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Computer-Aided Drug Design Modeling & Simulation Lab



Mechanisms of Herb-Drug Interactions Involving Cinnamon and Cytochrome P450 2A6: Focus on Time-dependent Inhibition by Cinnamaldehyde and 2-Methoxycinnamaldehyde

Michael J. EspirituJustin ChenJaydeep YadavMichael LarkinRobert D. PelletierJeannine M. ChanJeevan B. GCSenthil Natesan, and John P. Harrelson.  Drug Metabolism and Disposition August 12, 2020,

Binding mode for cinnamaldehyde within the CYP2A6 catalytic binding site

Molecular dynamics simulations provide insight into the loading efficiency of pro-resolving lipid mediators resolvin D1 and D2 in cell membrane-derived nanovesicles.

 GC, Jeevan B.; Szlenk, Christopher T.; Gao, J.; Dong, X.; Wang, Z.; Natesan, Senthil. Molecular Pharmaceutics May 6, 2020.

Membrane partitioning of resolvins D1 and D2

Functional analysis of thirty-four suspected pathogenic missense variants in ALDH5A1 gene associated with succinic semialdehyde dehydrogenase deficiency

Pop, A. et al.  Molecular Genetics and Metabolism  May 4, 2020.


Does the lipid bilayer orchestrate access and binding of ligands to transmembrane orthosteric/allosteric sites of GPCRs?

Szlenk, Christopher T.; GC, Jeevan B.; Natesan, Senthil. Molecular Pharmacology 2019, 96(5): 527-541.  DOI:

Membrane-facilitated ligand binding to GPCR

Integrin activation by the lipid molecule 25-hydroxycholesterol induces a proinflammatory response.

Pokharel, Swechha M.; Shil, Niraj K.; GC, Jeevan B.; Colburn, Zachary T.; Tsai, Su-Yu; Segovia, Jesus A.,; Chang, Te-Hung; Natesan, Senthil*; Jones, Jonathan C. R.*; Bose, Santanu*. Nature Communications 2019.  10, Article Number: 1482 (2019). *These authors jointly supervised this work.

Outside-in activation of integrins by 25-hydroxycholesterol

Cannabiboid receptor 2 agonist JWH-015 inhibits interleukin-1β-induced inflammation in rheumatoid arthritis synovial fibroblasts and in adjuvant induced arthritis rat via glucocorticoid receptor.

Fechtner, Sabrina; Singh, Anil K.; Srivastava, Ila, Szlenk, Christopher T.; Muench, Tim R.; Natesan, Senthil and Ahmed, Salahuddin. Frontiers in Immunology: Autoimmune and Autoinflammatory Disorders. 2019, 10:1027-38


Tian, Dandan; Natesan, Senthil; White, John R.; Paine, Mary F. Effects of common CYP1A2 genotypes and other key factors on intraindividual variation in the caffeine metabolic ratio: An exploratory analysis.  Clin. Transl. Sci. 2019. 12(1):39-46 doi: 10.1111/cts.12598 (published on November 2, 2018)


Natesan, Senthil; Pai, Manjunath P.; Lodise, Thomas. Determination of alternative ceftolozane/tazobactam (C/T) dosing regimens for patients with infections due to Pseudomonas aeruginosa with high (C/T) MIC values. J. Antimicrob. Chemoth. 2017 DOI:10.1093/jac/dkx221 


Hassan, Hazem; Keita, Jean-Arnaud; Narayan, Lawrence; Brady, Sean; Frederick, Richard; Carlson, Samuel; Glass, Karen; Natesan, Senthil; Buttolph, Thomm; Fandy, Tamer. The combination of dimethoxycurcumin with DNA methylation inhibitor enhances gene re-expression of promoter-methylated genes and antagonizes their cytotoxic effect. Epigenetics 2016, 11(10), 740-749

Kim, Sophia; Natesan, Senthil; Cornilescu, Gabriel; Carlson, Samuel; Tonelli, Marco; McClurg Urszula L.; Binda, Olivier; Robson, Craig N.; Markley, John L.; Balaz, Stefan; and Glass, Karen C. Mechanism of histone H3K4me3 recognition by the plant homeodomain of inhibitor of growth 3. J. Biol. Chem. 2016, 291(35), 18326-41

2014 – 2015

Natesan, Senthil; Lukacova, Viera; Peng, Ming; Subramaniam, Rajesh; Lynch, Sandra; Wang, Zhanbin; Tandlich, Roman; Balaz, Stefan. Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases. Mol. Pharmaceutics. 2014, 11(10), 3577-3595

Poplawski, Amanda; Hu, Kaifeng; Lee, Woonghee; Natesan, Senthil; Peng, Danni; Carlson, Samuel; Neuhardt, Elizabeth; Shi, Xiaobing; Balaz, Stefan; Markley, John L.; Glass, Karen C. Novel molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. J. Mol. Biol. 2014, 426 (8), 1661-1676


Lukacova, Viera; Natesan, Senthil; Peng, Ming; Tandlich, Roman; Wang, Zhanbin; Lynch, Sandra; Subramaniam, Rajesh; Balaz, Stefan. Structural determinants of drug partitioning in surrogates of phosphatidylcholine bilayer strata. Mol. Pharmaceutics 2013, 10 (10), 3684–3696

Natesan, Senthil; Wang, Zhanbin; Lukacova, Viera; Peng, Ming; Subramaniam, Rajesh; Lynch, Sandra; Tandlich, Roman; Balaz, Stefan. Structural determinants of drug partitioning in n-hexadecane/water system. J. Chem. Inf. Model. 2013, 53 (6), 1424–1435

Natesan, Senthil; Balaz, Stefan. Rigorous incorporation of tautomers, ionization species, and different binding modes into ligand-based and receptor-based 3D-QSAR methods. Curr. Pharm. Design 2013, 19(23), 4316-4322


Natesan, Senthil; Subramaniam, Rajesh; Bergeron, Charles; Balaz, Stefan. Binding affinity prediction for ligands and receptors forming tautomers and ionization species: Inhibition of mitogen-activated protein kinase-activated protein kinase 2 (MK2) inhibitors. JMed. Chem. 2012, 55 (5), 2035–2047

Natesan, Senthil; Wang, Tiansheng; Khandelwal, Akash; Lukacova, Viera; Bartus, Vladimir; Subramaniam, Rajesh; Balaz, Stefan. Cell-QSAR: Conceptual dissection of receptor binding and intracellular disposition in antifilarial activities of Selwood antimycins. J.  Med. Chem. 2012, 55(8), 3699-3712

Muthaiyan, Arunachalam; Martin, Elizebath; Natesan, Senthil; Crandall, Philip G.; Ricke, Steven C. Antimicrobial Effect and Mode of Action of Terpeneless Cold Pressed Valencia Orange Essential Oil on Methicillin-Resistant Staphylococcus aureus. J. Appl. Microbiol. 2012, 112, 1020-1033

Chalova, Vesela I; Hernandez-Hernandez, Oswaldo; Muthaiyan, Arunachalam; Sirsat, Sujata A; Natesan, Senthil; Sanz, Maria Luz; Moreno, F. Javier; O’Bryan, Corliss A.; Crandall, Philip G.; Ricke, Steven C. Growth and transcriptional response of Salmonella Typhimurium LT2 to glucose-lysine-based Maillard reaction products generated under low water activity conditions. Food Res. Int. 2012, 45, 1044-1053


Natesan, Senthil; Wang, Tiansheng; Khandelwal, Akash; Lukacova, Viera; Bartus, Vladimir; Balaz, Stefan. Rigorous treatment of multi-species multi-mode ligand-receptor interactions in 3D-QSAR: CoMFA analysis of thyroxine analogs binding to transthyretin. J. Chem. Inf. Model. 2011, 51 (5), 1132-1150

Giotis, Efstathios S; Muthaiyan, Arunachalam; Natesan, Senthil; Wilkinson, Brian J; Blair, Ian S; McDowell, David A. Transcriptome analysis of alkali shock and alkali adaptation in Listeria monocytogenes Foodborne Pathog. Dis. 2010, 7(10), 1147-1157