Ariel Fernandez

Summary

Affiliation: Rice University
Country: USA

Publications

  1. doi request reprint Modulating drug impact by wrapping target proteins
    Ariel Fernandez
    Karl F Hasselman Chair in Engineering, Professor of BioEngineering, Rice University, Department of Bioengineering, Houston, TX 77005, USA
    Expert Opin Drug Discov 2:249-59. 2007
  2. pmc An anticancer C-Kit kinase inhibitor is reengineered to make it more active and less cardiotoxic
    Ariel Fernandez
    Department of Bioengineering and Applied Physics Division, Rice Quantum Institute, Rice University, Houston, Texas 77005, USA
    J Clin Invest 117:4044-54. 2007
  3. ncbi request reprint The integrated development of network complexity modulates the diverse evolutionary mutation rates of individual proteins
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, 77005, USA
    FEBS Lett 579:5718-22. 2005
  4. doi request reprint Protein wrapping: a molecular marker for association, aggregation and drug design
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Chem Soc Rev 37:2373-82. 2008
  5. doi request reprint Is there a case for selectively promiscuous anticancer drugs?
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Drug Discov Today 14:1-5. 2009
  6. doi request reprint Taming the induced folding of drug-targeted kinases
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Trends Pharmacol Sci 30:66-71. 2009
  7. doi request reprint Bottom-up engineering of peptide cell translocators based on environmentally modulated quadrupole switches
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    ACS Nano 2:61-8. 2008
  8. doi request reprint Selective antagonism of anticancer drugs for side-effect removal
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Trends Pharmacol Sci 30:403-10. 2009
  9. ncbi request reprint Target Discovery--Select Biosciences' World Congress. 4-5 August 2009, San Francisco, CA, USA
    Ariel Fernandez
    Rice University, 6100 Main Street, Houston, TX 77005 1827, USA
    IDrugs 12:620-2. 2009
  10. pmc Human capacitance to dosage imbalance: coping with inefficient selection
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    Genome Res 19:2185-92. 2009

Research Grants

Collaborators

Detail Information

Publications31

  1. doi request reprint Modulating drug impact by wrapping target proteins
    Ariel Fernandez
    Karl F Hasselman Chair in Engineering, Professor of BioEngineering, Rice University, Department of Bioengineering, Houston, TX 77005, USA
    Expert Opin Drug Discov 2:249-59. 2007
    ..This fact suggests a broad applicability of the wrapping technology, ultimately leading to molecular therapies with tighter control of side effects...
  2. pmc An anticancer C-Kit kinase inhibitor is reengineered to make it more active and less cardiotoxic
    Ariel Fernandez
    Department of Bioengineering and Applied Physics Division, Rice Quantum Institute, Rice University, Houston, Texas 77005, USA
    J Clin Invest 117:4044-54. 2007
    ..These findings identify the reengineered imatinib as an agent to treat GISTs with curbed side effects and reveal a bottom-up approach to control drug specificity...
  3. ncbi request reprint The integrated development of network complexity modulates the diverse evolutionary mutation rates of individual proteins
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, 77005, USA
    FEBS Lett 579:5718-22. 2005
    ....
  4. doi request reprint Protein wrapping: a molecular marker for association, aggregation and drug design
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Chem Soc Rev 37:2373-82. 2008
    ..Finally, we survey the recent exploitation of dehydrons as targetable features to promote specificity in drug-based cancer therapy. Dehydrons prove to be valuable targets to reduce side effects and enhance drug safety...
  5. doi request reprint Is there a case for selectively promiscuous anticancer drugs?
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Drug Discov Today 14:1-5. 2009
    ..This control may be achieved by drug redesign guided by known selectivity-promoting molecular features...
  6. doi request reprint Taming the induced folding of drug-targeted kinases
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Trends Pharmacol Sci 30:66-71. 2009
    ..This concept is validated by dynamically examining structural adaptations promoted by imatinib redesigns intended to control drug specificity...
  7. doi request reprint Bottom-up engineering of peptide cell translocators based on environmentally modulated quadrupole switches
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    ACS Nano 2:61-8. 2008
    ..Lipid solubility is induced by a quadrupolar arrangement. Our passive translocation motif possesses the highest efficiency and is derived from cellular prions...
  8. doi request reprint Selective antagonism of anticancer drugs for side-effect removal
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Trends Pharmacol Sci 30:403-10. 2009
    ..Editor and primary drug have overlapping therapeutic impact, and the editor suppresses the downstream propagation of toxicity-related signaling...
  9. ncbi request reprint Target Discovery--Select Biosciences' World Congress. 4-5 August 2009, San Francisco, CA, USA
    Ariel Fernandez
    Rice University, 6100 Main Street, Houston, TX 77005 1827, USA
    IDrugs 12:620-2. 2009
    ....
  10. pmc Human capacitance to dosage imbalance: coping with inefficient selection
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    Genome Res 19:2185-92. 2009
    ..The results may clarify the evolutionary etiology of aggregation-related diseases, since aggregation is often promoted by overexpression (a dosage imbalance) and aggregation propensity is associated with extreme packing deficiency...
  11. doi request reprint Golden rule for buttressing vulnerable soluble proteins
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    J Proteome Res 9:2643-8. 2010
    ..The results are justified on thermodynamic grounds and have implications for biomolecular engineering as they introduce two constants of universal applicability determining the architecture of soluble proteins...
  12. pmc Passive water-lipid peptide translocators with conformational switches: from single-molecule probe to cellular assay
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    J Phys Chem B 111:13987-92. 2007
    ..The associated free-energy agrees with mesoscopic measurements, and the in vitro behavior is quantitatively reproduced in cellular assays. The prototypes herald the advent of novel nanobiomaterials for passive translocation...
  13. ncbi request reprint Wrapping technology and the enhancement of specificity in cancer drug treatment
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Front Biosci 12:3617-27. 2007
    ..In particular, we discuss a future strategy to develop highly selective inhibitors targeting a signaling complex critical to cancer metastasis...
  14. pmc Molecular basis for evolving modularity in the yeast protein interaction network
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas, United States of America
    PLoS Comput Biol 3:e226. 2007
    ..The molecular basis for the evolutionary trend is likely rooted in the high-entropy penalty entailed in the association of two intramodular hubs...
  15. ncbi request reprint What factor drives the fibrillogenic association of beta-sheets?
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, United States
    FEBS Lett 579:6635-40. 2005
    ..The driving force for the association arises from the mechanical equivalent of the dehydration propensity of pre-formed intra-sheet hydrogen bonds and dipole-dipole interactions...
  16. pmc Incomplete protein packing as a selectivity filter in drug design
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    Structure 13:1829-36. 2005
    ..In this way, the packing defects of a soluble protein may be used as selectivity filters for drug design...
  17. pmc Packing defects as selectivity switches for drug-based protein inhibitors
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Proc Natl Acad Sci U S A 103:323-8. 2006
    ..Thus, nonconserved packing defects may be used as selectivity switches across homolog targets, using spatial displacements of packing defects across aligned protein structures...
  18. ncbi request reprint A priori inference of cross reactivity for drug-targeted kinases
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    J Med Chem 49:3092-100. 2006
    ..Our packing distance metric is further extended to infer cross reactivity over all human tyrosine kinases. This tool should prove useful to target clinically relevant regions of the pharmacokinome, as our experimental assays reveal...
  19. pmc Rational drug redesign to overcome drug resistance in cancer therapy: imatinib moving target
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Cancer Res 67:4028-33. 2007
    ..The inhibitor redesign reported delineates a molecular engineering paradigm to impair routes for drug resistance...
  20. ncbi request reprint Solvent-exposed backbone loosens the hydration shell of soluble folded proteins
    Ariel Fernandez
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    J Chem Phys 126:245103. 2007
    ..These bonds are poorly wrapped by surrounding nonpolar groups from the side chains and their dehydration is energetically favored...
  21. doi request reprint Induced disorder in protein-ligand complexes as a drug-design strategy
    Alejandro Crespo
    Department of Bioengineering, Rice University, Houston, Texas 77005, Department of Experimental Therapeutics, M D Anderson Cancer Center University of Texas, Houston, Texas 77030, USA
    Mol Pharm 5:430-7. 2008
    ..Induced disorder thus becomes a promising concept for drug design...
  22. pmc Kinase packing defects as drug targets
    Alejandro Crespo
    Department of Bioengineering, Rice University, Houston, TX 77005, United States
    Drug Discov Today 12:917-23. 2007
    ..In this light, we review design strategies to achieve paralogue discrimination, to control cross reactivity and to overcome drug resistance induced by target mutations...
  23. doi request reprint Turning promiscuous kinase inhibitors into safer drugs
    Xi Zhang
    Program in Applied Physics, Rice Quantum Institute, Rice University, 6100 Main St, Houston, TX 77005, USA
    Trends Biotechnol 26:295-301. 2008
    ..Finally, we evaluate the possibility of turning multi-target kinase inhibitors into clinical opportunities through judicious chemical modifications...
  24. ncbi request reprint Selectivity filters to edit out deleterious side effects in kinase inhibitors
    Sean Sessel
    Department of Bioengineering, Rice University, Houston, TX 77005, USA
    Curr Top Med Chem 11:788-99. 2011
    ....
  25. pmc c-Jun-NH2-kinase-1 inhibition leads to antitumor activity in ovarian cancer
    Pablo Vivas-Mejia
    Department of Experimental Therapeutics, Center for RNAi and non coding RNA, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
    Clin Cancer Res 16:184-94. 2010
    ..To show the functional, clinical, and biological significance of c-Jun-NH(2)-kinase (JNK)-1 in ovarian carcinoma...
  26. ncbi request reprint Dehydration propensity of order-disorder intermediate regions in soluble proteins
    Natalia Pietrosemoli
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    J Proteome Res 6:3519-26. 2007
    ..The presence of these large clusters signals a structural vulnerability, a pronounced dehydration propensity, and a strong electrostatic enhancement...
  27. doi request reprint In silico drug profiling of the human kinome based on a molecular marker for cross reactivity
    Xi Zhang
    Division of Applied Physics and Rice Quantum Institute, Rice University, Houston, Texas 77005, USA
    Mol Pharm 5:728-38. 2008
    ..Our in silico tool is validated by contrasting predictions against reported high-throughput screening experiments...
  28. doi request reprint Redesigning kinase inhibitors to enhance specificity
    Alejandro Crespo
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    J Med Chem 51:4890-8. 2008
    ..Thus, our design strategy proves to be operative to reduce the inhibitory impact of promiscuous kinase ligands, enhancing their safety as therapeutic agents...
  29. pmc Molecular basis for specificity in the druggable kinome: sequence-based analysis
    Jianping Chen
    Program in Applied Physics and Rice Quantum Institute, Rice University, Houston, TX 77005, USA
    Bioinformatics 23:563-72. 2007
    ..This work answers the question for a sizable screened sample of the human pharmacokinome including targets with unreported structure...
  30. pmc Protein structure protection commits gene expression patterns
    Jianping Chen
    Program in Applied Physics, Rice Quantum Institute, Rice University, Houston, TX 77005, USA
    Genome Biol 9:R107. 2008
    ..Yet, little effort has been devoted to tracing coordinating signals for expression correlations to the three-dimensional structures of gene products...
  31. ncbi request reprint Therapeutic efficacy of a novel focal adhesion kinase inhibitor TAE226 in ovarian carcinoma
    Jyotsnabaran Halder
    Department of Gynecologic Oncology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Cancer Res 67:10976-83. 2007
    ..The novel FAK inhibitor, TAE226, offers an attractive therapeutic approach in ovarian carcinoma...

Research Grants4

  1. Protein Packing Defects as Functional Markers and Drug Targets
    Ariel Fernandez; Fiscal Year: 2007
    ..Thus, the novel design concept of "drug inhibitor as a wrapper of functional packing defects" will be explored and validated. ..