Faculty Profile Image

Rudi Fasan

he/him/his

  • Andrew S. Kende Professor in Synthetic Organic Chemistry

PhD, University of Zurich, Switzerland, 2005

418 Hutchison Hall
(585) 273-3504
fasan@chem.rochester.edu

Website


Research Overview

The research interests of our group lie in the areas of bioorganic chemistry, chemical biology, and biomolecular engineering and evolution. Our laboratory integrates methods and principles of organic chemistry, molecular biology, and molecular evolution to develop novel chemo-biosynthetic and chemo-enzymatic approaches to the discovery of biologically active molecules. Our goal is to investigate and apply these methodologies toward the development of chemical agents useful for probing cell signaling pathways and controlling biomolecular interactions implicated in cancer development.

A major project involves the development of new strategies to direct the synthesis, diversification, and evolution of macrocyclic peptide-based molecules as potent and selective modulators of protein-protein interactions (PPIs). PPIs are implicated in all cellular processes from signal transduction to gene regulation, cell proliferation and apoptosis. Chemical agents capable of targeting PPIs with high potency and selectivity can provide invaluable tools for the study of complex cellular pathways and useful starting points for development of new therapeutics, but the development of such compounds has constituted a major challenge in chemical biology and drug discovery. Our group has pioneered methods to generate Macrocyclic Organo-Peptide Hybrids (MOrPHs) via the modular assembly of synthetic organic moieties with genetically encoded polypeptide precursors. These molecules constitute attractive molecular scaffolds to mediate specific and high-affinity recognition of a target protein as they combine a high degree of chemical complexity with a compact and conformationally rigid architecture. In addition, the MOrPH approach enables to couple the versatility of chemical synthesis with the advantages of genetic encoding and power of genetic mutagenesis, providing unique opportunities for the creation and screening of highly diverse chemical libraries and the molecular evolution of organo-peptide macrocycles with tailored protein-binding selectivity. Our group is exploring the potential of this new class of macrocyclic structures to tackle challenging molecular recognition problems, such as the selective and efficient disruption of protein-protein and protein-DNA complexes of therapeutic relevance and the specific recognition of structural homologues and post-translational isoforms of human proteins. An integral component of these studies is the application of a variety of biophysical techniques (e.g. Surface Plasmon Resonance, NMR and fluorescence spectroscopy) and biological assays for the characterization of the conformational and binding properties and biological activity of these compounds.

Another major area of interest is concerned with the design and development of efficientbiological catalysts for the selective functionalization of aliphatic C—H bonds. The selective functionalization of unactivated C(sp3)—H bonds represents a most valuable but also one of the most challenging transformations in organic chemistry. Our group is investigating the use of engineered cytochrome P450s as well as other heme-containing proteins (e.g. myoglobin) as catalytic platforms for the direct conversion of C(sp3)—H bonds into C—O, C—N, and C—C bonds. With the latter two, we aim at expanding the reactivity scope of these protein-based catalysts beyond that exhibited by naturally occurring enzymes. As part of these projects, we are developing systematic, rationally-driven approaches to predict the reactivity of these P450- and myoglobin-based catalysts via the combination of high-throughput screening methods and computational tools. We are also exploring new protein engineering strategies to enable rapid fine-tuning of the regio- and stereoselectivity of these enzymes. The ultimate goal of these studies is to develop efficient and systematic approaches to expedite the development of C—H functionalization biocatalysts with tailored activity and site-selectivity for synthetic applications. Finally, the scope and synthetic value of these methodologies is being investigated through the synthesis and functional elaboration of complex natural product scaffolds of medical interest via chemoenzymatic synthesis.

All our projects involve the synergistic integration of rational design, chemical synthesis, protein chemistry, and molecular evolution methods toward the development of enabling molecular discovery platforms of practical and broad utility. Members of the Fasan group have thus the opportunity to receive training in these areas and conduct interdisciplinary research at the intersection of chemistry, biology, and biophysics.

Research Interests

  • Organic chemistry and chemoenzymatic synthesis
  • asymmetric biocatalysis
  • protein engineering
  • bioorganic chemistry and chemical biology

Selected Publications

  • Ren X, Chandgude AL, Carminati DM, Fasan* R, “Highly Stereoselective and Enantiodivergent Synthesis of Cyclopropylphosphonates with Engineered Carbene Transferases”, 2022, Chemical Science, 13, 8550-8556. DOI: 10.1039/d2sc01965e.
  • Iannuzzelli JA, Bacik JP, Moore EJ, Shen Z, Irving EM, Vargas DA, Khare* SD, Ando* N, Fasan* R, “Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization”, 2022, Biochemistry, 61(11): 1041-1054. DOI: 10.1021/acs.biochem.2c00033. 
  • Nam D, Tinoco A, Shen Z, Adukure RD, Sreenilayam G, Khare* SD, Fasan* R, “Enantioselective Synthesis of a-Trifluoromethyl Amines via Biocatalytic N−H Bond Insertion with Acceptor-Acceptor Carbene Donors”, 2022, Journal of the American Chemical Society, 144 (6): 2590-2602. DOI: 10.1021/jacs.1c10750.
  • Chavali SS, Mali SM, Jenkins JL, Bonn RMS, Saseendran Anitha A, Bennett, RP, Smith, HC, Fasan* R, Wedekind* JE, “Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells”, Journal of Biological Chemistry, 2021, 297(6): 101390. DOI: 10.1016/j.jbc.2021.101390.
  • Alwaseem H, Giovani S, Crotti M, Welle K, Jordan CT, Ghaemmaghami S, Fasan* R, “Comprehensive Structure-Activity Profiling of Micheliolide and its Targeted Proteome in Leukemia Cells via Probe-Guided Late-Stage C—H Functionalization”, ACS Central Science, 2021, 7 (5): 841–857. DOI: 10.1021/acscentsci.0c01624.
  • Ren X, Fasan* R, “Engineered and Artificial Metalloenzymes for Selective C–H Functionalization”, Current Opinion in Green and Sustainable Chemistry, 2021, 31: 100494.
  • Nam D, Steck V, Potenzino R, Fasan* R, “A Diverse Library of Chiral Cyclopropane Scaffolds via Chemoenzymatic Assembly and Diversification of Cyclopropyl Ketones”, Journal of the American Chemical Society, 2021, 143, 5, 2221-2231. DOI: 10.1021/jacs.0c09504.
  • Carminati DM, Decaens J, Couve-Bonnaire S, Jubault* P, Fasan* R, “Biocatalytic strategy for the highly stereoselective synthesis of CHF2-containing trisubstituted cyclopropanes”, Angewandte Chemie International Edition, 2021, 60(13), 7072-7076. DOI: 10.1002/anie.202015368.
  • Ren X, Liu N, Chandgude AL, Fasan* R, “An enzymatic platform for the highly enantioselective and stereodivergent construction of cyclopropyl-d-lactones”, Angewandte Chemie International Edition, 2020, 59(48): 21634-21639 ( equal contribution). DOI: 10.1002/anie.202007953.
  • Steck V, Carminati DM, Johnson NR, Fasan* R, “Enantioselective Synthesis of Chiral Amines via Biocatalytic Carbene N—H Insertion”, ACS Catalysis, 2020, 10: 10967−10977, DOI: 10.1021/acscatal.0c02794.
  • Iannuzzelli JA, Fasan* R, “Expanded toolbox for directing the biosynthesis of macrocyclic peptides in bacterial cells”, Chemical Science, 2020, 11, 6202-6208.
  • Steck V, Kolev JN, Ren X, Fasan* R, “Mechanism-Guided Design and Discovery of Efficient P450-Derived C—H Amination Biocatalysts”, Journal of the American Chemical Society, 2020, 142(23):10343-10357. ( equal contribution).
  • Owens AE, Iannuzzelli JA, Gu Y, Fasan* R, “MOrPH-PhD: an integrated phage display platform for the discovery of functional genetically-encoded peptide macrocycles”, ACS Central Science, 2020, 6 (3): 368-381. DOI: 10.1021/acscentsci.9b00927
  • Ren X, Chandgude AL, Fasan* R, “Highly Stereoselective Synthesis of Fused Cyclopropane-γ-Lactams via Biocatalytic Iron-Catalyzed Intramolecular Cyclopropanation”, ACS Catalysis, 2020, 10(3): 2308-2313. DOI: 10.1021/acscatal.9b05383
  • Carminati MD, Fasan* R, “Stereoselective cyclopropanation of electrondeficient olefins with a cofactor redesigned carbene transferase featuring radical reactivity”, ACS Catalysis, 2019, 9(10): 9683-9697. DOI: 10.1021/acscatal.9b02272
  • Vargas DA, Khade RL, Zhang* Y, Fasan* R, “Biocatalytic strategy for highly diastereo- and enantioselective synthesis of 2,3-dihydrobenzofuran based tricyclic scaffolds”, Angewandte Chemie International Edition, 2019, 58(30): 10148-10152. DOI: 10.1002/anie.201903455
  • Chandgude AL, Ren X, Fasan* R, “Stereodivergent Intramolecular Cyclopropanation Enabled by Engineered Carbene Transferases”, Journal of the American Chemical Society, 2019, 141(23): 9145-9150. DOI: 10.1021/jacs.9b02700.
  • Tinoco A, Wei Y, Bacik JP, Carminati DM, Moore EJ, Ando N, Zhang* Y, Fasan* R, “Origin of high stereocontrol in olefin cyclopropanation catalyzed by an engineered carbene transferase”, ACS Catalysis, 2019, 9: 1514−1524. DOI: 10.1021/acscatal.8b04073
  • Chandgude AL, Fasan* R, “Highly diastereo- and enantioselective synthesis of nitrile-substituted cyclopropanes via myoglobin-mediated carbene transfer catalysis”, Angewandte Chemie International Edition, 2018, 57(48): 15852-15856. DOI: 10.1002/anie.201810059.
  • Vargas D, Tinoco A, Tyagi V, Fasan* R, “Myoglobin-catalyzed C—H functionalization of unprotected indoles”, Angewandte Chemie International Edition, 2018, 57(31): 9911-9915.
  • Wei Y, Tinoco A, Steck V, Fasan* R, Zhang* Y, “Cyclopropanations via Heme Carbenes: Basic Mechanism and Effects of Carbene Substituent, Protein Axial Ligand, and Porphyrin Substitution”, Journal of the American Chemical Society, 2018, 140 (5) 1649–1662.
  • Alwaseem H, Frisch BJ, Fasan* R, “Anticancer activity profiling of parthenolide analogs generated via P450-mediated chemoenzymatic synthesis”, Bioorganic & Medicinal Chemistry, 2018, 26: 1365–1373.
  • Moore EJ, Zorine D, Hansen WA, Khare* SD, Fasan* R, “Enzyme stabilization via computationally guided protein stapling”, 2017, Proceedings of the National Academy of Sciences USA; 114(47):12472-12477.
  • Sreenilayam G, Moore EJ, Steck V, Fasan* R, “Stereoselective olefin cyclopropanation under aerobic conditions with an artificial enzyme incorporating an iron-chlorin e6 cofactor”, ACS Catalysis, 2017, 7, 7629-7633.
  • Owens AE, de Paola I, Hansen WA, Liu YW, Khare SD, Fasan* R, “Design and Evolution of a Macrocyclic Peptide Inhibitor of the Sonic Hedgehog/Patched Protein-Protein Interaction”, Journal of the American Chemical Society, 2017, 139 (36), 12559-12568.
  • Sreenilayam G, Moore E, Steck V, Fasan* R, “Metal substitution modulates the reactivity and extends the reaction scope of myoglobin carbene transfer catalysts”, Advanced Synthesis & Catalysis, 2017, 359, 2076-2089.
  • Owens AE, Grasso KT, Ziegler CA, Fasan* R, “Two-tier Screening Platform for Directed Evolution of Aminoacyl-tRNA Synthetases with Enhanced Stop Codon Suppression Efficiency”, ChemBioChem, 2017, 18 (12), 1109-1116.
  • Tinoco A, Steck V, Tyagi V, Fasan* R, “Highly diastereo- and enantioselective synthesis of trifluoromethyl-substituted cyclopropanes via myoglobin-catalyzed transfer of tri-fluoromethylcarbene”, Journal of the American Chemical Society, 2017, 139 (15), 5293–5296
  • Bajaj P, Sreenilayam G, Tyagi V, Fasan* R, "Gram-scale synthesis of chiral cyclopropane-containing drugs and drug precursors using engineered myoglobin catalysts with complementary stereoselectivity", Angewandte Chemie International Edition, 2016, 55(52), 16110–16114
  • Tyagi V, Sreenilayam G, Bajaj P, Tinoco A, Fasan* R, "Biocatalytic synthesis of allylic and allenyl sulfides via a myoglobin-catalyzed Doyle-Kirmse reaction", Angewandte Chemie International Edition, 2016, 55(43), 13562-13566.
  • Tyagi V, Alwaseem H, Fasan* R  “Chemoenzymatic synthesis and antileukemic activity of novel C9- and C14-functionalized parthenolide analogs,”  Bioorganic and Medicinal Chemistry  2016,  24(17),  3876-86.
  • Tyagi V, Fasan* R  “Myoglobin-catalyzed olefination of aldehydes,”  Angewandte Chemie International Edition  2016,  55(7),  2512-2516.
  • Giovani S, Singh R, Fasan* R  “Efficient conversion of primary azides to aldehydes catalyzed by active site variants of myoglobin,”  Chemical Science  2016,  7,  234-239.
  • Bionda N, Fasan* R  “Ribosomal synthesis of natural product-like bicyclic peptides in E. coli,”  ChemBioChem  2015,  16(14),  2011-2016.
  • Frost JR, Jacob NT, Papa LJ, Owens AE, Fasan* R  “Ribosomal Synthesis of Macrocyclic Peptides in Vitro and in Vivo Mediated by Genetically Encoded Amino-thiol Unnatural Amino Acids,”  ACS Chemical Biology  2015,  10(8),  1805-1816.
  • Tyagi V, Bonn RB, Fasan* R  “Intermolecular carbene S-H insertion catalysed by engineered myoglobin-based catalysts,”  Chemical Science  2015,  6,  2488-2494.
  • Bordeaux M, Tyagi V, Fasan* R  “Highly diastereo- and enantioselective olefin cyclopropanation via engineered myoglobin-based catalysts,”  Angewandte Chemie International Edition  2015,  54(6),  1744-1748.
  • Singh R, Kolev JN, Sutera PA, Fasan* R  “Enzymatic C(sp3)—H amination: P450-catalyzed conversion of carbonazidates into oxazolidinones>,”  ACS Catalysis  20155,  1685-1691.
  • Smith JM, Frost JR, Fasan* R  “Macrocyclic organo-peptide hybrids inhibit the interaction between p53 and HDM2/X by accommodating a functional α-helical motif,” Chem. Comm.  2014,  50(39),  5027-5030.
  • Kolev JN, Zaengle JM, Ravikumar R, Fasan* R  “Enhancing the Efficiency and Regioselectivity of P450 Oxidation Catalysts via Unnatural Amino Acid Mutagenesis,” Chembiochem.  2014,  15(7),  1001-1010.
  • Singh R, Bordeaux M, Fasan* R  “P450-catalyzed intramolecular sp3 C—H amination with arylsulfonyl azide substrates,”  ACS Catal.  2014,  4(2),  546-552.
  • Kolev JN, O'Dwyer KM, Jordan CT, Fasan* R  “Discovery of potent parthenolide-based antileukemic agents enabled by late-stage P450-mediated C―H functionalization,”  ACS Chem. Biol.  2014,  9(1),  164-173.
  • Frost JR, Vitali F, Jacob NT, Brown MD, Fasan* R  “Macrocyclization of organo-peptide hybrids via a dual bioorthogonal ligation; insights from structure-reactivity studies,”  Chembiochem  2013,  14(1),  146-160.
  • Zhang K, Shafer BM, Demars II MD, Stern HA, Fasan* R  “Controlled oxidation of remote sp3 C―H bonds in artemisinin via P450 catalysts with fine-tuned regio- and stereoselectivity,”  J. Am. Chem. Soc.  2012,  134(45),  18695-18704.
  • Smith, J. M., Vitali, F., Archer, S. A., Fasan* R  “Modular assembly of macrocyclic organo-peptide hybrids using synthetic and genetically encoded precursors,”  Angew. Chem. Int. Ed. Engl.  2011,  50(22),  5075-80.
  • Zhang, K., El Damaty, S., Fasan* R “P450 fingerprinting method for rapid discovery of terpene hydroxylating P450 catalysts with diversified regioselectivity,”  J. Am. Chem. Soc  2011,  133(10),  3242-3245.