Jeremie Vendome

Overview

Jeremie Vendome

Titles

Senior Computational Scientist

Email
jv2202@columbia.edu

Lab

Barry Honig

Jeremie Vendome is a visiting research scientist in the lab of Barry Honig. He established a computer aided drug design (CADD) collaborative platform integrated with the Columbia Genome Center, and developed translational research collaborations with groups of clinicians, medicinal chemists, and structural biologists at the Columbia Medical Center. Currently, Jeremie also works as a principal scientist at Schrödinger, a leading computational chemistry company, where he is involved in scientific interactions with various Pharmaceutical companies as well as in drug discovery projects.

Jeremie completed his PhD in Computational Chemistry and Molecular Modeling in 2005 at the Ecole Normale Superieure de Cachan, in Paris. While completing his doctoral study, from 2001 to 2006, he also worked for a start-up biopharmaceutical company where he used CADD methods to help develop new tyrosine kinase inhibitors.   

In 2006, Jeremie joined Barry Honig’s lab at Columbia University as a postdoctoral research scientist where he conducted several research projects within multidisciplinary teams focused on protein design, protein binding specificity, and cell-cell adhesion. In 2012, Jeremie explored a new direction and acquired business skills as he worked as a business management consultant with the Boston Consulting Group. In 2014, he returned to Columbia to start the CADD platform.

Education History

PhD, Ecole Normale Superieure de Cachan, France
Computational Chemistry and Molecular Modeling

MPhil, Ecole Normale Superieure rue d’Ulm, Paris, France
Biomathematics, Bioinformatics and Biostatistics,

MSc, and BSc Ecole Normale Supereieure rue d’Ulm, Paris, France
Biology-Biochemistry

Publications

* Indicates authors contributed equally

Mann G, Huo L, Adam S, Nardone B, Vendome J, Westwood NJ, Müller R, Koehnke J. Structure and Substrate Recognition of the Bottromycin Maturation Enzyme BotP. Chembiochem. 2016 Dec 2;17(23):2286-2292.  

Deng C, Lipstein MR, Scotto L, Jirau Serrano XO, Mangone MA, Li S, Vendome J, Hao Y, Xu X, Deng SX, Realubit RB, Tatonetti NP, Karan C, Lentzsch S, Fruman DA, Honig B, Landry DW, O'Connor OA. Silencing c-Myc translation as a therapeutic strategy through targeting PI3K delta and CK1 epsilon in hematological malignancies. Blood. 2016 Oct 26.  

Petrou VI, Herrera CM, Schultz KM, Clarke OB, Vendome J, Tomasek D, Banerjee S, Rajashankar KR, Belcher Dufrisne M, Kloss B, Kloppmann E, Rost B, Klug CS, Trent MS, Shapiro L, Mancia F. Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation. Science. 2016 Feb 5;351(6273):608-12.

Qin W, Liu NN, Wang L, Zhou M, Ren H, Bugnard E, Liu JL, Zhang LH, Vendôme J, Hu JS, Xi XG. Characterization of biochemical properties of Bacillus subtilis RecQ helicase. J Bacteriol. 2014 Dec;196(24):4216-28.

Vendome J, Felsovalyi K, Song H, Yang Z, Jin X, Brasch J, Harrison OJ, Ahlsen G, Bahna F, Kaczynska A, Katsamba PS, Edmond D, Hubbell WL, Shapiro L, Honig B. Structural and energetic determinants of adhesive binding specificity in type I cadherins . Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):E4175-84.

Houssen WE, Koehnke J, Zollman D, Vendome J, Raab A, Smith MC, Naismith JH, Jaspars M. The discovery of new cyanobactins from Cyanothece PCC 7425 defines a new signature for processing of patellamides. Chembiochem. 2012 Dec 21;13(18):2683-9. 

Harrison OJ, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B, Shapiro L. Nectin ectodomain structures reveal a canonical adhesive interface. Nat Struct Mol Biol. 2012 Sep;19(9):906-15.

Koehnke J, Bent A, Houssen WE, Zollman D, Morawitz F, Shirran S, Vendome J, Nneoyiegbe AF, Trembleau L, Botting CH, Smith MC, Jaspars M, Naismith JH. The mechanism of patellamide macrocyclization revealed by the characterization of the PatG macrocyclase domain. Nat Struct Mol Biol. 2012 Aug;19(8):767-72.

Jin X*, Walker MA*, Felsövályi K*, Vendome J*, Bahna F, Mannepalli S, Cosmanescu F, Ahlsen G, Honig B, Shapiro L. Crystal structures of Drosophila Neural cadherin ectodomain region reveal a widely used class of Ca2+-free interdomain linkers. Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):E127-34.

Wu Y, Vendome J, Shapiro L, Ben-Shaul A, Honig B. Transforming binding affinities from three dimensions to two with application to cadherin clustering. Nature. 2011 Jul 27;475(7357):510-3.

Vendome J*, Posy S*, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B. Molecular design principles underlying beta-strand swapping in the adhesive dimerization of cadherins. Nat Struct Mol Biol. 2011 Jun;18(6):693-700.

Behnke-Parks WM, Vendome J, Honig B, Maliga Z, Moores C, Rosenfeld SS. Loop L5 acts as a conformational latch in the mitotic kinesin Eg5. J Biol Chem. 2011 Feb 18;286(7):5242-53. 

Harrison OJ, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, Wu Y, Vendome J, Felsovalyi K, Hampton CM, Troyanovsky RB, Ben-Shaul A, Frank J, Troyanovsky SM, Shapiro L, Honig B. The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure. 2011 Feb 9;19(2):244-56.

Koehnke J, Katsamba PS, Ahlsen G, Bahna F, Vendome J, Honig B, Shapiro L, Jin X. Splice form dependence of beta-neurexin/neuroligin binding interactions. Neuron. 2010 Jul 15;67(1):61-74.

Harrison OJ, Bahna F, Katsamba PS, Jin X, Brasch J, Vendome J, Ahlsen G, Carroll KJ, Price SR, Honig B, Shapiro L. Two-step adhesive binding by classical cadherins. Nat Struct Mol Biol. 2010 Mar;17(3):348-57. 

Ciatto C, Bahna F, Zampieri N, VanSteenhouse HC, Katsamba PS, Ahlsen G, Harrison OJ, Brasch J, Jin X, Posy S, Vendome J, Ranscht B, Jessell TM, Honig B, Shapiro L. T-cadherin structures reveal a novel adhesive binding mechanism. Nat Struct Mol Biol. 2010 Mar;17(3):339-47.

Katsamba P, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price S, Jessell TM, Ben-Shaul A, Shapiro L, Honig BH. Linking molecular affinity and cellular specificity in cadherin-mediated adhesion. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11594-9.

Vendôme J, Letard S, Martin F, Svinarchuk F, Dubreuil P, Auclair C, Le Bret M. Molecular modeling of wild-type and D816V c-Kit inhibition based on ATP-competitive binding of ellipticine derivatives to tyrosine kinases. J Med Chem. 2005 Oct 6;48(20):6194-201.