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Caceres-Cortes J, Falk B, Mueller L, Dhar TGM. Perspectives on Nuclear Magnetic Resonance Spectroscopy in Drug Discovery Research. J Med Chem 2024; 67:1701-1733. [PMID: 38290426 DOI: 10.1021/acs.jmedchem.3c02389] [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: 02/01/2024]
Abstract
The drug discovery landscape has undergone a significant transformation over the past decade, owing to research endeavors in a wide range of areas leading to strategies for pursuing new drug targets and the emergence of novel drug modalities. NMR spectroscopy has been a technology of fundamental importance to these research pursuits and has seen its use expanded both within and outside of traditional medicinal chemistry applications. In this perspective, we will present advancement of NMR-derived methods that have facilitated the characterization of small molecules and novel drug modalities including macrocyclic peptides, cyclic dinucleotides, and ligands for protein degradation. We will discuss innovations in NMR spectroscopy at the chemistry and biology interface that have broadened NMR's utility from hit identification through lead optimization activities. We will also discuss the promise of emerging NMR approaches in bridging our understanding and addressing challenges in the pursuit of the therapeutic agents of the future.
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Affiliation(s)
- Janet Caceres-Cortes
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Bradley Falk
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Luciano Mueller
- Synthesis and Enabling Technologies, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - T G Murali Dhar
- Discovery Chemistry, Small Molecule Drug Discovery, Bristol-Myers Squibb Company, Princeton, New Jersey 085401, United States
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Li R, Chen L, He X, Cao D, Zhang Z, Jiang H, Chen K, Cheng X. Loops Mediate Agonist-Induced Activation of the Stimulator of Interferon Genes Protein. J Chem Inf Model 2023; 63:7373-7381. [PMID: 37831484 DOI: 10.1021/acs.jcim.3c00984] [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: 10/14/2023]
Abstract
The stimulator of interferon genes (STING) is an important therapeutic target for cancer diseases. The activated STING recruits downstream tank-binding kinase 1 (TBK1) to trigger several important immune responses. However, the molecular mechanism of how agonist molecules mediate the STING-TBK1 interactions remains elusive. Here, we performed molecular dynamics simulations to capture the conformational changes of STING and TBK1 upon agonist binding. Our simulations revealed that multiple helices (α5-α7) and especially three loops (loop 6, loop 8, and C-terminal tail) of STING participated in the allosteric mediation of the STING-TBK1 interactions. Consistent results were also observed in the simulations of the constitutive activating mutant of STING (R284S). We further identified α5 as a key region in this agonist-induced activation mechanism of STING. Free-energy perturbation calculations of multiple STING agonists demonstrated that an alkynyl group targeting α5 is a determinant for agonist activities. These results not only offer deeper insights into the agonist-induced allosteric mediation of STING-TKB1 interactions but also provide a guidance for future drug development of this important therapeutic target.
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Affiliation(s)
- Rui Li
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xinheng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Duanhua Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zehong Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Kaixian Chen
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, No.1 Xiangshan Branch Lane, Hangzhou 310024, China
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Shang M, Lu K, Guan W, Cao S, Ren M, Zhou C. 2',3'-Cyclic GMP-AMP Dinucleotides for STING-Mediated Immune Modulation: Principles, Immunotherapeutic Potential, and Synthesis. ChemMedChem 2021; 17:e202100671. [PMID: 34807508 DOI: 10.1002/cmdc.202100671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 11/09/2022]
Abstract
The cGAS-STING pathway discovered ten years ago is an important component of the innate immune system. Activation of cGAS-STING triggers downstream signalling, such as TBK1-IRF3, NF-κB and autophagy, which in turn leads to antipathogen responses, durable antitumour immunity or autoimmune diseases. 2',3'-Cyclic GMP-AMP dinucleotides (2',3'-cGAMP), the key second messengers produced by cGAS, play a pivotal role in cGAS-STING signalling by binding and activating STING. Thus, 2',3'-cGAMP has immunotherapeutic potential, which in turn has stimulated research on the design and synthesis of 2',3'-cGAMP analogues for clinical applications over the past ten years. This review presents the discovery, metabolism, and function of 2',3'-cGAMP in the cGAS-STING innate immune signalling axis. The enzymatic and chemical syntheses of 2',3'-cGAMP analogues as STING-targeting therapeutics are also summarized.
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Affiliation(s)
- Mengdi Shang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Wenli Guan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Shujie Cao
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Mengtian Ren
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
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Sun D, Wu DR, Li P, Yip H, Wang B, Hou X, Zhao R, Zhang H, Kempson J, Mathur A. Large-scale supercritical fluid chromatography purification of unstable STING agonist intermediates. J Chromatogr A 2021; 1651:462309. [PMID: 34147835 DOI: 10.1016/j.chroma.2021.462309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 02/02/2023]
Abstract
A regioisomeric mixture of the nucleoside derivative, Intermediate 1, required resolution by preparative supercritical fluid chromatography (SFC) in order to obtain the desired regioisomer as a key intermediate in a STING agonist program. Various chiral columns and solvents including methanol, acetonitrile, isopropanol, and the mixture of acetonitrile and isopropanol as organic modifiers in carbon dioxide at different temperatures were screened to obtain the best regioisomeric resolution. A key issue associated with interconversion between the regioisomers via silyl migration during purification was investigated in methanol, acetonitrile, and the mixture of acetonitrile and isopropanol, and the optimal organic modifier in CO2 was established to mitigate the interconversion to an acceptable level (<5%). Taking into account peak resolution, throughput, interconversion and operation robustness, an efficient SFC method for large-scale purification was successfully developed and scaled up onto a 5 cm I. D. Chiralcel OJ-H column using 25% acetonitrile: isopropanol [1:1 (v/v)] with 0.1% ammonium hydroxide as the modifier in CO2 at a total flow rate of 270 mL/min and a temperature of 30°C. In addition, continual evaporation (i.e. every hour) of the desired isomer fraction stream post-separation ensured minimal further interconversion. A total of 258 grams were separated at a high throughput of 8.6 g/h. Regioisomeric purity of the desired isomer of Intermediate 1 was ≥98.2% and the recovery was ≥90.2%. A similar purification strategy was applied to the regioisomeric resolution of Intermediate 2, an analog of Intermediate 1. In total, 1028 grams of Intermediate 2 were processed at a high throughput of 12.5 g/h on a Viridis BEH 2-EP column. The regioisomeric purity of the desired isomer was ≥96.8% and the recovery was ≥90.7%.
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Affiliation(s)
- Dawn Sun
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States.
| | - Dauh-Rurng Wu
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
| | - Peng Li
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
| | - Henry Yip
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
| | - Bei Wang
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
| | - Xiaoping Hou
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
| | - Rulin Zhao
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
| | - Huiping Zhang
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
| | - James Kempson
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
| | - Arvind Mathur
- Department of Discovery Synthesis, Research and Early Development, Bristol Myers Squibb, Princeton, NJ 08540, United States
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