Atomistic Simulations and Design in Biology
Dr. VERMA Chandra
Senior Principal Investigator

Group Members
Dr. VERMA Chandra Principal Investigator
Dr. LAMA DilrajResearch Scientist
Dr. NGUYEN Ngoc MinhResearch Scientist
Dr. KANNAN SrinivasaraghavanResearch Scientist
Dr. KHARE Shruti VijayPostdoctoral Fellow
Dr. FOX Stephen JohnPostdoctoral Fellow
Dr. TAN Yaw SingPostdoctoral Fellow
Dr. PRADHAN Mohan Rajan Postdoctoral Fellow
Dr. KUMAR AkshitaPostdoctoral Fellow - NTU
Dr. ARONICA PietroPostdoctoral Fellow
Dr. LI JianguoPostdoctoral Fellow - SERI
Dr. MALIK Ashar JamilPostdoctoral Fellow
Dr. YADAHALLI ShilpaPostdoctoral Fellow
Dr. THANH BINH NguyenPostdoctoral Fellow
Ms. SRINIVASAN Harini PhD student
Mr. SHIVGAN Aishwary Tukaram PhD student
Ms. MHOUMADI Yasmina PhD student
Ms. REID Lauren Marie PhD student
Ms. COWAN Megan Butler PhD student
Mr. Dale Stuchfield * PhD student
Dr. LIU Wei Collaborator
Research Overview

A combination of modeling, virtual screening and molecular dynamics in various flavours are used to understand the changing shapes and characters of biomolecules and their associated interactions with other biomolecules or small molecules/peptides. The work builds upon foundations that are rooted in rigorous computational biochemistry benchmarked extensively against available experimental data. We then combine our models with detailed experimental investigations to provide incisive insights into biology at an atomic level (EMBO Reports 9:144; 2008). Our current research attempts to bridge basic structural/computational biophysical chemistry with the mysteries of the p53 pathway, kinases, translation initiation, ion-channels, antibodies and translate our findings towards development of novel therapeutics including stapled peptides to tackle infections, cancer, inflammation and the menace of resistance. We work closely with experimental, clinical and pharma partners.
More Details

Selected Publications
  1. Liu BH, Jobichen C, Chia CSB, Chan THM, Tang JP, Chung TXY, Li J, Poulsen A, Hung AW, Koh-Stenta X, Tan YS, Verma CS, Tan HK, Wu CS, Li F, Hill J, Joy J, Yang H, Chai L, Sivaraman J, Tenen DG.
    Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide.
    Proc Natl Acad Sci USA. 2018 Jul 5. pii: 201801253. doi: 10.1073/pnas.1801253115.

  2. Kannan S, Venkatachalam G, Lim HH, Surana U, Verma C.
    Conformational landscape of the epidermal growth factor receptor kinase reveals a mutant specific allosteric pocket.
    Chem Sci. 2018 9:5212. doi: 10.1039/c8sc01262h.

  3. Iegre J, Ahmed NS, Gaynord JS, Wu Y, Herlihy KM, Tan YS, Lopes-Pires ME, Jha R, Lau YH, Sore HF, Verma C, O' Donovan DH, Pugh N, Spring DR.
    Stapled peptides as a new technology to investigate protein-protein interactions in human platelets.
    Chem Sci. 2018 Apr 25;9(20):4638-4643. doi: 10.1039/c8sc00284c.

  4. Lama D, Pradhan MR, Brown CJ, Eapen RS, Joseph TL, Kwoh CK, Lane DP, Verma CS.
    Water-Bridge Mediates Recognition of mRNA Cap in eIF4E.
    Structure. 2017 Jan 3;25(1):188-194. doi: 10.1016/j.str.2016.11.006.

  5. Tan YS, Reeks J, Brown CJ, Thean D, Ferrer Gago FJ, Yuen TY, Goh ET, Lee XE, Jennings CE, Joseph TL, Lakshminarayanan R, Lane DP, Noble ME, Verma CS.
    Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.
    J Phys Chem Lett. 2016 Sep 1;7(17):3452-7. doi: 10.1021/acs.jpclett.6b01525.

  6. Castel P, Ellis H, Bago R, Toska E, Razavi P, Carmona FJ, Kannan S, Verma CS, Dickler M, Chandarlapaty S, Brogi E, Alessi DR, Baselga J, Scaltriti M.
    PDK1-SGK1 Signaling Sustains AKT-Independent mTORC1 Activation and Confers Resistance to PI3Kα Inhibition.
    Cancer Cell. 2016 Aug 8;30(2):229-242. doi: 10.1016/j.ccell.2016.06.004.

  7. Petrone L, Kumar A, Sutanto CN, Patil NJ, Kannan S, Palaniappan A, Amini S, Zappone B, Verma C, Miserez A.
    Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins.
    Nat Commun. 2015 Oct 28;6:8737. doi: 10.1038/ncomms9737.

  8. Hoe KK, Verma CS, Lane DP.
    Drugging the p53 pathway: understanding the route to clinical efficacy.
    Nat Rev Drug Discov 13(3):217-236 (2014).

  9. Goh Wa, Lee MY, Joseph T, Quah S, Brown C, Verma C, Brenner S, Ghadessy F, Teo YN.
    Molecular rotors as conditionally fluorescent labels for rapid detection of biomolecular interactions.
    J Amer Chem Soc 2014 Apr 30;136(17):6159-62.

  10. Goudie DR, D'Alessandro M, Merriman B, Lee H, Szeverényi I, Avery S, O'Connor BD, Nelson SF, Coats SE, Stewart A, Christie L, Pichert G, Friedel J, Hayes I, Burrows N, Whittaker S, Gerdes AM, Broesby-Olsen S, Ferguson-Smith MA, Verma C, Lunny DP, Reversade B, Lane EB.
    Multiple self-healing squamous epithelioma is caused by a disease-specific spectrum of mutations in TGFBR1.
    Nat Genet. 2011 Feb 27;43(4):365-9. doi: 10.1038/ng.780.

  11. Cheok CF, Verma CS, Baselga J, Lane DP.
    Translating p53 into the clinic.
    Nat Rev Clin Oncol. 2011 Jan;8(1):25-37. doi: 10.1038/nrclinonc.2010.174. Review.

  12. Brown CJ, Lain S, Verma CS, Fersht AR, Lane DP.
    Awakening guardian angels: drugging the p53 pathway.
    Nat Rev Cancer. 2009 Dec;9(12):862-73. doi: 10.1038/nrc2763. Review.

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