1
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Gasparetto M, Fődi B, Sipos G. Negishi-coupling-enabled synthesis of α-heteroaryl-α-amino acid building blocks for DNA-encoded chemical library applications. Beilstein J Org Chem 2024; 20:1922-1932. [PMID: 39135657 PMCID: PMC11318629 DOI: 10.3762/bjoc.20.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/26/2024] [Indexed: 08/15/2024] Open
Abstract
Amino acids are vital motifs in the domain of biochemistry, serving as the foundational unit for peptides and proteins, while also holding a crucial function in many biological processes. Due to their bifunctional character, they have been also used for combinatorial chemistry purposes, such as the preparation of DNA-encoded chemical libraries. We developed a practical synthesis for α-heteroaryl-α-amino acids starting from an array of small heteroaromatic halides. The reaction sequence utilizes a photochemically enhanced Negishi cross-coupling as a key step, followed by oximation and reduction. The prepared amino esters were validated for on-DNA reactivity via a reverse amidation-hydrolysis-reverse amidation protocol.
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Affiliation(s)
- Matteo Gasparetto
- X-Chem Zrt., Záhony u. 7, DA Building, Graphisoft Park, Budapest, 1031, Hungary
| | - Balázs Fődi
- X-Chem Zrt., Záhony u. 7, DA Building, Graphisoft Park, Budapest, 1031, Hungary
| | - Gellért Sipos
- X-Chem Zrt., Záhony u. 7, DA Building, Graphisoft Park, Budapest, 1031, Hungary
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2
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Fitzgerald P, Dixit A, Zhang C, Mobley DL, Paegel BM. Building Block-Centric Approach to DNA-Encoded Library Design. J Chem Inf Model 2024; 64:4661-4672. [PMID: 38860710 PMCID: PMC11200258 DOI: 10.1021/acs.jcim.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Anjali Dixit
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Chris Zhang
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - David L. Mobley
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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3
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Ramos AL, Goedken ER, Frank KE, Argiriadi MA, Bazzaz S, Bian Z, Brown JTC, Centrella PA, Chen HJ, Disch JS, Donner PL, Duignan DB, Gikunju D, Greszler SN, Guié MA, Habeshian S, Hartl HE, Hein CD, Hutchins CW, Jetson R, Keefe AD, Khan H, Li HQ, Olszewski A, Ortiz Cardona BJ, Osuma A, Panchal SC, Phelan R, Qiu W, Shotwell JB, Shrestha A, Srikumaran M, Su Z, Sun C, Upadhyay AK, Wood MD, Wu H, Zhang R, Zhang Y, Zhao G, Zhu H, Webster MP. Discovery of Small Molecule Interleukin 17A Inhibitors with Novel Binding Mode and Stoichiometry: Optimization of DNA-Encoded Chemical Library Hits to In Vivo Active Compounds. J Med Chem 2024; 67:6456-6494. [PMID: 38574366 DOI: 10.1021/acs.jmedchem.3c02397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Dysregulation of IL17A drives numerous inflammatory and autoimmune disorders with inhibition of IL17A using antibodies proven as an effective treatment. Oral anti-IL17 therapies are an attractive alternative option, and several preclinical small molecule IL17 inhibitors have previously been described. Herein, we report the discovery of a novel class of small molecule IL17A inhibitors, identified via a DNA-encoded chemical library screen, and their subsequent optimization to provide in vivo efficacious inhibitors. These new protein-protein interaction (PPI) inhibitors bind in a previously undescribed mode in the IL17A protein with two copies binding symmetrically to the central cavities of the IL17A homodimer.
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Affiliation(s)
- Ashley L Ramos
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Eric R Goedken
- AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Kristine E Frank
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Maria A Argiriadi
- AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sana Bazzaz
- X-Chem, Waltham, Massachusetts 02453, United States
| | - Zhiguo Bian
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Jesse T C Brown
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | | | - Hui-Ju Chen
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | | | - Pamela L Donner
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - David B Duignan
- AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | | | | | | | | | | | | | | | | | | | - Hasan Khan
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Huan-Qiu Li
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | | | | | - Augustine Osuma
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Sanjay C Panchal
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Ryan Phelan
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Wei Qiu
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - J Brad Shotwell
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Anurupa Shrestha
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Myron Srikumaran
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Zhi Su
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Chaohong Sun
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Anup K Upadhyay
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Michael D Wood
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Haihong Wu
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Ruijie Zhang
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Ying Zhang
- X-Chem, Waltham, Massachusetts 02453, United States
| | - Gang Zhao
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
| | - Haizhong Zhu
- AbbVie Incorporated, North Chicago, Illinois 60064, United States
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4
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Dickson P. DNA-Encoded Library Technology─A Catalyst for Covalent Ligand Discovery. ACS Chem Biol 2024; 19:802-808. [PMID: 38527941 DOI: 10.1021/acschembio.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The identification of novel covalent ligands for therapeutic purposes has long depended on serendipity, with dedicated hit finding techniques emerging only in the early 2000s. Advances in chemoproteomics have enabled robust characterization of putative drugs to derisk the unique liabilities associated with covalent hit molecules, leading to a renewed interest in this targeting modality. DNA-encoded library (DEL) technology has similarly emerged over the past two decades as a highly efficient method to identify new chemical equity toward protein targets of interest. A number of commercial and academic groups have reported methods in covalent DEL synthesis and hit identification; however, it is evident that there is still much to be done to fully realize the power of this technology for covalent ligand discovery. This perspective will explore the current approaches in covalent DEL technology and reflect on the next steps to advance this field.
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Affiliation(s)
- Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
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5
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Rama-Garda R, Martin-Ortega MD, Sánchez ADJ, Priego J, de Blas J, Torrado A, Domínguez E, Haro R, Rivera-Sagredo A, Román JP, Lorite MJ, Johansson HE, Loza MI, Amigo J, Sobrino B, Lallena MJ, Toledo MÁ. Design, synthesis and validation of a new Crimped Head-Piece for DNA-Encoded libraries generation. Bioorg Med Chem 2024; 99:117596. [PMID: 38232459 DOI: 10.1016/j.bmc.2024.117596] [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] [Received: 10/13/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Codification of DNA Encoded Libraries (DELs) is critical for successful ligand identification of molecules that bind a protein of interest (POI). There are different encoding strategies that permit, for instance, the customization of a DEL for testing single or dual pharmacophores (single strand DNA) or for producing and screening large diversity libraries of small molecules (double strand DNA). Both approaches challenges, either from the synthetic and encoding point of view, or from the selection methodology to be utilized for the screening. The Head-Piece contains the DNA sequence that is attached to a chemical compound, allowing the encoding of each molecule with a unique DNA tag. Designing the Head-Piece for a DNA-encoded library involves careful consideration of several key aspects including DNA barcode identity, sequence length and attachment chemistry. Here we describe a double stranded DNA versatile Head-Piece that can be used for the generation of single or dual pharmacophore libraries, but also shows other advanced DEL functionalities, stability and enlarged encoding capacity.
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Affiliation(s)
- Ramón Rama-Garda
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain; BioFarma, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña 15782, Spain.
| | - María Dolores Martin-Ortega
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | | | - Julián Priego
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Jesús de Blas
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Alicia Torrado
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Eduardo Domínguez
- Genomic Medicine, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña, Spain
| | - Rubén Haro
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Alfonso Rivera-Sagredo
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - José Pablo Román
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - María José Lorite
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | | | - María Isabel Loza
- BioFarma, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña 15782, Spain
| | - Jorge Amigo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Servizo Galego de Saúde (SERGAS), Instituto de Investigaciones Sanitarias (IDIS), A Coruña 15706, Spain
| | - Beatriz Sobrino
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Servizo Galego de Saúde (SERGAS), Instituto de Investigaciones Sanitarias (IDIS), A Coruña 15706, Spain
| | - María José Lallena
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Miguel Ángel Toledo
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
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6
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Collie GW, Clark MA, Keefe AD, Madin A, Read JA, Rivers EL, Zhang Y. Screening Ultra-Large Encoded Compound Libraries Leads to Novel Protein-Ligand Interactions and High Selectivity. J Med Chem 2024; 67:864-884. [PMID: 38197367 PMCID: PMC10823476 DOI: 10.1021/acs.jmedchem.3c01861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
The DNA-encoded library (DEL) discovery platform has emerged as a powerful technology for hit identification in recent years. It has become one of the major parallel workstreams for small molecule drug discovery along with other strategies such as HTS and data mining. For many researchers working in the DEL field, it has become increasingly evident that many hits and leads discovered via DEL screening bind to target proteins with unique and unprecedented binding modes. This Perspective is our attempt to analyze reports of DEL screening with the purpose of providing a rigorous and useful account of the binding modes observed for DEL-derived ligands with a focus on binding mode novelty.
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Affiliation(s)
| | | | | | | | | | | | - Ying Zhang
- X-Chem,
Inc., Waltham, Massachusetts 02453, United States
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7
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Xue L, Zhou S, Wu J, Duchemin N, Chen B, Zhang J, Zhang H, Yang K, Hu YJ. Development of On-DNA Cyclic Imide Synthesis for DNA Encoded Library Construction. Chembiochem 2023; 24:e202300206. [PMID: 37380609 DOI: 10.1002/cbic.202300206] [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] [Received: 03/16/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 06/30/2023]
Abstract
Here, we describe a novel method for the on-DNA synthesis of cyclic imides, an important class of molecules that includes several well-known medications. Significantly, the new method enabled on-DNA synthesis under mild conditions with high conversions and a broad functional group tolerance, utilizing ubiquitous bifunctional amines and bis-carboxylic acid, or alkyl halides, and therefore served as the linchpin for DNA encoded library (DEL) synthesis. The mechanism study of off-DNA and on-DNA chemical transformations revealed unique insights in contrast to conventional chemical transformation.
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Affiliation(s)
- Lijun Xue
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Sufang Zhou
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Jing Wu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Nicolas Duchemin
- Pharmaron UK, Ltd., Innovation Park, West Cl, Hertford Rd, Hoddesdon, EN11 9FH, UK
| | - Bingxin Chen
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Jie Zhang
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Huanqing Zhang
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Kexin Yang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing, 100176, China
| | - Yun Jin Hu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
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8
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Fitzgerald P, Cochrane WG, Paegel BM. Dose-Response Activity-Based DNA-Encoded Library Screening. ACS Med Chem Lett 2023; 14:1295-1303. [PMID: 37736190 PMCID: PMC10510511 DOI: 10.1021/acsmedchemlett.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/04/2023] [Indexed: 09/23/2023] Open
Abstract
Dose-response, or "conforming" behavior, increases confidence in a screening hit's authenticity. Here, we demonstrate dose-response solid-phase DNA-encoded library (DEL) screening. Compound dose in microfluidic droplets is modulated via the UV intensity of photocleavage from DEL beads. A 55,296-member DEL was screened at different UV intensities against model enzyme drug targets factor Xa (FXa) and autotaxin (ATX). Both screens yielded photochemical dose-dependent hit rates (FXa hit rates of 0.08/0.05% at 100/30% UV exposure; ATX hit rates of 0.24/0.08% at 100/20% UV exposure). FXa hits contained structures reflective of FXa inhibitors and four hits inhibited FXa (IC50 = 4.2 ± 0.1, 7.4 ± 0.3, 9.0 ± 0.3, and 19 ± 2 μM.) The top ATX hits (two dihydrobenzamidazolones and a tetrahydroisoquinoline) were validated as inhibitors (IC50 = 7 ± 2, 13 ± 2, and 1 ± 0.3 μM). Photochemical dose-response DEL screening data prioritized hits for synthesis, the rate-limiting step in DEL lead identification.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Wesley G. Cochrane
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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9
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Xue L, Liu W, Li S, Duchemin N, Lou M, Yuan J, Zhang H, Chen J, Yu W, Yang K, Hu YJ. On-DNA Morita-Baylis-Hillman Reaction: Accessing Targeted Covalent Inhibitor Motifs in DNA-Encoded Libraries. Bioconjug Chem 2023; 34:1366-1373. [PMID: 37418679 DOI: 10.1021/acs.bioconjchem.3c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
We herein present the first application of the on-DNA Morita-Baylis-Hillman (MBH) reaction for the creation of pharmaceutically relevant targeted covalent inhibitors (TCIs) with an α-hydroxyl Michael acceptor motif. Adapting a DNA-compatible organocatalytic process, this MBH reaction for covalent selection-capable DNA encoded library (DEL) synthesis grants access to densely functionalized and versatile precursors to explore novel chemical space for molecule recognition in drug discovery. Most importantly, this methodology sheds light on potentially unexpected reaction outcomes of the MBH reaction.
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Affiliation(s)
- Lijun Xue
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
| | - Weijie Liu
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
| | - Shu Li
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
| | - Nicolas Duchemin
- Pharmaron U.K., Ltd., Innovation Park, West Cl, Hertford Rd, Hoddesdon EN11 9FH, United Kingdom
| | - Mengjia Lou
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
| | - Jingyu Yuan
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
| | - Huanqing Zhang
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
| | - Junyun Chen
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
| | - Weina Yu
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
| | - Kexin Yang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P.R. China
| | - Yun Jin Hu
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P.R. China
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10
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Abstract
DNA-encoded libraries (DELs) are widely used in the discovery of drug candidates, and understanding their design principles is critical for accessing better libraries. Most DELs are combinatorial in nature and are synthesized by assembling sets of building blocks in specific topologies. In this study, different aspects of library topology were explored and their effect on DEL properties and chemical diversity was analyzed. We introduce a descriptor for DEL topological assignment (DELTA) and use it to examine the landscape of possible DEL topologies and their coverage in the literature. A generative topographic mapping analysis revealed that the impact of library topology on chemical space coverage is secondary to building block selection. Furthermore, it became apparent that the descriptor used to analyze chemical space dictates how structures cluster, with the effects of topology being apparent when using three-dimensional descriptors but not with common two-dimensional descriptors. This outcome points to potential challenges of attempts to predict DEL productivity based on chemical space analyses alone. While topology is rather inconsequential for defining the chemical space of encoded compounds, it greatly affects possible interactions with target proteins as illustrated in docking studies using NAD/NADP binding proteins as model receptors.
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Affiliation(s)
- William K Weigel
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Alba L Montoya
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr., Salt Lake City, Utah 84112, United States
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11
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Luo A, Zhou H, Hua Q, An Y, Ma H, Zhao X, Yang K, Hu YJ. Development of the Inverse Sonogashira Reaction for DEL Synthesis. ACS Med Chem Lett 2023; 14:270-277. [PMID: 36923912 PMCID: PMC10009795 DOI: 10.1021/acsmedchemlett.2c00477] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
An efficient approach for aryl acetylene DNA-encoded library (DEL) synthesis was developed in this study by transition-metal-mediated inverse Sonogashira reaction of 1-iodoalkyne with boronic acid under ambient conditions, with moderate to excellent conversions and broad substrate adaptability for the first time. Compared to palladium-phosphine, copper iodide performed better in the on-DNA inverse Sonogashira reaction. Interestingly, substrate diversity can be enhanced by first interrogating coupling reagents under copper-promoted conditions, and then revalidating them under palladium-facilitated conditions for those reagents which failed under the former. This complementary validation strategy is particularly well-fitted to any DEL validation studies.
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Affiliation(s)
- Ayun Luo
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Hongxia Zhou
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Qini Hua
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Yufang An
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Hangke Ma
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Xue Zhao
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Kexin Yang
- Pharmaron
Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Yun Jin Hu
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
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12
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Montoya AL, Glavatskikh M, Halverson BJ, Yuen LH, Schüler H, Kireev D, Franzini RM. Combining pharmacophore models derived from DNA-encoded chemical libraries with structure-based exploration to predict Tankyrase 1 inhibitors. Eur J Med Chem 2023; 246:114980. [PMID: 36495630 PMCID: PMC9805525 DOI: 10.1016/j.ejmech.2022.114980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
DNA-encoded chemical libraries (DECLs) interrogate the interactions of a target of interest with vast numbers of molecules. DECLs hence provide abundant information about the chemical ligand space for therapeutic targets, and there is considerable interest in methods for exploiting DECL screening data to predict novel ligands. Here we introduce one such approach and demonstrate its feasibility using the cancer-related poly-(ADP-ribose)transferase tankyrase 1 (TNKS1) as a model target. First, DECL affinity selections resulted in structurally diverse TNKS1 inhibitors with high potency including compound 2 with an IC50 value of 0.8 nM. Additionally, TNKS1 hits from four DECLs were translated into pharmacophore models, which were exploited in combination with docking-based screening to identify TNKS1 ligand candidates in databases of commercially available compounds. This computational strategy afforded TNKS1 inhibitors that are outside the chemical space covered by the DECLs and yielded the drug-like lead compound 12 with an IC50 value of 22 nM. The study further provided insights in the reliability of screening data and the effect of library design on hit compounds. In particular, the study revealed that while in general DECL screening data are in good agreement with off-DNA ligand binding, unpredictable interactions of the DNA-attachment linker with the target protein contribute to the noise in the affinity selection data.
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Affiliation(s)
- Alba L Montoya
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Brayden J Halverson
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
| | - Lik Hang Yuen
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA
| | - Herwig Schüler
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 22100, Lund, Sweden.
| | - Dmitri Kireev
- Department of Chemistry, 36 Schlundt Hall, University of Missouri, Columbia, MO, 65211, USA.
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA; Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr., Salt Lake City, UT, 84112, USA.
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13
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
- Faculty of
Chemistry and Chemical Biology, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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14
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Cai K, Ran Y, Sun W, Gao S, Li J, Wan J, Liu G. Palladium-Mediated Hydroamination of DNA-Conjugated Aryl Alkenes. Front Chem 2022; 10:851674. [PMID: 35480389 PMCID: PMC9035600 DOI: 10.3389/fchem.2022.851674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
C-N bond formation is one of the most commonly used reactions in medicinal chemistry. Herein, we report an efficient Pd-promoted hydroamination reaction between DNA-conjugated aryl alkenes and a wide scope of aliphatic amines. The described reactions are demonstrated in good to excellent conversions to furnish C (sp3)–N bonds on DNA. This DNA-compatible transformation has strong potentials for the application into DNA-encoded library synthesis.
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Affiliation(s)
| | | | - Wenbo Sun
- *Correspondence: Guansai Liu, ; Wenbo Sun, ; Sen Gao,
| | - Sen Gao
- *Correspondence: Guansai Liu, ; Wenbo Sun, ; Sen Gao,
| | | | | | - Guansai Liu
- *Correspondence: Guansai Liu, ; Wenbo Sun, ; Sen Gao,
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15
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Škopić MK, Losch F, McMillan AE, Willeke N, Malenica M, Bering L, Bode J, Brunschweiger A. Reagent-Based Scaffold Diversity for DNA-Encoded Library Design: Solid Phase Synthesis of DNA-Tagged sp 3-Rich Heterocycles by SnAP Chemistry. Org Lett 2022; 24:1383-1387. [PMID: 35113572 DOI: 10.1021/acs.orglett.2c00228] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactions that require strictly dry conditions are challenging to translate to a DNA-encoded library format. Controlled pore glass solid support-connected DNA oligonucleotide-aldehyde conjugates could be condensed with SnAP reagents and cyclized to various sp3-rich heterocycles. The Boc-group of products provided a handle for product purification, and its facile removal under acidic conditions was tolerated by a chemically stabilized barcode. The reaction provides reagent-based scaffold diversity with functionalities for further library synthesis.
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Affiliation(s)
- Mateja Klika Škopić
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Florian Losch
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Angus E McMillan
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Niklas Willeke
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Mateo Malenica
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Luis Bering
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Jeffrey Bode
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Andreas Brunschweiger
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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