Dakshanamurthy Laboratory

Publications

Recent (20110 to present)

2014

  • Petrini I, Meltzer PS, Kim IK, Lucchi M, Park KS, Fontanini G, Gao J, Zucali PA, Calabrese F, Favaretto A, Rea F, Rodriguez-Canales J, Walker RL, Pineda M, Zhu YJ, Lau C, Killian KJ, Bilke S, Voeller D, Dakshanamurthy S, Wang Y, Giaccone G. A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors. Nat Genet. 2014 Aug;46(8):844-9. doi: 10.1038/ng.3016. Epub 2014 Jun 29.
  • Ellingson SR, Dakshanamurthy S, Brown M, Smith JC, Baudry J. Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer. Concurr Comput. 2014 Apr 25;26(6):1268-1277.
  • Issa NT, Byers SW, Dakshanamurthy S. Big data: the next frontier for innovation in therapeutics and healthcare. Expert Rev Clin Pharmacol. 2014 May;7(3):293-8. doi: 10.1586/17512433.2014.905201. Epub 2014 Apr 7.
  • Assefnia S, Dakshanamurthy S, Auvil JM, Hampel C, Anastasiadis PZ, Kallakury B, Uren A, Foley DW, Brown ML, Shapiro L, Brenner M, Haigh D, Byers SW. Cadherin-11 in poor prognosis malignancies and rheumatoid arthritis: common target, common therapies. Oncotarget. 2014 Mar 30;5(6):1458-74.
  • Steiner NK, Dakshanamurthy S, Nguyen N, Hurley CK. Allelic variation of killer cell immunoglobulin-like receptor 2DS5 impacts glycosylation altering cell surface expression levels. Hum Immunol. 2014 Feb;75(2):124-8. doi: 10.1016/j.humimm.2013.11.012. Epub 2013 Nov 20.

2013

  • Dinesh Bheeman, Sathish Sugumaran, Ramesh Mathan, Dakshanamurthy Sivanesan and Chandar Shekar Bellan. Oxidative Stress Induced Biochemical Alterations Due to InTiO Nanoparticles exposure. Nanoscience Nanotechnology Letters. In Press.
  • Dakshanamurthy S. Editorial Policy: Journal of Theoretical & Computational Science: Open Access. Editorial: J Theor Comput Sci 2013, 1:e101. doi: 10.4172/jtco.1000e101.
  • Sivanesan Dakshanamurthy and Jan Charles Biro. Welcome to the Journal of Theoretical & Computational Science: Open Access. Editorial: J Theor Comput Sci 2013, 1:e105. doi: 10.4172/jtco.1000e105.
  • Steiner NK, Dakshanamurthy S, Nguyen N, Hurley CK. Hum Immunol. Allelic variation of killer cell immunoglobulin-like receptor 2DS5 impacts glycosylation altering cell surface expression levels. 2014 Feb;75(2):124-8. doi: 10.1016/j.humimm.2013.11.012. Epub 2013 Nov 20.
  • Walls TH, Grindrod SC, Beraud D, Zhang L, Baheti AR, Dakshanamurthy S, Patel MK, Brown ML, MacArthur LH. Synthesis and biological evaluation of a fluorescent analog of phenytoin as a potential inhibitor of neuropathic pain and imaging agent. Bioorg Med Chem. 2012 Sep 1;20(17):5269-76.
  • Dakshanamurthy S, Issa NT, Assefnia S, Seshasayee A, Peters OJ, Madhavan S, Uren A, Brown ML, Byers SW. Predicting new indications for approved drugs using a proteochemometric method. J Med Chem. 2012 Aug 9;55(15):6832-48. PMID: 22780961 (Corresponding Author).
  • Naiem T Issa, Jordan Kruger, Stephen W Byers and Sivanesan Dakshanamurthy. Drug Repurposing a Reality: From Computers to the Clinic. Expert Rev Clin Pharmacol. 2013 Mar;6(2):95-7.
  • Elllingson Sellings, Sivanesan Dakshanamurthy, Milton Brown, Smith, Jeremy C and Jerome Baudry. Accelerating Virtual High-Throughput Ligand Docking: Current Technology and Case Study on a Petascale Supercomputer. Concurrency and Computation: Practice and Experience Concurrency Computat.: Pract. Exper. (June 2013). doi: 10.1002/cpe.3070
  • Naiem T Issa, Stephen W Byers, and Sivanesan Dakshanamurthy. Drug Repurposing: Translational Pharmacology, Chemistry, Computers and the Clinic. Cur. Topics in Med. Chem. 2013;13(18):2328-36..
  • William R. Frazier, Noriko Steiner, Lihua Hou, Sivanesan Dakshanamurthy, Carolyn Katovich Hurley. Allelic Variation in KIR2DL3 Generates a KIR2DL2-like Receptor with Increased Binding to Its HLA-C Ligand. J Immunol. 2013 Jun 15;190(12):6198-208
  • Naiem T Issa, Jordan Krugar, Stephen W Byers and Sivanesan Dakshanamurthy. At the Interface of Cancer Metabolomics and Therapeutics: A Drug Repurposing Opportunity. Review. Metabolomics 2013, S1. Metabolomics : Open Access.
  • Venkata Mahidhar Yenugonda, Yingxian Xiao, Edward D. Levin, Amir H. Rezvani, Thao Tran, Nour Al-Muhtasib, Niaz Sahibzada, Teresa Xie, Corinne Wells, Susan Slade, Joshua E. Johnson, Sivanesan Dakshanamurthy, Hye-Sik Kong, York Tomita, Yong Liu, Mikell A Paige, Kenneth J. Kellar, Milton L. Brown.Design. Synthesis and Discovery of Picomolar Selective α4β2 Nicotinic Acetylcholine Receptor Ligands. J Med Chem. 2013 Nov 14;56(21):8404-21. doi: 10.1021/jm4008455. Epub 2013 Oct 18.

2012

  • Shajahan AN, Dobbin ZC, Hickman FE, Dakshanamurthy S, Clarke R. Tyrosine-phosphorylated Caveolin-1 (Tyr-14) Increases Sensitivity to Paclitaxel by Inhibiting BCL2 and BCLxL Proteins via c-Jun N-terminal Kinase (JNK). Biol Chem. 2012 May 18;287(21):17682-92.
  • Timofeeva OA, Chasovskikh S, Lonskaya I, Tarasova NI, Khavrutskii L, Tarasov SG, Zhang X, Korostyshevskiy VR, Cheema A, Zhang L, Dakshanamurthy S, Brown ML, Dritschilo A. Mechanisms of Unphosphorylated STAT3 Transcription Factor Binding to DNA. J Biol Chem. 2012 Apr 20;287(17):14192-200.
  • Davis GC, Kong Y, Paige M, Li Z, Merrick EC, Hansen T, Suy S, Wang K, Dakshanamurthy S, Cordova A, McManus OB, Williams BS, Chruszcz M, Minor W, Patel MK, Brown ML. Asymmetric synthesis and evaluation of a hydroxyphenylamide voltage-gated sodium channel blocker in human prostate cancer xenografts. Bioorg Med Chem. 2012 Mar 15;20(6):2180-8.
  • Walls TH, Grindrod SC, Beraud D, Zhang L, Baheti AR, Dakshanamurthy S, Patel MK, Brown ML, MacArthur LH. Synthesis and biological evaluation of a fluorescent analog of phenytoin as a potential inhibitor of neuropathic pain and imaging agent. Bioorg Med Chem. 2012 Sep 1;20(17):5269-76.
  • Dakshanamurthy S, Issa NT, Assefnia S, Seshasayee A, Peters OJ, Madhavan S, Uren A, Brown ML, Byers SW. Predicting new indications for approved drugs using a proteochemometric method. J Med Chem. 2012 Aug 9;55(15):6832-48. PMID: 22780961. doi: 10.1021/jm300576q

2011

  • Divekar SD, Storchan GB, Sperle K, Veselik DJ, Johnson E, Dakshanamurthy S, Lajiminmuhip YN, Nakles RE, Huang L, Martin MB. The role of calcium in the activation of estrogen receptor-alpha. Cancer Res. 2011 71(5):1658-68. PMID: 21212417
  • Sahab ZJ, Hall MD, Me Sung Y, Dakshanamurthy S, Ji Y, Kumar D, Byers SW. Tumor suppressor RARRES1 interacts with cytoplasmic carboxypeptidase AGBL2 to regulate the α-tubulin tyrosination cycle. Cancer Res. 2011 71(4):1219-28. PMID: 21303978
  • De Oliveira EO, Graf KM, Patel MK, Baheti A, Kong HS, Macarthur LH, Dakshanamurthy S, Wang K, Brown ML, Paige M. Synthesis and evaluation of hermitamides A and B as human voltage-gated sodium channel blockers. Bioorg Med Chem. 2011 19(14):4322-9. PMID: 21683602
  • Kong Y, Jung M, Wang K, Grindrod S, Velena A, Lee SA, Dakshanamurthy S, Yang Y, Miessau M, Zheng C, Dritschilo A, Brown ML.Histone Deacetylase Cytoplasmic Trapping by a Novel Fluorescent HDAC Inhibitor. Mol Cancer Ther. 2011 Jun 22. [Epub ahead of print] PMID: 21697394
  • Bulut G, Hong SH, Chen K, Beauchamp EM, Rahim S, Kosturko GW, Glasgow E, Dakshanamurthy S, Lee HS, Daar I, Toretsky JA, Khanna C, Uren A. Small molecule inhibitors of ezrin inhibit the invasive phenotype of osteosarcoma cells. Oncogene. 2011. PMID: 21706056 doi: 10.1038/onc.2011.245.
  • Hartley RM, Peng J, Fest GA, Dakshanamurthy S, Frantz DE, Brown ML, Mooberry SL. Polygamain, a New Microtubule Depolymerizing Agent that Occupies a Unique Pharmacophore in the Colchicine Site. Mol Pharmacol. 2011 Dec 14. [Epub ahead of print]
  • Madhavan S, Gusev Y, Harris M, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet LA, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, Weiner LM. G-DOC: a systems medicine platform for personalized oncology. Neoplasia. 2011 Sep;13(9):771-83.
  • Yenugonda VM, Deb TB, Grindrod SC, Dakshanamurthy S, Yang Y, Paige M, Brown ML. Fluorescent cyclin-dependent kinase inhibitors block the proliferation of human breast cancer cells. Bioorg Med Chem. 2011 Apr 15;19(8):2714-25. Epub 2011 Mar 4.

2010

  • Prahalad P, Dakshanamurthy S, Ressom H, Byers SW. Retinoic acid mediates regulation of network formation by COUP-TFII and VE-cadherin expression by TGFbeta receptor kinase in breast cancer cells. PLoS One. 2010 5(4):e10023. PMID: 20386594
  • Minami SS, Cordova A, Cirrito JR, Tesoriero JA, Babus LW, Davis GC, Dakshanamurthy S, Turner RS, Pak DT, Rebeck GW, Paige M, Hoe HS. ApoE mimetic peptide decreases Abeta production in vitro and in vivo. Mol Neurodegener. 2010 Apr 20;5(1):16.
  • Cheema A, Knights CD, Rao M, Catania J, Perez R, Simons B, Dakshanamurthy S, Kolukula VK, Tilli M, Furth PA, Albanese C, Avantaggiati ML. Functional mimicry of the acetylated C-terminal tail of p53 by a SUMO-1 acetylated domain, SAD. J Cell Physiol. 2010 May 6.

2009

  • Lixin Mi, Amrita Seema, Sivanesan, D, David Yang, Fung Lung Jung. Cancer preventive isothiocyanates induce selective degradation of cellular alpha- and beta-tubulins by proteasomes. J Biol Chem. 2009 Jun 19;284(25):17039-51.
  • Federoff HJ, Brown ML, Sivanesan, D, and Maguire-Zeiss K. Potential of Nurr1 Interactions to disclose new Parkinson’s therapeutics. Future Neurology. Mar 2009, Vol. 4, No. 2, Pages 161-165.
  • Xiao Y, Lazaro AM, Masaberg C, Haagenson M, Vierra-Green C, Spellman S, Sivanesan, D, Ng J, Hurley CK. Evaluating the potential impact of mismatches outside the antigen recognition site in unrelated hematopoietic stem cell transplantation: HLA-DRB1*1454 and DRB1*140101. Tissue Antigens. 2009 Jun;73(6):595-8.
  • Hong YB, Kang HJ, Kim HJ, Rosen EM, Dakshanamurthy S, Rondanin R, Baruchello R, Grisolia G, Daniele S, Bae I. Inhibition of cell proliferation by a resveratrol analog in human pancreatic and breast cancer cells. Exp Mol Med. 2009 41(3):151-60. PMID: 19293634
  • Erkizan HV, Kong Y, Merchant M, Schlottmann S, Barber-Rotenberg JS, Yuan L, Abaan OD, Chou TH, Dakshanamurthy S, Brown ML, Uren A, Toretsky JA. A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma. Nat Med. 2009 15(7):750-6. PMID: 19584866
  • Lai H, Feng M, Roxas-Duncan V, Dakshanamurthy S, Smith LA, Yang DC. Quinolinol and peptide inhibitors of zinc protease in botulinum neurotoxin A: effects of zinc ion and peptides on inhibition. Arch Biochem Biophys. 2009 491(1-2):75-84. PMID: 19772855

2008

  • Lixin Mi, Brian L. Hood, Sivanesan D, Xiantao Wang, Sudha Govind, Timothy D. Veenstra, Thomas P. Conrads, and Fung-Lung Chung. Covalent Binding To Tubulin By Isothiocyanates: A Mechanism Of Cell-Growth Arrest And Apoptosis. J. Biol. Chem. 2008 Aug 8;283(32):22136-46).
  • Noriko S, Sivanesan D, C.J. VandenBussche, C.K. Hurley. Extracellular domain alterations impact surface expression of stimulatory natural killer cell receptor KIR2DS5. Immunogenetics. 2008 Nov;60(11):655-67.
  • Vandenbussche CJ, Mulrooney TJ, Frazier WR, Sivanesan, D, Hurley CK. Dramatically reduced surface expression of NK cell receptor KIR2DS3 is attributed to multiple residues throughout the molecule. Genes and Immunity, 2008, 13 Nov.
  • Veselik DJ, Divekar S, Dakshanamurthy S, Storchan GB, Turner JM, Graham KL, Huang L, Stoica A, Martin MB. Activation of estrogen receptor-alpha by the anion nitrite. Cancer Res 68(10):3950-3958, 2008.
  • Chinigo GM, Paige M, Grindrod S, Dakshanamurthy, S, Hamel E, , Chruszcz M, Minor W, Brown ML. Asymmetric synthesis of 2,3-dihydro-2-arylquinazolin-4-ones: methodology and application to a potent fluorescent tubulin inhibitor with anticancer activity. J Med Chem. 2008 Aug 14;51(15):4620-31
  • Oh AS, Lahusen JT, Chien CD, Fereshteh MP, Zhang X, Dakshanamurthy S, Xu J, Kagan BL, Wellstein A, Riegel AT. Tyrosine phosphorylation of the nuclear receptor coactivator AIB1/SRC-3 is enhanced by Abl kinase and is required for its activity in cancer cells. Mol Cell Biol 28(21):6580-93, 2008.

2007

  • Identification and Characterization of a New Tubulin-Binding Tetrasubstituted Brominated Pyrrole. Susan L. Mooberry, Kimberly N. Weiderhold, Sivanesan D, Milton L. Brown, Ernest Hamel, John T. Gupton. Mol Pharmacol. 2007 Jul;72(1):132-40.
  • Dakshanamurthy S, Kim M, Brown ML, Byers SW. In-Silico Fragment Based Identification of Novel Angiogenesis Inhibitors. Bioorg Med Chem Lett 17(16):4551-6, 2007. (corresponding author)

2006

  • Salimuddin Shah, Mohamad Naimul, D. Sivanesan, Roger Herrell, Imran Rizvi, Mahadev Rao, Glendon Zinger, Meggan Valrance, Ann Aranda, Dino Moraz, Anthony Norman, Joellen Welsh, and Stephan byers. Molecular basis of vitamin D receptor and beta catenin cross regulation. Mol Cell. 2006 Mar 17;21(6):799-809).
  • Christopher J V, D. Sivanesan, Phillip E. Posch, Carolyn K Hurley. A Single Polymorphism Disrupts the Killer Ig-Like Receptor 2DL2/2DL3 D1 Domain. J. Immunology. 2006 177: 5347-5357).

2005

  • D. Sivanesan, R.V. Rajnarayanan, J. Doherty and N. Pattabiraman. In-Silico Screening using Flexible Ligand Binding Pocket: A Molecular Dynamics-Based Approach. J. Comp.Aided. & Mol. Design. 19 (2005) 213-228.
  • S. Jayalakshmi, N. Akula, D.Sivanesan, M. Narasimman, A. Rathinavelu and N. Pattabiraman. Identification of novel compounds as angiogenesis inhibitors. Bioorg. Med. Chem.Lett. 15 (2005) 4125-4129 (first three authors contributed equally)

2004

  • G. Basu, D. Sivanesan, T. Kawabata, and N. Go. Electrostatic Potential of Nucleotide-Free Protein is Sufficient for Discrimination Between Adenine- and Guanine specific binding sites. J. Mol. Biol. 342 (2004) 1053-1066.
  • R.V. Rajnarayanan, D. Sivanesan, and N. Pattabiraman. Teaching Old Drugs to Kill New Bugs: Structure-Based Discovery of Potential Anti-SARS Drugs. Biophys. Biochem. Res. Comm. 321 (2004) 370-378 (first two authors contributed equally).

2003

  • D. Sivanesan, I. Sumathi and William J. Welsh. Comparative studies on hydrated H-bonded and stacked DNA base pair. Chem. Phys. Lett, 367 (2003) 351-360. (Corresponding Author)

2002

  • D.Sivanesan, Gautam Basu and Nobuhiro Go. The role of electrostatics in discrimination of Adenine and Guanine by Proteins. Genome Informatics series 13 (2002) 316-317.

2001

  • D. Sivanesan, V. Subramanian, Balachandran Unni Nair. Quantification of reactive sites in DNA bases using Condensed Fukui function calculation J. Mol. Struct. (THEOCHEM), 544 (2001) 123-139.
  • D. Sivanesan, V. Subramanian and Balachadra Unni Nair. Solvent Effect on DNA Base Stacked Dimers: an Isodensity Polarizable Continuum Model Approach. Int. J. Quantum Chemistry, 84 (2001) 750-758.

2000

  • D. Sivanesan, V. Subramanian, Balachandran Unni Nair and T.Ramasami. Hydration of DNA Base-pair: A Hartree-Fock Self-Consistant Reaction Field Study. Indian J. Chem. 39A, (2000) 132-138.
  • D. Sivanesan, K.Babu, S.R. Gadre, V. Subramanian and T.Ramasami. Does a stacked DNA base pair hydrate better than a base pair? : An ab initio study. J. Phys. Chem. A. 104, (2000) 10887-10894.

1999

  • V. Subramanian, K. Chitra, D. Sivanesan, R. Amutha, and S. Sankar. Ab initio potential energy surface of Ne…CO complex. Chem. Phys. Lett. 307 (1999) 493-496.
  • D. Sivanesan, R. Amutha, V. Subramanian, B. U. Nair and T. Ramasami. Assessment of importance of solvent in the calculation of condensed Fukui function: A self-consistent reaction field calculation study. Chem. Phys. Lett. 308 (1999) 223-228.

1998

  • V. Subramanian, K. Chitra, D. Sivanesan, M. Renuka, S. Sankar and T. Ramasami. Comparison of conventional ab initio and density functional methods for the Ar-HF interaction potential. J. Mol. Struct. (Theochem) 431 (1998) 181-185.
  • V. Subramanian, K. Venkatesh, D. Sivanesan and T. Ramasami. Comparative study of density functional theory and conventional ab initio methods: Electronic structure of Si2C cluster. Proc. Indian Acad. Sci. (Chemical Sciences) 110 (1998) 127-132.
  • V. Subramanian, D. Sivanesan and T. Ramasami. Electronic structure of NeHCl and NeClH using G1, G2, and MP4 methods. Chem. Phys. Lett. 295 (1998) 312-316.
  • V. Subramanian, D. Sivanesan and T. Ramasami. The role of solvent in DNA base pair stacking interaction. Chem.Phys.Lett. 290 (1998) 189-192.
  • V. Subramanian, D. Sivanesan, R. Amutha, J. Padmanabhan and T. Ramasami. Hardness profile of Interaction of HF with He, Ne and Ar: Density functional and MP2 calculation. Chem.Phys.Lett. 294 (1998) 285-291.