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Senior Scientist
sahmed [at] thsti [dot] res [dot] in
Staff Scientist, Drug Discovery and Structural Biology Core Facility. Beckman Research Institute, City of Hope, Duarte, California, USA.
Research Associate. Beckman Research Institute, City of Hope, Duarte, California, USA.
Research Associate. University of Southern California (USC), Keck School of Medicine, Department of Medicine, Los Angeles, California, USA.
Ph.D. Institute of Microbial Technology (IMTECH), Chandigarh, India.

The HIV/AIDS pandemic is a serious global health problem with high levels of morbidity and mortality. In 2015, India had more than 2 million people living with HIV/AIDS. Anti-retroviral therapy (ART) and other preventive measures have reduced the disease burden, prolonged life, and slowed down the HIV/AIDS epidemic. However, a vaccine against HIV-1 is expected to be the most efficient ways to control new infection and eradicate the disease. Traditional vaccine development approaches (inactivated, attenuated etc.) does not work for HIV for various reasons. Nonetheless, spontaneous generation of broad neutralizing antibodies (bNAbs) in 10-20% of HIV-1 infected patients suggests of the possibility of inducing protective antibody using suitable immunogens as vaccine.  

The only surface exposed antigen on the HIV viral surface is the envelope (Env) protein, gp140. The focus of my research is to develop protein subunit based vaccine against HIV-1. We use structure guided protein engineering work to design suitable (cleaved, trimeric native-like)  viral Env protein and characterize them by various biochemical (functional assays, antigenicity etc.) and biophysical (structure, stability etc.) methods for its appropriateness as vaccine candidate. 

Pubmed search: shubbir ahmed,

1.  Ahmed S*, Shrivastava T, Kumar N, Ozorowski G, Ward AB, Chakrabarti BK* (2017). Stabilization of a soluble, native-like trimeric form of an efficiently cleaved Indian HIV-1 clade C envelope glycoprotein. J Biol Chem. 292(20):8236-43. *Co-corresponding authors.

2. Yan S, Zhang H, Hou G, Ahmed S, Williams JC, Polenova T. (2015S) Internal Dynamics of Dynactin's CAP-Gly is Regulated by Microtubules and Plus End Tracking Protein EB1. J Biol Chem. 290(3):1607-22. 

3.   Chandrayan SK, Prakash S, Ahmed S, Guptasarma P. (2014)Hyperthermophile Protein Behavior: Partially-Structured Conformations of Pyrococcus furiosus Rubredoxin Monomers Generated through Forced Cold-Denaturation and Refolding.PLoS One 9(3):e80014. 

4.   Ahmed S,Xie, J, Horne, D and Williams JC. (2014) Photocleavable Dimerizer for the Rapid Reversal of Molecular Trap Antagonists. J Biol Chem 289(8):4546-52. (Report)

5.   Yan, S, Hou, G, Schwieters, CD, Ahmed S, Williams, JC, Polenova T. (2013) Three-Dimensional Structure of CAP-Gly Domain of Mammalian Dynactin Determined by Magic Angle Spinning NMR Spectroscopy: Conformational Plasticity and Interactions with End Binding Protein EB1. J Mol Biol 425(22):4249-69.

6.   Stuchell-Brereton MD, Siglin A, Li j, Moore JK, Ahmed S,Williams JC, Cooper JA. (2011) Functional interaction between dynein light chain and intermediate chain is required for mitotic spindle positioning. Mol Biol Cell 22(15):2690-701.

7.   Ahmed S, Sun S, Siglin AE, Polenova T, Williams JC. (2010) Disease-associated mutations in the p150Glued subunit destabilize the CAP-gly domain. Biochemistry 49(25):5083-5. (Rapid Report)

8.   Ahmed S,Guptasarma P. (2008) Design of a soluble mini-protein through tandem duplication of the minimally engineered beta hairpin 'tongue' motif of alpha-hemolysin. Biochimie90(6):957-67.

9.   Ahmed S, Shukla A, Guptasarma P. (2008) Folding behavior of a backbone-reversed protein: Reversible polyproline type II to beta-sheet thermal transitions in retro-GroES multimers with GroES-like features. Biochim Biophys Acta.–Proteins and Proteomics1784(6):916-23.

10. Ahmed S, Kapoor D, Singh B, Guptasarma P. (2008) Conformational behavior of polypeptides derived through simultaneous global conservative site-directed mutagenesis of chymotrypsin inhibitor 2. Biochim Biophys Acta.-Proteins and Proteomics1784(5):796-805.

11. Kapoor D, Kumar V, Chandrayan SK, Ahmed S,Sharma S, Dutt M, Singh B, Karthikeyan S, Guptasarma P. (2008) Replacement of the active surface of a thermophile protein by that of a homologous mesophile protein through structure-guided 'protein surface grafting. Biochim Biophys Acta.-Proteins and Proteomics 1784(11):1771-6.

12. Kapoor D, Kumar S, Ahmed S,Guptasarma P. (2007) Using DNA sequencing electrophoresis compression artifacts as reporters of stable mRNA structures affecting gene expression. Electrophoresis28(21):3862-7.

13. Das U, Hariprasad G, Ethayathulla AS,Manral P, Das TK, Pasha S, Mann A, Ganguli M, Verma AK, Bhat R, Chandrayan SK, Ahmed S, Sharma S, Kaur P, Singh TP, Srinivasan A. (2007) Inhibition of protein aggregation: supramolecular assemblies of arginine hold the key. PLoS One2(11):e1176.

1.      US provisional patent submitted

Title: Stabilized Indian Clade C ENV. Shubbir Ahmed, Tripti Shrivastava and Bimal Chakrabarti. (US Provisional Patent Application No. 62/407,729)


2.      US patent Submitted

Title:Photoclevable Linker. John C. Williams, David Horne, Jun Xie and Shubbir Ahmed. (US Patent Application No. 2014015477)


3.      US, EP and India patent approved

Title:A recombinant meso-active thermo-stable protein and the process of design and biosynthesis thereof. Divya Kapoor, Sanjeev Kumar, Shubbir Ahmed, Swati Sharma, Manish Dutt, Balvinder Singh, Karthikeyan Subramanian and Purnananda Guptasarma. (US Patent No. 11/936,009, EP patent No. 2099820, India Patent No. 2411/DEL/2006)


  • Selected for full scholarship to attend ‘HIV Research for Prevention 2016: AIDS Vaccine, Microbicide and ARV-based Prevention Science (HIVR4P)’ conference held at Chicago, USA, Oct., 2016
  • Bagged 2nd prize for project development in technological entrepreneurship workshop hosted jointly by Indian Institute of Management, Bangalore (IIMB) and CSIR, 2005.2
  • Council for Scientific and Industrial Research - Senior Research fellowship (CSIR-SRF), Govt. of India, 2004.7 - 2007.7
  • Council for Scientific and Industrial Research - Junior Research fellowship (CSIR-JRF), Govt. of India, 2002.6-2004.6
  • Nominated for CSIR-SPM Fellowship Exam. (top 20% among CSIR-NET qualifier), 2002
  • Graduate Aptitude Test for Engineering (GATE), 2001.