Email: YRODRIGUEZ@HOSTOS.CUNY.EDU
 

Office Number:A-507F

Office Tel: (718) 518-4134

Courses Teaching:

PHY 210 – General Physics I
CHE 210 – General Chemistry I
CHE 220 – General Chemistry II
ENV 110 – Environmental Science I

Areas of Expertise:

General and Physical Chemistry, General Physics, Metabolic Networks Dynamics, Computational and Theoretical Biophysics
 

Research

Application of Computational and Theoretical Biophysics approaches:
  • To the design of small-molecule chemical ligands that selectively modulate the biological function of the bromodomain (BRD) of the human transcriptional coactivator CBP (CREB binding protein) (and other BRDs such as BRD41, BRD42 and BRD4ET). CBP BRD plays an important role in the regulation of chromatin-mediated gene transcription and has major implication to cancer.
  • To understand the fundamental molecular mechanisms of histone lysine-methylation-directed control of gene transcription. Towards this goal, we propose using structure-based rational methods to design small molecules that selectively modulate the biological functions of EED to histone H3 peptide trimethylated at Lys 27.

Recent Publications

Scientific

  • Rodríguez, Y., Gerona-Navarro, G., Osman, R. and Zhou, M.-M. (2019) “In Silico Design and Molecular Basis for the Selectivity of Olinone Towards the First over the Second Bromodomain of BRD4.” PROTEINS: Struct, Funct, and Bioinf. (In press)
  • Pérez-Gordillo, F. L., Pérez de Vega, M. J., Gerona-Navarro, G., Rodríguez, Y., Alvarez de la Rosa, D., González-Muñiz, R. and Martín-Martínez, M. (2019) “Advances in the Development of Non-steroidal Mineralocorticoid-receptor Antagonists.” Chapter in Book Aldosterone-Mineralocorticoid Receptor - Cell Biology to Translational Medicine. ISBN 978-1-83962-199-4.
  •  Zhang, G., Barragan, F., Wilson, K., Levy, N., Herskovits, A., Sapozhnikov, M., Rodríguez, Y., Kelmendi, L., Alkasimi, H., Korsmo, H., Chowdhury, M., Gerona-Navarro, G. (2018) “A Solid-Phase Approach to Accessing Bisthioether-Stapled Peptides Resulting in a Potent Inhibitor of PRC2 Catalytic Activity.” Angew Chem Int Ed Engl, 57(52):17073-17078.
  •  Martín-Martínez, M., Pérez-Gordillo, F.L., Álvarez de la Rosa, D., Rodríguez, Y., Gerona-Navarro, G., González-Muñiz, R., and Zhou, M.-M. (2017) “Modulating Mineralocorticoid Receptor with Non-steroid Antagonists. New Opportunities for the Development of Potent and Selective Ligands without Off-target Side-effects.” J Med Chem, 60(7):2629-2650.
  •  Li, J., Rodríguez, Y., Cheng, C., Zeng, L., Wong, E.Y., Xu, C.Y., Zhou, M.-M. and Xu, P.X. (2016) “EYA1's conformation-specificity in dephosphorylating phosphothreonine in Myc and its activity on Myc stabilization in breast cancer.” Mol Cell Biol, 37(1). pii: e00499-16. Print 2017 Jan 1.
  •  Ren, C., Morohashi, K., Plotnikov, A.N., Jakoncic, J., Smith, S.G., Li, J., Zeng. L., Rodríguez, Y., Stojanoff, V., Walsh, M. and Zhou, M.-M. (2015) “Small Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain.” Chem Biol, 22(2): 161-8.
  •  Gacias-Monserrat, M., Gerona-Navarro, G., Plotnikov, A.N., Zhang, G.T., Zeng, L., Kaur, J., Moy, G., Rusinova, E., Rodríguez, Y., Matikainen, Joshua, J., Vincek, A., Joshua, J., Casaccia, P., & Zhou, M.-M. (2014) “Selective Chemical Modification of Gene Transcription Favors Oligodendrocyte Lineage Progression.” Chem Biol, 21(7): 841-54.
  •  Gerona-Navarro, G., Rodríguez, Y., Mujtaba, S., Frasca, A., Patel, J., Zeng, L., Plotnikov, A.N., Osman, R. and Zhou, M.-M. (2011) “Rational Design of Cyclic Peptide Modulators of the Transcriptional Coactivator CBP: A New Class of p53 Inhibitors.” J Am Chem Soc, 133(7):2040-2043.
  •  Eichenbaum, K.D., Rodríguez, Y., Mezei, M. and Osman, R. (2010) “The energetics of the acetylation switch in p53-mediated transcriptional activation.” Proteins, 78(2): 447-456.
  •  Rodríguez, Y., Mezei, M. and Osman R. (2008) “PT1 Gla domain binds to membrane through two dipalmitoylphosphatidylserines. A computational study.” Biochemistry, 47(50):13267-13278.
  •  Rodríguez, Y., Mezei, M. and Osman, R. (2007) “Association free energy of dipalmitoylphosphatidylserines in a mixed dipalmitoylphosphatidylcholine membrane.” Biophys J, 92(9):3071-3080.
  •  Torralba, A. and Rodríguez, Y. (2006) “Susceptibilities of an irreversible Michaelis-Menten enzyme.” Bull Math Biol, 68:1335-1353.
Education
  • Rodríguez, Y. and Gorr, A. (2019) “Decoding Literal Equations by Undressing the Process.” Curriculum Alignment. CCRP - Graduate NYC (www.graduatenyc.org).
  • Rodríguez, Y., Cardona, F, DePass, A.L. (2015) “A joint dual degree program en New York City” Understanding Interventions that Broaden Participation in Science Careers: Translating Research, Imapacting Practice, Vol VII, San Diego, California, May 15 – 17, 2015.
  •  Flek, F., Rodríguez, Y. and Fernández, F. “Chapter 4.4 bridging theory and applications: improving students' mathematical proficiency for the physical sciences with emphasis on physics.” Mathematics Teaching-Research Journal Online, 7(1):331-348, Summer 2014. 
  • Rodríguez, Y. (2012) “Teaching Philosophy.” Touchstone, 5.1:71-73. Center for Teaching and Learning. Hostos Community College (HCC).
  • Trachman, J., Casari, W., Nuñez-Rodríguez, N., Henderson, F., Rodríguez, Y. and Libfeld, J. (2011) “Saturday in the Park with Franz and Joyce.” Touchstone, 4(1):23-27. Center for Teaching and Learning. HCC. 
  • Henderson F., Trachman J., Steinberg, O., Nuñez-Rodriguez, N. and Rodríguez, Y. (2010) “Carving a Path of Sustainability in Hostos Community College.” Touchstone, 3(1):53-56 Center for Teaching and Learning. HCC. 
  • Rodríguez, Y. and Nuñez-Rodríguez, N. (2009) “Promoting the use of the flow chart in chemistry.” Touchstone, 2(1):33–37. Center for Teaching and Learning. HCC. 
  • Henderson F., Rodríguez Y. and Pelicot L. “Hostos goes green: The recycling program.” (2009) !Escriba!!Write!, 7:79-80. HCC Library.

Patents

  • Gerona-Navarro, G., Zhou, M.-M., Casaccia, P. and Rodríguez, Y. “Small Molecule Transcription Modulators of Bromodomains.” US Provisional Application No.: USP201462005645 | Filed: May 30, 2014. European Patent Office: 80298 Munich, Germany | Application No/Patent No. 15800337.6 – 1453 PCT/US2015033178 | Filed May 29, 2015.

Grants  and Fellowships

  • Rodríguez, Y., Angulo, N., Nieto-Wire, C. and Varelas A. The Hostos Engineering Academic Talent (HEAT) Scholarship Program | National Science Foundation (NSF 1833767, $999,400, 2019-2024).
  •  Rodríguez, Y. “Novel Small-Molecule Inhibitors for Investigating the Role of AF9 YEATS Domain in Gene Transcription” PSC-CUNY 50 Research Award 62748-00 50 ($6,000, Round 2019 – 2020)
  •  Rodríguez, Y. Community College Research Grant Program (Grant No. 1532) / CUNY ($10,000) 02/01/2018 – 01/31/2019 “In Silico Discovery of Small-Molecule Modulators of the AF9 YEATS Domain”
  •  Rodríguez, Y. CUNY Chancellor’s Research Fellowship Award for the 2018 – 2019 Academic Year.
  • Rodríguez, Y. Fulbright Scholar Award, 2016 – 2017 Academic Year to the Slovak Republic.
  • Rodríguez, Y. CUNY Chancellor’s Research Fellowship Award for the 2015 – 2016 Academic Year. 
  • Rodríguez, Y. Structure-Guided Design of BRD4-BrD1 Small-Molecule Inhibitors. PSC-CUNY 45 Research Award # 67708-00 45 for $6,000.00. (Round 2014 – 2015) 
  • Rodríguez, Y. Non-coding RNAs for Epigenetic Transcriptional Silencing in Prostate Cancer. Research Supplements to Promote Diversity in Health-Related Research. NIH/NCI Award 1R01CA154809-01 for $94,854 (09/01/2011 – 08/31/2013). Parent Grant PIs: Walsh, M. and Zhou, MM. 
  • Rodríguez, Y., Gerona-Navarro, G., Martínez, M., Pérez Vega, M., Zhou, M.M., González Muñiz, R. The Mineralocorticoid Receptor in Disease States: Integrative Approach to New Small-Molecule Modulators. International i-LINK Research Award 0312 for 23,200 Euros. Ministry of Economy and Competitivity, Spanish Government. (January 2012 – December 2013) 
  • Rodríguez, Y. Structure-Based Discovery of EED Chemical Inhibitors. PSC-CUNY 42 Research Award 64663-00 42 for $6,000. (Round 2011 – 2012) 
  • Rodríguez, Y. and Luján J. In Newton’s Footprints: Learning Physics by Doing Physics. COBI Project HCC Presented at COBI Retreat, Bronx Zoo, NY, June 1, 2011. (Award for $2,000, Round 2011 – 2012) 
  • Rodríguez, Y. Novel Small Molecules for Investigating Mechanisms of MLL-CBP-Induced Leukemia. PSC-CUNY 41 Research Award 63571-00 41 for $6,000. (Round 2010 – 2011) 
  • Rodríguez, Y. and Luján J. In Galileo’s Footprints: Learning Physics by Doing Physics. COBI Project HCC Presented at COBI Retreat, Bear Mountain, NY, March 18 – 20, 2010. (Award for $2,000, Round 2010 – 2011) 
  • Rodríguez, Y. Rational Design of Novel Chemical Modulators for Epigenetic Gene Silencing. PSC-CUNY 40 Research Award 62197-00 40 for $4,500. (Round 2009 – 2010) 
  • Rodríguez, Y. and Fernández F. Navigating the World of Chemistry through the Lab. COBI project, HCC $2,000. (Round 2009 – 2010)

Presentations

  • Rodríguez, Y., Plenary at 11th Joint Meeting of Medicinal Chemistry, Prague, Czech Republic, June 27 – 30, 2019 and Guest Speaker at IQM of CSIC in Madrid, Spain, July 4, 2019 on “In Silico Design of Chemical Modulator for Chromatin Biology.”
  •  Majekova, M., Viskupicova, J., Horakova, L., Rodríguez, Y. “Polypharmacology of Rutin Fatty Acid Esters” 22th EuroQSAR 2018 Translational and Health Informatics: Implications for Drug Discovery Conference, Thessaloniki, Greece - September 16-20, 2018. (Poster Presentation)
  •  Majekova, M., Viskupicova, J., Rodriguez, Y. Horakova, L. “Rutin Fatty Acid Esters As Multi-Target Compounds” MuTaLig COST ACTION CA15135 Annual meeting 2018 - Valletta (Malta), October 18-19 2018. (Poster Presentation)
  • Rodríguez, Y., “Structure-Based Design of Selective Small-Molecule Inhibitors for the First Bromodomain of BRD4.” Institute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences, November 28, 2016. (Guest speaker)
  •  Rodríguez, Y., Gerona-Navarro, G., Osman, R. and Zhou, M.-M. “Structure-Based Design of Selective BRD4-BrD1 Small-Molecule Inhibitors.” 21th EuroQSAR 2016 Where Molecular Simulations Meet Drug Discovery Conference in Verona, Italy, September 4 – 8, 2016. (Poster Presentation)
  •  Nuñez-Rodríguez N., Henderson F., Rodríguez, Y. and Varelas, A. “Enabling Success of Community College STEM Students through a NIH IRACDA Program.” Poster Presentation, 8th Conference on Understanding interventions that Broaden Participation in Science Careers, Philadelphia, PA, February 26 – 28, 2016.
  •  Rodríguez, Y., Fernández, F. and Flek, R. “Bridging Theory and Applications | Improving Students Mathematical Proficiency for Physical Sciences.” 12th Annual CUE Conference. HCC, CUNY. May 13, 2016. 
  • Fernández, W., Garrido-Rodríguez, I. and Rodríguez, Y. “Structure-Based Discovery of EED Inhibitors.” Hostos Research Day 2016, The Senate Grants Committee, the Grants Office, the Office of Academic Affair and the Senior Vice President for Administration and Finance. HCC. March 18, 2016.
  •  Rodríguez, Y. and Nuñez-Rodríguez, N. “Classroom Management I and II.” Hostos Teaching Institute (Fall 2015 and Spring 2016).
  • Pérez-Gordillo, F., Sierra Ramos, C., Gerona-Navarro, G., Álvarez de la Rosa, D., Zhou, M.-M., Rodríguez, Y., González-Muñiz, R. and Martín-Martínez, M. “Search for new non-steroidal mineralocorticoid receptor antagonist: structure-based virtual screening.” Spanish-Italian Medicinal Chemistry Congress, Barcelona, España, July 12 – 15, 2015. (Poster Presentation)
  •  Pérez-Gordillo, F., Sierra Ramos, C., Gerona-Navarro, G., Álvarez de la Rosa, D., Zhou, M.-M., Rodríguez, Y., González-Muñiz, R. and Martín-Martínez, M. “Structure-based virtual screening for novel non-steroidal mineralocorticoid receptor antagonists.” 8th International Symposium and Annual ADMIRE Cost Meeting: Aldosterone, MR and Salt-What´s new? Zermatt, Switzerland October 7 – 11, 2015. (Poster Presentation)
  •  Rodríguez, Y. Guest Speaker at the 15th Annual Biomedical Research Conference for Minority Students (ABRCMS) in Seattle, Washington, November 11 – 14, 2015 on “Community College Students: Tips for Transitioning to a Four-Year Institution.”
  •  Rodríguez, Y. Plenary Presentation at 7th Conference on Understanding Interventions that Broaden Participation in Science Careers, San Diego, California, May 15 – 17, 2015 on “Hostos Community College-The City College of New York Joint Dual Engineering Degree Program: A Successful Marriage.”
  •  Smith, S.G., Ren, C., Plotnikov A.N., Zeng, L., Rodríguez, Y., and Zhou, M.-M. “Synthesis of Small Molecule Inhibitors of the CBX7 Chromodomain.” Seventh Departmental Research Retreat. Structural and Chemical Biology Department. Mount Sinai School of Medicine, (Chappaqua, New York, October, 2014). (Poster Presentation)
  •  Ren, C., Smith, S.G., Plotnikov A.N., Zeng, L., Rodríguez, Y., and Zhou, M.-M. “Identification of Small Molecule Inhibitors for CBX7 Chromodomain.” Sixth Departmental Research Retreat. Structural and Chemical Biology Department. Mount Sinai School of Medicine, (Chappaqua, New York, October, 2013). (Poster Presentation)
  •  Gerona-Navarro, G., Rodríguez, Y. and Zhou, M.-M. “Design and Synthesis of Novel Conformationally Restricted Peptides as Chemical Modulators for CBP Bromodomain.” Fifth Departmental Research Retreat. Structural and Chemical Biology Department. Mount Sinai School of Medicine, (Chappaqua, New York, October, 2012). (Poster Presentation)
  •  Ren C., Morohashi K., Plotnikov A.N., Rodríguez, Y., Li, J., Zeng, L. and Zhou, M.-M. “Identification of Small Molecule Inhibitors for CBX7 Chromodomain-Methylated Lysine Interaction in Gene Silencing.” Fifth Departmental Research Retreat. Structural and Chemical Biology Department. Mount Sinai School of Medicine, (Chappaqua, New York, October, 2012). (Poster Presentation)
  •  Rodríguez, Y., Steinberg, O., Fernández, F., Mitchell, S., Nuñez-Rodríguez, N., Trachman, J. and Ostrin, Z. “Learning Physics by Doing Physics“ within the Roundtable “Alternative Medicine.” 2012 International Learning Styles Conference, Bronx, New York, July 10, 2012.
  •  Rodríguez, Y. “Rational Design of Small-Molecule Modulators of the Transcriptional Coactivator CBP and CBX7 Chromodomain.” Structural and Chemical Biology Department, Mount Sinai School of Medicine, New York, June 8, 2012.
  •  Rodríguez, Y. “Rational Design of Small-Molecule Modulators of the Transcriptional Coactivator CBP.” North American UGM and Conference. Montreal, Canada, June 28 – 29, 2012. (Poster Presentation)
  •  Rodríguez, Y. Physics Problems: How To Solve It. Second Annual Problem Solving at Hostos Community College (HCC), November 10, 2011.
  •  Gerona-Navarro, G., Rodríguez, Y., Mujtaba, S., Osman, R., Casaccia, P. and Zhou, M.-M. “Chemical modulation of gene transcription favors oligodendrocyte lineage progression.” Third Departmental Research Retreat. Structural and Chemical Biology Department. Mount Sinai School of Medicine, (Chappaqua, New York, October, 2010). (Oral Presentation)
  •  Rodríguez, Y., Flek, R., and Fernández, F. Engineering Institute: Bridge to PHY 210 / CHE 220. Faculty Development Initiative (FDI). Center for Teaching and Learning. HCC (June 4, 2010). (Oral Presentation)
  •  Nuñez-Rodríguez, N., Rodríguez, Y. and Fernández, F. “Online Assessment: What works? What does not work? Instructional Technology Showcase.” HCC (April 30, 2010). (Oral Presentation)
  •  Nuñez-Rodríguez, N. and Rodríguez, Y. “Toward an Enjoyable Experience of Learning Sciences. Synergy in STEM: Bringing Mathematics, Physics and Engineering Together.” New York City College of Technology, CUNY. (October 30, 2009). (Poster Presentation)
  •  Gerona-Navarro, G., Rodríguez, Y., Mujtaba, S., Osman, R. and Zhou, M.-M. “Design and Synthesis of Novel Conformationally Restricted Peptides as Chemical Modulators for CBP Bromodomain.” Second Departmental Research Retreat. Structural and Chemical Biology Department. Mount Sinai School of Medicine, (New York, October, 2009). (Poster presentation)
  •  Rodríguez, Y., Lundberg, K., Ordoñez, F., Guevara, C. and Willians, S. “ePortfolios in Action: An Exploration of New Practices.” FDI Week Events, Center for Teaching and Learning. FDR, HCC (June 1, 2009)
  •  Nuñez-Rodríguez, N. and Rodríguez, Y. “Toward an Enjoyable Experience of Learning Sciences.” 5th Annual Gen Ed Conference. Lehman College, CUNY. (May 8, 2009). (Poster Presentation)
  •  Eichenbaum, K.D., Rodríguez, Y., Mezei, M. and Osman, R. “Recognition of Acetylated p53 by the CBP Bromodomain. Biophysical Society.” 53th Annual Meeting. Boston, Massachusetts, February 28-March 4, 2009.
  •  Gerona-Navarro, G., Rodríguez, Y., Osman, R. and Zhou, M.-M. “Design and Synthesis of Novel Conformationally Restricted Peptides as Chemical Modulators for CBP Bromodomain.” Cancer Health Disparities Summit. Eliminating Cancer Health Disparities through Science, Training and Community. Bethesda, MD, July 14-16, 2008. (Poster presentation)
  •  Gerona-Navarro, G., Rodríguez, Y., Osman, R. and Zhou, M.-M. “Design and Synthesis of Novel Conformationally Restricted Peptides as Chemical Modulators for CBP Bromodomain.” First Departmental Research Retreat. Structural and Chemical Biology Department. Mount Sinai School of Medicine, New York, September 5, 2008. (Poster presentation)
  •  Baron, E.L, Rodríguez, Y., Cui, M., Max, M. and Osman, R. “Effects of R813 in hT1R3 on sweet receptor function. Biophysical Society.” 52th Annual Meeting. Long Beach, California, February 2-6, 2008. (Poster Presentation)