorodiamidate Morpholino Oligonucleotides Using Trityl and Fmoc Chemistry in an Automated Oligo Synthesizer. J. Org. Chem. 2022, 87, 15, 9466–9478 https://doi.org/10.1021/acs.joc.2c00265
 

Mana, T.; Kundu, J.; Lahiri, H.; Bera, S.; Kolay, J.; Sinha, S.; Mukhopadhyay, R. Molecularly Resolved, Label-free Nucleic Acid Sensing at Solid-liquid Interface using Non-ionic DNA Analogues. RSC Adv. 2022, 12, 9263-9274, https://doi.org/10.1039/D2RA00386D
 

Bose, C.; Das, U.; Kuilya, T. K.; Mondal, J.; Bhadra, J.; Banerjee, P.; Goswami, R. K. and Sinha, S. Cananginone Abrogates EMT in Breast Cancer Cells through Hedgehog Signaling. Chem. Biodiversity 2022, e202100823 (https://doi.org/10.1002/cbdv.202100823)
 

Gupta, S.; Qasim, Md.; Gupta, A.; Kundu, J.; Sinha, S. Structural Modifications to the Internal Oligoguanidinium Transporter Uncover Two Potent Analogues that Effectively Deliver the Pro-apoptotic Peptide in Multiple Cancer Cell Lines. Bioconj. Chem. 2022, 33 (1), 121-133, doi.org/10.1021/acs.bioconjchem.1c00456

 
 

2021

Kundu, J.; Das, U.; Bose, C.; Bhadra, J. and Sinha, S. Self-transfecting GMO-PMO and PMO-GMO chimeras enable gene silencing in vitro and in vivo zebrafish model and NANOG Inhibition Induce the Apoptosis in Breast and Prostate Cancer Cells. BioRxiv 2021, https://doi.org/10.1101/2021.06.04.447039
 

Banerjee, I. ; Ghosh, K. C. ; Oheix, E. ; Jean, M.; Naubron, J-V.; Réglier, M.; Iranzo, O.* and Sinha, S.* Synthesis of Protected 3,4- and 2,3-Dimercaptophenylalanines as Building Blocks for Fmoc-Peptide Synthesis and Incorporation of the 3,4-Analogue in a Decapeptide Using Solid-Phase Synthesis. J. Org. Chem. 2021, 86, 2210−2223, doi.org/10.1021/acs.joc.0c02359.

 

2020

Chandra Bose, Priyanjalee Banerjee, Jayanta Kundu, Biswadeb Dutta, Indranil Ghosh, Shreya Sinha, Argha Ghosh, Abhishek Barua, Shalini Gupta, Ujjal Das, Siddhartha S. Jana, Surajit Sinha. Evaluation of tubulin targeted pyrimidine indole hybrid molecule as an anticancer agent. ChemSelect 2020, 5, 14021‒14031.

 

J. Kundu, P. Banerjee, C. Bose, U. Das, U. Ghosh and S. Sinha: Internal Oligoguanidinium Transporter: Mercury Free Scalable Synthesis, Improvement of Cellular Localization, Endosomal Escape, Mitochondrial Localization and Conjugation with Antisense Morpholino for NANOG Inhibition to Induce Chemosensitisation of Taxol in MCF-7 Cells. Bioconj. Chem. 2020, 31 (10), 2367‒2382, doi.org/10.1021/acs.bioconjchem.0c00444.

 

J. Kundu, U. Ghosh, A. Ghosh, A. Das, D. Nagar, A. Ghose and S. Sinha: Synthesis of Phosphorodiamidate Morpholino Oligonucleotides Using Trityl and Fmoc Chemistry-A New Method Amenable to Automated Synthesizer. ChemRxiv 2020, 10.26434/chemrxiv.12765563

 

2018-2019

Ghosh, K. C.; Duttagupta, I.; Bose, C.; Banerjee, P.; Gayen, A. K. and Sinha, S. Synthesis and anti-cancer activities of prolein-containing cyclic peptides and their linear analogs and congeners Syn. Commun. 2019, 49, 221‒236.

 

Ghosh K. C.; Banerjee, I. And Sinha, S. Montrillonite K 10 catalysed highly regioselective azidolysis of epoxides. A short and efficinat synthesis of phenylglycine. Syn. Commun. 2018, 48, 2923‒2934.
 

Khatra, H.; Khan, P. P.; Pattanayak, S.; Bhadra, J.; Rather, B.; Chakrabarti, S.; Saha, T. and Sinha, S. Hedgehog antagonist pyrimidine-indole-hybrid molecule inhibits ciliogenesis through microtubule destabilization. ChemBioChem 2018, 19, 723–735.

 
2010-2017
Nandi, B.; Khatra, H.; Khan, P. P.; Bhadra, J.; Pattanayak, S. and Sinha, S. “Cationic Cytosine Morpholino-Based Transporters: Synthesis and Regulation of Intracellular Localization”. ChemSelect 2017, 2, 5059–5067.
 
Khatra, H.; Bose, C. and Sinha, S. "Discovery of hedgehog antagonists for cancer therapy". Current Med. Chem. 2017, 24, 1–26, invited review).
 
Bhadra, J.; Pattanayak, S.; Khan, P. P.; Kundu, J.; Sinha, S. “Internal Oligoguanidinium-based Cellular Transporter Enhances Antisense Efficacy of Morpholinos in in vitro and Zebrafish model”. Bioconjugate Chem. 2016, 27, 2254–2259.
 
Khatra, H.; Kundu, J.; Khan, P. P.; Duttagupta, I.; Pattanayak, S. and Sinha, S. “Piperazic Acid Derivatives Inhibit Gli1 in Hedgehog Signaling Pathway”. Bioorg. Med. Chem. Lett. 2016, 26, 4423–4426.
 
Duttagupta, I.; Bhadra, J.; Das, S. K.; Sinha, S. “Proteolytic stability of α-hydrazino acid-containing peptides: a qualitative study”. Tetrahedron Lett. 2016, 57, 3858–3861.
 
Duttagupta, I.; Ghosh, K. C.; Sinha, S. “Synthetic Studies Toward Nonribosomal Peptides”. Studies in Natural Product Chem. (Elsevier, UK) (Elsevier, UK) 2016, 48, 31–66 (invited).
 
Duttagupta, I.; Misra, D.; Bhunya, S.; Paul, A.; Sinha, S. “Cis - Trans Conformational Analysis of δ – Azaproline in Peptides”. J. Org. Chem. 2015, 80, 10585−10604.
 
Bhadra, J.; Pattanayak, S. “Synthesis of Morpholino Monomers, Chlorophosphoramidate Monomers and Solid Phase Synthesis of Short Morpholino Oligomers”. Current Protocols in Nucl. Acid Chem. 2015, 4.65.1–4.65.26 (Wiley).
 
Bhadra, J.; Kundu, J.; Ghosh, K.; Sinha, S. “Synthesis of phosphorodiamidate morpholino oligonucleotides by H-phosphonate method”. Tetrahedron Lett. 2015, 56, 4565–4568.
 
Banerjee, T. S.; Paul, S.; Sinha, S.*; Das, S.* “Synthesis of iboga-like isoquinuclidines: Dual opioid receptors agonists having antinociceptive properties”. Bioorg. Med. Chem. 2014, 22, 6062–6070.
 
Chakraborty, A.; Jyothi, K.; Sinha, S. “Palladium-catalyzed synthesis of 2-allylindole and 2-allylbenzofuran derivatives from 2-((trimethylsilyl)ethynyl)arenes.” Tetrahedron Lett. 2014, 55, 6795–6798.
 
Duttagupta, I.; Goswami, K.; Chatla, P. and Sinha, S. “Improved Synthesis of Cyclic α-Hydrazino Acids of 5 to 9-Membered Rings and Optical Resolution of 5, 6, 7-Membered Ring Hydrazino Acids” Syn.Commun. 2014, 44, 2510–2519.
 
Paul, S.; Pattanayak, S.; Sinha, S. “Synthesis and Cell Transfection Properties of cationic uracil-morpholinotetramer”. Tetrahedron Lett. 2014, 55, 1072–1076.
 
Pattanayak, S.; Khatra, H.; Saha, S. and Sinha, S. “Cationic Morpholino Antisense Oligomer Conjugate: Synthesis, Cellular uptake and Inhibition of Gli1 in Hedgehog Hedgehog Signalling Pathway” RSC Advances 2014, 4, 1951–1954.
 
Paul, S.; Jana, S.; Bhadra, J.; Sinha, S. “Photophysical Studies and Submicron Ring Formation of Morpholino U-Nucleoside Monomers” Chem. Commun. 2013, 49, 11278–11280.
 
Chakraborty, A.; Goswami, K.; Adiyala, A.; Sinha, S. “Syntheses of Spiro[cyclopent[3]ene-1,3_-indole]s and Tetrahydrocyclo-hepta[b]indoles from 2,3-Disubstituted Indoles through Sigmatropic Rearrangement” Euro. J. Org. Chem. 2013, 7117–7127.
 
Goswami, K.; Chakraborty, A.; Sinha, S. “Synthesis of Optically Active Selenium-Containing Isotryptophan, Homoisotryptophan and Homotryptophan” Euro. J. Org. Chem. 2013, 3645–3647.
 
Nandi, B.; Pattanayak, S.; Paul, S. and Sinha, S. “Synthesis of Nucleobase-Functionalized Morpholino Modified Nucleoside Monomers Through Palladium-Catalyzed Cross-Coupling Reactions” Euro. J. Org. Chem. 2013, 1271–1286.
 
Pattanayak, S.; Paul, S.; Nandi, B. and Sinha, S. “Improved protocol for the synthesis of Flexibly ProtectedMorpholino Monomers from Unprotected Ribonucleosides” Nucleosides, Nucleotides and Nucleic Acids 2012, 31, 763–782.
 
Pattanayak, S.; Sinha, S. “Lithium bromide–DBU mediated synthesis of chlorophosphoramidate-activatedmorpholino nucleoside subunits” Tetrahedron Lett. 2012, 53, 6714–6717.
 
Duttagupta, I.; Goswami, K.; Sinha, S. “Synthesis of cyclic α-hydrazino acids” Tetrahedron 2012, 68,8347–8357.
 
Jana, G. K. and Sinha, S. “Total synthesis of ibogaine, epiibogaine and their analogues” Tetrahedron 2012,68, 7155–7165.
 
Paul, S.; Nandi, B.; Pattanayak, S.; Sinha, S. “Synthesis of 5-alkynylated uracil–morpholino monomersusing Sonogashira coupling” Tetrahedron Lett. 2012, 53, 4179–4183.
 
Jana, G. K. and Sinha, S. “Reductive Heck coupling: an efficient approach toward the iboga alkaloids.Synthesis of ibogamine, epiibogamine and iboga analogs” Tetrahedron Lett. 2012, 53, 1671-1674.
 
Goswami, K.; Duttagupta, I.; Sinha, S. “Synthesis of optically active homotryptophan and its oxygen andand sulfur analogues” Tetrahedron 2012, 68, 280–286.
 
Goswami, K.; Duttagupta, I.; Sinha, S. “Synthesis of Optically Active 2- and 3-Indolylglycine derivatives and their Oxygen Analogues” J. Org. Chem. 2012, 77, 7081−7085.
 
Pattanayak, S.; Sinha, S. “Ceric ammonium nitrate-mediated detritylation of tritylated amines” TetrahedronLett. 2011, 52, 34–37.
 
Paul, S.; Pattanayak, S.; Sinha, S. “Synthesis of new series of iboga analogues” Tetrahedron Lett. 2011,52, 6166–6169.
 
Chakraborty, A.; Sinha, S. “Synthesis of 3-[2-(1,3-butadienyl)]-1H-indoles en route to murrapanineanalogue” Tetrahedron Lett. 2011, 52, 6635–6638.
 
Jana, G. K.; Paul, S.; Sinha, S. “Recent Progress in the Synthesis of Iboga-alkaloids and their congeners”Org. Prep. Proc. International (Invited Review) 2011, 43, 541–573.
 
Nandi, B.; Sinha, S. “Alkylation of acylmetalates with alkyl halides to prepare Fischer carbine complexes:an improved protocol” Tetrahedron 2011, 67, 106–113.
 
Jana, G. K.; Sinha, S. “Synthesis of iboga alkaloids by Pd-catalyzed heteroannulation of 2-iodoaniline with an internal alkyne as the key step” Tetrahedron Lett. 2010, 51,1441–1443.
 

Jana, G. K.; Sinha, S. “A concise route to iboga-analogues via the formation of suitably substituted-2-indoles” Tetrahedron Lett. 2010, 51, 1994–1996.

 

 
Hyman, J. M.; Firestone, A. J.; Heine, V. M.; Zhao, Y.; Ocasio, C. A.; Han, K.; Sun, M.; Rack, P. G.; Surajit Sinha; Wu, J. J.; Solow-Cordero, D. E.; Jiang, J.; Rowitch, D. H.; James K. Chen. “Small-molecule inhibitors reveal multiple Strategies for Hedgehog pathway blockade” Proc. Natl. Acad. Sci USA 2009, 106,14132 – 14137.
 
Ouyang, X.; Shestopalov, I. A.; Surajit Sinha, Zheng, G.; Pitt, C. L. W.; Li, W. H.; Olson, A. J.; James K. Chen. “Versatile Synthesis and Rational Design of Caged Morpholinos” J. Am. Chem. Soc. 2009, 131, 13255–13269.
 
Cupido, T.; Rack, P. G.; Firestone, A. J.; Hyman, J. M.; Han, K.; Surajit Sinha; Ocasio, C. A. and James K. Chen. “The Imidazopyridine Derivative JK184 Reveals Dual Roles for Microtubules in Hedgehog Signaling.” Angew. Chem. Int. Ed. 2009, 48, 2321 – 2324.
 
Shestopalov, I. A.; Sinha, S.; Chen, J. K. “Light-controlled gene silencing in zebrafish embryos”. Nature Chemical Biology. 2007, 3, 650 - 651. (Authors contributed equally). (It was cited by the Faculty of 1000 as a "must read" with an F1000 factor of 6.4 and won ‘2008 NIH Pioneer Awards’).
 
Sinha, S.; Chen, J. K. “Purmorphamine activates the hedgehog pathway by targeting smoothened”. Nature Chemical Biology. 2006, 2, 29 – 30. (Work appeared as news and views in this issue).
 
Switzer, C.; Sinha S.; Kim, P. H.; Heuberger, B. D. “A purine-like Nickel (II) base-pair for DNA”. Angew. Chem. Int. Ed. 2005, 44, 1529 – 1532. (Hot off the Press, Mol. BioSyst. 2005, 1, 109-111).
 
Sinha S.; Kim, P. H.; Switzer, C. “2’-5’-linked DNA is a template for polymerase-directed DNA synthesis J. Am. Chem. Soc. 2004, 126, 40-41.
 
Post doctoral work: Chaput, J. C.; Sinha, S.; Switzer, C. “5-Propynyluracil diaminopurine: an efficient base-pair for non-enzymatic transcription of DNA”. Chem. Commun. 2002, 1568-1569.
 
Sinha, S.; Tilve, S.; Chandrasekaran, S. “A convenient synthesis of trans-3-hydroxy-L-proline” ARKIVOC (Gainesville, FL, United States). 2005, 11, 209-217.
 
Bhat, R. G.; Sinha, S.; Chandrasekaran, S. “Propargyloxycarbonyl (Poc) amino acid chlorides asefficient coupling reagents for the synthesis of 100% diastereopure peptides and resin boundtetrathiomolybdate as an effective deblocking agent for the Poc group”. Chem. Commun. 2002, 812-813.
 
Sridhar, P. R.; Sinha, S.; Chandrasekaran, S. “Highly selective deprotection of tert-butyl estersusing ytterbium triflate as a catalyst under mild conditions”. Indian Journal of Chemistry, SectionB, 2002, 41B(1), 157-160.
 
Sinha, S.; Mandal, B.; Chandrasekaran, S. “Insertion of ethyl acetate to aromatic compounds by meansof Friedel-Crafts reaction with -chloro--(ethylthio)-acetate catalyzed by ytterbium triflate.” Tetrahedron Lett. 2000, 41, 9109-9112.
 
Sinha, S.; Mandal, B.; Chandrasekaran, S. “Selective para metalation of 3-methoxy and 3,5-dimethoxy benzoic acids with LIC-KOR: synthesis of 3,5-dimethoxy-4-methyl benzoic acid”. Tetrahedron Lett.2000, 41, 3157-60.
 
Sinha, S.; Ilankumaran, P.; Chandrasekaran, S. “The prop-2-ynyloxy carbonyl function (POC):a new amino-protecting group removable from sulfur-containing peptides by ultrasonicirradiation with tetrathiomolybdate under mild and neutral conditions”. Tetrahedron Lett. 1999, 40, 771-774.
 
Ravikumar, K. S.; Sinha, S.; Chandrasekaran, S. “Diastereoselectivity in the reduction of acycliccarbonyl compounds with diisopropoxytitanium(III) tetrahydroborate”. J. Org. Chem. 1999, 64, 5841-5844.
 
Sinha, S.; Ilankumaran, P.; Chandrasekaran, S. “One pot conversion of alcohols to disulfides mediated by tetrathiomolybdate”. Tetrahedron. 1999, 55, 14769-14776.

 


Teaching

  • Organic Synthesis-I; Subject Code(s): CHS4203 (for SCS)

  • Oragnic Chemistry-II; Subject Code(s): AIS4201 (for SAIS)/ PHD208

  • Drug Design and Delivery; Subject Code(s):AIS5103/ PHD114


Facilities

  • Synthetic Organic Chemistry Lab(M-048)
  • Oligosynthesizer for RNA/DNA Synthesis(M-154,B)
  • Molecular Biology and Zebrafish Lab (M-052)
  • Cell culture Lab(M-044)


Patents

1) Sinha, S.; Pattanayak, S.; Paul, S.; Nandi, B.  Morpholino based antisense agent. WO 2011/018798, US20120296087; File no. IACS/NPA04/2009; Office filing no. 1059/KOL/2009. International publication date 17.02.2011. US 9,914,745B2, date of patent 13th March, 2018

2) Sinha, S.; Pattanayak, S. Substituted Internal Ologo-Guanidines As Cellular Penetrating Agents. 71/KOL/2013 dated 21th January, 2013.

3) Sinha, S.; Das, S.; Banerjee, T.; Paul, S. Isoquinuclidine Derivatives as Antinociceptive Agents for Pain Relief. 946/KOL/2014 dated 16th September,2014.

4) Sinha, S.; Bhadra, J.; Pattanayak, S.; Kundu, J. OLIGO-GUANIDINES composed of heterocyclic rings with hydrophobic/ lipophilic group at the N-terminal based cellular transporter for effective delivery of nonpenetrable cargos in vitro and in vivo 1328/KOL/2015, 23.12.2015, PCT/IN2016/000150, 10th June, 2016.

5) Sinha, S.; Kundu, J.; Bhadra, J. MMTr-protected H-phosphonate monomers and MMTr-deprotection by organic acids are the right combination of morpholino oligonucleotides synthesis (Patent Application No. as 201631037420, 2nd November, 2016).

6) Sinha, S. and Shastry, A. jointly with DART, Bengaluru “IGT Conjugated Antisense Oligonucleotides for inducing exon skipping in Duchenne Muscular Dystrophy.” Ref. No./Application No: 201741040678; App. Number: TEMP/E- 1/41357/2017- CHE


Alumni

Ph.D Awarded and current position:

1) Dr. Goutam Kumar Jana. Now at Pharma Co. ChemBiotek.

  1. Thesis Title: Studies directed towards the synthesis of indolazepine-based alkaloid called "Ibogaine and its analogues".
  2.  

2) Dr. Sankha Pattanayak. Postdoctoral Research Associate under Prof. James K. Chen Group, Chemical & Systems Biology, School of Medicine, Stanford University, USA.

  1. Thesis Title: 
  2.  

3) Dr. Sibasish Paul. Postdoctoral Research Associate under Prof. Marvin H Caruther's group at the Department of Chemistry & Biochemistry, University of Colorado, Boulder, USA. now as a scientist in Agilent Technologies, Colorado, USA. 

  1. Thesis Title: Synthesis and biological evaluation of alkaloids and modified nucleotides.
  2.  

4) Dr. Koushik Goswami. Post Doctoral Research Fellow under Dr. Stéphane P. Roche at the Department of Chemistry and Biochemistry, Florida Atlantic University. At present a guest Lecturer in Belur Ramkrishna Mission Vidyamandir and Research Associate by Kothari fellowship (UGC) in Kalyani University. At present Assistant professor in Amity University, Kolkata.

  1. Thesis Title: 
  2.  

5) Dr. Amrita Chakraborty. Research Associate by Kothari fellowship (UGC) in Visva Bharati University, Santiniketan, W. B. and also a guest lecturer. At present Assistant Professor, A. N. College, Patna.

  1. Thesis Title: 
  2.  

6) Dr. Indranil Duttagupta. Postdoctoral Research Associate under Prof. Gérard Audran in Aix-Marseille University, France. At present Durham University, UK.

  1. Thesis Title: Synthesis and biological applications of artificial amino acids.
  2.  

7) Dr. Bappaditya Nandi. Research Associate in my lab (2015 to till date). At present Assistant Professor in Budge Budge Engineering College, Kolkata.

  1. Thesis Title: Synthesis of modified morpholino nucleoside monomers, cationic oligomers and their cellular transfection studies.
  2.  

8) Dr. Jhuma Bhadra. Post doctoral fellow at Clemson University, USA (May 2017). At present March 1 st Boston College.

  1. Thesis Title: 
  2.  

9) Dr. Harleen Khatra. Assistant Professor, SUS College of Engineering.

  1. Thesis Title: 
  2.  

10) Dr. Keshab Chandra Ghosh. now at IOCL.

  1. Thesis Title: Synthesis of biologically important cyclic peptides non proteinogenic amino acids and peptides.
  2.  

11) Dr. Isita Banerjee. now at Chembiotek, Kolkata.

  1. Thesis Title: Development of methodology for C-2 Arylation of Indoles and synthesis of Mercaptophenylalanines and their peptides.
  2.  

12) Dr. Jayanta Kundu. now at Alnylam Pharmaceuticals, USA.

  1. Thesis Title: Design and synthesis of cellular transporter as a novel delivery vehicle for antisense oligonucleotides and towards the development of antisense therapy for the treatment of duchenne muscular dystrophy.
  2.  

13) Dr. Chandra Bose.

  1. Thesis Title: Regulation of Hedgehog Signaling by Chemical Tools.
  2.  

14) Dr. Ujjwal Ghosh. Research Scientist at GenELixir India Ltd, Visakhapatnam.

  1. Thesis Title: Exploring PMOs from different perspectives: A novel synthesis strategy of 5’-thiol functionalization and incorporation of guanidinium groups in their delivery.

 

Research Associate Alumni:

1) Dr. Pragya P. Khan (DBT RA-1 for 3 years, Ph.D in Zoology, Visva Bharati University). At present working as a post doc Sunnyvale, California.

2) Dr. Priyanjalee Banerjee, (DBT RA-1), now Assisstant Professor, Raiganj Surendranath Mahavidyalaya, Raiganj. 

3) Dr. Ujjwal Das, (RA-1), now at Rutgers University, New Jersey, USA.

4) Dr. Pallab Shaw, (RA-1), now at University of Oklahoma (Health Stephenson Cancer Centre), USA.

 

Project Students Alumni(2019 and later):

 

1) Ms. Shreya Sinha (IntPhD, SAIS, project duration: July 2019-March 2020)

2) Mr. Abhishek Barua (IntPhD, SBS, project duration: June 2019-March 2020)

3) Ms. Shayari Bhattacharya (IntPhD, SAIS, project duration: June 2020-May 2021)

4) Ms. Firdaus Ahmed (IntPhD, SBS, project duration: June 2020-May 2021)

5) Mr. Swapnendu Deb (IntPhD, SAIS, project duration: September 2021-June 2022)

6) Ms. Neha Poddar (IntPhD, SAIS, project duration: September 2021-June 2022) 

7) Ms. Gargi Sarkar (IntPhD, SAIS, project duration: September 2022-May 2023)

8) Mr. Rohan Sharma (IntPhD, SAIS, project duration: September 2023-June 2024)

9) Mr. Bikram Das (IntPhD, SAIS, project duration: September 2023-June 2024)

10) Ms. Latanjali Maharana (IntPhD, SAIS, project duration: September 2023-June 2024)

11) Mr. Arpan banerjee (BS-MS, project duration: September 2022-June 2024)

 


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