Ariel Fernández Stigliano*
Updated 9.2020
*Also styled as Ariel Fernández
Born in Bahía Blanca, Argentina, April 8, 1957
American and Argentine citizen
Private address:
1419 Montrose Blvd.
Houston, TX 77019
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Current Positions
Head, Daruma Institute for Artificial Intelligence in Pharmaceutical Research, AF Innovation, GmbH
["Artificial Intelligence Platform for Molecular Targeted Therapy", the new book on AI by Ariel Fernandez
https://www.amazon.com/Artificial.../dp/981123230X]
President, AF Innovation, GmbH, a Pharmaceutical Consultancy (2010-).
Vicepresident and Chief Scientific Officer at Ariel Fernandez Consultancy, GmbH, a Biotechnology firm specialized in dynamic molecular design (2013-)
Expert scientifique, Comité d’Evaluation Scientifique, Innovation Biomédicale (CE18), Agence Nationale de la Recherche, France (2015-)
Senior Investigator, National Research Council (CONICET) (2011-).
Argentine Mathematics Institute
1083 Buenos Aires, Argentina
Honorary Investigator, Collegium Basilea, Institute of Advanced Study, CH 4053 Basel, Switzerland (2006-)
Visiting Professor, National Tsing-Hua University, Hsinchu, Republic of China (2010-)
Past Appointments
Distinguished Investigator, PI Pharmaceutical Informatics, Morgridge Institute for Research at the University of Wisconsin-Madison, Madison, Wisconsin 53715 (2011-2012)
Karl F. Hasselmann Chaired Professor of Engineering, Rice University, Department of Bioengineering, Rice University, Houston, TX 77005 (2005-2011)
Professor of Bioengineering, Rice University, 2005-2011 (retired)
Rice Research Professor (2011)
Adjunct Professor of Molecular Therapy, M. D. Anderson Cancer Center (UTMC) (2006-)
Adjunct Professor (2006-2008) and Visiting Scholar (2008-2012), Computer Science Department, The University of Chicago.
Senior Scientific Consultant, Eli Lilly and Company (2004- ).
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Primary research foci
Pharmacoinformatics and Pharmacogenomics; Translational Medical Informatics; Molecularly Targeted Cancer Therapy; Clinical Kinomics; Integrative Biology; Bioinformatics; Discovery Informatics; Systems Bioengineering; Molecular Theranostic Engineering; Physical Chemistry; Molecular Biophysics, Dehydron Physics
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Education
Ph. D., M. Sc., M. Phil., Yale University, 1981-1984 (fastest awarded Yale Ph. D.).
Sr. Research Scientist, Max-Planck-Institut fuer biophysikalische Chemie, Division of Nobel Laureate Manfred Eigen, Goettingen, Germany, 1986-1989.
Research Associate (1985-1987), Visiting Senior Research Scientist (1994-1996), Princeton University.
Licenciado en Matematica (1980), Quimico (1979), Universidad Nacional del Sur, Bahia Blanca, Argentina.
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Summary of Personal Accomplishments
Ariel Fernández (IQ 151, test# e2a3fa0b) introduced what appears to be the correct formulation for self-organization in nonequilibrium thermodynamics by realizing that the thermodynamically relevant degrees of freedom must belong to a center manifold, an algebraically closed entity, and not to an attractor, as Ilya Prigogine previously assumed. He has provided a semiempirical solution to the protein folding problem by introducing the episteric tension, a measure of the distortion of the water structural matrix that requires a multi-scale theory of dielectrics. He rationally discovered a ligand that would competitively disrupt a protein-protein interface for therapeutic purposes (patent pending, ref. 347). He also managed to predict and control induced folding in drug-target associations. Together with Ridgway Scott, he introduced the dehydron, a structural defect in proteins that promotes its own dehydration. A dehydron is a meta-structural feature of relevance in drug design, enzyme catalysis and protein folding. Ariel Fernández determined and measured the dehydronic field, the mechanical equivalent of the dehydration propensity of a dehydron exerted on a test nonpolar molecule and orthogonal to the Coulombic field. His current efforts are devoted to show that dehydrons are enablers and stimulators of enzyme catalysis.
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Awards and Previous Appointments
Camille and Henry Dreyfus Teacher-Scholar Awardee, 1991
Camille and Henry Dreyfus Distinguished New Faculty Awardee, 1989
John S. Guggenheim Memorial Foundation Fellow, 1995-1996
Consultant to U.S. Federal Government, NIH, Special Panel on Centers of Excellence in Systems Biology, 2003-
National Cancer Institute (NCI) Reviewer. NIH Study Section RFA-07-005 "Advanced Proteomic Platforms and Computational Sciences for NCI Clinical Proteomic Technologies Initiative", 2006-
Guest Professor, Institute for Protein Research, Osaka University, Japan, 2003
Visiting Senior Researcher, Max-Planck-Institut fuer Biochemie, Abteilung Robert Huber, Martinsried, Germany, 2000-
Visiting Senior Scientist, Institute for Nonlinear Science, University of California at San Diego, 1989
Managing Editor, Frontiers in Bioscience, Encyclopedia of Bioscience, 2006-
Editor, Journal of Biological Physics and Chemistry, Basel, Switzerland, 2000-
Fulbright Scholar, US Information Agency, 1999 and Fulbright Fellow, 1981
Alexander von Humboldt Foundation Awardee (1995)
Max Planck Society Scholar, Goettingen, Germany (1987-1989)
Feinberg Fellow, Israel, 1984-1985
Full Professor, Indiana University School of Informatics, 2003-2005.
Full Professor, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 2003-2005.
Elected Fellow, American Institute for Medical and Biological Engineering, 2006
Full Professor and Principal Investigator, UNS and Natl. Res. Council of Argentina, 1994-2003.
Medal "State of Buenos Aires" to the best graduate, Argentina, 1980
Deputy Governor, American Biographical Institute, 1998-
Co-organizer and Proceedings Editor of the Miami Bio/Technology Winter Symposium, Nature-sponsored, 1993.
Chair, “Resistance and Safety”/Kinase Inhibitors, Cambridge Healthtech Institute’s Sixth Annual “Discovery on Target” Symposium; October 20-23, Boston, MA, USA, 2008.
Honorary Member, Collegium Basilea, Institute for Advanced Study, Basel, Switzerland, 2006-
Adjunct Professor of Computer Science, The University of Chicago (2005-2008).
Distinguished Scientific Leader Lecturer, Georgia Institute of Technology, 11/10/2010, Lecture title: “Evolutionary insights into the control of drug specificity”. URL: https://smartech.gatech.edu/handle/1853/36240?show=full
Columnist at Project Syndicate, The World’s Opinion Page (2011-)
Legal Consultancies - Pharmaceutical Patent Litigation
Schiff/Hardin, LLP (Chicago-based Law Firm).
Racoczy, Molino, Mazzocchi and Siwik, LLP (Chicago-based Law Firm)
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Grant support, PI: Ariel Fernandez
NIH Grant Award 1R01 GM072614 from the National Institute of General Medical Sciences (NIGMS). Title: “Protein packing defects as functional markers and drug targets”. Total amount of award: $1.6million (2005-2009).
Eli Lilly and Company, Unrestricted research funds (2004-)
Recent Lectures
Seminar lecture: “Curbing drug side effects by exploiting integrative ideas in molecular biophysics”, Computations in Science Seminars, Kersten Physics Teaching Center, The University of Chicago, November 28 (2007).
Keynote speaker: “Curbing the Cardiotoxicity of Kinase Inhibitors: The Methyl that Saved the Heart”, Discovery on Target 2007, Cambridge Healthtech Institute Fifth Annual, “Developing inhibitors for Promising Drug Targets”, World Trade Center, Boston, MA, October 15-18 (2007).
"7th International Workshop on Pharmacodynamics of Anticancer Agents”, organized by the University of Chicago, Guanacaste, Costa Rica, September 16-20 (2007).
“Re-engineering of Imatinib to Decrease Cardiac Risk: Translational Ideas in Drug Discovery”, World Pharmaceutical Congress, Cambridge Healthtech Institute Second Annual “Cardiotoxicity and Drug Safety”, Philadelphia, PA, May 12-13 (2008).
“Curbing side effects in anticancer drugs”, in “Science for Health with a Human Face”, International Symposium (4 Nobel laureates in attendance), Madrid, Spain, November 4-7 (2008).
“Translational ideas in drug discovery”, Guest lecturer, Genomics Research Center, Academia Sinica, Taipei, Taiwan, June 14-21 (2008).
Keynote speaker and Chair, “Resistance and Safety”. Lecture title: “Translational ideas to curb side effects in anticancer kinase-targeting therapy: Reducing cardiotoxicity through inhibitor redesign”. Cambridge Healthtech Institute’s Sixth Annual “Discovery on Target”/KINASE INHIBITORS; October 20-23, 2008, Boston, MA, USA.
Lecturer, 238th American Chemical Society National Meeting & Exposition. ACS paper 251: “Translational ideas in molecular therapy: Re-engineering anticancer drugs to curb side effects”; section “Novel Approaches to fine tune anticancer drugs to achieve acceptable clinical outcomes, Walter E. Washington Convention Center, August 16-20, 2009, Washington DC, USA.
Lecturer, “Frontiers in Pharmacology” Seminar Series, University of California at Davis, Department of Pharmacology, GBSF Auditorium, October 23, 2009, UC Davis, Davis CA, USA.
Keynote speaker, “Origin of Life: Molecular origins, Extinction, Life in Extremes, Species Diversification”, Vienna Biocenter, Noviembre 18, 2010, Vienna, Austria, sitio web: www.originoflife2010.com
Distinguished Scientific Leader Lecturer, Georgia Institute of Technology, 11/10/2010, Lecture title: “Evolutionary insights into the control of drug specificity”. URL: https://smartech.gatech.edu/handle/1853/36240?show=full
Chair of Session “Protein Kinase Inhibitors in Cancer” (# 5-8), Speech title: “Translational Ideas in Molecular Cancer Therapy”, BIT Life Sciences’ 4th Annual Protein & Peptide Conference (PepCon 2011), Beijing, China, March 23-25, 2011.
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Patents
US 8,466,154 B2 (granted)
Ariel Fernández et al.: “Methods and Composition of Matter Related to Wrapping of Dehydrons”. Inventors: Ariel Fernández, William Bornmann, Gabriel Lopez-Berestein, Angela Sanguino, Zeng-Hong Peng, Anil K. Sood. Awarded: June 18, 2013.
US 20130345135A1 (granted)
Richard L. Moss and Ariel Fernández: “Inhibition of MYBP-C binding to myosin as a treatment for heart failure”. Inventors: Richard L. Moss and Ariel Fernández; Asignee: Wisconsin Alumni Research Foundation.
Books
Author: Ariel Fernández (2010)
Title: “Transformative Concepts for Drug Design: Target Wrapping”
Publisher: Springer, Heidelberg, Berlin (240 pages)
ISBN: 978-3-642-11791-6
Author: Ariel Fernández Stigliano (2015)
Title: “Biomolecular Interfaces: Interactions, Functions and Drug Design”
Publisher: Springer, Heidelberg, Berlin (372 pages)
ISBN: 978-3319168494
Author: Ariel Fernández (2016)
Title: “Physics at the Biomolecular Interface: Fundamentals for Molecular Targeted Therapy” (488 pages)
Publisher: Springer International Publishing, Switzerland
Soft and Biological Matter Series
ISBN: 978-3-319-30851-7
Authors: L. Ridgway Scott, Ariel Fernández (2017)
Title: “A Mathematical Approach to Protein Biophysics”
Publisher: Springer International Publishing, Switzerland
ISBN: 978-3319660318
Author: Ariel Fernández (2021)
Title: “Artificial Intelligence Platform for Molecular Targeted Therapy”
DOI: https://doi.org/10.1142/12160
Publisher: World Scientific Press Company, Singapore
ISBN: 978-981-123-230-5 (hardcover)
Critiques on recent work
Nature 432, 688 (2004)
News and Views article on: Despa, F., Fernandez, A. and Berry, R.S. Dielectric modulation of biological water. Phys. Rev. Lett. 93, 228104 (2004)
Journal of Clinical Investigation 117, 3650-3653 (2007)
Commissioned Editorial Commentary by George Demetri on: Fernández, A. et al. An anticancer C-Kit kinase inhibitor is re-engineered to make it more active and less cardiotoxic. Journal of Clinical Investigation 117, 4044-4054 (2007)
Nature Reviews Drug Discovery 7, 120-121 (2008)
Research Highlights, “Anticancer drugs: Redesigning kinase inhibitors”, on: Fernández, A. et al. An anticancer C-Kit kinase inhibitor is re-engineered to make it more active and less cardiotoxic. Journal of Clinical Investigation 117, 4044-4054 (2007)
Chemical & Engineering News (ACS) 86, number 09, p.31 (2008)
Science & Technology Concentrates: “Drug Design Strategy Aims for Disorder”, on: Crespo, A. and Fernández, A. Induced disorder in protein-ligand complexes as a drug-design strategy”. Molecular Pharmaceutics (ACS), published online February 16, 2008.
Nature, News and Views on Ariel Fernandez and Michael Lynch, Nature 474, 502-505 (2011). Philip Ball “The Achilles Heel of Biological Complexity” Published online 18 May 2011 | Nature | doi:10.1038/news.2011.294
Critique Excerpts
The research by Fernández and collaborators (cf. Journal of Clinical Investigation 117, 4044-4054 (2007)) has been auspiciously received by key researchers in cancer therapy and is being perceived as a conceptual and technical breakthrough. Thus, Harvard Medical School Professor George Demetri, director of the Center for Sarcoma and Bone Oncology at Dana-Farber Cancer Institute, wrote:
“The approach used here by Fernández et al. holds great promise to allow more customized development of rationally designed therapeutic agents.”
“…with tools such as those described by Fernández et al., the future certainly looks bright for constructing ever-better agents that can be combined safely and effectively to manage, and eventually cure, many forms of human cancer.”
(from Demetri’s Commentary, Journal of Clinical Investigation 117, 3650-3653, 2007).
Thomas Force, Wilson Professor of Medicine at Thomas Jefferson University, who first characterized and reported imatinib cardiotoxicity in his 2006 Nature Medicine article, said:
“…this knowledge could potentially steer drug development away from targets and pathways that would lead to toxicity, but would leave tumor cell killing intact. Fernández and co-workers, in this really remarkable piece of work, have proven that this is indeed possible. Their findings will hopefully encourage drug makers to pursue a similar approach of “rational drug re-design” (and drug design) in the development of new anti-cancer agents...”
http://www.media.rice.edu/media/NewsBot.asp?MODE=VIEW&ID=10334&SnID=1798653505
http://www.medicalnewstoday.com/articles/90646.php
In “Chemistry World” (Royal Society of Chemistry, UK), Force added:
“The biggest message of this paper is that a cardiotoxic cause can be identified and steered away from. There are hundreds of agents in development that could benefit from this research.”
http://www.rsc.org/chemistryworld/News/2007/December/03120703.asp
The research by Fernández also received coverage from the popular press (Reuters):
http://www.reuters.com/article/healthNews/idUSN0341290220071203
The Fernandez contribution was highlighted in Nature Reviews Drug Discovery 7, 120-121 (February 2008). (Research Highlights, “Anticancer drugs: Redesigning kinase inhibitors”). Thus, Nature Reviews editor Sarah Crunkhorn wrote:
“In summary, WBZ_4 [the drug designed by the Fernandez team] could have potential as a novel therapy for GISTs [gastro-intestinal stromal tumors], and the approach demonstrated in the study might also be applied to engineer the specificity of other kinase inhibitors with the aim of creating safer and more effective drugs.”
Other Recent Critiques
The paper: Ariel Fernández (2012) Epistructural tension promotes protein associations, Physical Review Letters 108, 188102 has been reviewed in Chemical & Engineering News and Physics/Focus (American Physical Society):
“Protein Binding Hot Spots” by Jyllian Kemsley
Chemical & Engineering News, 90(20), May 14, 2012 [Science & Technology, Concentrates]
“Focus: Proteins Hook up Where Water Allows”. May 4, 2012, Physics 5, 51 (2012), DOI: 10.1103/Physics.5.51, URL: http://physics.aps.org/articles/v5/51
The paper: Ariel Fernández and Michael Lynch, Nonadaptive origins of interactome complexity”. Nature 474, 502-505 (2011) has been reviewed in Scientific American and Nature/News:
“Why Are You So Complex? Complicated Protein Interactions Evolved to Stave Off Mutations” by Philip Ball. Scientific American, May 18, 2011. URL:http://www.scientificamerican.com/article/complicated-protein-interactions-evolved-to-stave-off-mutations/
“The Achilles' heel of biological complexity” by Philip Ball, Nature, 18 May 2011, doi:10.1038/news.2011.294 URL:http://www.nature.com/news/2011/110518/full/news.2011.294.html
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SELECTED RECENT PUBLICATIONS BY ARIEL FERNANDEZ
(350 TOTAL)
242. Ariel Fernández, Tobin R. Sosnick and Andrés Colubri: “Dynamics of hydrogen-bond desolvation in folding proteins”, Journal of Molecular Biology 321, 659-675 (2002).
243. Ariel Fernández: “Insufficient hydrogen-bond desolvation and prion-related disease”, European Journal of Biochemistry 269, 4165-4172 (2002). Priority paper; cover for September issue.
244. Ariel Fernández: “Desolvation shell of hydrogen bonds in folded proteins, protein complexes and folding pathways”, FEBS Letters (Fed. Eur. Biochem. Soc.) 527, 166-170 (2002).
245. Ariel Fernández: “The protective shell of a hydrogen bond: A motif in protein folding pathways”, Physics Letters A 302, 144-148 (2002).
246. Ariel Fernández and Mercedes Boland: “Solvent environment conducive to protein aggregation”, FEBS Letters (Fed. Eur. Biochem. Soc.) 529, 298-302 (2002).
247. Florin Despa, Ariel Fernández, R. Stephen Berry, Yaakov Levy and Joshua Jortner: “Interbasin-motion approach to dynamics of conformationally constrained peptides”. Journal of Chemical Physics 118, 5673-5684 (2003).
248. Ariel Fernández and Mercedes Boland: “What is inherently wrong with the prion structure?” Journal of Biological Physics & Chemistry 2, 98-100 (2002).
249. Ariel Fernández, Min-yi Shen, Andrés Colubri, Tobin R. Sosnick, R. Stephen Berry and Karl F. Freed: “Large-scale context in protein folding: villin headpiece”, Biochemistry 42, 664-671 (2003).
250. Ariel Fernández and Harold A. Scheraga: “Insufficiently dehydrated hydrogen bonds as determinants for protein interactions”, Proceedings of the National Academy of Sciences, USA 100, 113-118 (2003).
251. Ariel Fernández, Jozsef Kardos and Yuji Goto: “Protein folding: Could hydrophobic collapse be coupled with hydrogen-bond formation? FEBS Letters (Fed. Eur. Biochem. Socs.) 536, 187-192 (2003).
252. Ariel Fernández and Mercedes Boland: “Protein folding: where is the paradox?”, Journal of Biomolecular Structure and Dynamics 20, 331-2 (2002).
253. Ariel Fernández and R. Stephen Berry: “Proteins with hydrogen-bond packing defects are highly interactive with lipid bilayers: Implications for amyloidogenesis”,
Proceedings of the National Academy of Sciences, USA 100, 2391-2396 (2003).
254. Ariel Fernández: “Record reveals simplicity of primeval protein alphabet”. J. Biol. Phys. Chem. 3, 1 (2003).
255. Ariel Fernández: “Lower limit to the size of the primeval aminoacid alphabet”, Zeitschrift für Naturforschung 59c, 151-2 (2004).
256. Ariel Fernández and Ridgway Scott: “Adherence of packing defects in soluble proteins”, Physical Review Letters 91, 018102, 4 pages (2003).
257. Ariel Fernández, Jozsef Kardos, Ridgway Scott, Yuji Goto and R. Stephen Berry: “Structural defects and the diagnosis of amyloidogenic propensity”, Proceedings of the National Academy of Sciences, USA 100, 6446-6451 (2003).
258. Ariel Fernández: “Dehydron: a guidance in protein supramolecular organization”, Annual Report, The Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Japan (ISSN 1348-0022) 24, 22-26 (2003).
259. Ariel Fernández: “What caliber pore is like a pipe? Nanotubes as modulators of ion gradients”, Journal of Chemical Physics 119, 5315-5319
Communication (2003).
Featured in Virtual Journal of Nanoscale Science and Technology 8, September 8, 2003, Section on Carbon Nanotubes, C60, and Related Topics).
260. Ariel Fernández and Ridgway Scott: “Dehydron: A structure-encoded signal for protein interactions”, Biophysical Journal 85, 1914-1928 (2003).
261. Ariel Fernández and Ridgway Scott: “Under-wrapped soluble proteins as signals triggering membrane morphology”, Journal of Chemical Physics 119, 6911-6915 (2003).
262. Ariel Fernández: “Oncogenic mutations and packing defects in protein structure”, Journal of Biomolecular Structure and Dynamics 21, 9-15 (2003).
263. Ariel Fernández, Ridgway Scott and Harold A. Scheraga: “Amino-acid residues at protein-protein interfaces: Why is propensity so different from relative abundance?”, Journal of Physical Chemistry B 107, 9929-9932 (2003).
264. Kristina Rogale and Ariel Fernández: “Protein folding: a good structure protector is also a good structure seeker”. Physics Letters A 321, 263-266 (2004).
265. Ariel Fernández: “Functionality of wrapping defects in soluble proteins: What cannot be kept dry must be conserved”. Journal of Molecular Biology 337, 477-483 (2004).
266. Ariel Fernández and Kristina Rogale: “Charge screening in confined water: frequency dissection”. Journal of Biological Physics and Chemistry 3, 82-84 (2003).
267. Ariel Fernández, L. Ridgway Scott and R. Stephen Berry: “The nonconserved wrapping of conserved folds reveals a trend towards increasing connectivity in proteomic networks”. Proceedings of the National Academy of Sciences, USA 101, 2823-2827 (2004).
268. Ariel Fernández and Kristina Rogale: “Sequence-space selection of cooperative model proteins”. Journal of Physics A: Mathematical & General 37, 197-202 (2004).
269. Ariel Fernández, Kristina Rogale, L. Ridgway Scott and Harold A. Scheraga: “Inhibitor design by wrapping packing defects in HIV-1 proteins”.
Proceedings of the National Academy of Sciences, USA 101, 11640-11645 (2004).
270. Ariel Fernández and R. Stephen Berry: “Molecular dimension explored in evolution to promote proteomic complexity”. Proceedings of the National Academy of Sciences, USA 101, 13460-13465 (2004).
271. Ridgway Scott, Mercedes Boland, Kristina Rogale and Ariel Fernández: “Continuum equations for dielectric response to macromolecular assemblies at the nanoscale”.
Journal of Physics A: Mathematical and General 37, 9791-9803 (2004).
272. Ariel Fernández: “Keeping Dry and Crossing Membranes”. Nature Biotechnology 22, 1081-1084 (2004).
273. Ariel Fernández: “Buffering the entropic cost of hydrophobic collapse in folding proteins”. Journal of Chemical Physics 121, 11501-11502 (Letter to the Editor) (2004).
Featured in Virtual Journal of Biological Physics Research, Vol. 8, issue 11, December 1, 2004.
274. Florin Despa, Ariel Fernández and R. Stephen Berry: “Dielectric modulation of biological water”. Physical Review Letters 93, 228104 (4 pages) (2004).
Featured in Nature (News and Views) 432, 688 (2004).
275. Ariel Fernández: “Direct nanoscale dehydration of hydrogen bonds”.
Journal of Physics D, Applied Physics 38, 2928-2932 (2005).
276. Vladimir N. Uversky, Ariel Fernández and Anthony L. Fink. “Structural and conformational prerequisites of amyloidogenesis”. In: Protein Misfolding, Aggregation and Conformational Diseases. Vol. I: Protein Aggregation and Conformational Diseases (Uversky V.N., Fink A.L., Eds.) Springer, New York, pages 1-20, ISBN 038725918X (2006).
277. Ariel Fernández: “Protein function with concurrent promiscuity”, Opinions and Commentary, Journal of Biomolecular Structure & Dynamics 22, 615-624 (2005).
278. Ariel Fernández: “Incomplete protein packing as a selectivity filter in drug design”. Structure 13, 1829-1836 (2005).
279. Ariel Fernández: “The integrated development of network complexity modulates the diverse evolutionary mutation rates of individual proteins”,
FEBS Letters (Fed. Eur. Biochem. Soc.) 579, 5718-5722 (2005).
280. Ariel Fernández: “Wrapping a hydrogen bond with a molecular force probe: the mechanical equivalent of dehydration propensity”. Journal of Biological Physics and Chemistry 6, 3-7 (2006).
281. Ariel Fernández: “What factor drives the fibrillogenic association of beta-sheets?”
FEBS Letters (Fed. Eur. Biochem. Soc.) 579, 6635-6640 (2005).
282. Ariel Fernández and Sridhar Maddipati: “The a-priori inference of cross reactivity for drug targeted kinases”. Journal of Medicinal Chemistry 49, 3092-3100 (2006).
283. Sridhar Maddipati and Ariel Fernández: “Feature-similarity kinase classifier as a ligand engineering tool”. Biomolecular Engineering 23, 307-315 (2006).
284. Ariel Fernández and L. Ridgway Scott: “Modulating drug impact by wrapping target proteins”. Expert Opinion on Drug Discovery 2, 249-259 (doi:10.1517/17460441.2.2.249)
(2007).
285. Jianping Chen, Xi Zhang and Ariel Fernández: “Molecular basis for specificity in the druggable kinome: sequence-based analysis”. Bioinformatics 23, 563-572 (2007).
286. Sridhar Maddipati and Ariel Fernández: “Peptide translocators with engineered dehydration-prone hydrogen bonds”. Journal of Chemical Physics 126, 061102, Communication (2007).
287. A. Keith Dunker and Ariel Fernandez: “Engineering a productive enzyme confinement”. Trends in Biotechnology 25, 189-190, Research Focus (2007).
288. Ariel Fernández and Alejandro Crespo: “Wrapping technology and the enhancement of specificity in cancer drug treatment”. Frontiers in Bioscience 12, 3617-3627 (2007).
289. Ariel Fernández et al.: “Rational Drug Redesign to overcome drug resistance in cancer therapy: Imatinib moving target”. Cancer Research 67, 4028-4033, Priority Report, Cover featured (2007).
290. Ariel Fernández, Jianping Chen and Alejandro Crespo: “Solvent-exposed backbone loosens the hydration shell of soluble folded proteins”. Journal of Chemical Physics 126, 245103 (2007).
291. Natalia Pietrosemoli, Alejandro Crespo and Ariel Fernández:
“Dehydration propensity of order-disorder intermediate regions in soluble proteins”.
Journal of Proteome Research 6, 3519-3526 (2007).
292. Jyotsnabaran Halder, …, Ariel Fernández, Gabriel Lopez-Berestein, Anil K. Sood: “Therapeutic efficacy of a novel FAK inhibitor TAE226 in ovarian carcinoma”.
Cancer Research 67, 10976-10983 (2007).
293. Ariel Fernández, et al.: “An anticancer C-kit kinase inhibitor is re-engineered to make it more active and less cardiotoxic”. Journal of Clinical Investigation 117, 4044-4054 (2007). (featured in Press Releases).
Commentary by George Demetri: Structural reengineering of imatinib to decrease cardiac risk in cancer therapy. Journal of Clinical Investigation 117, 3650-3653 (2007).
294. Ariel Fernández: “Molecular basis for evolving self-dissimilarity in the yeast protein interaction network”. PLoS Computational Biology 3, e226 (2007).
295. Alejandro Crespo and Ariel Fernández: “Kinase packing defects as drug targets.”
Drug Discovery Today 12, 917-923 (2007).
296. Ariel Fernández, Alejandro Crespo and Axel Blau: “Passive Water-Lipid Peptide Translocators with Conformational Switches: From Single-Molecule Probe to Cellular Assay”. Journal of Physical Chemistry B 111, 13987-13992 (2007).
297. Han Liang, Kristina Rogale-Plazonic, Jianping Chen, Wen-Hsiung Li and
Ariel Fernández: “Protein under-wrapping causes dosage sensitivity and decreases gene duplicability”. PLoS Genetics 4, e11 (2008).
298. Ariel Fernández, Xi Zhang and Jianping Chen: “Folding and wrapping soluble proteins: Exploring the molecular basis of cooperativity and aggregation”.
Progress in Molecular Biology and Translational Science 83, 53-88 (2008).
299. Ariel Fernández, Alejandro Crespo, Sridhar Maddipati and Ridgway Scott: “Bottom-up engineering of peptide cell translocators based on environmentally modulated quadrupole switches”. ACS Nano 2, 61-68 (2008).
300. Alejandro Crespo and Ariel Fernández: “Induced disorder in protein-ligand complexes as a drug-design strategy”. Molecular Pharmaceutics (ACS) 5, 430-437 (2008).
301. Xi Zhang, Alejandro Crespo and Ariel Fernández: “Turning promiscuous kinase inhibitors into safer drugs”. Trends in Biotechnology 26, 295-301 (2008).
302. Xi Zhang and Ariel Fernández: “In silico drug profiling of the human kinome based on a molecular marker for cross reactivity”. Molecular Pharmaceutics (ACS) 5, 728-738 (2008).
303. Han Liang and Ariel Fernández: “Evolutionary constraints imposed by gene dosage balance”. Frontiers in Bioscience 13, 4373-8 (2008).
304. Ariel Fernández and Alejandro Crespo: “Protein wrapping: a marker for association, aggregation and molecular targeted therapy”. Chemical Society Reviews (Royal Society of Chemistry, UK) 37, 2373-2382, Tutorial Review (2008).
305. Alejandro Crespo, Xi Zhang and Ariel Fernández: "Redesigning kinase inhibitors to enhance specificity". Journal of Medicinal Chemistry 51, 4890-4898 (2008).
306. Jianping Chen, Han Liang and Ariel Fernández: “Protein structure protection commits gene expression patterns”. Genome Biology 9, R107 (2008).
307. Ariel Fernández: “Structural Basis for Specificity in Drug Therapy” (Plenary Inaugural Lecture BIOMAT 2008). Actas de la Academia Nacional de Ciencias (Córdoba, Argentina) Tomo XIV, pages 11-22 (2008).
308. Ariel Fernández, Alejandro Crespo and Abhinav Tiwari: “Is there a case for selectively promiscuous anticancer drugs?”. Drug Discovery Today 14, 1-5 (2009)
309. Ariel Fernández, Soledad Bazán and Jianping Chen: “Taming the induced folding of drug-targeted kinases”. Trends in Pharmacological Sciences 30, 66-71 (2009).
310. Ariel Fernández and Sean Sessel: “Selective antagonism of anticancer drugs for side-effect removal”. Trends in Pharmacological Sciences 30, 403-410 (2009).
311. Ariel Fernández: “Target Discovery”, iDrugs 12, 620-622 (2009)
312. Ariel Fernández and Jianping Chen: “Human capacitance to dosage imbalance: Coping with inefficient selection”. Genome Research 19, 2185-2192 (2009).
313. P. Vivas-Mejia, J. Benito, Ariel Fernández, et al.: “c-Jun-NH2-kinase-1 inhibition leads to antitumor activity in ovarian cancer”. Clinical Cancer Research 16, 184-194 (2010).
314. Ariel Fernández and R. Stephen Berry: “Golden rule for buttressing vulnerable soluble proteins”. Journal of Proteome Research (ACS) 9, 2643-2648 (2010).
315. Sean Sessel and Ariel Fernández: “Selectivity filters to edit out side effects in molecular anticancer therapy”. Current Topics in Medicinal Chemistry 11, 788-799 (2010).
316. Larisa Cybulski, Mariana Martin, Maria Mansilla, Ariel Fernández and Diego de Mendoza: “Membrane Thickness Cue for Cold Sensing in a Bacterium”. Current Biology 20, 1539-1544 (2010).
Editorially commissioned review by Kumaran Ramamurthi, Current Biology 20, R707-R709 (2010).
Research Highlight in Nature Reviews/Microbiology:
Lucie Wootton: “Bacillus takes the temperature”. Nature Reviews/Microbiology 8, 680 (2010).
317. Ariel Fernández: “Nanoscale Thermodynamics of Biological Interfacial Tension”, Proceedings of The Royal Society A 467, 559-568 (2010).
318. Christopher Fraser, Ariel Fernández and Ridgway Scott: “Dehydron analysis: Quantifying the effect of hydrophobic groups on the strength and stability of hydrogen bonds”. Advances in Experimental Medicine and Biology 680, 473-479 (2010).
319. Erica Schulz, Marisa Frechero, Gustavo Appignanesi and Ariel Fernández: “Sub-nanoscale surface ruggedness provides a water-tight seal for exposed regions in soluble protein structure”. PLoS One (Public Library of Science) 5, e12844, PMID: 20862253 (2010).
320. Ariel Fernández: “Variational mechanics of water at biological interfaces”. Fast Track Communication. Journal of Physics A: Math. Theor. 44, 292001 (2011).
321. Ariel Fernández: “Biology avoids phase separations”. Journal of Physics A / Insights (2011) Online: http://iopscience.iop.org/1751-8121/labtalk-article/46468?labTalkTab
322. Ariel Fernández and Michael Lynch: “Nonadaptive origins of interactome complexity”. Nature 474, 502-505 (2011).
323. Ariel Fernández, Christopher Fraser and L. Ridgway Scott: “Purposely engineered drug-target mismatches for entropy-based drug optimization”. Trends in Biotechnology 30, 1-7 (2012).
324. Ariel Fernández, Yun-Huei Tzeng and Sze-Bi Hsu: “Subfunctionalization reduces the fitness cost of gene duplication in humans by buffering dosage imbalances”.
BMC Genomics 12, 604 (2011).
325. Ariel Fernández: “Mathematical modeling in biology: A mixed picture”. Journal of Biological Physics and Chemistry (Collegium Basilea and AMSI) 11, 124 (2011).
326. Christopher M. Fraser, Ariel Fernández and L. Ridgway Scott. WRAPPA: A Screening Tool for Candidate Dehydron Identification. University of Chicago, Department of Computer Science Technical Report TR-2011-05, Communicated by L. Ridgway Scott on December 4, 2011.
URL: http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-05
327. Ariel Fernández: “Communication: Epistructural thermodynamics of soluble proteins”. Journal of Chemical Physics 136, 091101 (2012).
328. Sebastián Accordino, Marcela A. Morini, María B. Sierra, Ariel Rodriguez-Fris, Gustavo Appignanesi and Ariel Fernández: “Wrapping mimicking in drug-like small molecules disruptive of protein-protein interfaces”. Proteins: Structure, Function, Bioinformatics 80, 1755-1765 (2012).
329. Sebastián Accordino, Ariel Rodriguez-Fris, Gustavo Appignanesi and Ariel Fernández: “A unifying motif of intermolecular cooperativity in protein associations”. European Physical Journal E: Soft Matter and Biological Physics 35, 59 (2012).
330. Ariel Fernández: “Epistructural tension promotes protein associations”.
Physical Review Letters 108, 188102 (2012).
Reviewed in Physics (American Physical Society).
Focus: “Proteins Hook up Where Water Allows”. Physics 5, 51 (2012).
Reviewed in Chemical & Engineering News
“Protein Binding Hot Spots”. Chemical & Engineering News 90 (20), 39 (2012)
331. Ariel Fernández: “Comunication: Nanoscale electrostatic theory of epistructural fields at the protein-water interface”. Journal of Chemical Physics 137, 231101 (2012).
332. Quoc-Nam Tran, Valentin Andreev and Ariel Fernández: "Likelihood of side effects depends on desired clinical impact: Affinities within a very small set of targets enables inference of promiscuity or specificity of kinase inhibitors," IEEE International Conference on Bioinformatics and Biomedicine Workshops, bibmw, pp.151-158 (2012).
URL:
http://www.computer.org/csdl/proceedings/bibmw/2012/2746/00/06470297-abs.html
333. Ariel Fernández Stigliano: “Breakdown of the Debye polarization ansatz at protein-water interfaces”. Journal of Chemical Physics 138, 225103 (2013).
334. Maria B. Sierra, Sebastian Accordino, Ariel Rodriguez-Fris, Marcela Morini, Gustavo Appignanesi and Ariel Fernández Stigliano: “Protein packing defects ‘heat up’ interfacial water”. European Physical Journal E 36, 62 (2013).
335. Ariel Fernández Stigliano: “Provisional theory of nanoscale water dielectrics”. Journal of Biological Physics and Chemistry 13, 9-11 (2013).
336. Ariel Fernández: “Supramolecular evolution of protein organization”.
Annual Reviews of Genetics, in press (2015).
337. L. Ridgway Scott and Ariel Fernández Stigliano. A disruptive dipole-dipole alignment promotes a stable molecular association. University of Chicago, Department of Computer Science Technical Report TR-2013-10, Communicated by L. Ridgway Scott on November 22, 2013.
URL: http://www.cs.uchicago.edu/research/publications/techreports/TR-2013-10
338. Ariel Fernández: “The principle of minimal episteric distortion of the water matrix and its steering role in protein folding”. Journal of Chemical Physics 139, 085101 (2013).
339. María Eugenia Inda, Michel Vandenbranden, Ariel Fernández, et al.: “A lipid-mediated conformational switch modulates the thermosensing activity in DesK”. Proceedings of the National Academy of Sciences USA 111, 3579-3584 (2014).
Reviewed in Research Highlights - Nature Chemical Biology 10, 240 (2014)
340. Ariel Fernández: “Synergizing immunotherapy with molecularly targeted anticancer treatment”. Drug Discovery Today 19, 1427-1432 (2014).
Published online at
http://www.sciencedirect.com/science/article/pii/S135964461400107X
DOI information: 10.1016/j.drudis.2014.03.022
341. Ariel Fernández: “Water promotes the sealing of nanoscale packing defects in folding proteins”. Journal of Physics: Condensed Matter – Fast Track Communications 26, 202101 (2014).
342. Ariel Fernández: “How do proteins dry in water?” Journal of Physics: Condensed Matter – News Item, May 1 (2014).
Published at: http://iopscience.iop.org/0953-8984/labtalk-article/57046
343. Joan Montes de Oca, Ariel Rodriguez Fris, Gustavo Appignanesi and Ariel Fernández: “Productive induced metastability in allosteric modulation of kinase function”. FEBS Journal (Federation European Biochemical Societies) 281, 3079-3091 (2014).
Published online at: http://onlinelibrary.wiley.com/doi/10.1111/febs.12844/abstract;jsessionid=CF42405D678C5BC7A0C43AD3B80785C2.f03t04
344. Ariel Fernández: “Communication: Chemical functionality of interfacial water enveloping nanoscale structural defects in proteins”. Journal of Chemical Physics 140, 221102 (2014).
http://scitation.aip.org/content/aip/journal/jcp/140/22/10.1063/1.4882895
________________________________________________________________
345. BOOK
Author: Ariel Fernández
Title: “Transformative Concepts for Drug Design: Target Wrapping”
Publisher: Springer, Heidelberg, Berlin
ISBN: 978-3-642-11791-6
Publication year: 2010.
PATENTS
346.
US 8,466,154 B2 (awarded)
Ariel Fernández et al.: “Methods and Composition of Matter Related to Wrapping of Dehydrons”. Inventors: Ariel Fernández, William Bornmann, Gabriel Lopez-Berestein, Angela Sanguino, Zeng-Hong Peng, Anil K. Sood. Awarded: June 18, 2013.
347.
US 20130345135A1 (pending)
Richard L. Moss and Ariel Fernández: “Inhibition of MYBP-C binding to myosin as a treatment for heart failure”. Inventors: Richard L. Moss and Ariel Fernández; Asignee: Wisconsin Alumni Research Foundation.
___________________________________________________________
SYNDICATED PRESS COLUMNIST
348. Ariel Fernández: “Human Evolution: No Easy Fix”. Project Syndicate (The World’s Opinion Page), Culture and Society Section, October 3, 2011.
Published at:
http://www.project-syndicate.org/commentary/human-evolution--no-easy-fix
349. Ariel Fernández: “Structural Defects in Proteins May Function as Catalysts, Study Reveals”, Press Release: Discovery of the Catalytic Dehydron, WebWire, July 6, 2014.
350. Ariel Fernández: “Protein Structural Defects Are Enablers and Stimulators of Enzyme Catalysis”. PR Newswire, July 14, 2014.
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My Resume
COVID 19
In these three papers, Ariel Fernandez outlines a plausible route to defuse COVID19:
https://pubs.acs.org/doi/10.1021/acsmedchemlett.0c00410
https://pubs.acs.org/doi/10.1021/acsptsci.0c00114
https://pubs.acs.org/doi/10.1021/acsptsci.0c00128
Ariel Fernandez
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