Department of Chemistry and Biochemistry

Department of Chemistry and Biochemistry
Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Chapter 2. Design and Synthesis of Synthetic Receptors for Biomolecule Recognition Katharine L. Diehl, James L. Bachman, Brette M. Chapin, Ramakrishna Edupuganti, P. Rogelio Escamilla, Alexandra M. Gade, Erik T. Hernandez, Hyun Hwa Jo, Amber M. Johnson, Igor V. Kolesnichenko, Jaebum Lim, Chung-Yon Lin, Margaret K. Meadows, Helen M. Seifert, Diana Zamora-Olivares, Eric V. Anslyn* Department of Chemistry and Biochemistry 1 University Station A1590 Austin, TX 78712 *

Figure 2.1 Intermolecular interactions involved in complexation.
Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.1 Intermolecular interactions involved in complexation.

© The Royal Society of Chemistry 2015
Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.1 Binding affinities of cyclic and acyclic polyethers for K+.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.2 Conformational change required for K+ binding in 18-crown-6.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.3 Barbital binding by macrocyclic Hamilton receptor and deconstructed acyclic hosts.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.4 Adenosine binding by cleft-shaped receptor.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.5 Pinwheel host 2.6 with six guanidinium groups binds strongly to inositol-1,4,5-triphosphate.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.6 Inward binding conformation of pinwheel host is induced by the presence of Br- guest.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.2 Strengths of covalent bonds and noncovalent interactions. asingle covalent bond or monovalent interaction.

Figure 2.3 Cation···π interaction.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.4 Three types of molecular torsion balances designed by the groups of: A) Ōki, B) Wilcox, and C) Shimizu.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.5 Host guest association in solution.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Table 2.1 Log K and ΔG° values for complexation of pyrene by cyclophane host 2.8 in various solvents that differ in polarity as expressed by ET(30) values, T = 303 K. Scheme 2.7 Structures of cyclophane host 2.8 and pyrene guest.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Table 2.2 Log K values for complexation of K+ by 18-crown-6 in various solvents that differ in surface tension.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Table 2.3 Reversible covalent reactions.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.8 Reversible covalent bonding of diol-containing guest using boronic acids. (Adapted with permission from Org. Lett., 2010, 12, 4804, © 2010 American Chemical Society)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.9 Reversible nucleophilic attack on a boronic acid.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Table 2.4 Common carbonyl-based indicators and associated analytes.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.10 Nucleophilic attack by a thiolate on a disulfide.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.6 CPK models of α-cyclodextrin showing toluene outside (left) and inside (right) the cavity. (Reproduced with permission from Adv. Chem. Ser., 1971, 100, 21, © 1971 American Chemical Society)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.11 Design of a glucopyranose receptor using CAVEAT.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.12 Structure designed using CAVEAT.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.13 Dopamine binding by Wang's receptor.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.7 Example of the scoring method from HostDesigner's LINKER algorithm. The degree of overlap of the oxoanion guests of the two original fragments determines the score. The top left structure with a RMSD=0.29 is the highest scoring candidate, the bottom right structure with RMSD=3.21 is the lowest scoring. (Reproduced with permission from J. Am. Chem. Soc., 2006, 128, 2035, © 2006 American Chemical Society)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.8 Input fragments for generating a host for oxygen mustard. Arrows indicate where new bonds will be formed. (Reproduced with permission from Comput. Theor. Chem., 2014, 1028, 72, © 2014 Elsevier)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.14 Top five synthetically accessible host structures for oxygen mustard generated using HostDesigner. (Reproduced with permission from Comput. Theor. Chem., 2014, 1028, 72, © 2014 Elsevier)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.15 Common scaffolds for synthetic organic receptors.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.16 Water soluble crown ether host for NAD+.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.9 Protein immobilization on glass slides with calix[4]crown-5 derivative (Adapted with permission from Proteomics, 2003, 3, 2289, © 2003 Wiley)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.17 Structures showing receptor 2.15 (a calixcrown linked to a calixpyrrole), receptors and 2.17 immobilized on silica gel, and calixpyrrole 2.18 delivering Pt(II) drug to AMP.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.18 A) Schematic representation of the synthesis of CB8 under acidic conditions. B) CB8 forms ternary complexes with electron-deficient methyl viologen (2.19) and a second electron-rich partner (2.20). (Adapted with permission Angew. Chem. Int. Ed., 2001, 113, 1574, © 2001 Wiley)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.19 Three most common cyclodextrins.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.20 Structures of pinwheel hosts.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.10 A) Parallel synthesis method of combinatorial library generation, B) Split-mix method of combinatorial library generation, also called split-and-pool, C) Combinatorial library generated through coupling of mixtures.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.21 Guanidiniocarbonyl-pyrrole receptors generated using parallel synthesis. All of the R groups are directly attached to the amide nitrogen.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.22 Peptide substituted-TAC generated by split-mix synthesis. The library consists of amino acids at the specified positions, resulting in 66 = 46,456 members.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.11 SELEX protocol for artificial evolution of a complex biopolymer library.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.12 Cartoon depiction of building blocks assembling in a dynamic system, with their respective concentrations dependent upon the depth of the thermodynamic wells. Persistent template binding produces a new low-energy library member, and the equilibrium shifts towards the amplified member. (Adapted with permission from Dynamic Combinatorial Chemistry, Wiley-VCH: Weinheim, 2010, © 2010 Wiley-VCH Verlag GmbH & Co. KGaA)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.23 Cyclic monomeric host 2.23 and dimeric host 2.24 where X is one of the disulfide linkages a to f.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.24 Dimeric host with two covalent linkers (X) incorporating the disulfide linkages a to d.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.13 General illustrations of systems utilizing cooperativity: A) oxygen binding to hemoglobin and, B) folding of DNA/RNA. (Reproduced with permission from Angew. Chem. Int. Ed., 2009, 48, © 2009 Wiley)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.14 Speciation profile of a system exhibiting positive cooperativity. Note the sharp transition and the low build-up of intermediates. (Reproduced with permission from Angew. Chem. Int. Ed., 2009, 48, © 2009 Wiley)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.25 Monovalent and divalent β-cyclodextrin receptors and guest.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.15 Model of binding interaction caused by tethering, with the bottom two images showing complete and incomplete binding interaction, respectively. (Reproduced with permission from Proc. Natl. Acad. Sci. USA, 2007, 104, 6538, © 2007 National Academy of Sciences, U.S.A.)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.16 Example of an entropy-enthalpy compensation plot.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.17 Compensation behavior exhibited by a variety of guests to p-sulfonatocalix[n]arenes in water. (Reproduced with permission J. Chem. Soc., Perkin Trans. 2, 2002, 2, 524, © 2002 Royal Society of Chemistry)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.26 Structure of cucurbit[7]uril host and ferrocence guests. (Reproduced with permission from Proc. Nat. Acad. Sci. USA, 2007, 104, 20737, © 2007 National Academy of Sciences, U.S.A.)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.18 Differential sensing using a hypothetical array-based sensor. To a 16-element array, A), analyte 1 (later identified as a beer) and analyte 2 (whisky) are applied. The response patterns B, E are used directly, or the pattern A is subtracted to obtain differential patterns C, F. (Reproduced with permission from Chem. Soc. Rev., 2010, 39, 3954, © 2010 Royal Society of Chemistry)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.19 Array-based sensor utilizing analyte binding by differential receptors. Regardless of whether the analyte is a single- or multi-component analyte, receptors bind a number of analytes, but each receptor binds the analytes differently thus providing a differential response. (Reproduced with permission from Chem. Soc. Rev., 2010, 39, 3954, © 2010 Royal Society of Chemistry)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Figure 2.20 Schematic presentation of a cell detection assay and the interactions between polymers (ribbons) and cell types (surface). Fluorescence of the polymer is quenched upon binding to the cell surface. (Reproduced with permission from J. Am. Chem. Soc., 2010, 132, 1018, © 2010 American Chemical Society)

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.27 Calixpyrrole scaffold used to create carboxylate indicators.

Supplementary information for Synthetic Receptors for Biomolecules: Design Principles and Applications © The Royal Society of Chemistry 2015 Scheme 2.28 Cucurbituril hosts used to target nitrosamines.

Department of Chemistry and Biochemistry

Similar presentations

Presentation on theme: "Department of Chemistry and Biochemistry"— Presentation transcript:

Similar presentations

About project

Feedback

Log in

Auth with social network:

Department of Chemistry and Biochemistry

Similar presentations

Presentation on theme: "Department of Chemistry and Biochemistry"— Presentation transcript:

Similar presentations

About project

Feedback