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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 2020, 48(10), 1028-1043. Article LINK

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 2020, 17(6), 2155-2164.  Article LINK

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 2020, 130(3), 172-178. Article LINK


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.  Article LINK

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(1), 1482 (2019). Article LINK  *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 Article LINK


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