Umesh Prasad Singh , Ph.D. ( IISc, Bengaluru)

Senior Principal Scientist
Infectious Diseases and Immunology
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Research Focus

Drug Discovery (anti-viral for dengue and SARS-Cov2), Computational Chemistry, Molecular modeling, Structural Biology, Structural Chemistry (non-coded amino acid based peptides)

Research Interest

Discovery scientist in preclinical translational research for about 20 years

Drug Discovery achievements:

  • Part of the discovery team that characterized atomic resolution structure of the ribonuclease ONCONASE. As part of the confirmatory stage of phase III, the U.S. Food and Drug Administration (FDA) has given Onconase orphan and fast-track drug status for Malignant Pleural Mesothelioma.
  • Part of the innovation teams that innovated the molecule Licogliflozin, which is currently in human clinical trials (Phase-II) for Diabetes Mellitus-2.
  • Part of the innovation teams that innovated the molecule GKM-001, which successfully completed Phase-Ib clinical trials and is about to enter Phase II for Diabetes Mellitus-2.
  • Part of innovation teams that have innovated selective JAK kinases (for RA, SLE and other autoimmune and inflammatory diseases), BTK kinases (for MCL, CLL and RA etc.) and FAAH inhibitors as potent antinociceptive therapeutic agents. 

Translational Drug discovery - areas of experience (mainly industry based): 

  • Translation Drug discovery areas: Present focus is mainly Infectious viral diseases like dengue and SARS-Cov2. Earlier experience (mainly industry based): Metabolic diseases (Diabetes, Asthma, allergy, COPD, IBD), Alzheimer’s, Pain/Inflammation, and ribonuclease based protein cancer-therapeutics
  • Drug targets like viral proteases, GPCRs, Kinases, solute transporter(s), and their role in different diseases, solving problems of developing therapeutics through understanding molecular mechanisms
  • Structure/ligand based drug design, Protein homology modeling, Molecular modeling of proteins/ protein-drug complexes, High Throughput Virtual Screening (HTVS), Pharmacophore based modeling, molecular docking, molecular dynamics, compound database management
  • Protein-based activity assays, biophysical assays
  • X-ray crystallographic studies of proteins, peptides, protein-ligand complexes
  • Design of novel non-coded amino acid based peptides, peptide-based inhibitors as anti-viral agents
  • Natural product discovery for therapeutic applications (anti-viral and anti-cancer)

 

Credentials

Ph.D, Science (Structural Biology/ Biophysics), Indian Institute of Science (IISc), Bangalore [1997 – 2004].

MSc (Research), Interdisciplinary (physics & Chemistry), Institute of Chemical Technology (ICT) Mumbai [1993 – 1996]. 

BSc, Physics (Major), Chemistry and Mathematics, DG Ruparel College, University of Mumbai [1989 – 1992].

 

Patents & Publications

  1. Solid-state green synthesis of two (1:1) organic intermolecular compounds; their physico-chemical, thermal, single crystal growth, and atomic packing studies , Sumit Chaudhary, Rama Nand Rai, Deeti Jyothi, Umesh Prasad Singh, Abhinav Kumar, Materials Chemistry and Physics,Volume 322, 1 August 2024, 129541. https://doi.org/10.1016/j.matchemphys.2024.129541
  2. Melatonin Inhibits AGS Cell Proliferation by Binding to the ATP Binding Site of CDK2 Under Hyperglycemic Conditions; Abhishek Chatterjee, Tapasi Roy, Deeti Jyothi, Vineet Kumar Mishra, Umesh Prasad Singh, Snehasikta Swarnakar; Cell Biochem Biophys 2024 Mar 7. ( https://doi.org/10.1007/s12013-024-01241-9.)
  3. Swietenolide isolated from Swietenia macrophylla King in Hook seeds shows in vitro anti-colorectal cancer activity through inhibition of mouse double minute 2 (MDM2) homolog; Purna Chandra Pal, Sayoni Nag, Deeti Jyothi, Sudesna Das, Krishna Das Saha and Umesh Prasad Singh; Natural Products Research, 2023 ( https://doi.org/10.1080/14786419.2023.2233045.)
  4. Targeting DPP4-RBD interactions by sitagliptin and linagliptin delivers a potential hostdirected therapy against pan-SARS-CoV-2 infections; Shailendra Mani, Anupamjeet Kaur, Kamini Jakhar, Geetika Kumari, Sudipta Sonar, Amit Kumar, Sudesna Das, Santosh Kumar, Vijay Kumar, Rakesh Kundu, Anil Kumar Pandey, Umesh Prasad Singh and Tanmay Majumdar; Int J Biol Macromol. 2023 Aug 1; 245: 125444; Published online 2023 Jun 27. https://doi.org/10.1016/j.ijbiomac.2023.125444
  5. Solid state synthesis, thermal, spectral, optical, crystal structure and atomic packing studies of 2-(3-Hydroxyphenyl)-2,3-dihydroquinazolin-4(1H)-one, Sumit Chaudhary, R.N. Rai, Deeti Jyothi, Umesh Prasad Singh, Materials Lett. (2023); 341; 134253 (https://doi.org/10.1016/j.matlet.2023.134253)
  6. Design and synthesis of novel spirocyclic carboxylic acids as potent and orally bioavailable DGAT1 inhibitors and their biological evaluation, Summon Koul, Suresh Kurhade, Sandeep Bhosale, Keshav Naik, Videsh Salunkhe, Sudhir Ravula, Prasad Punde, Ravikumar Velayutham, Atul Tiwari, Daniela Ahl, Srividya Malkapuram, Vamsi Mudagala, Amol Raje, Dhananjay Umrani, Suhas Tambe, Poonam Patil, Umesh Singh, Debnath Bhuniya, Narayanan Hariharan, Kasim Mookhtiar  Bioorg. Med. Chem. Lett. (2022); 62: 128632 ( https://doi.org/10.1016/j.bmcl.2022.128632 )
  7. Conformation of Achiral α/β Hybrid Peptides Containing Glycine and 1-Aminocyclohexaneacetic Acid Sudha Shankar, Deeti Jyothi, Junaid ur Rahim, Purna Chandra Pal, Umesh Prasad Singh* and Rajkishor Rai* ChemistrySelect (2022), 7(10), e202104453 ( https://doi.org/10.1002/slct.202104453 )
  8. Therapeutic Effect of Combinatorial Probiotics to Protect Intestinal Barrier Function, Rintu Das, Srabani Kar, Silpak Biswas, Umesh P Singh and Ena Ray Banerjee, EC Microbiology 9.2 (2017): 84-95
  9. Tamarixetin 3-O-β-d-Glucopyranoside from Azadirachta indica Leaves: Gastroprotective Role through Inhibition of Matrix Metalloproteinase-9 Activity in Mice, Yadav DK, Bharitkar YP1, Hazra A1, Pal U, Verma S, Jana S, Singh UP, Maiti NC, Mondal NB, Swarnakar S., J Nat Prod. 2017 May 26;80(5):1347-1353 ( https://doi.org/10.1021/acs.jnatprod.6b00957 )
  10. C11/C9 Helical Folding in αβ Hybrid Peptides Containing 1-Amino-cyclohexane acetic acid (β3, 3-Ac6c) Naiem Ahmad Wani, Srinivasarao Raghothama,Umesh Prasad Singh,* and Rajkishor Rai* Chem. Eur. J. 2017 DOI: 10.1002/chem.201700265 ( https://doi.org/10.1002/chem.201700265 )
  11. Incipient Twisted Ribbon Structure Stabilized by C 12 Helical Turns in γ 4 /α Hybrid Peptide Sudha Shankar · Naiem Ahmad Wani · Umesh Prasad Singh* · Rajkishor Rai* ChemistrySelect (2016), 1(13):3675-3678 ( https://doi.org/10.1002/slct.201600793 )
  12. Folded Structure Stabilized by C7, C10 and C12 Hydrogen Bonds in α/γ Hybrid Peptides Naiem Ahmad Wani, Vivek Kumar Gupta, Umesh Prasad Singh, Subrayashastry Aravinda, and Rajkishor Rai * ChemistrySelect (2016), 1, 1674 – 1677 ( https://doi.org/10.1002/slct.201600389 )
  13. Anti-Oxiflammatory profile of date extracts (Phoenix sylvestris) Rintu Das, Shinjini Mitra, Kaustab Mukherjee, Umesh P. Singh, Ena Ray Banerjee Biomedical Research and Therapy (2015) 2(6): 297-317 ( https://doi.org/10.15419/bmrat.v2i06.53 )
  14. Anti-Oxidant and Anti-Inflammatory Activities of Different Varieties of Piper Leaf extracts (Piper betle L.), Rintu Das, Shinjini Mitra, Kaustab Mukherjee, Pramathadhip Paul, Umesh P. Singh, and Ena Ray Banerjee J Nutr Food Sci (2015), 5(5) 415. http://dx.doi.org/10.4172/2155-9600.1000415
  15. Substituted fused tricyclic compounds, compositions and medicinal applications thereof Barawkar, Dinesh; Bende, Tanushree ; Zahler, Robert; Bandyopadhyay, Anish; Sarangthem, Robindro Singh; Doshi, Jignesh; Waman, Yogesh; Jadhav, Rushikesh, Singh, Umesh Prasad.United States Patent Application: US2014/0023614 A1 · Filed: 03/21/2012 · Published: 01/23/2014 ( https://patents.google.com/patent/US9115133B2/en )
  16. Bicyclic compounds, compositions and medicinal applications thereof  Thakkar, Mahesh; Koul, Summon; Bhuniya, Debnath; Singh, Umesh. , WIPO Patent Application: WO/2013/157021 A1 · Filed: 04/18/2013 · Published: 10/24/2013 ( https://patents.google.com/patent/WO2013157021A1/en )
  17. Amide compounds, compositions and applications thereof Kharul, Rajendra; BHUNIYA, Debnath;  MOOKHTIAR, Kasim A.; SINGH, Umesh; HAZARE, Atul ; PATIL, Satish; DATRANGE, Laxmikant; THAKKAR, Mahesh. WIPO Patent Application WO/2013/042139 A1 · Filed: 09/21/2012 · Published: 03/28/2013  ( https://patents.google.com/patent/WO2009110985A2/en )
  18. Discovery of pyrazole carboxylic acids as potent inhibitors of rat long chain L-2-hydroxy acid oxidase , Dinesh A. Barawkar,§,* Anish Bandyopadhyay,§ Anil Deshpande,§ Summon Koul,§ Sachin Kandalkar,§ Pradeep Patil,§ Goraksha Khose,§ Samir Vyas,§ Mahesh Mone,§ Shubhangi Bhosale,§ Umesh Singh,§ Siddhartha De,§ Ashwin Meru,§ Jayasagar Gundu,§Anita Chugh,§ Venkata P. Palle,§ Kasim A. Mookhtiar,§ Joseph P. Vacca,† Prasun K. Chakravarty,† Ravi P. Nargund,† Samuel D. Wright,† Sophie Roy,†Michael P. Graziano,† Doris Cully,† Tian-Quan Cai,† Sheo B. Singh†.  J. Biog Med Chem Lett, Volume 22 (2012) 4341-4347.  ( https://doi.org/10.1016/j.bmcl.2012.05.020 )
  19. Discovery of novel and potent  heterocyclic carboxylic acid derivatives as Protein Tyrosine Phosphatase 1B inhibitors, Sujay Basu, Uppuleti Viplava Prasad, Dinesh A. Barawkar, Suraj Menon, Siddhartha De, Meena S Patel,Venkata P Palle, Sachin Thorat, Umesh P. Singh, Yogesh Waman, Sanjay Niranjan, Vishal Pathade, Ashwani Gaur. Bioorganic & Medicinal Chemistry Letters, Volume 22 (2012), Pages 2843-2849) ( https://doi.org/10.1016/j.bmcl.2012.02.070 )
  20. Potent and Selective Inhibitors of Long Chain L-2-Hydroxy Acid Oxidase-2 Reduced Blood Pressure in DOCA-Salt Treated Rats. Dinesh A Barawkar, Ashwin Meru, Anish Bandyopadhyay, Abir Banerjee, Anil M Deshpande,Chandrashekhar Athare, Chandrasekhar Koduru, Goraksha Khose, Jayasagar Gundu, Koshu Mahajan, Pradeep Patil, Sachin R Kandalkar, Sanjay Niranjan, Shubhangi Bhosale, Siddhartha De, Sudit Mukhopadhyay, Sumit Chaudhary, Summon Koul, Umesh Singh, Anita Chugh, Venkata P. Palle, Kasim A Mookhtiar, Joseph Vacca, Prasun K Chakravarty, Ravi P. Nargund, Samuel, D. Wright, Sophie Roy, Michael P Graziano, Sheo Bux Singh, Doris Cully, and Tian-Quan Cai, ACS Med. Chem. Lett. (2011), 2, 919−923 ( https://doi.org/10.1021/ml2001938 )
  21. Crystal structure of Onconase at 1.1-Å resolution. Insights into substrate binding and collective motion. Daniel E. Holloway, Umesh P. Singh, Kuslima Shogen and K. Ravi Acharya FEBS Journal 278 (2011) 4136–4149. ( https://doi.org/10.1111/2Fj.1742-4658.2011.08320.x )
  22. Structure of a Cyclic Water Tetramer in a Nucleotide Crystal Host and a Hypothetical Model for Water Cluster Growth. Umesh Prasad Singh* J. Mol Structure (2010) 983, 73-75. ( https://doi.org/10.1016/J.MOLSTRUC.2010.08.034 )
  23. Enzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes, Umesh P. Singh, Wojciech Ardelt, Shailendra K. Saxena, Daniel E. Holloway, Eugene Vidunas, Hung-Suen Lee, Abha Saxena, Kuslima Shogen and K. Ravi Acharya, J. Miol. Biol. (2007) 371, 93-111 ( https://doi.org/10.1016/j.jmb.2007.04.071 )
  24. Correlating Miscibility of PVC/PMMA blend with Polymer Chain Orientation.  Vineeta D. Deshpande and Umesh Singh*. J. Appl. Polym. Sci. (2006). 101, 624-630. ( https://doi.org/10.1002/app.23322 )
  25. Ethyl 2-[N-(tert-butyloxycarbonyl)-L-alanylamino]-4-methyl-1, 3-thiazole-5-carboxylate reveals a trans orientation of the preceding amide N-H with respect to the thiazole-ring sulfur. Umesh Prasad Singh, Mini Thomas, T.P. Seshadri and Shantanu Bhattacharya.  Acta. Cryst. (2000) C56, 1482-1483. ( https://dx.doi.org/10.1107/S0108270100012439 )
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