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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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2
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Huang Z, Bi T, Jiang H, Liu H. Review on NMR as a tool to analyse natural products extract directly: Molecular structure elucidation and biological activity analysis. PHYTOCHEMICAL ANALYSIS : PCA 2024; 35:5-16. [PMID: 37789666 DOI: 10.1002/pca.3292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
INTRODUCTION Natural products, the small organic molecules produced by plants, microbes and invertebrates, often present in the form of a mixture, this leads to the structural characterisation of natural extracts often requiring time-consuming multistep purification procedures. Nuclear magnetic resonance (NMR) technology is traditionally utilised as a tool for the structural elucidation of pure compounds. Contemporarily, an up-to-date trend in the application of NMR in natural product research is shifting to the direct NMR analysis of crude mixtures, to obtain molecular structure and biological activity information without performing cumbersome separation. OBJECTIVE To review works of literature on the evolution, principle and progress of NMR technologies for analysing mixtures, we focus on the successful application of NMR technologies in direct analysis of natural product extracts. METHODOLOGY Based on our research experience, academic tracking and extensive literature search, which involved, but not limited to, the use of various databases, like Web of Knowledge and PubMed. The keywords used, in various combinations, to retrieve recent literature on the successful application of NMR technologies to sheer natural product extracts, and excluded artificially natural product mixture and biofluid. RESULTS NMR technologies for direct natural extracts analysis, including two-dimensional J-resolved spectroscopy (2D-JRES), pure shift NMR, diffusion-ordered NMR spectroscopy (DOSY), statistical correlation spectroscopy (STOCSY), concentration-ordered NMR spectroscopy (CORDY), saturation transfer difference (STD) and water-ligand observed via gradient spectroscopy (WaterLOGSY) were illustrated. CONCLUSIONS By these methods, molecular structure and biological activity information will be directly obtained from NMR analysis of natural products extract, aiming to save experimental time and expenses.
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Affiliation(s)
- Zhouman Huang
- College of Life Sciences, Wuchang University of Technology, Wuhan, China
| | - Tian Bi
- College of Life Sciences, Wuchang University of Technology, Wuhan, China
| | - Haipeng Jiang
- College of Life Sciences, Wuchang University of Technology, Wuhan, China
| | - Huwei Liu
- College of Life Sciences, Wuchang University of Technology, Wuhan, China
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Zhang M, Liu L, Zhao Y, Cao Y, Zhu Y, Han L, Yang Q, Wang Y, Wang C, Zhang H, Wang Y, Zhang J. Discovery and evaluation of active compounds from Xuanfei Baidu formula against COVID-19 via SARS-CoV-2 M pro. Chin Med 2023; 18:94. [PMID: 37528477 PMCID: PMC10394814 DOI: 10.1186/s13020-023-00790-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/25/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) is still a widespread concern. As one of the effective traditional Chinese medicine (TCM) formulae, Xuanfei Baidu formula (XFBD) shows significant efficacy for treatment of COVID-19 patients. However, its antiviral active compounds and mechanism are still unclear. PURPOSE In this study, we explored the bioactive compounds of XFBD and its antiviral mechanism by integrating computational analysis and experimental testing. METHODS Focusing on the SARS-CoV-2 main protease (Mpro), as a key target in virus transcription and replication, the fluorescence resonance energy transfer (FRET) assay was built to screen out satisfactory natural inhibitors in XFBD. The surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) were undertaken to verify the binding affinity of ligand-Mpro. Omicron BA.1.1 and BA.2.3 variants were used to evaluate the antiviral activity of the focused compounds in non-cytotoxicity concentrations. For introducing the molecular mechanism, computational modeling and NMR spectra were employed to characterize the ligand-binding modes and identify the ligand-binding site on Mpro. RESULTS From a library of 83 natural compounds, acteoside, licochalcone B, licochalcone D, linoleic acid, and physcion showed the satisfactory inhibition effects on Mpro with IC50 ranging from 1.93 to 42.96 µM, which were further verified by SPR. Showing the excellent binding affinity, acteoside was witnessed to gain valuable insights into the thermodynamic signatures by ITC and presented antiviral activity on Omicron BA.1.1 and BA.2.3 variants in vitro. The results revealed that acteoside inhibited Mpro via forming the hydrogen bond between 7-H of acteoside and Mpro. CONCLUSION Acteoside is regarded as a representative active natural compound in XFBD to inhibit replication of SARS-CoV-2, which provides the antiviral evidence and some insights into the identification of SARS-CoV-2 Mpro natural inhibitors.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Ministry of Education), Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Liting Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
| | - Yao Zhao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 200031, China
| | - Yipeng Cao
- National Supercomputer Center in Tianjin, Tianjin, 300457, China
| | - Yan Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 200031, China
| | - Lifeng Han
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
- Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
| | - Qi Yang
- Guangzhou Laboratory, Guangzhou, 510005, China
| | - Yu Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Ministry of Education), Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Changjian Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China
| | - Han Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China.
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae (Ministry of Education), Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China.
| | - Yuefei Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China.
- Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China.
| | - Junhua Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, China.
- Evidence-Based Medicine Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
- Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China.
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Rai R, Dawodu OI, Johnson SM, Vilseck JZ, Kelley MR, Ziarek JJ, Georgiadis MM. Chemically induced partial unfolding of the multifunctional Apurinic/apyrimidinic endonuclease 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547112. [PMID: 37425839 PMCID: PMC10327033 DOI: 10.1101/2023.06.29.547112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Targeting of the multifunctional enzyme apurinic/apyrimidinic endonuclease I/redox factor 1 (APE1) has produced small molecule inhibitors of both its endonuclease and redox activities. While one of the small molecules, the redox inhibitor APX3330, completed a Phase I clinical trial for solid tumors and a Phase II clinical trial for Diabetic Retinopathy/Diabetic Macular Edema, the mechanism of action for this drug has yet to be fully understood. Here, we demonstrate through HSQC NMR studies that APX3330 induces chemical shift perturbations (CSPs) of both surface and internal residues in a concentration-dependent manner, with a cluster of surface residues defining a small pocket on the opposite face from the endonuclease active site of APE1. Furthermore, APX3330 induces partial unfolding of APE1 as evidenced by a time-dependent loss of chemical shifts for approximately 35% of the residues within APE1 in the HSQC NMR spectrum. Notably, regions that are partially unfolded include adjacent strands within one of two beta sheets that comprise the core of APE1. One of the strands comprises residues near the N-terminal region and a second strand is contributed by the C-terminal region of APE1, which serves as a mitochondrial targeting sequence. These terminal regions converge within the pocket defined by the CSPs. In the presence of a duplex DNA substrate mimic, removal of excess APX3330 resulted in refolding of APE1. Our results are consistent with a reversible mechanism of partial unfolding of APE1 induced by the small molecule inhibitor, APX3330, defining a novel mechanism of inhibition.
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Bai Y, Jiao W, Vörster J, Parker EJ. Conformational interdomain flexibility in a bacterial α-isopropylmalate synthase is necessary for leucine biosynthesis. J Biol Chem 2022; 299:102789. [PMID: 36509144 PMCID: PMC9860122 DOI: 10.1016/j.jbc.2022.102789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
α-Isopropylmalate synthase (IPMS) catalyzes the first step in leucine (Leu) biosynthesis and is allosterically regulated by the pathway end product, Leu. IPMS is a dimeric enzyme with each chain consisting of catalytic, accessory, and regulatory domains, with the accessory and regulatory domains of each chain sitting adjacent to the catalytic domain of the other chain. The IPMS crystal structure shows significant asymmetry because of different relative domain conformations in each chain. Owing to the challenges posed by the dynamic and asymmetric structures of IPMS enzymes, the molecular details of their catalytic and allosteric mechanisms are not fully understood. In this study, we have investigated the allosteric feedback mechanism of the IPMS enzyme from the bacterium that causes meningitis, Neisseria meningitidis (NmeIPMS). By combining molecular dynamics simulations with small-angle X-ray scattering, mutagenesis, and heterodimer generation, we demonstrate that Leu-bound NmeIPMS is in a rigid conformational state stabilized by asymmetric interdomain polar interactions. Furthermore, we found removing these polar interactions by mutagenesis impaired the allosteric response without compromising Leu binding. Our results suggest that the allosteric inhibition of NmeIPMS is achieved by restricting the flexibility of the accessory and regulatory domains, demonstrating that significant conformational flexibility is required for catalysis.
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Affiliation(s)
- Yu Bai
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Jan Vörster
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Emily J. Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand,For correspondence: Emily J. Parker
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6
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Murray NH, Lewis A, Rincon Pabon JP, Gross ML, Henzler-Wildman K, Pagliarini DJ. 2-Propylphenol Allosterically Modulates COQ8A to Enhance ATPase Activity. ACS Chem Biol 2022; 17:2031-2038. [PMID: 35904798 PMCID: PMC9586199 DOI: 10.1021/acschembio.2c00434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
COQ8A is an atypical kinase-like protein that aids the biosynthesis of coenzyme Q, an essential cellular cofactor and antioxidant. COQ8A's mode of action remains unclear, in part due to the lack of small molecule tools to probe its function. Here, we blend NMR and hydrogen-deuterium exchange mass spectrometry to help determine how a small CoQ precursor mimetic, 2-propylphenol, modulates COQ8A activity. We identify a likely 2-propylphenol binding site and reveal that this compound modulates a conserved COQ8A domain to increase nucleotide affinity and ATPase activity. Our findings promise to aid further investigations into COQ8A's precise enzymatic function and the design of compounds capable of boosting endogenous CoQ production for therapeutic gain.
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Affiliation(s)
- Nathan H. Murray
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Adam Lewis
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Juan P. Rincon Pabon
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | | | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Correspondence and requests for materials should be addressed to D.J.P.,
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Di Carluccio C, Forgione RE, Bosso A, Yokoyama S, Manabe Y, Pizzo E, Molinaro A, Fukase K, Fragai M, Bensing BA, Marchetti R, Silipo A. Molecular recognition of sialoglycans by streptococcal Siglec-like adhesins: toward the shape of specific inhibitors. RSC Chem Biol 2021; 2:1618-1630. [PMID: 34977577 PMCID: PMC8637897 DOI: 10.1039/d1cb00173f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/14/2021] [Indexed: 01/16/2023] Open
Abstract
Streptococcus gordonii and Streptococcus sanguinis, commensal bacteria present in the oral cavity of healthy individuals, upon entry into the bloodstream can become pathogenic, causing infective endocarditis (IE). Sialic acid-binding serine-rich repeat adhesins on the microbial surface represent an important factor of successful infection to cause IE. They contain Siglec-like binding regions (SLBRs) that variously recognize different repertoires of O-glycans, with some strains displaying high selectivity and others broader specificity. We here dissect at an atomic level the mechanism of interaction of SLBR-B and SLBR-H from S. gordonii with a multivarious approach that combines NMR spectroscopy and computational and biophysical studies. The binding pockets of both SLBRs are broad enough to accommodate extensive interactions with sialoglycans although with key differences related to strain specificity. Furthermore, and significantly, the pattern of interactions established by the SLBRs are mechanistically very different from those reported for mammalian Siglecs despite them having a similar fold. Thus, our detailed description of the binding modes of streptococcal Siglec-like adhesins sparks the development of tailored synthetic inhibitors and therapeutics specific for Streptococcal adhesins to counteract IE, without impairing the interplay between Siglecs and glycans. We here present a detailed molecular description of sialoglycans recognition by Siglec-like adhesins from S. gordonii opening the venue for the design of specific inhibitors to influence the propensity of streptococci to cause infective endocarditis.![]()
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Affiliation(s)
- Cristina Di Carluccio
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Rosa Ester Forgione
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Andrea Bosso
- Department of Biology, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Shinji Yokoyama
- Department of Chemistry, Graduate School of Science, Osaka University 1-1 Machikaneyama Toyonaka Osaka 560-0043 Japan
| | - Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University 1-1 Machikaneyama Toyonaka Osaka 560-0043 Japan
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy .,Department of Chemistry, Graduate School of Science, Osaka University 1-1 Machikaneyama Toyonaka Osaka 560-0043 Japan
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University 1-1 Machikaneyama Toyonaka Osaka 560-0043 Japan
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy.,Department of Chemistry "Ugo Schiff", University of Florence Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
| | - Barbara A Bensing
- Division of Infectious Diseases, Veterans Affairs Medical Center, Department of Medicine, University of California San Francisco California 94121 USA.,Northern California Institute for Research and Education San Francisco California 94121 USA
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
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McPherson KS, Korzhnev DM. Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy. RSC Chem Biol 2021; 2:1167-1195. [PMID: 34458830 PMCID: PMC8342002 DOI: 10.1039/d1cb00101a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Cellular DNA damage response (DDR) is an extensive signaling network that orchestrates DNA damage recognition, repair and avoidance, cell cycle progression and cell death. DDR alteration is a hallmark of cancer, with the deficiency in one DDR capability often compensated by a dependency on alternative pathways endowing cancer cells with survival and growth advantage. Targeting these DDR pathways has provided multiple opportunities for the development of cancer therapies. Traditional drug discovery has mainly focused on catalytic inhibitors that block enzyme active sites, which limits the number of potential drug targets within the DDR pathways. This review article describes the emerging approach to the development of cancer therapeutics targeting essential protein-protein interactions (PPIs) in the DDR network. The overall strategy for the structure-based design of small molecule PPI inhibitors is discussed, followed by an overview of the major DNA damage sensing, DNA repair, and DNA damage tolerance pathways with a specific focus on PPI targets for anti-cancer drug design. The existing small molecule inhibitors of DDR PPIs are summarized that selectively kill cancer cells and/or sensitize cancers to front-line genotoxic therapies, and a range of new PPI targets are proposed that may lead to the development of novel chemotherapeutics.
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Affiliation(s)
- Kerry Silva McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
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Bu C, Jin L. NMR Characterization of the Interactions Between Glycosaminoglycans and Proteins. Front Mol Biosci 2021; 8:646808. [PMID: 33796549 PMCID: PMC8007983 DOI: 10.3389/fmolb.2021.646808] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Glycosaminoglycans (GAGs) constitute a considerable fraction of the glycoconjugates found on cellular membranes and in the extracellular matrix of virtually all mammalian tissues. The essential role of GAG-protein interactions in the regulation of physiological processes has been recognized for decades. However, the underlying molecular basis of these interactions has only emerged since 1990s. The binding specificity of GAGs is encoded in their primary structures, but ultimately depends on how their functional groups are presented to a protein in the three-dimensional space. This review focuses on the application of NMR spectroscopy on the characterization of the GAG-protein interactions. Examples of interpretation of the complex mechanism and characterization of structural motifs involved in the GAG-protein interactions are given. Selected families of GAG-binding proteins investigated using NMR are also described.
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Affiliation(s)
- Changkai Bu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Lan Jin
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
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10
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Applications of Solution NMR in Drug Discovery. Molecules 2021; 26:molecules26030576. [PMID: 33499337 PMCID: PMC7865596 DOI: 10.3390/molecules26030576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.
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11
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Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein-protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
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Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
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12
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Bataille CJR, Rabbitts TH, Claridge TDW. NMR waterLOGSY as An Assay in Drug Development Programmes for Detecting Protein-Ligand Interactions-NMR waterLOGSY. Bio Protoc 2020; 10:e3666. [PMID: 33659336 PMCID: PMC7842718 DOI: 10.21769/bioprotoc.3666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/27/2020] [Accepted: 05/18/2020] [Indexed: 11/02/2022] Open
Abstract
In drug development programmes, multiple assays are needed for the determination of protein-compound interactions and evaluation of potential use in assays with protein-protein interactions. In this protocol we describe the waterLOGSY NMR method for confirming protein-ligand binding events.
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Affiliation(s)
- Carole J. R. Bataille
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Terence H. Rabbitts
- Institute of Cancer Research. Division of Cancer Therapeutics, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Timothy D. W. Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
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Raingeval C, Cala O, Brion B, Le Borgne M, Hubbard RE, Krimm I. 1D NMR WaterLOGSY as an efficient method for fragment-based lead discovery. J Enzyme Inhib Med Chem 2019; 34:1218-1225. [PMID: 31286785 PMCID: PMC6691826 DOI: 10.1080/14756366.2019.1636235] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
WaterLOGSY is a sensitive ligand-observed NMR experiment for detection of interaction between a ligand and a protein and is now well-established as a screening technique for fragment-based lead discovery. Here we develop and assess a protocol to derive ligand epitope mapping from WaterLOGSY data and demonstrate its general applicability in studies of fragment-sized ligands binding to six different proteins (glycogen phosphorylase, protein peroxiredoxin 5, Bcl-xL, Mcl-1, HSP90, and human serum albumin). We compare the WaterLOGSY results to those obtained from the more widely used saturation transfer difference experiments and to the 3D structures of the complexes when available. In addition, we evaluate the impact of ligand labile protons on the WaterLOGSY data. Our results demonstrate that the WaterLOGSY experiment can be used as an additional confirmation of the binding mode of a ligand to a protein.
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Affiliation(s)
- Claire Raingeval
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Olivier Cala
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Béatrice Brion
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Marc Le Borgne
- b Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453 - INSERM US7 , Lyon , France
| | - Roderick Eliot Hubbard
- c YSBL, University of York , Heslington , York , UK.,d Vernalis (R&D) Ltd, Granta Park, Abington , Cambridge , UK
| | - Isabelle Krimm
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
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14
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Dalvit C, Parent A, Vallée F, Mathieu M, Rak A. Fast NMR Methods for Measuring in the Direct and/or Competition Mode the Dissociation Constants of Chemical Fragments Interacting with a Receptor. ChemMedChem 2019; 14:1115-1127. [DOI: 10.1002/cmdc.201900152] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Indexed: 12/16/2022]
Affiliation(s)
| | - Annick Parent
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Francois Vallée
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Magali Mathieu
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
| | - Alexey Rak
- Bio Structure and BiophysicsIntegrated Drug DiscoverySanofi R&D 13, Quai Jules Guesde—BP 14 94403 Vitry sur Seine Cedex France
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