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Computer-aided Drug Design
Computer-aided Drug Design
Computational approaches such as Site-Identification by Ligand Competitive Saturation for Drug Design (SILCS) in combination with structural biology aim to facilitate the discovery of novel therapeutic agents in rational drug design. In searching of drug-like inhibitors of B-cell lymphoma 6 BTB domain (BCL6) for anti-cancer therapeutics, SILCS method has proved to help identify a thiourea compound scaffold (7CC5) and analogs that bind to BCL6 BTB domain, which demonstrated over 100-fold improved potency.
Publications
- Cheng, Huimin; Linhares, Brian; Yu, Wenbo; Cardenas, Mariano; Ai, Yong; Jiang, Wenjuan; Melnick, Ari; MacKerell, Alex; Cierpicki, Tomasz; Xue, Fengtian. Thiourea-Based Inhibitors of the BCL6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design, Journal of Medicinal Chemistry, 2018 [DOI]
Drug-Specific Design Using Coarse-grained Martini Model
Drug-Specific Design Using Coarse-grained Martini Model
Computational Molecular dynamics have been widely used to investigate molecular level information such as molecular packing and interactions in computer-aided drug design. For macromolecules like polymers, micelles, nanoparticles used in drug delivery, CG Martini force field model is powerful in simulating the self-assembly process, preserve the chemical properties while reducing the number of particles in the system. This model is successfully used to design a novel nanoparticle platform called "Telodendrimers" for effective drug (like paclitaxel and doxorubicin) encapsulation together with experimental scientists in Juntao Luo's group.
PTX200.mpgSelf-Assembly Process: Box size=30nm; Simulation time= 1.5 microseconds; Temperature=300K; 17% weight percentage Paclitaxel (PTX) drug loading PEG5KCA8 system, PTX (=270 molecules) in Orange ; PEG in Gray; Lysine in Red; Cholic acid in Blue; Water (=196,276 molecules )not shown, CPU: Intel R Xeon(R) @2.20 GHz, Simulation was finished in 2014@Syracuse University Synergy Clusters.
Publications
- Wenjuan Jiang, Juntao Luo, and Shikha Nangia, “Multiscale approach to investigate self?assembly of telodendrimer based nanocarriers for anticancer drug-delivery”, Langmuir, 31, 4270-4280, 2015 [DOI]
- Wenjuan Jiang, Xiaoyi Wang, Dandan Guo, Juntao Luo, and Shikha Nangia, “Drug-Specific Design of Telodendrimer Architecture for Effective Doxorubicin Encapsulation” J. Phys. Chem. B, 120(36), 9766-9777, 2016 [DOI]
- Reem Eldawud, Manuela Reitzig, Jörg Opitz, Yon Rojansakul, Wenjuan Jiang, Shikha Nangia, and Cerasela Zoica Dinu. “Combinatorial approaches to evaluate nanodiamond uptake and induced cellular fate”, Nanotechnology, 27(8), 085107, 2016 [DOI]
- Huilin Ma, Flaviyan Jerome Irudayanathan, Wenjuan Jiang, and Shikha Nangia, “Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model”, J. Phys. Chem. B, 119, 14668-14682, 2015 [DOI]
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