Insights in Biological and Synthetic Medicinal Chemistry
Larry H. Bernstein, M.D., FCAP, Curator
Leaders in Pharmaceutical Intelligence
Series E. 2; 10
Selected Articles Linking the Biological and Synthetic Worlds
The worlds of biological and synthetic chemistry both offer incredible diversity. Biology provides complex architectures including proteins, nucleic acids, and polysaccharides. Synthetic chemistry, on the other hand, provides a tool for atom-by-atom control over molecular structure that can be used to obtain molecules and materials inaccessible through biology.
In this ACS Select Virtual Issue, we highlight some of the recent advances in bioconjugation chemistry. These publications describe new strategies for functionalization of biomacromolecules, as well as the use of synthetic molecules as building blocks for assembly using biological machinery. The resultant conjugate systems have new and exciting properties, as demonstrated in new therapeutic and imaging applications.
– Vincent Rotello, Editor-in-Chief, Bioconjugate Chemistry
– C. Dale Poulter, Editor-in-Chief, The Journal of Organic Chemistry
– Amos Smith, III, Editor-in-Chief, Organic Letters
10.1 Bioconjugate Chemistry
10.1.1 Production of Site-Specific Antibody-Drug Conjugates Using Optimized Non-Natural Amino Acids in a Cell-Free Expression System
Zimmerman, E. S.; Heibeck, T. H.; Gill, A.; Li, X. F.; Murray, C. J.; Madlansacay, M. R.; Tran, C.; Uter, N. T.; Yin, G.; Rivers, P. J.; Yam, A. Y.; Wang, W. D.; Steiner, A. R.; Bajad, S. U.; Penta, K.; Yang, W. J.; Hallam, T. J.; Thanos, C. D.; Sato, A. K.
Bioconjugate Chem., 2014, 25 (2), pp 351-361
DOI: 10.1021/bc400490z
10.1.2 General Chemoselective and Redox-Responsive Ligation and Release Strategy
Park, S.; Westcott, N. P.; Luo, W.; Dutta, D.; Yousaf, M. N.
Bioconjugate Chem., 2014, 25 (3), pp 543-551
DOI: 10.1021/bc400565y
10.1.3 Chemoenzymatic Fc Glycosylation via Engineered Aldehyde Tags
Smith, E. L.; Giddens, J. P.; Iavarone, A. T.; Godula, K.; Wang, L. X.; Bertozzi, C. R.
Bioconjugate Chem., 2014, 25 (4), pp 788-795
DOI: 10.1021/bc500061s
10.1.4 Triazine-Based Tool Box for Developing Peptidic PET Imaging Probes: Syntheses, Microfluidic Radio labeling, and Structure-Activity Evaluation
Li, H. R.; Zhou, H. Y.; Krieger, S.; Parry, J. J.; Whittenberg, J. J.; Desai, A. V.; Rogers, B. E.; Kenis, P. J. A.; Reichert, D. E.
Bioconjugate Chem., 2014, 25 (4), pp 761-772
DOI: 10.1021/bc500034n
10.1.5 Developments in the Field of Bioorthogonal Bond Forming Reactions-Past and Present Trends
King, M.; Wagner, A.
Bioconjugate Chem., 2014, 25 (5), pp 825-839
DOI: 10.1021/bc500028d
10.1.6 Diels-Alder Cycloadditions on Synthetic RNA in Mammalian Cells
Pyka, A. M.; Domnick, C.; Braun, F.; Kath-Schorr, S.
Bioconjugate Chem., 2014, 25 (8), pp 1438-1443
DOI: 10.1021/bc500302y
10.1.7 High-Density Functionalization and Cross-Linking of DNA: “Click” and “Bis-Click” Cycloadditions Performed on Alkynylated Oligonucleotides with Fluorogenic Anthracene Azides
Pujari, S. S.; Ingale, S. A.; Seela, F.
Bioconjugate Chem., 2014, 25 (10), pp 1855-1870
DOI: 10.1021/bc5003532
10.1.8 Surface Functionalization of Exosomes Using Click Chemistry
Smyth, T.; Petrova, K.; Payton, N. M.; Persaud, I.; Redzic, J. S.; Gruner, M. W.; Smith-Jones, P.; Anchordoquy, T. J.
Bioconjugate Chem., 2014, 25 (10), pp 1777-1784
DOI: 10.1021/bc500291r
10.1.9 Site-Specific Antibody-Drug Conjugates: The Nexus of Biciorthogonal Chemistry, Protein Engineering, and Drug Development.
Agarwal, P.; Bertozzi, C. R.
Bioconjugate Chem., 2015, 26 (2), pp 176-192
DOI: 10.1021/bc5004982
10.1.10 Strain-Promoted Oxidation-Controlled Cyclooctyne-1,2-Quinone Cycloaddition (SPOCQ) for Fast and Activatable Protein Conjugation
Borrmann, A.; Fatunsin, O.; Dommerholt, J.; Jonker, A. M.; Lowik, D.; van Hest, J. C. M.; van Delft, F. L.
Bioconjugate Chem., 2015, 26 (2), pp 257-261
DOI: 10.1021/bc500534d
10.2 The Journal of Organic Chemistry
10.2.1 Sequential “Click” – “Photo-Click” Cross-Linker for Catalyst-Free Ligation of Azide-Tagged Substrates
Arumugam, S.; Popik, V. V.
J. Org. Chem., 2014, 79 (6), pp 2702-2708
DOI: 10.1021/jo500143v
10.2.3 Diazirine-Containing RNA Photo-Cross-Linking Probes for Capturing microRNA Targets
Nakamoto, K.; Ueno, Y.
J. Org. Chem., 2014, 79 (6), pp 2463-2472
DOI: 10.1021/jo402738t
10.2.4 Interstrand Cross-Link and Bioconjugate Formation in RNA from a Modified Nucleotide
Sloane, J. L.; Greenberg, M. M.
J. Org. Chem., 2014, 79 (20), pp 9792-9798
DOI: 10.1021/jo501982r
10.2.5 Synthesis of Base-Modified 2 ‘-Deoxyribonucleoside Triphosphates and Their Use in Enzymatic Synthesis of Modified DNA for Applications in Bioanalysis and Chemical Biology
Hocek, M.
J. Org. Chem., 2014, 79 (21), pp 9914-9921
DOI: 10.1021/jo5020799
10.2.6 Site-specific PEGylation of Proteins: Recent Developments
Nischan, N.; Hackenberger, C. P. R.
J. Org. Chem., 2014, 79 (22), pp 10727-10733
DOI: 10.1021/jo502136n
10.3 Organic Letters
10.3.1 One-Pot Peptide Ligation-Desulfurization at Glutamate
Cergol, K. M.; Thompson, R. E.; Malins, L. R.; Turner, P.; Payne, R. J.
Org. Lett., 2014, 16 (1), pp 290-293
DOI: 10.1021/ol403288n
10.3.2 Semisynthesis of Peptoid-Protein Hybrids by Chemical Ligation at Serine
Levine, P. M.; Craven, T. W.; Bonneau, R.; Kirshenbaum, K
Org. Lett., 2014, 16 (2), pp 512-515
DOI: 10.1021/ol4033978
10.3.3 A Photoinduced, Benzyne Click Reaction
Gann, A. W.; Amoroso, J. W.; Einck, V. J.; Rice, W. P.; Chambers, J. J.; Schnarr, N. A.
Org. Lett., 2014, 16 (7), pp 2003-2005
DOI: 10.1021/ol500389t
10.3.4 Amine-Selective Bioconjugation Using Arene Diazonium Salts
Diethelm, S.; Schafroth, M. A.; Carreira, E. M.
Org. Lett., 2014, 16 (15), pp 3908-3911
DOI: 10.1021/ol5016509
10.3 5 Efficient and Facile Synthesis of Acrylamide Libraries for Protein-Guided Tethering
Allen, C. E.; Curran, P. R.; Brearley, A. S.; Boissel, V.; Sviridenko, L.; Press, N. J.; Stonehouse, J. P.; Armstrong, A.
Org. Lett., 2015, 17 (3), pp 458-460
DOI: 10.1021/ol503486t
10.4 Synthesis, Design and Molecular Function
This Special Issue on “Synthesis, Design and Molecular Function”, guest-edited by Paul Wender, is intended to explore the many exciting new advances and challenges associated with designing and making molecules in the 21st century. It features contributions from thought leaders in the field directed at new reactions, reagents and catalysts, process technologies and screening strategies.
See guest editorial by Paul Wender
10.4.1 Art, Architecture, and the Molecular Frontier
Paul A. Wender (Guest Editor)
DOI: 10.1021/acs.accounts.5b00332
10.4.2 From Synthesis to Function via Iterative Assembly of N-Methyliminodiacetic Acid Boronate Building Blocks
Junqi Li, Anthony S. Grillo, and Martin D. Burke *
DOI: 10.1021/acs.accounts.5b00128
10.4.3 Trimethylenemethane Diyl Mediated Tandem Cycloaddition Reactions: Mechanism Based Design of Synthetic Strategies
Hee-Yoon Lee *
DOI: 10.1021/acs.accounts.5b00178
10.4.4 Intermolecular Reaction Screening as a Tool for Reaction Evaluation
Karl D. Collins* and Frank Glorius*
DOI: 10.1021/ar500434f
10.4.5 Development of Globo-H Cancer Vaccine
Samuel J. Danishefsky*, Youe-Kong Shue, Michael N. Chang, and Chi-Huey Wong*
DOI: 10.1021/ar5004187
10.4.6 Total Synthesis of Vinblastine, Related Natural Products, and Key Analogues and Development of Inspired Methodology Suitable for the Systematic Study of Their Structure–Function Properties
Justin E. Sears and Dale L. Boger*
DOI: 10.1021/ar500400w
10.4.7 Reaction Design, Discovery, and Development as a Foundation to Function-Oriented Synthesis
Glenn C. Micalizio* and Sarah B. Hale
DOI: 10.1021/ar500408e
10.4.8 Copy, Edit, and Paste: Natural Product Approaches to Biomaterials and Neuroengineering
Karl Gademann*
DOI: 10.1021/ar500435b
10.4.9 Catalytic Enantioselective Construction of Quaternary Stereocenters: Assembly of Key Building Blocks for the Synthesis of Biologically Active Molecules
Yiyang Liu, Seo-Jung Han, Wen-Bo Liu, and Brian M. Stoltz*
DOI: 10.1021/ar5004658
10.4.10 Focused Library with a Core Structure Extracted from Natural Products and Modified: Application to Phosphatase Inhibitors and Several Biochemical Findings
Go Hirai* and Mikiko Sodeoka*
DOI: 10.1021/acs.accounts.5b00048
10.5 Ionization Methods in Mass Spectrometry
Mass spectrometry has undoubtedly boomed over the last two decades and has become a major analytical tool in many disciplines. The technique relies on the separation of ions of different m/z, and its success hinges on efficient ionization methods that furthermore should be tailored to the task at hand. Depending on the application, ionization should be soft, hard, selective, as efficient as possible, etc. This virtual issue pulls together publications from Analytical Chemistry that showcase the exemplary developments in ionization techniques.
10.5.1 From the editorial by Renato Zenobi
DOI 10.1021/acs.analchem.5b01062
10.5.2 Nanophotonic Ionization for Ultratrace and Single-Cell Analysis by Mass Spectrometry
Bennett N. Walker, Jessica A. Stolee, and Akos Vertes
DOI: 10.1021/ac301238k
10.5.3 Unraveling the Mechanism of Electrospray Ionization
Lars Konermann, Elias Ahadi, Antony D. Rodriguez, and Siavash Vahidi
DOI: 10.1021/ac302789c
10.5.4 Ambient Surface Mass Spectrometry Using Plasma-Assisted Desorption Ionization: Effects and Optimization of Analytical Parameters for Signal Intensities of Molecules and Polymers
T. L. Salter, I. S. Gilmore, A. Bowfield, O. T. Olabanji, and J. W. Bradley
DOI: 10.1021/ac302677m
10.5.5 Fast Surface Acoustic Wave-Matrix-Assisted Laser Desorption Ionization Mass Spectrometry of Cell Response from Islets of Langerhans
Loreta Bllaci, Sven Kjellström, Lena Eliasson, James R. Friend, Leslie Y. Yeo, and Staffan Nilsson
DOI: 10.1021/ac3019125
10.5.6 Electrospun Nanofibers as Substrates for Surface-Assisted Laser Desorption/Ionization and Matrix-Enhanced Surface-Assisted Laser Desorption/Ionization Mass Spectrometry
Tian Lu and Susan V. Olesik
DOI: 10.1021/ac303292e
10.5.7 Capillary Photoionization: A High Sensitivity Ionization Method for Mass Spectrometry
Markus Haapala, Tina Suominen, and Risto Kostiainen
DOI: 10.1021/ac4002673
10.5.8 High-Speed Tandem Mass Spectrometric in Situ Imaging by Nanospray Desorption Electrospray Ionization Mass Spectrometry
Ingela Lanekoff, Kristin Burnum-Johnson, Mathew Thomas, Joshua Short, James P. Carson, Jeeyeon Cha, Sudhansu K. Dey, Pengxiang Yang, Maria C. Prieto Conaway, and Julia Laskin
DOI: 10.1021/ac401760s
10.5.9 Atomic Force Microscope Controlled Topographical Imaging and Proximal Probe Thermal Desorption/Ionization Mass Spectrometry Imaging
Olga S. Ovchinnikova, Kevin Kjoller, Gregory B. Hurst, Dale A. Pelletier, and Gary J. Van Berkel
DOI: 10.1021/ac4026576
10.5.10 Droplet Electrospray Ionization Mass Spectrometry for High Throughput Screening for Enzyme Inhibitors
Shuwen Sun and Robert T. Kennedy
DOI: 10.1021/ac502542z
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