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Mahmood A, Samad A, Bano S, Umair M, Ajmal A, Ilyas I, Shah AA, Li P, Hu J. Structural and dynamics insights into the GBA variants associated with Parkinson's disease. J Biomol Struct Dyn 2024; 42:6256-6268. [PMID: 37434319 DOI: 10.1080/07391102.2023.2233617] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/01/2023] [Indexed: 07/13/2023]
Abstract
The GBA1 gene encodes for the lysosomal enzyme glucocerebrosidase (GCase), which maintains glycosphingolipid homeostasis and regulates the autophagy process. Genomic variants of GBA1 are associated with Goucher disease; however, several heterozygous variants of GBA (E326K, T369M, N370S, L444P) are frequent high-risk factors for Parkinson's disease (PD). The underlying mechanism of these variants has been revealed through functional and patient-centered research, but the structural and dynamical aspects of these variants have not yet been thoroughly investigated. In the current study, we used a thorough computational method to pinpoint the structural changes that GBA underwent because of genomic variants and drug binding mechanisms. According to our findings, PD-linked nsSNP variants of GBA showed structural variation and abnormal dynamics when compared to wild-typ. The docking analysis demonstrated that the mutants E326K, N370S, and L444P have higher binding affinities for Ambroxol. Root means square deviation (RMSD), Root mean square fluctuation analysis (RMSF), and MM-GBSA analysis confirmed that the Ambroxol are more stable in the binding site of N370S and L444P, and that their binding affinities are stronger as compared to the wild-type and T369M variants of GBA. The evaluation of hydrogen bonds and the calculation of the free binding energy provided additional evidence in favor of this conclusion. When docked with Ambroxol, GBA demonstrated an increase in binding affinity and catalytic activity. Understanding the therapeutic efficacy and potential against the aforementioned changes in the GBA will be beneficial in order to use more efficient methods for developing novel drugs.
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Affiliation(s)
- Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Shazia Bano
- Department of Optometry and Vision Sciences, University of Lahore, Lahore, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Iqra Ilyas
- National Centre of Excellence in Molecular Biology (CEMB), University of The Punjab, Lahore, Pakistan
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Ping Li
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Junjian Hu
- Department of Central Laboratory, SSL Central Hospital of Dongguan City, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, China
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2
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Lan T, Dong Y, Jiang L, Zhang Y, Sui X. Analytical approaches for assessing protein structure in protein-rich food: A comprehensive review. Food Chem X 2024; 22:101365. [PMID: 38623506 PMCID: PMC11016869 DOI: 10.1016/j.fochx.2024.101365] [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: 10/05/2023] [Revised: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
This review focuses on changes in nutrition and functional properties of protein-rich foods, primarily attributed to alterations in protein structures. We provide a comprehensive overview and comparison of commonly used laboratory methods for protein structure identification, aiming to offer readers a convenient understanding of these techniques. The review covers a range of detection technologies employed in food protein analysis and conducts an extensive comparison to identify the most suitable method for various proteins. While these techniques offer distinct advantages for protein structure determination, the inherent complexity of food matrices presents ongoing challenges. Further research is necessary to develop and enhance more robust detection methods to improve accuracy in protein conformation and structure analysis.
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Affiliation(s)
- Tian Lan
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yabo Dong
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lianzhou Jiang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yan Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaonan Sui
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
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3
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Akbari B, Huber BR, Sherman JH. Unlocking the Hidden Depths: Multi-Modal Integration of Imaging Mass Spectrometry-Based and Molecular Imaging Techniques. Crit Rev Anal Chem 2023:1-30. [PMID: 37847593 DOI: 10.1080/10408347.2023.2266838] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Multimodal imaging (MMI) has emerged as a powerful tool in clinical research, combining different imaging modes to acquire comprehensive information and enabling scientists and surgeons to study tissue identification, localization, metabolic activity, and molecular discovery, thus aiding in disease progression analysis. While multimodal instruments are gaining popularity, challenges such as non-standardized characteristics, custom software, inadequate commercial support, and integration issues with other instruments need to be addressed. The field of multimodal imaging or multiplexed imaging allows for simultaneous signal reproduction from multiple imaging strategies. Intraoperatively, MMI can be integrated into frameless stereotactic surgery. Recent developments in medical imaging modalities such as magnetic resonance imaging (MRI), and Positron Emission Topography (PET) have brought new perspectives to multimodal imaging, enabling early cancer detection, molecular tracking, and real-time progression monitoring. Despite the evidence supporting the role of MMI in surgical decision-making, there is a need for comprehensive studies to validate and perform integration at the intersection of multiple imaging technologies. They were integrating mass spectrometry-based technologies (e.g., imaging mass spectrometry (IMS), imaging mass cytometry (IMC), and Ion mobility mass spectrometry ((IM-IM) with medical imaging modalities, offering promising avenues for molecular discovery and clinical applications. This review emphasizes the potential of multi-omics approaches in tissue mapping using MMI integrated into desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI), allowing for sequential analyses of the same section. By addressing existing knowledge gaps, this review encourages future research endeavors toward multi-omics approaches, providing a roadmap for future research and enhancing the value of MMI in molecular pathology for diagnosis.
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Affiliation(s)
- Behnaz Akbari
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Bertrand Russell Huber
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
- Boston University Alzheimer's Disease and CTE Center, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
- US Department of Veteran Affairs, VA Boston Healthcare System, Boston, Massachusetts USA
- US Department of Veterans Affairs, National Center for PTSD, Boston, Massachusetts USA
| | - Janet Hope Sherman
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts, USA
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4
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Radford HM, Toft CJ, Sorenson AE, Schaeffer PM. Inhibition of Replication Fork Formation and Progression: Targeting the Replication Initiation and Primosomal Proteins. Int J Mol Sci 2023; 24:ijms24108802. [PMID: 37240152 DOI: 10.3390/ijms24108802] [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: 03/31/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Over 1.2 million deaths are attributed to multi-drug-resistant (MDR) bacteria each year. Persistence of MDR bacteria is primarily due to the molecular mechanisms that permit fast replication and rapid evolution. As many pathogens continue to build resistance genes, current antibiotic treatments are being rendered useless and the pool of reliable treatments for many MDR-associated diseases is thus shrinking at an alarming rate. In the development of novel antibiotics, DNA replication is still a largely underexplored target. This review summarises critical literature and synthesises our current understanding of DNA replication initiation in bacteria with a particular focus on the utility and applicability of essential initiation proteins as emerging drug targets. A critical evaluation of the specific methods available to examine and screen the most promising replication initiation proteins is provided.
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Affiliation(s)
- Holly M Radford
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Casey J Toft
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Alanna E Sorenson
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Patrick M Schaeffer
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
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5
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Li C, Xiao J, Wu S, Liu L, Zeng X, Zhao Q, Zhang Z. Clinical application of serum-based proteomics technology in human tumor research. Anal Biochem 2023; 663:115031. [PMID: 36580994 DOI: 10.1016/j.ab.2022.115031] [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: 10/28/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 12/27/2022]
Abstract
The rapid development of proteomics technology in the past decades has led to further human understanding of tumor research, and in some ways, the technology plays a very important supporting role in the early detection of tumors. Human serum has been shown to contain a variety of proteins closely related to life activities, and the dynamic change in proteins can often reflect the physiological and pathological conditions of the body. Serum has the advantage of easy extraction, so the application of proteomics technology in serum has become a hot spot and frontier area for the study of malignant tumors. However, there are still many difficulties in the standardized use of proteomic technologies, which inevitably limit the clinical application of proteomic technologies due to the heterogeneity of human proteins leading to incomplete whole proteome populations, in addition to most serum protein markers being now not highly specific in aiding the early detection of tumors. Nevertheless, further development of proteomics technologies will greatly increase our understanding of tumor biology and help discover more new tumor biomarkers with specificity that will enable medical technology.
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Affiliation(s)
- Chen Li
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Juan Xiao
- Department of Otorhinolaryngology, The Second Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Shihua Wu
- Department of Pathology, The Second Hospital of Shaoyang College, Hunan, Shaoyang, 422000, Hunan Province, China
| | - Lu Liu
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Xuemei Zeng
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang, 421001, China
| | - Qiang Zhao
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China.
| | - Zhiwei Zhang
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China; Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang, 421001, China.
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6
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Gopal J, Hua PY, Muthu M, Wu HF. A MALDI-MS-based impact assessment of ZnO nanoparticles, nanorods and quantum dots on the lipid profile of bacterial pathogens. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 15:87-98. [PMID: 36484165 DOI: 10.1039/d2ay01640k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
MALDI-MS was used for studying the impact of zinc oxide (ZnO) nanomaterials on Pseudomonas aeruginosa and Staphylococcus aureus. The growth patterns of both these bacterial pathogens in the presence of the ZnO nanomaterials and the subsequent lipidomic changes were assessed using an optimized simple, rapid MALDI-MS based methodology. All three nanostructures tested exhibited differential bactericidal activity unique to P. aeruginosa and S. aureus. The results indicated that the ZnO nanomaterials were highly inhibitory to S. aureus even at 70 mg L-1, while in the case of P. aeruginosa, the ZnO nanomaterials were compatible for up to 10 h and beyond 10 h only marginal growth inhibition was observed. The results proved that the shapes of the ZnO nanomaterials did not affect their toxicity properties. MALDI-MS was applied to study the lipidomic changes of P. aeruginosa and S. aureus after nanomaterial treatment, in order to throw light on the mechanism of growth inhibition. The results from the MALDI-MS studies showed that the ZnO nanostructures exhibited only marginal changes in the lipidomic profile both in the case of P. aeruginosa and S. aureus. These preliminary results indicate that the mechanism of growth inhibition by the ZnO nanomaterial is not through lipid-based interactions, but apparently more so via protein inhibitions.
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Affiliation(s)
- Judy Gopal
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai 602105, Tamil Nadu, India.
| | - Pei-Yang Hua
- Department of Chemistry, National Sun Yat Sen University, Kaohsiung, 804, Taiwan.
| | - Manikandan Muthu
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai 602105, Tamil Nadu, India.
| | - Hui-Fen Wu
- Department of Chemistry, National Sun Yat Sen University, Kaohsiung, 804, Taiwan.
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 800, Taiwan
- Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
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7
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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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8
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D'Amico CI, Polasky DA, Steyer DJ, Ruotolo BT, Kennedy RT. Ion Mobility-Mass Spectrometry Coupled to Droplet Microfluidics for Rapid Protein Structure Analysis and Drug Discovery. Anal Chem 2022; 94:13084-13091. [PMID: 36098981 DOI: 10.1021/acs.analchem.2c02307] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Native mass spectrometry coupled to ion mobility (IM-MS) has become an important tool for the investigation of protein structure and dynamics upon ligand binding. Additionally, collisional activation or collision induced unfolding (CIU) can further probe conformational changes induced by ligand binding; however, larger scale screens have not been implemented due to limitations associated with throughput and sample introduction. In this work we explore the high-throughput capabilities of CIU fingerprinting. Fingerprint collection times were reduced 10-fold over traditional data collections through the use of improved smoothing and interpolation algorithms. Fast-CIU was then coupled to a droplet sample introduction approach using 40 nL droplet sample volumes and 2 s dwell times at each collision voltage. This workflow, which increased throughput by ∼16-fold over conventional nanospray CIU methods, was applied to a 96-compound screen against Sirtuin-5, a protein target of clinical interest. Over 20 novel Sirtuin-5 binders were identified, and it was found that Sirtuin-5 inhibitors will stabilize specific Sirtuin-5 gas-phase conformations. This work demonstrates that droplet-CIU can be implemented as a high-throughput biophysical characterization approach. Future work will focus on improving the throughput of this workflow and on automating data acquisition and analysis.
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Affiliation(s)
- Cara I D'Amico
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Daniel A Polasky
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Daniel J Steyer
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert T Kennedy
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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9
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Cu and Zn Interactions with Peptides Revealed by High-Resolution Mass Spectrometry. Pharmaceuticals (Basel) 2022; 15:ph15091096. [PMID: 36145317 PMCID: PMC9504920 DOI: 10.3390/ph15091096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/26/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease characterized by abnormal extracellular amyloid-beta (Aβ) peptide depositions in the brain. Among amorphous aggregates, altered metal homeostasis is considered a common risk factor for neurodegeneration known to accelerate plaque formation. Recently, peptide-based drugs capable of inhibiting amyloid aggregation have achieved unprecedented scientific and pharmaceutical interest. In response to metal ions binding to Aβ peptide, metal chelation was also proposed as a therapy in AD. The present study analyzes the interactions formed between NAP octapeptide, derived from activity-dependent neuroprotective protein (ADNP), amyloid Aβ(9–16) fragment and divalent metal ions such as Cu and Zn. The binding affinity studies for Cu and Zn ions of synthetic NAP peptide and Aβ(9–16) fragment were investigated by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), electrospray ion trap mass spectrometry (ESI-MS) and atomic force microscopy (AFM). Both mass spectrometric methods confirmed the formation of metal–peptide complexes while the AFM technique provided morphological and topographic information regarding the influence of metal ions upon peptide crystallization. Our findings showed that due to a rich histidine center, the Aβ(9–16) fragment is capable of binding metal ions, thus becoming stiff and promoting aggregation of the entire amyloid peptide. Apart from this, the protective effect of the NAP peptide was found to rely on the ability of this octapeptide to generate both chelating properties with metals and interactions with Aβ peptide, thus stopping its folding process.
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10
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Lusci G, Pivetta T, Carucci C, Parsons DF, Salis A, Monduzzi M. BSA fragmentation specifically induced by added electrolytes: An electrospray ionization mass spectrometry investigation. Colloids Surf B Biointerfaces 2022; 218:112726. [PMID: 35914467 DOI: 10.1016/j.colsurfb.2022.112726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/16/2022] [Accepted: 07/24/2022] [Indexed: 10/16/2022]
Abstract
Biointerfaces are significantly affected by electrolytes according to the Hofmeister series. This work reports a systematic investigation on the effect of different metal chlorides, sodium and potassium bromides, iodides and thiocyanates, on the ESI/MS spectra of bovine serum albumin (BSA) in aqueous solution at pH = 2.7. The concentration of each salt was varied to maximize the quality of the ESI/MS spectrum, in terms of peak intensity and bell-shaped profile. The ESI/MS spectra of BSA in the absence and in the presence of salts showed a main protein pattern characterized by the expected mass of 66.5 kDa, except the case of BSA/RbCl (mass 65.3 kDa). In all systems we observed an additional pattern, characterized by at least three peaks with low intensity, whose deconvolution led to suggest the formation of a BSA fragment with a mass of 19.2 kDa. Only NaCl increased the intensity of the peaks of the main BSA pattern, while minimizing that of the fragment. NaCl addition seems to play a crucial role in stabilizing the BSA ionized interface against hydrolysis of peptide bonds, through different synergistic mechanisms. To quantify the observed specific electrolyte effects, two "Hofmeister" parameters (Hs and Ps) are proposed. They are obtained using the ratio of (BSA-Salt)/BSA peak intensities for both the BSA main pattern and for its fragment. SYNOPSIS: NaCl stabilizes BSA ion and almost prevents fragmentation due to denaturing pH.
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Affiliation(s)
- Gloria Lusci
- Dept. Chemical and Geological Science, University of Cagliari, Cittadella Universitaria, S.S. 554 bivio Sestu, 09042 Monserrato, Cagliari, Italy
| | - Tiziana Pivetta
- Dept. Chemical and Geological Science, University of Cagliari, Cittadella Universitaria, S.S. 554 bivio Sestu, 09042 Monserrato, Cagliari, Italy
| | - Cristina Carucci
- Dept. Chemical and Geological Science, University of Cagliari, Cittadella Universitaria, S.S. 554 bivio Sestu, 09042 Monserrato, Cagliari, Italy; Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy. Unità Operativa University of Cagliari, Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
| | - Drew Francis Parsons
- Dept. Chemical and Geological Science, University of Cagliari, Cittadella Universitaria, S.S. 554 bivio Sestu, 09042 Monserrato, Cagliari, Italy; Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy. Unità Operativa University of Cagliari, Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy.
| | - Andrea Salis
- Dept. Chemical and Geological Science, University of Cagliari, Cittadella Universitaria, S.S. 554 bivio Sestu, 09042 Monserrato, Cagliari, Italy; Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy. Unità Operativa University of Cagliari, Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy.
| | - Maura Monduzzi
- Dept. Chemical and Geological Science, University of Cagliari, Cittadella Universitaria, S.S. 554 bivio Sestu, 09042 Monserrato, Cagliari, Italy; Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy. Unità Operativa University of Cagliari, Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy.
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11
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Mak T, Rossjohn J, Littler DR, Liu M, Quinn RJ. Collision-Induced Affinity Selection Mass Spectrometry for Identification of Ligands. ACS BIO & MED CHEM AU 2022; 2:450-455. [PMID: 37101899 PMCID: PMC10125361 DOI: 10.1021/acsbiomedchemau.2c00021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hyphenated mass spectrometry has been used to identify ligands binding to proteins. It involves mixing protein and compounds, separation of protein-ligand complexes from unbound compounds, dissociation of the protein-ligand complex, separation to remove protein, and injection of the supernatant into a mass spectrometer to observe the ligand. Here we report collision-induced affinity selection mass spectrometry (CIAS-MS), which allows separation and dissociation inside the instrument. The quadrupole was used to select the ligand-protein complex and allow unbound molecules to be exhausted to vacuum. Collision-induced dissociation (CID) dissociated the protein-ligand complex, and the ion guide and resonance frequency were used to selectively detect the ligand. A known SARS-CoV-2 Nsp9 ligand, oridonin, was successfully detected when it was mixed with Nsp9. We provide proof-of-concept data that the CIAS-MS method can be used to identify binding ligands for any purified protein.
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Affiliation(s)
- Tin Mak
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3168, Australia
| | - Dene R. Littler
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3168, Australia
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
| | - Ronald J. Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
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12
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Hu Q, Chen M, Yan M, Wang P, Lei H, Xue H, Ma Q. Comprehensive analysis of Sini decoction and investigation of acid-base self-assembled complexes using cold spray ionization mass spectrometry. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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13
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Zhu D, Su H, Ke C, Tang C, Witt M, Quinn RJ, Xu Y, Liu J, Ye Y. Efficient discovery of potential inhibitors for SARS-CoV-2 3C-like protease from herbal extracts using a native MS-based affinity-selection method. J Pharm Biomed Anal 2021; 209:114538. [PMID: 34929567 PMCID: PMC8670146 DOI: 10.1016/j.jpba.2021.114538] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022]
Abstract
The 3C-like protease (3CLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to the virus life cycle and is supposed to be a potential target for the treatment of coronaviral infection. Traditional Chinese medicines (TCMs) have played an impressive role in the treatment of COVID-19 in China. The effectiveness of TCM formulations prompts scientists to take continuous effort on searching for bioactive small molecules from the ancient resources. Herein, we developed a native mass spectrometry-based affinity-selection method for rapid screening of active small molecules from crude herbal extracts applied for COVID-19 therapy. Six common herbs named Lonicera japonica, Scutellaria baicalensis, Forsythia suspensa, Glycyrrhiza uralensis, Cirsium japonicum, and Andrographis paniculata were investigated. After preliminary separation of the crude extracts, the fractions were incubated with 3CLpro. A native MS-based affinity screening assay was then conducted to search for the protein-ligand complexes. A UHPLC-Q/TOF-MS with UNIFI data acquisition and data processing software was applied to identify the hit compounds. Standard compounds were used to verify the outcomes. Among the 16 hits, three flavonoids, baicalein, scutellarein and ganhuangenin, were identified as potential noncovalent inhibitors against 3CLpro with IC50 values of 0.94, 3.02, and 0.84 μM, respectively. Their binding affinities were further characterized by native MS, with Kd values being 1.43, 3.85, and 1.09 μM, respectively. Overall, we established an efficient native MS-based strategy for discovering 3CLpro ligands from crude mixtures, which supplies a potential strategy of small molecule lead discovery from TCMs.
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Affiliation(s)
- Dafu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China; State Key Laboratory of Drug Research, and Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Changqiang Ke
- State Key Laboratory of Drug Research, and Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chunping Tang
- State Key Laboratory of Drug Research, and Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Yechun Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310058, China.
| | - Jia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310058, China.
| | - Yang Ye
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China; State Key Laboratory of Drug Research, and Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Hanna GS, Choo YM, Harbit R, Paeth H, Wilde S, Mackle J, Verga JU, Wolf BJ, Thomas OP, Croot P, Cray J, Thomas C, Li LZ, Hardiman G, Hu JF, Wang X, Patel D, Schinazi RF, O’Keefe BR, Hamann MT. Contemporary Approaches to the Discovery and Development of Broad-Spectrum Natural Product Prototypes for the Control of Coronaviruses. JOURNAL OF NATURAL PRODUCTS 2021; 84:3001-3007. [PMID: 34677966 PMCID: PMC8547502 DOI: 10.1021/acs.jnatprod.1c00625] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 05/25/2023]
Abstract
The pressing need for SARS-CoV-2 controls has led to a reassessment of strategies to identify and develop natural product inhibitors of zoonotic, highly virulent, and rapidly emerging viruses. This review article addresses how contemporary approaches involving computational chemistry, natural product (NP) and protein databases, and mass spectrometry (MS) derived target-ligand interaction analysis can be utilized to expedite the interrogation of NP structures while minimizing the time and expense of extraction, purification, and screening in BioSafety Laboratories (BSL)3 laboratories. The unparalleled structural diversity and complexity of NPs is an extraordinary resource for the discovery and development of broad-spectrum inhibitors of viral genera, including Betacoronavirus, which contains MERS, SARS, SARS-CoV-2, and the common cold. There are two key technological advances that have created unique opportunities for the identification of NP prototypes with greater efficiency: (1) the application of structural databases for NPs and target proteins and (2) the application of modern MS techniques to assess protein-ligand interactions directly from NP extracts. These approaches, developed over years, now allow for the identification and isolation of unique antiviral ligands without the immediate need for BSL3 facilities. Overall, the goal is to improve the success rate of NP-based screening by focusing resources on source materials with a higher likelihood of success, while simultaneously providing opportunities for the discovery of novel ligands to selectively target proteins involved in viral infection.
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Affiliation(s)
- George S. Hanna
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Yeun-Mun Choo
- Department of Chemistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Ryan Harbit
- College of Charleston, Charleston, South Carolina 29425, United States
| | - Heather Paeth
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Sarah Wilde
- Department of Biology, Clemson University, Clemson, South Carolina 29631, United States
| | - James Mackle
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Jacopo-Umberto Verga
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Bethany J. Wolf
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Olivier P. Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway, Galway H91Tk33, Ireland
| | - Peter Croot
- Irish Centre for Research in Applied Geoscience, Earth and Ocean Sciences and Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
| | - James Cray
- Department of Biomedical Education and Anatomy, College of Medicine and Division of Biosciences, College of Dentistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Courtney Thomas
- Department of Chemistry, South Carolina State University, Orangeburg, South Carolina, United States
| | - Ling-Zhi Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University/SPU, Shenyang, China
| | - Gary Hardiman
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Jin-Feng Hu
- School of Advanced Study, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang 318000, China
| | - Xiaojuan Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Dharmeshkhumar Patel
- Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine, and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Raymond F. Schinazi
- Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine, and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Barry R. O’Keefe
- Molecular Targets Program, Center for Cancer Research, Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mark T. Hamann
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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15
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Sakallioglu IT, Barletta RG, Dussault PH, Powers R. Deciphering the mechanism of action of antitubercular compounds with metabolomics. Comput Struct Biotechnol J 2021; 19:4284-4299. [PMID: 34429848 PMCID: PMC8358470 DOI: 10.1016/j.csbj.2021.07.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB), one of the oldest and deadliest bacterial diseases, continues to cause serious global economic, health, and social problems. Current TB treatments are lengthy, expensive, and routinely ineffective against emerging drug resistant strains. Thus, there is an urgent need for the identification and development of novel TB drugs possessing comprehensive and specific mechanisms of action (MoAs). Metabolomics is a valuable approach to elucidating the MoA, toxicity, and potency of promising chemical leads, which is a critical step of the drug discovery process. Recent advances in metabolomics methodologies for deciphering MoAs include high-throughput screening techniques, the integration of multiple omics methods, mass spectrometry imaging, and software for automated analysis. This review describes recently introduced metabolomics methodologies and techniques for drug discovery, highlighting specific applications to the discovery of new antitubercular drugs and the elucidation of their MoAs.
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Affiliation(s)
- Isin T. Sakallioglu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska Lincoln, Lincoln, NE 68583-0905, USA
| | - Patrick H. Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
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16
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Gogolashvili A, Lomsadze K, Chankvetadze L, Takaishvili N, Peluso P, Dallocchio R, Salgado A, Chankvetadze B. Separation of tetrahydrozoline enantiomers in capillary electrophoresis with cyclodextrin-type chiral selectors and investigation of chiral recognition mechanisms. J Chromatogr A 2021; 1643:462084. [PMID: 33789195 DOI: 10.1016/j.chroma.2021.462084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022]
Abstract
The recognition power and affinity pattern of various cyclodextrins (CD) towards the enantiomers of tetrahydrozoline (THZ) were studied using capillary electrophoresis (CE). As expected, affinity of THZ enantiomers and selectivity of recognition towards CD derivatives was strongly dependent on the cavity size and substituent type and pattern on the CD rims. Not only were the affinity strength and selectivity of recognition affected by the size of the cavity and chemistry of the CDs but also the affinity pattern. Another interesting example of opposite affinity pattern of enantiomers towards α- and β-CD was observed here. In addition, opposite affinity pattern of THZ enantiomers was seen towards β-CD and its acetylated derivatives, while methylation of β-CD did not affect the affinity pattern of THZ enantiomers. In order to get more information about structural mechanisms of the multivariate dependences mentioned above, rotating frame Overhauser enhancement spectroscopy (ROESY) and computation techniques were used. Significant differences between the structure of THZ complexes with different CDs with both methods were encountered. Good correlations between experimentally determined and computed structure of complexes, as well as between computed complex stabilities and enantiomer migration order (EMO) in CE were observed.
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Affiliation(s)
- Ann Gogolashvili
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, Tbilisi 0179, Georgia
| | - Ketevan Lomsadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, Tbilisi 0179, Georgia; School of Science and Technology, The University of Georgia, 77a, M. Kostava Str., Tbilisi 0171, Georgia
| | - Lali Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, Tbilisi 0179, Georgia
| | - Nino Takaishvili
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, Tbilisi 0179, Georgia
| | - Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondary a di Sassari, Traversa La Crucca 3, Regione Baldinca, Sassari, Li Punti 07100, Italy
| | - Roberto Dallocchio
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondary a di Sassari, Traversa La Crucca 3, Regione Baldinca, Sassari, Li Punti 07100, Italy
| | - Antonio Salgado
- NMR Spectroscopy Centre (CERMN), CAI Químicas, Faculty of Pharmacy, University of Alcalá, Alcalá de Henares, Madrid E-28805, Spain
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, Tbilisi 0179, Georgia.
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17
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Chen X, Wu X, Luan T, Jiang R, Ouyang G. Sample preparation and instrumental methods for illicit drugs in environmental and biological samples: A review. J Chromatogr A 2021; 1640:461961. [PMID: 33582515 DOI: 10.1016/j.chroma.2021.461961] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022]
Abstract
Detection of illicit drugs in the environmental samples has been challenged as the consumption increases globally. Current review examines the recent developments and applications of sample preparation techniques for illicit drugs in solid, liquid, and gas samples. For solid samples, traditional sample preparation methods such as liquid-phase extraction, solid-phase extraction, and the ones with external energy including microwave-assisted, ultrasonic-assisted, and pressurized liquid extraction were commonly used. The sample preparation methods mainly applied for liquid samples were microextraction techniques including solid-phase microextraction, microextraction by packed sorbent, dispersive solid-phase extraction, dispersive liquid-liquid microextraction, hollow fiber-based liquid-phase microextraction, and so on. Capillary microextraction of volatiles and airborne particulate sampling were primarily utilized to extract illicit drugs from gas samples. Besides, the paper introduced recently developed instrumental techniques applied to detect illicit drugs. Liquid chromatograph mass spectrometry and gas chromatograph mass spectrometry were the most widely used methods for illicit drugs samples. In addition, the development of ambient mass spectrometry techniques, such as desorption electrospray ionization mass spectrometry and paper spray mass spectrometry, created potential for rapid in-situ analysis.
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Affiliation(s)
- Xinlv Chen
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Xinyan Wu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Tiangang Luan
- Guangdong Provincial Key Laboratory of Psychoactive Substances Monitoring and safety, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, 100 Waihuanxi Road, Guangzhou 510006, China
| | - Ruifen Jiang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China.
| | - Gangfeng Ouyang
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis (China National Analytical Center Guangzhou), Guangzhou, 510070, China; Chemistry College, Center of Advanced Analysis and Gene Sequencing, Zhengzhou University, Kexue Avenue 100, Zhengzhou 450001, China.
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18
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Development of a target identification approach using native mass spectrometry. Sci Rep 2021; 11:2387. [PMID: 33504855 PMCID: PMC7840913 DOI: 10.1038/s41598-021-81859-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
A key step in the development of new pharmaceutical drugs is the identification of the molecular target and distinguishing this from all other gene products that respond indirectly to the drug. Target identification remains a crucial process and a current bottleneck for advancing hits through the discovery pipeline. Here we report a method, that takes advantage of the specific detection of protein-ligand complexes by native mass spectrometry (MS) to probe the protein partner of a ligand in an untargeted method. The key advantage is that it uses unmodified small molecules for binding and, thereby, it does not require labelled ligands and is not limited by the chemistry required to tag the molecule. We demonstrate the use of native MS to identify known ligand-protein interactions in a protein mixture under various experimental conditions. A protein-ligand complex was successfully detected between parthenolide and thioredoxin (PfTrx) in a five-protein mixture, as well as when parthenolide was mixed in a bacterial cell lysate spiked with PfTrx. We provide preliminary data that native MS could be used to identify binding targets for any small molecule.
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19
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Wilkinson IVL, Terstappen GC, Russell AJ. Combining experimental strategies for successful target deconvolution. Drug Discov Today 2020; 25:S1359-6446(20)30373-1. [PMID: 32971235 DOI: 10.1016/j.drudis.2020.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/10/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Investment in phenotypic drug discovery has led to increased demand for rapid and robust target deconvolution to aid successful drug development. Although methods for target identification and mechanism of action (MoA) discovery are flourishing, they typically lead to lists of putative targets. Validating which target(s) are involved in the therapeutic mechanism of a compound poses a significant challenge, requiring direct binding, target engagement, and functional studies in relevant physiological contexts. A combination of orthogonal approaches can allow target identification beyond the proteome as well as aid prioritisation for resource-intensive target validation studies.
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Affiliation(s)
- Isabel V L Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Georg C Terstappen
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK.
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20
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Probing the mechanisms of inhibition for various inhibitors of metallo-β-lactamases VIM-2 and NDM-1. J Inorg Biochem 2020; 210:111123. [PMID: 32622213 DOI: 10.1016/j.jinorgbio.2020.111123] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
To probe the mechanism of inhibition of several previously-published metallo-β-lactamase (MBL) inhibitors for the clinically-important MBL Verona integron-encoded metallo-β-lactamase 2 (VIM-2), equilibrium dialyses with metal analyses, native state electrospray ionization mass spectrometry (ESI-MS), and UV-Vis spectrophotometry were utilized. The mechanisms of inhibition were analyzed for ethylenediaminetetraacetic acid (EDTA); dipicolinic acid (DPA) and DPA analogs 6-(1H-tetrazol-5-yl)picolinic acid (1T5PA) and 4-(3-aminophenyl)pyridine-2,6-dicarboxylic acid (3AP-DPA); thiol-containing compounds, 2,3-dimercaprol, thiorphan, captopril, and tiopronin; and 5-(pyridine-3-sulfonamido)-1,3-thiazole-4-carboxylic acid (ANT-431). UV-Vis spectroscopy and native-state ESI-MS results showed the formation of ternary complexes between VIM-2 and 1T5PA, ANT-431, thiorphan, captopril, and tiopronin, while a metal stripping mechanism was shown with VIM-2 and EDTA and DPA. The same approaches were used to show the formation of a ternary complex between New Delhi Metallo-β-lactamase (NDM-1) and ANT-431. The studies presented herein show that most of the inhibitors utilize a similar mechanism of inhibition as previously reported for NDM-1. These studies also demonstrate that native mass spectrometry can be used to probe the mechanism of inhibition at lower enzyme/inhibitor concentrations than has previously been achieved.
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21
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Multi-instrumental approach to unravel molecular mechanisms of natural bioactive compounds: Case studies for flavonoids. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115865] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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