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Stincone P, Naimi A, Saviola AJ, Reher R, Petras D. Decoding the molecular interplay in the central dogma: An overview of mass spectrometry-based methods to investigate protein-metabolite interactions. Proteomics 2024; 24:e2200533. [PMID: 37929699 DOI: 10.1002/pmic.202200533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
With the emergence of next-generation nucleotide sequencing and mass spectrometry-based proteomics and metabolomics tools, we have comprehensive and scalable methods to analyze the genes, transcripts, proteins, and metabolites of a multitude of biological systems. Despite the fascinating new molecular insights at the genome, transcriptome, proteome and metabolome scale, we are still far from fully understanding cellular organization, cell cycles and biology at the molecular level. Significant advances in sensitivity and depth for both sequencing as well as mass spectrometry-based methods allow the analysis at the single cell and single molecule level. At the same time, new tools are emerging that enable the investigation of molecular interactions throughout the central dogma of molecular biology. In this review, we provide an overview of established and recently developed mass spectrometry-based tools to probe metabolite-protein interactions-from individual interaction pairs to interactions at the proteome-metabolome scale.
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Affiliation(s)
- Paolo Stincone
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of Tuebingen, Center for Plant Molecular Biology, Tuebingen, Germany
| | - Amira Naimi
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | | | - Raphael Reher
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | - Daniel Petras
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of California Riverside, Department of Biochemistry, Riverside, USA
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2
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Tomoya K, Komiya K, Nakajima D, Umekubo N, Yokoshima S. Total Synthesis of Kopsone. Org Lett 2023; 25:2718-2721. [PMID: 37036762 DOI: 10.1021/acs.orglett.3c00838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
A total synthesis of kopsone was achieved, featuring stereoselective preparation of an acyclic aldehyde having a protected hydroxylamine moiety via Ireland-Claisen rearrangement and intramolecular cycloaddition of an eight-membered cyclic nitrone to form the 2-azabicyclo[3.3.1]nonane skeleton.
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Affiliation(s)
- Kazutoshi Tomoya
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Kazuaki Komiya
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Daisuke Nakajima
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Nariyoshi Umekubo
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Satoshi Yokoshima
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
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3
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Dekker T, Harteveld JW, Wágner G, de Vries MCM, Custers H, van de Stolpe AC, de Esch IJP, Wijtmans M. Green Drug Discovery: Novel Fragment Space from the Biomass-Derived Molecule Dihydrolevoglucosenone (Cyrene TM). Molecules 2023; 28:molecules28041777. [PMID: 36838763 PMCID: PMC9967789 DOI: 10.3390/molecules28041777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Biomass-derived molecules can provide a basis for sustainable drug discovery. However, their full exploration is hampered by the dominance of millions of old-fashioned screening compounds in classical high-throughput screening (HTS) libraries frequently utilized. We propose a fragment-based drug discovery (FBDD) approach as an efficient method to navigate biomass-derived drug space. Here, we perform a proof-of-concept study with dihydrolevoglucosenone (CyreneTM), a pyrolysis product of cellulose. Diverse synthetic routes afforded a 100-membered fragment library with a diversity in functional groups appended. The library overall performs well in terms of novelty, physicochemical properties, aqueous solubility, stability, and three-dimensionality. Our study suggests that Cyrene-based fragments are a valuable green addition to the drug discovery toolbox. Our findings can help in paving the way for new hit drug candidates that are based on renewable resources.
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4
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Zothantluanga JH, Umar AK, Lalhlenmawia H, Vinayagam S, Borthakur MS, Patowary L, Tayeng D. Computational screening of phytochemicals for anti-parasitic drug discovery. PHYTOCHEMISTRY, COMPUTATIONAL TOOLS AND DATABASES IN DRUG DISCOVERY 2023:257-283. [DOI: 10.1016/b978-0-323-90593-0.00005-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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5
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Moinul M, Khatun S, Amin SA, Jha T, Gayen S. Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review. Biochem Pharmacol 2022; 206:115301. [DOI: 10.1016/j.bcp.2022.115301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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6
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Ji X, Li J, Sharma PP, Jiang X, Rathi B, Gao Z, Hu L, Kang D, De Clercq E, Cocklin S, Liu C, Pannecouque C, Dick A, Liu X, Zhan P. Design, Synthesis and Structure-Activity Relationships of Phenylalanine-Containing Peptidomimetics as Novel HIV-1 Capsid Binders Based on Ugi Four-Component Reaction. Molecules 2022; 27:molecules27185995. [PMID: 36144727 PMCID: PMC9502897 DOI: 10.3390/molecules27185995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
As a key structural protein, HIV capsid (CA) protein plays multiple roles in the HIV life cycle, and is considered a promising target for anti-HIV treatment. Based on the structural information of CA modulator PF-74 bound to HIV-1 CA hexamer, 18 novel phenylalanine derivatives were synthesized via the Ugi four-component reaction. In vitro anti-HIV activity assays showed that most compounds exhibited low-micromolar-inhibitory potency against HIV. Among them, compound I-19 exhibited the best anti-HIV-1 activity (EC50 = 2.53 ± 0.84 μM, CC50 = 107.61 ± 27.43 μM). In addition, I-14 displayed excellent HIV-2 inhibitory activity (EC50 = 2.30 ± 0.11 μM, CC50 > 189.32 μM) with relatively low cytotoxicity, being more potent than that of the approved drug nevirapine (EC50 > 15.02 μM, CC50 > 15.2 μM). Additionally, surface plasmon resonance (SPR) binding assays demonstrated direct binding to the HIV CA protein. Moreover, molecular docking and molecular dynamics simulations provided additional information on the binding mode of I-19 to HIV-1 CA. In summary, we further explored the structure—activity relationships (SARs) and selectivity of anti-HIV-1/HIV-2 of PF-74 derivatives, which is conducive to discovering efficient anti-HIV drugs.
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Affiliation(s)
- Xiangkai Ji
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Jing Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Prem Prakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Zhen Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Lide Hu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapym, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19104, USA
| | - Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapym, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19104, USA
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
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7
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Willis N, Mahy W, Sipthorp J, Zhao Y, Woodward HL, Atkinson BN, Bayle ED, Svensson F, Frew S, Jeganathan F, Monaghan A, Benvegnù S, Jolly S, Vecchia L, Ruza RR, Kjær S, Howell S, Snijders AP, Bictash M, Salinas PC, Vincent JP, Jones EY, Whiting P, Fish PV. Design of a Potent, Selective, and Brain-Penetrant Inhibitor of Wnt-Deactivating Enzyme Notum by Optimization of a Crystallographic Fragment Hit. J Med Chem 2022; 65:7212-7230. [PMID: 35536179 PMCID: PMC9150124 DOI: 10.1021/acs.jmedchem.2c00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 12/26/2022]
Abstract
Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human diseases such as colorectal cancer and Alzheimer's disease, supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we have described the discovery and profile of 8l (ARUK3001185) as a potent, selective, and brain-penetrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identified 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases, and drug targets.
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Affiliation(s)
- Nicky
J. Willis
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - William Mahy
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - James Sipthorp
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Yuguang Zhao
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Hannah L. Woodward
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Benjamin N. Atkinson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Elliott D. Bayle
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Sarah Frew
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Fiona Jeganathan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Amy Monaghan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Stefano Benvegnù
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Sarah Jolly
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Luca Vecchia
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Reinis R. Ruza
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Svend Kjær
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Steven Howell
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | | | - Magda Bictash
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Patricia C. Salinas
- Department
of Cell and Developmental Biology, Laboratory for Molecular and Cellular
Biology, University College London, London WC1E 6BT, U.K.
| | - Jean-Paul Vincent
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - E. Yvonne Jones
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Paul Whiting
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
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8
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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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9
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Chavda VP, Ertas YN, Walhekar V, Modh D, Doshi A, Shah N, Anand K, Chhabria M. Advanced Computational Methodologies Used in the Discovery of New Natural Anticancer Compounds. Front Pharmacol 2021; 12:702611. [PMID: 34483905 PMCID: PMC8416109 DOI: 10.3389/fphar.2021.702611] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Natural chemical compounds have been widely investigated for their programmed necrosis causing characteristics. One of the conventional methods for screening such compounds is the use of concentrated plant extracts without isolation of active moieties for understanding pharmacological activity. For the last two decades, modern medicine has relied mainly on the isolation and purification of one or two complicated active and isomeric compounds. The idea of multi-target drugs has advanced rapidly and impressively from an innovative model when first proposed in the early 2000s to one of the popular trends for drug development in 2021. Alternatively, fragment-based drug discovery is also explored in identifying target-based drug discovery for potent natural anticancer agents which is based on well-defined fragments opposite to use of naturally occurring mixtures. This review summarizes the current key advancements in natural anticancer compounds; computer-assisted/fragment-based structural elucidation and a multi-target approach for the exploration of natural compounds.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad, India
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey.,ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey
| | - Vinayak Walhekar
- Department of Medicinal Chemistry, Bharati Vidyapeeth's Poona College of Pharmacy, Pune, India
| | - Dharti Modh
- Department of Medicinal Chemistry, Bharati Vidyapeeth's Poona College of Pharmacy, Pune, India
| | - Avani Doshi
- Department of Chemistry, SAL Institute of Pharmacy, Ahmedabad, India
| | - Nirav Shah
- Department of Pharmaceutics, SAL Institute of Pharmacy, Ahmedabad, India
| | - Krishna Anand
- Faculty of Health Sciences and National Health Laboratory Service, Department of Chemical Pathology, School of Pathology, University of the Free State, Bloemfontein, South Africa
| | - Mahesh Chhabria
- Department of Pharmaceutical Chemistry, L.M. College of Pharmacy, Ahmedabad, India
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10
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Hoarau M, Vanichtanankul J, Srimongkolpithak N, Vitsupakorn D, Yuthavong Y, Kamchonwongpaisan S. Discovery of new non-pyrimidine scaffolds as Plasmodium falciparum DHFR inhibitors by fragment-based screening. J Enzyme Inhib Med Chem 2021; 36:198-206. [PMID: 33530764 PMCID: PMC8759724 DOI: 10.1080/14756366.2020.1854244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In various malaria-endemic regions, the appearance of resistance has precluded the use of pyrimidine-based antifolate drugs. Here, a three-step fragment screening was used to identify new non-pyrimidine Plasmodium falciparum dihydrofolate reductase (PfDHFR) inhibitors. Starting from a 1163-fragment commercial library, a two-step differential scanning fluorimetry screen identified 75 primary fragment hits. Subsequent enzyme inhibition assay identified 11 fragments displaying IC50 in the 28-695 μM range and selectivity for PfDHFR. In addition to the known pyrimidine, three new anti-PfDHFR chemotypes were identified. Fragments from each chemotype were successfully co-crystallized with PfDHFR, revealing a binding in the active site, in the vicinity of catalytic residues, which was confirmed by molecular docking on all fragment hits. Finally, comparison with similar non-hit fragments provides preliminary input on available growth vectors for future drug development.
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Affiliation(s)
- Marie Hoarau
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Nitipol Srimongkolpithak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Danoo Vitsupakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
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11
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Feature-Based Molecular Network-Guided Dereplication of Natural Bioactive Products from Leaves of Stryphnodendron pulcherrimum (Willd.) Hochr. Metabolites 2021; 11:metabo11050281. [PMID: 33946668 PMCID: PMC8147077 DOI: 10.3390/metabo11050281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Stryphnodendron pulcherrimum is a species known to have a high content of tannins. Accordingly, its preparations are used in southern Pará, Brazil, for their anti-inflammatory and antimicrobial activities, but so far, its chemical profile composition remains essentially unknown. We herein describe the compounds present in a hydro-acetonic extract from S. pulcherrimum leaves as revealed by dereplication via ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry. The data were combined with spectral organization, spectral matching through the Global Natural Products Social platform, in silico annotation and taxonomical ponderation. Several types of phenolic compounds were identified such as gallic acids, flavan-3-ols and flavone-like compounds. From these, 5 have been recently reported by our group, whereas 44 are reported here for the first time in this tree species, and 41 (out of 49) for this genus. The results highlight the possible role of Stryphnodendron pulcherrimum as a renewable source for natural bioactive products with potential pharmaceutical applications.
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12
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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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Chachulski L, Windshügel B. LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance. J Chem Inf Model 2020; 60:6544-6554. [PMID: 33289563 DOI: 10.1021/acs.jcim.0c00693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fragment-based drug design is a popular approach in drug discovery, which makes use of computational methods such as molecular docking. To assess fragment placement performance of molecular docking programs, we constructed LEADS-FRAG, a benchmark data set containing 93 high-quality protein-fragment complexes that were selected from the Protein Data Bank using a rational and unbiased process. The data set contains fully prepared protein and fragment structures and is publicly available. Moreover, we used LEADS-FRAG for evaluating the small-molecule docking programs AutoDock, AutoDock Vina, FlexX, and GOLD for their fragment docking performance. GOLD in combination with the scoring function ChemPLP and AutoDock Vina performed best and generated near-native conformations (root mean square deviation <1.5 Å) for more than 50% of the data set considering the top-ranked docking pose. Taking into account all docking poses, the tested programs generated near-native conformations for up to 86% of the fragments in LEADS-FRAG. By rescoring all docking poses with the GOLD scoring functions and the Protein-Ligand Informatics force field, the number of near-native conformations increased up to 40% with respect to the top-rescored poses. Our results show that conventional small-molecule docking programs achieve a satisfactory fragment docking performance when utilizing rescoring.
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Affiliation(s)
- Laura Chachulski
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, ScreeningPort, Hamburg 22525, Germany.,Jacobs University Bremen gGmbH, Bremen 28759, Germany
| | - Björn Windshügel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, ScreeningPort, Hamburg 22525, Germany.,Institute for Biochemistry and Molecular Biology, Department of Chemistry, Universität Hamburg, Hamburg 20146, Germany
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Jiang X, Huang B, Olotu FA, Li J, Kang D, Wang Z, De Clercq E, Soliman MES, Pannecouque C, Liu X, Zhan P. Exploiting the tolerant region I of the non-nucleoside reverse transcriptase inhibitor (NNRTI) binding pocket. Part 2: Discovery of diarylpyrimidine derivatives as potent HIV-1 NNRTIs with high Fsp 3 values and favorable drug-like properties. Eur J Med Chem 2020; 213:113051. [PMID: 33279288 DOI: 10.1016/j.ejmech.2020.113051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 01/18/2023]
Abstract
To yield potent HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) with favorable drug-like properties, a series of novel diarylpyrimidine derivatives targeting the tolerant region I of the NNRTI binding pocket were designed, synthesized and biologically evaluated. The most active inhibitor 10c exhibited outstanding antiviral activity against most of the viral panel, being about 2-fold (wild-type, EC50 = 0.0021 μM), 1.7-fold (K103N, EC50 = 0.0019 μM), and slightly more potent (E138K, EC50 = 0.0075 μM) than the NNRTI drug etravirine (ETR). Additionally, 10c was endowed with relatively low cytotoxicity (CC50 = 18.52 μM). More importantly, 10c possessed improved drug-like properties compared to those of ETR with an increased Fsp3 (Fraction of sp3 carbon atoms) value. Furthermore, the molecular dynamics simulation and molecular docking studies were implemented to reveal the binding mode of 10c in the binding pocket. Taken together, 10c is a promising lead compound that is worth further investigation.
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Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Boshi Huang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Jing Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Leuven, B-3000, Belgium
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Leuven, B-3000, Belgium.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong, Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012, Ji'nan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong, Province, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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Tunstall T, Portelli S, Phelan J, Clark TG, Ascher DB, Furnham N. Combining structure and genomics to understand antimicrobial resistance. Comput Struct Biotechnol J 2020; 18:3377-3394. [PMID: 33294134 PMCID: PMC7683289 DOI: 10.1016/j.csbj.2020.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobials against bacterial, viral and parasitic pathogens have transformed human and animal health. Nevertheless, their widespread use (and misuse) has led to the emergence of antimicrobial resistance (AMR) which poses a potentially catastrophic threat to public health and animal husbandry. There are several routes, both intrinsic and acquired, by which AMR can develop. One major route is through non-synonymous single nucleotide polymorphisms (nsSNPs) in coding regions. Large scale genomic studies using high-throughput sequencing data have provided powerful new ways to rapidly detect and respond to such genetic mutations linked to AMR. However, these studies are limited in their mechanistic insight. Computational tools can rapidly and inexpensively evaluate the effect of mutations on protein function and evolution. Subsequent insights can then inform experimental studies, and direct existing or new computational methods. Here we review a range of sequence and structure-based computational tools, focussing on tools successfully used to investigate mutational effect on drug targets in clinically important pathogens, particularly Mycobacterium tuberculosis. Combining genomic results with the biophysical effects of mutations can help reveal the molecular basis and consequences of resistance development. Furthermore, we summarise how the application of such a mechanistic understanding of drug resistance can be applied to limit the impact of AMR.
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Affiliation(s)
- Tanushree Tunstall
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Stephanie Portelli
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - David B. Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Combined Protein- and Ligand-Observed NMR Workflow to Screen Fragment Cocktails against Multiple Proteins: A Case Study Using Bromodomains. Molecules 2020; 25:molecules25173949. [PMID: 32872491 PMCID: PMC7504435 DOI: 10.3390/molecules25173949] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
As fragment-based drug discovery has become mainstream, there has been an increase in various screening methodologies. Protein-observed 19F (PrOF) NMR and 1H CPMG NMR are two fragment screening assays that have complementary advantages. Here, we sought to combine these two NMR-based assays into a new screening workflow. This combination of protein- and ligand-observed experiments allows for a time- and resource-efficient multiplexed screen of mixtures of fragments and proteins. PrOF NMR is first used to screen mixtures against two proteins. Hit mixtures for each protein are identified then deconvoluted using 1H CPMG NMR. We demonstrate the benefit of this fragment screening method by conducting the first reported fragment screens against the bromodomains of BPTF and Plasmodium falciparum (Pf) GCN5 using 467 3D-enriched fragments. The hit rates were 6%, 5% and 4% for fragments binding BPTF, PfGCN5, and fragments binding both proteins, respectively. Select hits were characterized, revealing a broad range of affinities from low µM to mM dissociation constants. Follow-up experiments supported a low-affinity second binding site on PfGCN5. This approach can be used to bias fragment screens towards more selective hits at the onset of inhibitor development in a resource- and time-efficient manner.
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Kirsch P, Hartman AM, Hirsch AKH, Empting M. Concepts and Core Principles of Fragment-Based Drug Design. Molecules 2019; 24:molecules24234309. [PMID: 31779114 PMCID: PMC6930586 DOI: 10.3390/molecules24234309] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/11/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
In this review, a general introduction to fragment-based drug design and the underlying concepts is given. General considerations and methodologies ranging from library selection/construction over biophysical screening and evaluation methods to in-depth hit qualification and subsequent optimization strategies are discussed. These principles can be generally applied to most classes of drug targets. The examples given for fragment growing, merging, and linking strategies at the end of the review are set in the fields of enzyme-inhibitor design and macromolecule–macromolecule interaction inhibition. Building upon the foundation of fragment-based drug discovery (FBDD) and its methodologies, we also highlight a few new trends in FBDD.
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Affiliation(s)
- Philine Kirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
| | - Alwin M. Hartman
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-988-062-031
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