Torrey Pines Institute for Molecular Studies science image
Torrey Pines Institute for
Molecular Studies
11350 SW Village Parkway
Port St. Lucie, FL 34987-2352
USA
Scientists
Photo by M. Lynn
Karina Martínez Mayorga
Assistant Member
Conformational analysis

772.345.4688 - phone
772.345.3649 - fax

Dr. Karina Martínez-Mayorga earned a Bachelor of Science in Chemistry in 1997 and a Ph.D. in 2005 with Professor Gabriel Cuevas, both from the National Autonomous University of Mexico in Mexico City. During her doctoral studies, she participated in research visits with Professor Jesus Jimenez-Barbero in Madrid, Spain and instructed in the School of Chemistry at UNAM and La Salle University. In February 2005, Dr. Martínez-Mayorga joined the group of Professor Michael F. Brown at the University of Arizona as a postdoctoral fellow, conducting experimental and computational research on membrane proteins and membrane lipids in collaboration with groups at Wabash Collage, Indiana, IBM TJ Watson Research Center, New York, and recently with the University of California at Santa Cruz and Albert-Ludwigs University in Freiburg, Germany. In August 2007, she joined the Torrey Pines Institute for Molecular Studies in Florida as Assistant Member.

Research Focus

Dr. Martínez-Mayorga focuses on the development of structural models by computational techniques to aid on the design of new compounds.  Some of the methodologies employed are: Molecular similarity searching, ligand-based virtual screening, conformational analysis, quantum chemical calculations, and molecular dynamics simulations.

Honors and Awards

  • Member of the National Researcher System, National Council of Science and Technology, Mexico,
    (SNI-CONACyT), Mexico, January 2006-2008
  • Antonio Caso Medal postulate for PhD studies. National Autonomous University of Mexico, 2005.
  • Science and Technology National Council Fellowship at the National Autonomous University of Mexico, PhD studies, 2001-2004.
  • Outstanding Teacher, La Salle University, 2004.
  • Science and Technology National Council Fellowship at the National Autonomous University of Mexico, M.Sc. studies, 1998-2000.
  • Postgraduate Studies Scholarship at the National Autonomous University of Mexico, 2003.


Current Projects


A) Design, binding mode prediction and ligand-based virtual screening of painkillers.
 G-Protein Coupled Receptors (GPCR) superfamily plays a significant role in drug discovery and development; they are involved in ca. 45% of all current therapy.  Opioid receptors are GPCRs currently used as the most effective analgesics available in the clinical treatment of moderate and severe pain. Nevertheless, there is still the need for potent painkillers with lesser side effects. We are developing binding mode models to identify key structural features involved in the ligand-receptor recognition process, as well as searching for new opioid ligands by means of ligand-based virtual screening.




B) Physicochemical characterization of metal-polyamine complexes.  Metal containing compounds; have successfully been used in therapy, such as cisplatin as an anticancer agent.  The presence of the metal confers particular chemical properties participating in electron transferring processes.  It also induces and stabilizes geometrical arrangements that might not be favorable otherwise.  In terms of novel drugs, this scenario shows opportunities of new areas in the chemical and property space.  Our current work focuses on the analysis of the energy profile that influence the formation, stability and conformational (geometrical) preferences of Pt- polyamine complexes.




C) Conformation and dynamics of rhodopsin chromophore, retinal.  Rhodopsin is responsible for the dim light vision in eukaryotes; it has been used as a representative prototype of the GPCR superfamily.  Rhodopsin activation starts with the absorption of light by its chromophore called retinal.  This event produces the cis to trans isomerization of retinal.  We are studying the conformational and dynamical properties of retinal into rhodopsin binding pocket.





Publications

  1. Li, Y, Yongye, BA, Giulianotti, MA, Martínez-Mayorga, K, Yu, Y, Houghten, RA. Synthesis of Cyclic Peptide through Direct Aminolysis of a Peptide Thioester in an Aqueous Organic Solvent. J Comb Chem. Epub Oct 6, 2009. [Epub ahead of print]
  2. Yongye, AB, Li, Y, Giulianotti, MA, Yu, Y, Houghten, RA, Martínez-Mayorga, K. Modeling of Peptides Containing D-Amino Acids: Implications on Cyclization. J Comput Aided Mol Des. 23(9):677-89, 2009.
  3. Scior, J. T.; Medina-Franco, J. L.; Do, Q.-T.; Martínez-Mayorga, K.; Yunes Rojas, J. A.; Bernard, P. How to Recognize and Workaround Pitfalls in QSAR Studies. Curr. Med. Chem. 2009, 16, 4297-4313.
  4. Brown, M.F., Martínez-Mayorga, K., Nakanishi, K., Salgado, G.F., Struts, A.V. Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid-state H NMR Spectroscopy. Photochem. Photobiol. 85(2):442-53, 2009.
  5. Medina-Franco, J.L., Martínez-Mayorga, K., Bender, A., Marín, R.M., Giulianotti, M.A., Pinilla, C., Houghten, R.A. Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs. J. Chem. Inf. Model. 49:477-91, 2009.
  6. Navarrete-Vazquez, G., Paoli, P., León-Rivera, I., Villalobos-Molina, R., Medina-Franco, J.L., Ortiz-Andrade, R., Estrada-Soto, S., Camici, G., Diaz-Coutiño, D., Gallardo-Ortiz, I., Martínez-Mayorga, K., Moreno-Díaz, H. Synthesis, in vitro and computational studies of protein tyrosine phosphatase 1B inhibition of a small library of 2-arylsulfonylaminobenzothiazoles with antihyperglycemic activity. Bioorg. Med. Chem. 17(9):3332-41, 2009. Epub Mar 26, 2009.
  7. Yongye, A.B., Appel, J.R., Giulianotti, M.A., Dooley, C.T., Medina-Franco, J.L., Nefzi, A., Houghten, R.A., Martínez-Mayorga, K. Identification, structure-activity relationships and molecular modeling of potent triamine and piperazine opioid ligands. Bioorg. Med. Chem. Epub Jun 21, 2009. [Epub ahead of print.]
  8. Medina-Franco, J.L., Martínez-Mayorga, K., Giulianotti, M.A., Houghten, R.A., Pinilla, C. Visualization of the Chemical Space in Drug Discovery. Curr.Comput.Aided Drug Des. 4:323-334, 2008.
  9. Medina-Franco, J.L., Martínez-Mayorga, K., Juárez-Gordiano, C., Castillo R. Pyridin-2(1H)-ones: A promising class of HIV-1 non-nucleoside reverse transcriptase inhibitors. ChemMedChem (2):1141-1147, 2007.
  10. Tanaka, K., Struts, A.V., Krane, S., Fujioka, N., Job, C., Salgado, G., Martínez-Mayorga, K. Brown, M.F. and Nakanishi, K.. Synthesis of CD3-labeled 11-cis-Retinals and Application to Solid-State Deuterium NMR Spectroscopy of Rhodopsin. Bull. Chem. Soc. Japan 80:2177-2184, 2007.
  11. Martínez-Mayorga, K., Pitman, M.C., Groessfield, A., Feller, S.E., Brown, M.F. Retinal Counterion Switch Mechanism in Vision Evaluated by Molecular Simulations. J. Am. Chem. Soc. 128:16502-16503, 2006.
  12. Martínez-Mayorga, K., Juaristi, E. and Cuevas, G. Manifestation of Steroelectronic Effects on the Calculated Carbon-Hydrogen Bond Lengths and One Bond 1JC-H NMR Coupling Constants. Relative Acceptor Ability of the Carbonyl Group (C=O), Thiocarbonil (C=S), and Methyleden (C=CH2) Groups Towards C-H Donor Bonds. J.O. Chem. 69:7266-7276, 2004.
  13. Martínez-Mayorga, K., Medina-Franco, J. L., Mari, S., Cañada, F. Javier, Rodríguez-García E., Vogel, P., Li, H., Blériot, Y., Sinaÿ, P., Jiménez-Barbero, J. The Conformational Behavior of Novel Glycosidase Inhibitors with Substituted Azepan Structures. A NMR and Modeling Study. Eur. J. Org. Chem. 10:4119-4129, 2004.
  14. Martínez-Mayorga, K., Cortes, F., Leal, I., Reyna, V., Quintana, D., Antúnez, S., Cuevas, G. Toward the Origin of the Conformational Preference of 2-methoxyoxane, a Model Useful to Study the Anomeric Effect. ARKIVOC 132-148, 2003.

Presentations

Oral

  1. Brown, M. F.; Martínez-Mayorga, K.; Salgado, G. F. J.; Struts, A. V. "Solid-State NMR Relaxation of Rhodopsin in Membranes" International Conference on Magnetic Resonance in Biological Systems, San Diego, CA, August 24-29, 2008.
  2. Medina-Franco, J. L.; Martínez-Mayorga, K. "2D- vs. 3D-Similarity Studies in Combinatorial Libraries and Other Large Compound Collections" ACS National Meeting Philadelphia, PA August 18, 2008.
  3. Brown, M. F.; Martínez-Mayorga, K.; Nakanishi, K.; Salgado, G. F. J.; Struts, A. V. "Retinylidene Structure and Dynamics in Activation of Rhodopsin as Detected by Solid-State 2H NMR Relaxation"  13th International Conference on Retinal Proteins. Barcelona, Spain, June 15-19, 2008.
  4. Martínez-Mayorga, K.; Pitman, M. C.; Grossfield, A.; Feller, S. E; Brown, M. F. "Visual Receptor Activation Evaluated by Molecular Dynamics Simulations and Solid State 2H NMR" Spectroscopy51st Biophysical Society Meeting, Baltimore, MD, USA February 3-7, 2007.
  5. Martínez-Mayorga, K.; Pitman, M. C.; Grossfield, A.; Feller, S. E; Brown, M. F. "Rhodopsin Activation Studied by Microsecond-Time Scale Molecular Dynamic Simulations" 19th Rocky Mountain Regional ACS Meeting, Tucson AZ, USA October 17, 2006.
  6. Martínez-Mayorga, K.; Pitman, M. C.; Grossfield, A.; Feller, S. E. "Molecular Dynamics Simulation of Light Activation of Rhodopsin" 50th Biophysical Society Meeting, Salt Lake City Utah, USA February 2006.
  7. Juaristi, E.; Cuevas, G.; Martínez-Mayorga, K. "Manifestations of Stereoelectronic Interactions in C-13/H-1 Bond Coupling Constants" 17th International Conference on Organic Synthesis, Shanghai China, August 15-20, 2004.

Poster

  1. Martínez-Mayorga, K. "3D-Molecular Similarity Applied to Food Chemistry" general session and Sci-Mix ACS National Meeting Philadelphia. 18, 19 August, 2008
  2. Medina-Franco, J. L.; Martínez-Mayorga, K.; Giulianotti, M. A. ; Scior, T.; Yu, Y.; Pinilla, C.; Houghten, R. A. "Dynamic interplay between chemotype, similarity and docking studies: Towards a virtual screening approach for protein kinase B inhibitors"  8th International Conference on Chemical Structures (ICCS) Noordwijkerhouth, The Netherlands, 1-5 June, 2008.
  3. Martínez-Mayorga, K.; Medina-Franco, J. L.; Giulianotti, M. A.; Pinilla, C.; Dooley, C. T.; Houghten, R. A. "Binding Conformation Of A Set of Bicyclic Guanidines to k-Opioid Receptor As Suggested By 3D Shape Similarity Analysis" Keystone Symposia, Silberthorne, Colorado, USA March 29-April 2, 2008.
  4. Medina-Franco, J. L.; Giulianotti, M.; Pinilla, C.; Martínez-Mayorga, K.; Ghosh, S.; An, J.; Huang, Z.; Weish, K.; Reed, J.; Houghten, R. A. "Insights into the mechanism of action of phenylurea-based XIAP inhibitors by molecular docking" Keystone Symposia, Silberthorne, Colorado, USA March 29-April 2, 2008.
  5. Martínez-Mayorga, K.; Grossfield, A.; Medina-Franco, J. L.; Pitman, M. C.; Feller, S. E.; Brown, M. F. "Retinal Relaxation in Rhodopsin Activation Viewed by Large-Scale Molecular Dynamics Simulations" 52nd Biophysical Society Meeting & 16th International Biophysics Congress, Long Beach CA, USA February 2-6, 2008.
  6. Lewis, J.W.; Martínez-Mayorga, K.; Szundi, I.; Epps, J.; Constantino, V. U.; Kliger, D. S.; Brown, M. F. "Influence of Lipid Membrane Composition on the Kinetics of Rhodopsin Activation by Time-Resolved UV-Visible Spectroscopy" 52nd Biophysical Society Meeting & 16th International Biophysics Congress, Long Beach CA, USA February 2-6, 2008.
  7. Vogel, R.; Martínez-Mayorga, K.; Mahalingam, M.; Constantino, V. U.; Brown, M. F. "Activation of Rhodopsin at Physiological Temperatures: Structural and Thermodynamic Characterization of the Two Protonation Switches" 52nd Biophysical Society Meeting & 16th International Biophysics Congress, Long Beach CA, USA February 2-6, 2008.
  8. Vogel, R.; Martínez-Mayorga, K.; Mahalingam, M.; Constantino, V. U.; Brown, M. F. "Membrane Lipid Modification of Rhodopsin Activation Studied by FTIR Spectroscopy" 52nd Biophysical Society Meeting & 16th International Biophysics Congress, Long Beach CA, USA February 2-6, 2008.
  9. Struts, A. V.; Salgado, G. F. J.; Martínez-Mayorga, K.; Leftin, A.; Job, C.; Brown, M. F. "Site-Directed 2H NMR Reveals Functional Dynamics of Retinal due to Light Activation of Rhodopsin" 52nd Biophysical Society Meeting & 16th International Biophysics Congress, Long Beach CA, USA February 2-6, 2008.
  10. Lau, P.-W.; Grossfield, A.; Feller, S. E.; Martínez-Mayorga, K.; Struts, A. V.; Pitman, M. C.; Brown, M. F. "Molecular Dynamics Simulations Unveil Dynamic Flexibility of Retinal within Binding Pocket of Rhodopsin" 52nd Biophysical Society Meeting & 16th International Biophysics Congress, Long Beach CA, USA February 2-6, 2008.
  11. Struts, A. V.; Salgado, G. F. J.; Martínez-Mayorga, K.; Job, C.; Tanaka, K.; Krane, S.; Nakanishi, K.; Brown, M. F. "2H NMR Relaxation and Dynamics of Retinal Cofactor in Dark, Meta I, and Meta II States of Rhodopsin" 51st Biophysical Society Meeting, Baltimore MD, USA February 3-7, 2007.
  12. Martínez-Mayorga, K.; Medina-Franco, J. L.; Mari, S.; Cañada, F. J.; Rodríguez-García, E.; Vogel, P.; Li, H.; Bleriot, Y.; Sinaÿ, P.;  Jiménez-Barbero, J. "Conformational Study of Monosacharide Analogues with 1H NMR, NOE experiments and Molecular Dynamics"ACS 228th National Meeting, Philadelphia PA USA, August 22-26, 2004.
  13. Martínez-Mayorga, K.; Cuevas, G. "Are the Changes of One-Bond 1JC-H Coupling Constatns a Real Index of Stereoelectronic Manifestation?" Institute of Chemistry Internal Symposia -UNAM, March 8-11, 2004.
  14. Roura Pérez, G.; Cuevas, G.; Martínez-Mayorga, K. "Computational Evaluation of the 1JC-H Coupling Constants in Ketones" XXXIX Mexican Chemical Society Meeting, Mérida, Yucatán, Mexico October 3-7, 2004.
  15. Martínez-Mayorga, K.; Medina-Franco, J. L.; Mari, S.; Cañada, F. J.; Rodríguez-García, E.; Vogel, P.; Li, H.; Bleriot, Y.; Sinaÿ, P.; Jiménez-Barbero, J. Small Molecule NMR Conference, SMASH, Verona Italy September 14-17, 2003.
  16. Martínez-Mayorga, K.; Cuevas, G.; Juarista, E. "Stereoelectronic Effects Manifestation in 1JC-H Coupling Constants and C-H Distances in Cyclohexanone, Thiocyclohexanone, Lactone and Thiolactone Derivatives" First Meeting of the NMR Group of the Royal Society of Chemistry of Spain, Calella Barcelona, Spain, October 20-23, 2002.
  17. Martínez-Mayorga, K.; Chavez-Uribe, M. C. I.; Cuevas, G. "Participation of Stereoelectronic Effects in the Grob Fragmentation Towards 1JC-C Coupling Constants" XXV Latin-American Chemistry Meeting, Cancun Quintana Roo, Mexico, September 22-26, 2002.
Copyright © 2010 Torrey Pines Institute for Molecular Studies. All rights reserved.