1
|
Sunkari YK, Nguyen TL, Siripuram VK, Flajolet M. Impact of organic chemistry conditions on DNA durability in the context of DNA-encoded library technology. iScience 2023; 26:107573. [PMID: 37664608 PMCID: PMC10470182 DOI: 10.1016/j.isci.2023.107573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023] Open
Abstract
High-power screening (HPS) technologies, such as DNA-encoded library (DEL) technology, could exponentially increase the dimensions of the chemical space accessible for drug discovery. The intrinsic fragile nature of DNA is associated with cumbersome limitations and DNA durability (e.g., depurination, loss of phosphate groups, adduct formation) is compromised in numerous organic chemistry conditions that require empirical testing. An atlas of reaction conditions (temperature, pH, solvent/buffer, ligands, oxidizing reagents, catalysts, scavengers in function of time) that have been systematically tested in multiple combinations, indicates precisely limits useful for DEL construction. More importantly, this approach could be used broadly to effectively evaluate DNA-compatibility of any novel on-DNA chemical reaction, and it is compatible with different molecular methodologies. This atlas and the general approach presented, by allowing novel reaction conditions to be performed in presence of DNA, should greatly help in expanding the DEL chemical space as well as any field involving DNA durability.
Collapse
Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thu-Lan Nguyen
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| |
Collapse
|
2
|
Ganguly S, Bhakta S, Ghosh T. Gold‐Catalyzed Synthesis of Spirocycles: Recent Advances. ChemistrySelect 2022. [DOI: 10.1002/slct.202201407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Somnath Ganguly
- Department of Applied Chemistry Maulana Abul Kalam Azad University of Technology Simhat, Haringhata 741249, Nadia West Bengal India
| | - Sayantika Bhakta
- Department of Applied Chemistry Maulana Abul Kalam Azad University of Technology Simhat, Haringhata 741249, Nadia West Bengal India
| | - Tapas Ghosh
- Department of Applied Chemistry Maulana Abul Kalam Azad University of Technology Simhat, Haringhata 741249, Nadia West Bengal India
| |
Collapse
|
3
|
Kosińska A, Virieux D, Pirat JL, Czarnecka K, Girek M, Szymański P, Wojtulewski S, Vasudevan S, Chworos A, Rudolf B. Synthesis and Biological Studies of Novel Aminophosphonates and Their Metal Carbonyl Complexes (Fe, Ru). Int J Mol Sci 2022; 23:ijms23158091. [PMID: 35897660 PMCID: PMC9330042 DOI: 10.3390/ijms23158091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
The quest to find new inhibitors of biologically relevant targets is considered an important strategy to introduce new drug candidates for the treatment of neurodegenerative diseases. A series of (aminomethyl)benzylphosphonates 8a–c and their metallocarbonyl iron 9a–c and ruthenium 10a–c complexes were designed, synthesized, and evaluated for their inhibitory potentials against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) by determination of IC50. Metallocarbonyl derivatives, in general, did not show significant inhibition activity against these enzymes, the most potent inhibitor was the (aminomethyl)benzylphosphonate 8a (IC50 = 1.215 µM against AChE). Molecular docking analysis of AChE and (aminomethyl)benzylphosphonates 8a–c showed the strongest interactions of 8a and AChE compared to isomers 8b and 8c. Cytotoxicity studies of synthesized compounds towards the V79 cell line were also performed and discussed.
Collapse
Affiliation(s)
- Aneta Kosińska
- Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, 91-403 Lodz, Poland
- ICGM, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France; (D.V.); (J.-L.P.)
- Correspondence: (A.K.); (B.R.)
| | - David Virieux
- ICGM, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France; (D.V.); (J.-L.P.)
| | - Jean-Luc Pirat
- ICGM, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France; (D.V.); (J.-L.P.)
| | - Kamila Czarnecka
- Department of Pharmaceutical Chemistry, Drug Analyses and Radiopharmacy, Faculty of Pharmacy, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (K.C.); (P.S.)
| | - Małgorzata Girek
- Animal House, Faculty of Pharmacy, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland;
| | - Paweł Szymański
- Department of Pharmaceutical Chemistry, Drug Analyses and Radiopharmacy, Faculty of Pharmacy, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (K.C.); (P.S.)
- Department of Radiobiology and Radiation Protection, Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland
| | - Sławomir Wojtulewski
- Department of Structural Chemistry, Faculty of Chemistry, University of Bialystok, Ciołkowskiego 1K, 15-245 Bialystok, Poland;
| | - Saranya Vasudevan
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (S.V.); (A.C.)
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (S.V.); (A.C.)
| | - Bogna Rudolf
- Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, 91-403 Lodz, Poland
- Correspondence: (A.K.); (B.R.)
| |
Collapse
|
4
|
Sun J, Nie Q, Fang X, He Z, Zhang G, Li Y, Li Y. Vinyl azide as a synthon for DNA-compatible divergent transformations into N-heterocycles. Org Biomol Chem 2022; 20:5045-5049. [PMID: 35703385 DOI: 10.1039/d2ob00862a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Inspired by diversity-oriented synthesis, we have developed a series of DNA-compatible transformations utilizing on-DNA vinyl azide as a synthon to forge divergent N-heterocyclic scaffolds. Polysubstituted imidazoles and isoquinolines were efficiently obtained with moderate-to-excellent conversions. Besides, the "one-pot" strategy to prepare in-house on-DNA vinyl azides afforded synthons readily. Results from substrate scope exploration and enzymatic ligation further demonstrate the feasibility of these N-heterocycle syntheses in DNA-encoded chemical library construction.
Collapse
Affiliation(s)
- Jie Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Zhiwei He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China.,Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
| |
Collapse
|
5
|
Škopić MK, Dos Santos Smith D, Gohla A, Kunig VBK, Brunschweiger A. Initiating DNA-Encoded Library Synthesis with a Hexathymidine DNA Oligonucleotide. Methods Mol Biol 2022; 2541:89-104. [PMID: 36083549 DOI: 10.1007/978-1-0716-2545-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Libraries of DNA-encoded compounds (DELs) are a validated screening technology for drug discovery. Here we describe a library synthesis strategy that starts with a solid phase-bound, chemically very stable hexathymidine DNA sequence "hexT." Different heterocycle conjugates of the hexT oligonucleotide were synthesized from simple starting materials using metal or acid catalysts. The hexT conjugates were isolated, characterized, and ligated to coding DNA sequences.
Collapse
Affiliation(s)
- Mateja Klika Škopić
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | | | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
| |
Collapse
|
6
|
Zhang J, Li X, Wei H, Li Y, Zhang G, Li Y. Sequential DNA-Encoded Building Block Fusion for the Construction of Polysubstituted Pyrazoline Core Libraries. Org Lett 2021; 23:8429-8433. [PMID: 34652930 DOI: 10.1021/acs.orglett.1c03145] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The construction of chemical libraries containing polysubstituted pyrazoline scaffolds is highly desirable for the discovery of novel chemical ligands for biological targets. Herein, we report a sequential DNA-encoded synthesis strategy for polysubstituted pyrazoline heterocycles, which fuses a broad panel of aldehydes, aryl amines, and alkenes as building blocks. Furthermore, mock library synthesis and selection demonstrated the ability of the method to produce DNA-encoded focused libraries with highly functionalized pyrazoline cores.
Collapse
Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Haimei Wei
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| |
Collapse
|
7
|
Fair RJ, Walsh RT, Hupp CD. The expanding reaction toolkit for DNA-encoded libraries. Bioorg Med Chem Lett 2021; 51:128339. [PMID: 34478840 DOI: 10.1016/j.bmcl.2021.128339] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022]
Abstract
Over the past decade, DNA-encoded libraries (DELs) have emerged as a leading platform for small molecule drug discovery among pharmaceutical companies, biotech companies and academic drug hunters alike. This revolutionary technology has tremendous potential that is yet to be fully realized, as the exploration of therapeutically relevant chemical space is fueled by the ever-expanding repertoire of DNA-compatible reactions used to construct the libraries. Advances in direct coupling reactions, like photo-catalytic cross couplings, unique cyclizations such as the formation of 1,2,4-oxadiazoles, and new functional group transformations are valuable contributions to the DEL reaction toolkit, and indicate where future reaction development efforts should focus in order to maximize the productivity of DELs.
Collapse
Affiliation(s)
| | - Ryan T Walsh
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA
| | | |
Collapse
|
8
|
Potowski M, Kunig VBK, Eberlein L, Vakalopoulos A, Kast SM, Brunschweiger A. Chemisch stabilisierte DNA‐Codes für DNA‐kodierte Chemie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marco Potowski
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Verena B. K. Kunig
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Lukas Eberlein
- TU Dortmund University Faculty of Chemistry and Chemical Biology Physical Chemistry Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | | | - Stefan M. Kast
- TU Dortmund University Faculty of Chemistry and Chemical Biology Physical Chemistry Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Andreas Brunschweiger
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| |
Collapse
|
9
|
Potowski M, Kunig VBK, Eberlein L, Vakalopoulos A, Kast SM, Brunschweiger A. Chemically Stabilized DNA Barcodes for DNA-Encoded Chemistry. Angew Chem Int Ed Engl 2021; 60:19744-19749. [PMID: 34153170 PMCID: PMC8456907 DOI: 10.1002/anie.202104348] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/10/2021] [Indexed: 12/18/2022]
Abstract
DNA‐encoded compound libraries are a widely used small molecule screening technology. One important aim in library design is the coverage of chemical space through structurally diverse molecules. Yet, the chemical reactivity of native DNA barcodes limits the toolbox of reactions for library design. Substituting the chemically vulnerable purines by 7‐deazaadenine, which exhibits tautomerization stability similar to natural adenine with respect to the formation of stable Watson–Crick pairs, yielded ligation‐competent, amplifiable, and readable DNA barcodes for encoded chemistry with enhanced stability against protic acid‐ and metal ion‐promoted depurination. The barcode stability allowed for straightforward translation of 16 exemplary reactions that included isocyanide multicomponent reactions, acid‐promoted Pictet–Spengler and Biginelli reactions, and metal‐promoted pyrazole syntheses on controlled pore glass‐coupled barcodes for diverse DEL design. The Boc protective group of reaction products offered a convenient handle for encoded compound purification.
Collapse
Affiliation(s)
- Marco Potowski
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Verena B K Kunig
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Lukas Eberlein
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | | | - Stefan M Kast
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| |
Collapse
|
10
|
Abstract
Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.
Collapse
Affiliation(s)
- Patrick R Fitzgerald
- Skaggs Doctoral Program in the Chemical and Biological Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Departments of Pharmaceutical Sciences, Chemistry, & Biomedical Engineering, University of California, Irvine, 101 Theory Suite 100, Irvine, California 92617, United States
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| |
Collapse
|
11
|
Salehpour M, Azizian J. Exploration of interaction behavior between spiro[indene-2,2'-[1,3,5]oxathiazine]-1,3-diones and DNA with the help of DFT, molecular docking, and MD simulations. J Biomol Struct Dyn 2021; 40:9194-9213. [PMID: 33998964 DOI: 10.1080/07391102.2021.1924266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A detailed computational study covering density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulations of some spirocyclic compounds interacting with a B-DNA has been performed. DFT calculations were performed using the B3LYP functional with 6-311++G(d,p) basis set and were used to identify the electrophilic and nucleophilic centers in electrostatic forces. NMR results were in agreement with previous experimental data and approved the reliability of the used method and basis set. The in silico screening results showed that spirocyclic compounds fulfill the Lipinski's rule of five and can be developed as potential oral bioavailable drug candidates. Based on molecular docking results, the binding affinities follow the 4c < 4d < 4a = 4b < 4e < 4g < 4f order and ranged from -8.6 to -9.7 kcal/mol indicating a reasonably favorable interaction between DNA and investigated compounds. The adducts were stabilized by hydrophobic and hydrogen bonding interactions. The MD simulations performed for 100 ns and the results are reported in terms of variables such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), center of mass (COM) separation distance between DNA and ligands, intermolecular hydrogen bonds, and radial distribution functions (RDF). The MD simulations demonstrated that compounds 4a and 4d bind into the minor groove of 1BNA and may act as potential biological probes for B-DNA.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mahboobeh Salehpour
- Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Javad Azizian
- Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
12
|
Shi Y, Wu YR, Yu JQ, Zhang WN, Zhuang CL. DNA-encoded libraries (DELs): a review of on-DNA chemistries and their output. RSC Adv 2021; 11:2359-2376. [PMID: 35424149 PMCID: PMC8693808 DOI: 10.1039/d0ra09889b] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
A DNA-encoded library is a collection of small molecules covalently linked to DNA that has unique information about the identity and the structure of each library member. A DNA-encoded chemical library (DEL) is broadly adopted by major pharmaceutical companies and used in numerous drug discovery programs. The application of the DEL technology is advantageous at the initial period of drug discovery because of reduced cost, time, and storage space for the identification of target compounds. The key points for the construction of DELs comprise the development and the selection of the encoding methods, transfer of routine chemical reaction from off-DNA to on-DNA, and exploration of new chemical reactions on DNA. The limitations in the chemical space and the diversity of DEL were reduced gradually by using novel DNA-compatible reactions based on the formation and the cleavage of various bonds. Here, we summarized a series of novel DNA-compatible chemistry reactions for DEL building blocks and analysed the druggability of screened hit molecules via DELs in the past five years.
Collapse
Affiliation(s)
- Ying Shi
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Yan-Ran Wu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Jian-Qiang Yu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Wan-Nian Zhang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
| | - Chun-Lin Zhuang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
| |
Collapse
|
13
|
Price AK, Paegel BM. Considerations for Achieving Maximized DNA Recovery in Solid-Phase DNA-Encoded Library Synthesis. ACS COMBINATORIAL SCIENCE 2020; 22:649-655. [PMID: 32786319 DOI: 10.1021/acscombsci.0c00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded library (DEL) technology enables rapid, economical synthesis, and exploration of novel chemical space. Reaction development for DEL synthesis has recently accelerated in pace with a specific emphasis on ensuring that the reaction does not compromise the integrity of the encoding DNA. However, the factors that contribute to a reaction's "DNA compatibility" remain relatively unknown. We investigated several solid-phase reactions and encoding conditions and determined their impact on DNA compatibility. Conditions that minimized the accessibility of reactive groups on the DNA encoding tag (switching solvent, low temperature, double-stranded encoding tag) significantly improved compatibility. We showcased this approach in the multistep synthesis of an acyldepsipeptide (ADEP1) fragment, which preserved 73% of DNA for a >100-fold improvement over canonical conditions. These results are particularly encouraging in the context of multistep reaction sequences to access natural product-like scaffolds and more broadly underscore the importance of reconciling the biophysical properties and reactivity of DNA with chemistry development to yield high-quality libraries of those scaffolds.
Collapse
Affiliation(s)
- Alexander K. Price
- Department of Chemistry Scripps Research 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry Scripps Research 130 Scripps Way, Jupiter, Florida 33458, United States
| |
Collapse
|
14
|
Potowski M, Kunig VBK, Losch F, Brunschweiger A. Synthesis of DNA-coupled isoquinolones and pyrrolidines by solid phase ytterbium- and silver-mediated imine chemistry. MEDCHEMCOMM 2019; 10:1082-1093. [PMID: 31391880 PMCID: PMC6644566 DOI: 10.1039/c9md00042a] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
DNA-encoded libraries of chemically synthesized compounds are an important small molecule screening technology. The synthesis of encoded compounds in solution is currently restricted to a few DNA-compatible and water-tolerant reactions. Encoded compound synthesis of short DNA-barcodes covalently connected to solid supports benefits from a broad range of choices of organic solvents. Here, we show that this encoded chemistry approach allows for the synthesis of DNA-coupled isoquinolones by an Yb(iii)-mediated Castagnoli-Cushman reaction under anhydrous reaction conditions and for the synthesis of highly substituted pyrrolidines by Ag(i)-mediated 1,3-dipolar azomethine ylide cycloaddition. An encoding scheme for these DNA-barcoded compounds based on a DNA hairpin is demonstrated.
Collapse
Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| |
Collapse
|
15
|
Zhao G, Huang Y, Zhou Y, Li Y, Li X. Future challenges with DNA-encoded chemical libraries in the drug discovery domain. Expert Opin Drug Discov 2019; 14:735-753. [DOI: 10.1080/17460441.2019.1614559] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Guixian Zhao
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yiran Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yizhou Li
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
16
|
Wang X, Sun H, Liu J, Zhong W, Zhang M, Zhou H, Dai D, Lu X. Palladium-Promoted DNA-Compatible Heck Reaction. Org Lett 2019; 21:719-723. [DOI: 10.1021/acs.orglett.8b03926] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P.R. China
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Company, Limited, 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P.R. China
| | - Hui Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P.R. China
| | - Jiaxiang Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P.R. China
| | - Wenge Zhong
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Company, Limited, 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P.R. China
| | - Mingqiang Zhang
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Company, Limited, 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P.R. China
| | - Hu Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P.R. China
| | - Dongcheng Dai
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Company, Limited, 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P.R. China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P.R. China
| |
Collapse
|
17
|
Yepremyan A, Mehmood A, Asgari P, Janesko BG, Simanek EE. Synthesis of Macrocycles Derived from Substituted Triazines. Chembiochem 2019; 20:241-246. [PMID: 30311340 DOI: 10.1002/cbic.201800475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Indexed: 11/11/2022]
Abstract
A triazine ring derivatized with morpholine, an N-alkyl-N'-BOC-hydrazine (alkyl=isopropyl or benzyl) and the diethylacetal of glycinylpropionaldehyde undergoes spontaneous dimerization in good yields upon acid-catalyzed deprotection. The resulting 24-member macrocycles can be characterized by NMR spectroscopy, mass spectrometry, and single crystal X-ray diffraction. In the solid state, both homodimers adopt a taco-like conformation. Although each shows π-π stacking between the triazine rings, different patterns of hydrogen bonds emerge. The crystal structure of the isopropyl dimer shows that it includes two molecules of trifluoracetic acid per macrocycle. The trifluoroacetate anion charge balances the protonated triazines, which engage in bifurcated hydrogen bonds with the carbonyl acceptor of the distant glycine. This carbonyl also forms a hydrogen bond with the NH of the proximate glycine. The crystal structure of the benzyl derivative does not include trifluoracetic acid. Instead, two hydrogen bonds form, each between a glycine NH and the lone pair of the C=N nitrogen of the hydrazine group. In the solid state, both molecules present the alkyl side chains and morpholine groups in close proximity. A heterodimer is accessible in approximately statistical yields-along with both homodimers-by mixing the two protected monomers prior to subjecting them to deprotection.
Collapse
Affiliation(s)
- Akop Yepremyan
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 S. University Avenue, Fort Worth, TX, 76109, USA
| | - Arshad Mehmood
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 S. University Avenue, Fort Worth, TX, 76109, USA
| | - Parham Asgari
- Shimadzu Center of the University of Texas at Arlington, 505 W. Nedderman Drive, Arlington, TX, 76019, USA
| | - Benjamin G Janesko
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 S. University Avenue, Fort Worth, TX, 76109, USA
| | - Eric E Simanek
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 S. University Avenue, Fort Worth, TX, 76109, USA
| |
Collapse
|
18
|
Li H, Sun Z, Wu W, Wang X, Zhang M, Lu X, Zhong W, Dai D. Inverse-Electron-Demand Diels-Alder Reactions for the Synthesis of Pyridazines on DNA. Org Lett 2018; 20:7186-7191. [PMID: 30365326 DOI: 10.1021/acs.orglett.8b03114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The synthesis of pyridazines on DNA has been developed on the basis of inverse-electron-demand Diels-Alder (IEDDA) reactions of 1,2,4,5-tetrazines. The broad substrate scope is explored. Functionalized pyridazine products are selected for subsequent DNA-compatible Suzuki-Miyaura coupling, acylation, and SNAr substitution reactions, demonstrating the feasibility and versatility of IEDDA reactions for DNA-encoded library synthesis.
Collapse
Affiliation(s)
- Hailong Li
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Zhen Sun
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Wenting Wu
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Xuan Wang
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica , Chinese Academy of Science , 501 Haike Road, Zhang Jiang Hi-Tech Park , Pudong, Shanghai 201203 , P. R. China
| | - Mingqiang Zhang
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica , Chinese Academy of Science , 501 Haike Road, Zhang Jiang Hi-Tech Park , Pudong, Shanghai 201203 , P. R. China
| | - Wenge Zhong
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Dongcheng Dai
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| |
Collapse
|
19
|
Favalli N, Bassi G, Scheuermann J, Neri D. DNA-encoded chemical libraries - achievements and remaining challenges. FEBS Lett 2018; 592:2168-2180. [PMID: 29683493 PMCID: PMC6126621 DOI: 10.1002/1873-3468.13068] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 11/10/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of compounds, individually coupled to DNA tags serving as amplifiable identification barcodes. Since individual compounds can be identified by the associated DNA tag, they can be stored as a mixture, allowing the synthesis and screening of combinatorial libraries of unprecedented size, facilitated by the implementation of split-and-pool synthetic procedures or other experimental methodologies. In this review, we briefly present relevant concepts and technologies, which are required for the implementation and interpretation of screening procedures with DNA-encoded chemical libraries. Moreover, we illustrate some success stories, detailing how novel ligands were discovered from encoded libraries. Finally, we critically review what can realistically be achieved with the technology at the present time, highlighting challenges and opportunities for the future.
Collapse
Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| |
Collapse
|