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Research Interests

1. Mutational Effects on Biomolecular Systems

One of the my main research interest includes understanding the effect of mutations on overall structure and dynamics of different bio-molecular systems. In these studies, molecular dynamics simulations and enhanced post-dynamics analyses were employed in order to understand the protein dynamics, free energy landscapes and several other parameters in order to understand the impact of mutations on bio-molecular dynamics and free energy landscape.

Softwares used: AMBER, UCSF Chimers, Visual Molecular Dynamics (VMD), Residue Interaction Network (RIN), H++, PCASuite, Maestro (academic version), LigPlot

rin_mbs

image courtesy:Bhakat S, Martin A and Soliman M.E. (2014) An Integrated Molecular Dynamics, Principal Component Analysis and Residue Interaction Network Approach Reveals the Impact of M184V Mutation on HIV Reverse Transcriptase Resistance to Lamivudine, Molecular Biosystems, 10, 2215-2228

2. Structure Based Drug Design towards Neglected Tropical Diseases

Neglected tropical diseases (NTDs) such as dengue virus (DENV), west nile virus (WNV) and chikungunya virus (CHIKV) re-emerged as a major global threat due to its recent outbreaks in several developed nations. Despite its rapid emergence, till date no approved drugs.vaccines were available in order to counter these NTDs. One of my main research interest is to design novel small molecule inhibitors targeting several non-structural proteins of these neglected viral diseases.

Targets of interest: Dengue NS2B-NS3 serine protease, WNV serine protease, CHIKV NSP2, CHIKV macrodomain

Techniques used: Combined structure and pharmacophore based drug design, MM/GBSA rescoring, biological testing

Softwares used: Autodock, ZINC Pharmer, ZINC, Mcule, AMBER, UCSF Chimera, Maestro (academic version), GLIDE, LigPlot

figure 4

image courtesy: Bhakat S, Karubiu W, Venkatesan J and Soliman M.E. (2014) A perspective on targeting non-structural proteins to combat Neglected Tropical Diseases: Dengue, West Nile and Chikungunya viruses, European Journal of Medicinal Chemistry, 87, 677-702 [LINK

3. Dimerization and Protein Folding

One of my key interest includes understanding dimerization of protein subunits in order to understand the inhibitor uptake mechanism as well as drug binding landscape.

Proteins of interests: Plasmepsin-II and V, HIV-NEF, HIV-Protease, BACE-1 & 2, Hsp90

Softwares used: AMBER, UCSF Chimera, VMD, Maestro (academic version), LigPlot

nef_picimage courtesy: Moonsamy S., Bhakat S. and Soliman M.E. (2014) Dynamic features of apo and bound HIV-Nef protein reveal the anti-HIV dimerization inhibition mechanism, Journal of Receptors and Signal Transduction, In Press [LINK]

 4. Other Interests

Besides these, my research interest also span across studies related to structure activity relationship, medicinal chemistry, biophyscics and bio-informatics


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