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Rodrigo Galindo-Murillo

Assistant Research Professor of Medicinal Chemistry

 

CONTACT

Phone: 801.581.3285

Fax: 801.585.6208

Email: rodrigo.galindo@utah.edu

Education

  • B.S. 2002, Pharmaceutical Biochemistry, Universidad Autónoma de México (UNAM)

  • M.S. 2006, Quantum Chemistry, Universidad Autónoma de México (UNAM)

  • Ph.D. 2011, Physical Chemistry, Universidad Autónoma de México (UNAM)

  • 2012-2017, Postdoctoral fellow, Medicinal Chemistry Department, College of Pharmacy, University of Utah.  Mentor: Thomas E. Cheatham III

 

Research Interests

Computational chemistry approaches to study the structure, ligand binding and dynamics of nucleic acids

DNA/RNA-drug binding studies

Molecules that contain transition metals like Co, Ni, Cu and Zn are gaining interest as part of therapeutic drugs for cancer treatment, parasitic anti-viral infections. These compounds interact directly with nucleic acids in different configurations such as intercalation, groove binders or stacking. Using computational tools that include Molecular Dynamics, Quantum Chemistry and Quantum Theory of Atoms in Molecules we study the specific interactions of nucleic acids and transition metal complexes to gain insight into their binding affinity, energetics and the effect in the structure and dynamics.

Of special interest is the binding mode known as base-pair eversion, which consist of a ligand of planar structure and with aromatic rings, binds through the minor groove of DNA and pushing an AT or GC pair, breaking the Watson-Crick pairing of the nucleotides and pushing both bases toward the major groove, flipping the bases. This results in the ligand inserting into the DNA in the resulting cavity.

Galindo-Murillo Lab Molecules

Learn more about this process with the videos below:

Molecular dynamics simulation of Cu(4,7-dimethyl-bipiridine-acac) d(GAGAAATTGAGA)2

Molecular Dynamics of Cu[4,4'-dimetil-bipyridine-acetilacetonate]+ with DNA

Nucleic acids dynamics

The dynamic properties and the normal “breathing” modes of nucleic acids are deeply involved in molecular recognition processes. I am interested in studying these properties of nucleic acids as a mean to understand the molecular recognition system inside the cell and how enzymes that repair DNA damage are able to quickly locate and identify mismatches, bulges, oxidation or similar type of molecular errors.

Using computational chemistry tools and spectroscopic tools, we are interested in the time-range and the modes of motion of non-canonical structures such as those present in damaged DNA.

Examples can be viewed here:

Water density of DNA morphing between two GAAC sites

Non canonical DNA bases

The genetic code of every living organism on Earth is a quaternary or base four code, increasing it to a higher base system could open a wide range of possibilities for genetic marking, signaling and eventually even for coding and transcription which in turn would allow for an artificially enhanced control of genetics. The search for modified base pairs capable of extending the genetic alphabet remains an open challenge in chemistry and synthetic biology. We employ high throughput screening and computational chemistry methodologies to search for new molecules that match the stability of the double DNA strand, and at the same time, allow the biomolecular machinery to replicate this structures in-vivo.

Shown here:

DNA with heterobases, Molecular Dynamics Simulation

Publications

    1. Galindo-Murillo R, Garcia-Ramos, JC, Ruiz-Azuara L, T. E. Cheatham III, Cortes-Guzman, F. Intercalation processes of copper complexes in DNA. Nucleic Acids Research (2015) doi: 10.1093/nar/gkv467. Link
    2. Galindo-Murillo R, Roe D, T. E. Cheatham III. On the absence of intra-helical DNA dynamics on the microsecond timescale) Nature Communications 5:5152 doi: 10.1038/ncomms6152 (2014). Link
    3. Galindo-Murillo R. Roe DR, Cheatham TE III, Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochimica et Biophysica Acta (BBA)-General Subjects, (In press, DOI: 10.1016/j.bbagen.2014.09.00 Link
    4. Toledano-Magana Y, Garca-Ramos J C, Torres-Gutierrez C, Vazquez-Gasser C, Esquivel-Sanchez J M, Perez-Jimenez A, Ortiz-Frade L, Galindo-Murillo R, Laclette J P, Ruiz-Azuara L, Cesar Carrero J. Metal-based drugs for neglected tropical diseases treatment. Ruthenium (II) complexes with potential amoebicidal activity. Journal of Medicinal Chemistry (Submitted)
    5. The π-back-bonding modulation and its impact in the electronic properties of Cu(II) antineoplastic compounds. Experimental and theoretical study.” performed by Juan Carlos García-Ramos, Rodrigo Galindo-Murillo, Araceli Tovar-Tovar, Ana Luisa Alonso-Saenz, Virginia Gómez-Vidales, Marcos Flores-Álamo, Luis Ortiz-Frade,Fernando Cortes-Guzmán, Rafael Moreno-Esparza,Antonio Campero and Lena Ruiz-Azuara. Chemistry- A European Journal, 2014, 20, pp 13730-13741 Link
    6. Zhenjian Lin, Michael Koch, May Hamdy Abdel Aziz, Rodrigo Galindo-Murillo, Ma Diarey Tianero, Thomas E Cheatham, Louis R Barrows, Chris A Reilly, Eric W Schmidt. Oxazinin A, a Pseudodimeric Natural Product of Mixed Biosynthetic Origin from a Filamentous Fungus. 2014, 16, pp 4774-4777 Link
    7. Galindo-Murillo R, Thomas E. Cheatham III. DNA Binding Dynamics and Energetics of Cobalt, Nickel, and Copper Metallopeptides. ChemMedChem 9 (6), 1252-1259. Link
    8. Galindo-Murillo R, Alberto Olmedo-Romero, Eduardo Cruz-Flores, P.M. Petrar, Sandor Kunsagi-Mate, Joaquín Barroso-Flores, Calix[n]arene-based drug carriers: A DFT study of their electronic interactions with a chemotherapeutic agent used against leukemia, Computational and Theoretical Chemistry, Volume 1035, 1 May 2014, Pages 84-91. Link
    9. Galindo-Murillo R, María Eugenia Sandoval-Salinas, and Joaquín Barroso-Flores. In Silico Design of Monomolecular Drug Carriers for the Tyrosine Kinase Inhibitor Drug Imatinib Based on Calix- and Thiacalix[n]arene Host Molecules: A DFT and Molecular Dynamics Study. Journal of Chemical Theory and Computation 2014 10 (2), 825-834 Link
    10. Garca-Ramos J C, Galindo-Murillo R, Cortes-Guzman F, Ruiz-Azuara L. Metal-based drug-DNA interactions. Journal of the Mexican Chemical Society 2013 Aug 28;57(3):245-259.
    11. Bergonzo C, Galindo-Murillo R, T. E. Cheatham, III. Molecular modeling of nucleic acid structure: Electrostatics and Solvation. Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.9.1-7.9.22 (2013)
    12. Bergonzo C, Galindo-Murillo R, T. E. Cheatham, III. Molecular modeling of nucleic acid structure: Energy and Sampling. Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.8.1-7.8.21 (2013). Link
    13. Galindo-Murillo R, Bergonzo C, T. E. Cheatham, III. Molecular modeling of nucleic acid structure. Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.5.1-7.5.12 (2013). Link
    14. Valencia-Cruz AI, Uribe-Figueroa LI, Galindo-Murillo R, Baca-Lopez K, Gutierrez AG, Vazquez- Aguirre A, Ruiz-Azuara L, Hernandez-Lemus E, Meja C. Whole genome gene expression analysis reveals Casiopena-induced apoptosis pathways. PLoS One. 2013;8(1). Link
    15. Galindo-Murillo R, Ruiz-Azuara L, Moreno-Esparza R, Cortes-Guzman F. Molecular recognition between DNA and a copper-based anticancer complex. Physical Chemistry Chemical Physics. 2012 Nov 28;14(44):15539-46. Link
    16. Galindo-Murillo R, Hernandez-Lima J, Gonzales-Rendon M, Cortes-Guzman F, Ruiz-Azuara L, Moreno-Esparza R. Stacking betwen Casiopeinas and DNA bases. Physical Chemistry Chemical Physics. 2011 Aug 28;13(32):14510-5. Link