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Li Q, Zhou SR, Kim H, Wang H, Zhu JJ, Yang JK. Discovering novel Cathepsin L inhibitors from natural products using artificial intelligence. Comput Struct Biotechnol J 2024; 23:2606-2614. [PMID: 39006920 PMCID: PMC11245987 DOI: 10.1016/j.csbj.2024.06.009] [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: 02/05/2024] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 07/16/2024] Open
Abstract
Cathepsin L (CTSL) is a promising therapeutic target for metabolic disorders. Current pharmacological interventions targeting CTSL have demonstrated potential in reducing body weight gain, serum insulin levels, and improving glucose tolerance. However, the clinical application of CTSL inhibitors remains limited. In this study, we used a combination of artificial intelligence and experimental methods to identify new CTSL inhibitors from natural products. Through a robust deep learning model and molecular docking, we screened 150 molecules from natural products for experimental validation. At a concentration of 100 µM, we found that 36 of them exhibited more than 50 % inhibition of CTSL. Notably, 13 molecules displayed over 90 % inhibition and exhibiting concentration-dependent effects. The molecular dynamics simulation on the two most potent inhibitors, Plumbagin and Beta-Lapachone, demonstrated stable interaction at the CTSL active site. Enzyme kinetics studies have shown that these inhibitors exert an uncompetitive inhibitory effect on CTSL. In conclusion, our research identifies Plumbagin and Beta-Lapachone as potential CTSL inhibitors, offering promising candidates for the treatment of metabolic disorders and illustrating the effectiveness of artificial intelligence in drug discovery.
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Affiliation(s)
- Qi Li
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Si-Rui Zhou
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Hanna Kim
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Hao Wang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Juan-Juan Zhu
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Jin-Kui Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
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2
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Park JY, Park KM. Recent discovery of natural substances with cathepsin L-inhibitory activity for cancer metastasis suppression. Eur J Med Chem 2024; 277:116754. [PMID: 39128327 DOI: 10.1016/j.ejmech.2024.116754] [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: 07/02/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Cathepsin L (CTSL), a cysteine cathepsin protease of the papain superfamily, plays a crucial role in cancer progression and metastasis. Dysregulation of CTSL is frequently observed in tumor malignancies, leading to the degradation of extracellular matrix and facilitating epithelial-mesenchymal transition (EMT), a key process in malignant cancer metastasis. This review mainly provides a comprehensive information about recent findings on natural inhibitors targeting CTSL and their anticancer effects, which have emerged as potent anticancer therapeutic agents or metastasis-suppressive adjuvants. Specifically, inhibitors are categorized into small-molecule and macromolecule inhibitors, with a particular emphasis on cathepsin propeptide-type macromolecules. Additionally, the article explores the molecular mechanisms of CTSL involvement in cancer metastasis, highlighting its regulation at transcriptional, translational, post-translational, and epigenetic levels. This work underscores the importance of understanding natural CTSL inhibitors and provides researchers with practical insights to advance the relevant fields and discover novel CTSL-targeting inhibitors from natural sources.
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Affiliation(s)
- Jun-Young Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyung-Min Park
- Department of Food Science and Biotechnology, Wonkwang University, Iksan, 54538, Republic of Korea.
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3
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Li Z, Yang Y, Gao F. Monomeric compounds from natural products for the treatment of pulmonary fibrosis: a review. Inflammopharmacology 2024; 32:2203-2217. [PMID: 38724690 DOI: 10.1007/s10787-024-01485-0] [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: 01/09/2024] [Accepted: 04/23/2024] [Indexed: 08/06/2024]
Abstract
Pulmonary fibrosis (PF) is the end stage of lung injury and chronic lung diseases that results in diminished lung function, respiratory failure, and ultimately mortality. Despite extensive research, the pathogenesis of this disease remains elusive, and effective therapeutic options are currently limited, posing a significant clinical challenge. In addition, research on traditional Chinese medicine and naturopathic medicine is hampered by several complications due to complex composition and lack of reference compounds. Natural product monomers, possessing diverse biological activities and excellent safety profiles, have emerged as potential candidates for preventing and treating PF. The effective anti-PF ingredients identified can be generally divided into flavonoids, saponins, polysaccharides, and alkaloids. Specifically, these monomeric compounds can attenuate inflammatory response, oxidative stress, and other physiopathological processes of the lung through many signaling pathways. They also improve pulmonary factors. Additionally, they ameliorate epithelial-mesenchymal transition (EMT) and fibroblast-myofibroblast transdifferentiation (FMT) by regulating multiple signal amplifiers in the lungs, thereby mitigating PF. This review highlights the significant role of monomer compounds derived from natural products in reducing inflammation, oxidative stress, and inhibiting EMT process. The article provides comprehensive information and serves as a solid foundation for further exploration of new strategies to harness the potential of botanicals in the treatment of PF.
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Affiliation(s)
- Zhuqing Li
- University of Shanghai for Science and Technology, 516, Jungong Road, Shanghai, 200093, China
| | - Yanyong Yang
- Basic Medical Center for Pulmonary Disease, Naval Medical University, 800, Xiangyin Road, Shanghai, 200433, China.
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, Shanghai, 200433, People's Republic of China.
| | - Fu Gao
- University of Shanghai for Science and Technology, 516, Jungong Road, Shanghai, 200093, China.
- Basic Medical Center for Pulmonary Disease, Naval Medical University, 800, Xiangyin Road, Shanghai, 200433, China.
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, Shanghai, 200433, People's Republic of China.
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4
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Kim Y, Kim Y, Lim HJ, Kim DK, Park JH, Oh CM. Integrative single-cell transcriptome analysis provides new insights into post-COVID-19 pulmonary fibrosis and potential therapeutic targets. J Med Virol 2023; 95:e29201. [PMID: 37966390 DOI: 10.1002/jmv.29201] [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: 07/26/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
The global COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 virus has resulted in a significant number of patients experiencing persistent symptoms, including post-COVID pulmonary fibrosis (PCPF). This study aimed to identify novel therapeutic targets for PCPF using single-cell RNA-sequencing data from lung tissues of COVID-19 patients, idiopathic pulmonary fibrosis (IPF) patients, and a rat transforming growth factor beta-1-induced fibrosis model treated with antifibrotic drugs. Patients with COVID-19 had lower alveolar macrophage counts than healthy controls, whereas patients with COVID-19 and IPF presented with elevated monocyte-derived macrophage counts. A comparative transcriptome analysis showed that macrophages play a crucial role in IPF and COVID-19 development and progression, and fibrosis- and inflammation-associated genes were upregulated in both conditions. Functional enrichment analysis revealed the upregulation of inflammation and proteolysis and the downregulation of ribosome biogenesis. Cholesterol efflux and glycolysis were augmented in both macrophage types. The study suggests that antifibrotic drugs may reverse critical lung fibrosis mediators in COVID-19. The results help clarify the molecular mechanisms underlying pulmonary fibrosis in patients with severe COVID-19 and IPF and highlight the potential efficacy of antifibrotic drugs in COVID-19 therapy. Collectively, all these findings may have significant implications for the development of new treatment strategies for PCPF.
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Affiliation(s)
- Yumin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Yeongmin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Hyobin Julianne Lim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Dae-Kyum Kim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ji-Hwan Park
- Korea Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Chang-Myung Oh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
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Sukumaran S, Zochedh A, Viswanathan TM, Sultan AB, Kathiresan T. Theoretical Investigation of 5-Fluorouracil and Tamoxifen Complex – Structural, Spectrum, DFT, ADMET and Docking Simulation. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2022.2164018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sureba Sukumaran
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Azar Zochedh
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Thimma Mohan Viswanathan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Asath Bahadur Sultan
- Department of Physics, Condensed Matter Physics Laboratory, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Thandavarayan Kathiresan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
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Biasizzo M, Javoršek U, Vidak E, Zarić M, Turk B. Cysteine cathepsins: A long and winding road towards clinics. Mol Aspects Med 2022; 88:101150. [PMID: 36283280 DOI: 10.1016/j.mam.2022.101150] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 12/03/2022]
Abstract
Biomedical research often focuses on properties that differentiate between diseased and healthy tissue; one of the current focuses is elevated expression and altered localisation of proteases. Among these proteases, dysregulation of cysteine cathepsins can frequently be observed in inflammation-associated diseases, which tips the functional balance from normal physiological to pathological manifestations. Their overexpression and secretion regularly exhibit a strong correlation with the development and progression of such diseases, making them attractive pharmacological targets. But beyond their mostly detrimental role in inflammation-associated diseases, cysteine cathepsins are physiologically highly important enzymes involved in various biological processes crucial for maintaining homeostasis and responding to different stimuli. Consequently, several challenges have emerged during the efforts made to translate basic research data into clinical applications. In this review, we present both physiological and pathological roles of cysteine cathepsins and discuss the clinical potential of cysteine cathepsin-targeting strategies for disease management and diagnosis.
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Affiliation(s)
- Monika Biasizzo
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Urban Javoršek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Eva Vidak
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Miki Zarić
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000, Ljubljana, Slovenia.
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7
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Braccia C, Christopher JA, Crook OM, Breckels LM, Queiroz RML, Liessi N, Tomati V, Capurro V, Bandiera T, Baldassari S, Pedemonte N, Lilley KS, Armirotti A. CFTR Rescue by Lumacaftor (VX-809) Induces an Extensive Reorganization of Mitochondria in the Cystic Fibrosis Bronchial Epithelium. Cells 2022; 11:1938. [PMID: 35741067 PMCID: PMC9222197 DOI: 10.3390/cells11121938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/12/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cystic Fibrosis (CF) is a genetic disorder affecting around 1 in every 3000 newborns. In the most common mutation, F508del, the defective anion channel, CFTR, is prevented from reaching the plasma membrane (PM) by the quality check control of the cell. Little is known about how CFTR pharmacological rescue impacts the cell proteome. METHODS We used high-resolution mass spectrometry, differential ultracentrifugation, machine learning and bioinformatics to investigate both changes in the expression and localization of the human bronchial epithelium CF model (F508del-CFTR CFBE41o-) proteome following treatment with VX-809 (Lumacaftor), a drug able to improve the trafficking of CFTR. RESULTS The data suggested no stark changes in protein expression, yet subtle localization changes of proteins of the mitochondria and peroxisomes were detected. We then used high-content confocal microscopy to further investigate the morphological and compositional changes of peroxisomes and mitochondria under these conditions, as well as in patient-derived primary cells. We profiled several thousand proteins and we determined the subcellular localization data for around 5000 of them using the LOPIT-DC spatial proteomics protocol. CONCLUSIONS We observed that treatment with VX-809 induces extensive structural and functional remodelling of mitochondria and peroxisomes that resemble the phenotype of healthy cells. Our data suggest additional rescue mechanisms of VX-809 beyond the correction of aberrant folding of F508del-CFTR and subsequent trafficking to the PM.
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Affiliation(s)
- Clarissa Braccia
- D3 PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (C.B.); (T.B.)
| | - Josie A. Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
| | - Oliver M. Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
- Department of Statistics, University of Oxford, 29 St Giles’, Oxford OX1 3LB, UK
| | - Lisa M. Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
| | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
| | - Nara Liessi
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (V.T.); (V.C.); (S.B.)
| | - Valeria Capurro
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (V.T.); (V.C.); (S.B.)
| | - Tiziano Bandiera
- D3 PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy; (C.B.); (T.B.)
| | - Simona Baldassari
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (V.T.); (V.C.); (S.B.)
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (V.T.); (V.C.); (S.B.)
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; (J.A.C.); (O.M.C.); (L.M.B.); (R.M.L.Q.)
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
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8
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Santiago C, Jiménez-Aberasturi X, Leicea E, Lete MG, Sotomayor N, Lete E. Microwave-assisted palladium catalysed C-H acylation with aldehydes: synthesis and diversification of 3-acylthiophenes. Org Biomol Chem 2022; 20:852-861. [PMID: 35001098 DOI: 10.1039/d1ob02176a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of MW allows the efficient palladium(II)-catalysed C-3 acylation of thiophenes with aldehydes via C(sp2)-H activation for the synthesis of (cyclo)alkyl/aryl thienyl ketones (43 examples). Compared to standard thermal conditions, the use of MW reduces the reaction time (15 to 30 min vs. 1 to 3 hours), leading to improved yields of the ketones (up to 92%). The control of positional selectivity is achieved by 2-pyridinyl and 2-pyrimidyl ortho-directing groups at C-2 of the thiophene scaffold. To show the synthetic applicability, selected ketones were subjected to further transformations, including intramolecular reactions to directly embed the directing group in the core structure of the new molecule.
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Affiliation(s)
- Carlos Santiago
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
| | - Xabier Jiménez-Aberasturi
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
| | - Eztizen Leicea
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
| | - Marta G Lete
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, Derio 48170, Spain
| | - Nuria Sotomayor
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
| | - Esther Lete
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
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9
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Mule S, Singh A, Greish K, Sahebkar A, Kesharwani P, Shukla R. Drug repurposing strategies and key challenges for COVID-19 management. J Drug Target 2021; 30:413-429. [PMID: 34854327 DOI: 10.1080/1061186x.2021.2013852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
COVID-19 is a clinical outcome of viral infection emerged due to strain of beta coronavirus which attacks the type-2 pneumocytes in alveoli via angiotensin-converting enzyme 2 (ACE2) receptors. There is no satisfactory drug developed against 'SARS-CoV2', highlighting an immediate necessity chemotherapeutic repurposing plan COVID-19. Drug repurposing is a method of selection of approved therapeutics for new use and is considered to be the most effective drug finding strategy since it includes less time and cost to obtain treatment compared to the de novo drug acquisition process. Several drugs such as hydroxychloroquine, remdesivir, teicoplanin, darunavir, ritonavir, nitazoxanide, chloroquine, tocilizumab and favipiravir (FPV) showed their activity against 'SARS-CoV2' in vitro. This review has emphasized on repurposing of drugs, and biologics used in clinical set up for targeting COVID-19 and to evaluate their pharmacokinetics, pharmacodynamics and safety with their future aspect. The key benefit of drug repurposing is the wealth of information related to its safety, and easy accessibility. Altogether repurposing approach allows access to regulatory approval as well as reducing sophisticated safety studies.
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Affiliation(s)
- Shubham Mule
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research-Raebareli, Lucknow, India
| | - Ajit Singh
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research-Raebareli, Lucknow, India
| | - Khaled Greish
- Nanomedicine Unit, College of Medicine and Medical Sciences, Al-Jawhara Center for Molecular Medicine and Inherited Disorders, Arabian Gulf University, Manama, Bahrain
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Rahul Shukla
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research-Raebareli, Lucknow, India
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10
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Ayele AG, Enyew EF, Kifle ZD. Roles of existing drug and drug targets for COVID-19 management. Metabol Open 2021; 11:100103. [PMID: 34222852 PMCID: PMC8239316 DOI: 10.1016/j.metop.2021.100103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023] Open
Abstract
In December 2019, a highly transmissible, pneumonia epidemic caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), erupted in China and other countries, resulting in devastation and health crisis worldwide currently. The search and using existing drugs support to curb the current highly contagious viral infection is spirally increasing since the pandemic began. This is based on these drugs had against other related RNA-viruses such as MERS-Cov, and SARS-Cov. Moreover, researchers are scrambling to identify novel drug targets and discover novel therapeutic options to vanquish the current pandemic. Since there is no definitive treatment to control Covid-19 vaccines are remain to be a lifeline. Currently, many vaccine candidates are being developed with most of them are reported to have positive results. Therapeutic targets such as helicases, transmembrane serine protease 2, cathepsin L, cyclin G-associated kinase, adaptor-associated kinase 1, two-pore channel, viral virulence factors, 3-chymotrypsin-like protease, suppression of excessive inflammatory response, inhibition of viral membrane, nucleocapsid, envelope, and accessory proteins, and inhibition of endocytosis were identified as a potential target against COVID-19 infection. This review also summarizes plant-based medicines for the treatment of COVID-19 such as saposhnikoviae divaricata, lonicerae japonicae flos, scutellaria baicalensis, lonicera japonicae, and some others. Thus, this review aimed to focus on the most promising therapeutic targets being repurposed against COVID-19 and viral elements that are used in COVID-19 vaccine candidates.
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Key Words
- 3CLpro, 3-chymotrypsin-like protease
- AAK1, adaptor-associated kinase 1
- ACE-2, Angiotensin-Converting Enzyme-2
- CEF, Cepharanthine
- COVID-19
- COVID-19, coronavirus disease-2019
- Existing drug
- GAK, cyclin G-associated kinase
- MERS-CoV, Middle East respiratory syndrome coronavirus
- Management
- Nsp, non-structure protein
- ORF, open reading frame
- PLpro, papain-like protease
- RdRp, RNA-dependence RNA-polymerase
- SARS-COV-2, severe acute respiratory syndrome coronavirus-2
- TMPRSS2, transmembrane Serine Protease 2
- TPC2, two-pore channel 2
- Therapeutic target
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Affiliation(s)
- Akeberegn Gorems Ayele
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Engidaw Fentahun Enyew
- Department of Human Anatomy, School of Medicine, College of Medicine and Health Sciences, Gondar, Ethiopia
| | - Zemene Demelash Kifle
- Department of Pharmacology, School of Pharmacy, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
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11
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Li Y, Ai X, Zou C, Liu Y, Ma L, Men J, Liu D, Sheng L, Ruan X, Liu H, Li W, Ma E, Yuan L. Discovery of a novel and selective cathepsin L inhibitor with anti-metastatic ability in vitro and in vivo against breast cancer cells. Bioorg Chem 2021; 115:105256. [PMID: 34426153 DOI: 10.1016/j.bioorg.2021.105256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 12/31/2022]
Abstract
Asperphenamate is a natural product that has attracted considerable interest from researchers worldwide. In the last decade, aiming to increase the biological activity and improve druggability, modifications of the A-ring moiety in asperphenamate have been performed. Our laboratory has also recently reported functional derivatizations of the A ring and studied its effect on the inhibition of cysteine cathepsin L. However, the functional significance of the B-ring fragment toward cathepsin L has not been evaluated thus far. In this paper, forty-four derivatives of the B-ring substituted with different N-phenylsulfonyl groups were designed and synthesized. Among them, the paratrifluromethyl analog B-2a and the 2, 4-difluoro-5-chloro derivative B-11b showed more potent inhibitory activity against cathepsin L than the control compound, ABR, which displayed the strongest inhibitory effect on cathepsin L and S among all reported asperphenamate derivatives. In particular, compound B-2a showed more pronounced selectivity against cathepsin L than the other derivatives. Molecular docking revealed that the N-phenylsulfonylamide moiety was vital for the interactions between B-2a and cathepsin L. Moreover, B-2a displayed no toxicity against normal cells. Therefore, compound B-2a was selected for further studies. Wound-healing assays, Transwell chamber assays and breast cancer lung metastasis mouse models demonstrated that B-2a exhibited antimetastatic ability in vitro and in vivo.
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Affiliation(s)
- Yanchun Li
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Xinyu Ai
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University), Ministry of Education, Shenyang 110016, PR China; Institute of Drug Research in Medicine Capital of China, Benxi 117000, PR China
| | - Chunyang Zou
- Department of Pharmacy, Liaoning Vocational College of Medicine, Shenyang 110101, PR China
| | - Yutong Liu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Lili Ma
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University), Ministry of Education, Shenyang 110016, PR China
| | - Jinyu Men
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University), Ministry of Education, Shenyang 110016, PR China
| | - Dongyue Liu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Lei Sheng
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University), Ministry of Education, Shenyang 110016, PR China; Institute of Drug Research in Medicine Capital of China, Benxi 117000, PR China
| | - Xinhui Ruan
- Department of Pharmacy, Liaoning Vocational College of Medicine, Shenyang 110101, PR China
| | - Haihan Liu
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University), Ministry of Education, Shenyang 110016, PR China
| | - Weixia Li
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University), Ministry of Education, Shenyang 110016, PR China
| | - Enlong Ma
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Lei Yuan
- Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University), Ministry of Education, Shenyang 110016, PR China; Institute of Drug Research in Medicine Capital of China, Benxi 117000, PR China.
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12
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Smith EA, Hill NT, Gelb T, Garman KA, Goncharova EI, Bokesch HR, Kim CK, Wendt KL, Cichewicz RH, Gustafson KR, Brownell I, Henrich CJ. Identification of natural product modulators of Merkel cell carcinoma cell growth and survival. Sci Rep 2021; 11:13597. [PMID: 34193920 PMCID: PMC8245553 DOI: 10.1038/s41598-021-93097-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/21/2021] [Indexed: 12/04/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a rare, but aggressive skin cancer the incidence of which has increased significantly in recent years. The majority of MCCs have incorporated Merkel cell polyomavirus (VP-MCC) while the remainder are virus-negative (VN-MCC). Although a variety of therapeutic options have shown promise in treating MCC, there remains a need for additional therapeutics as well as probes for better understanding MCC. A high-throughput screening campaign was used to assess the ability of > 25,000 synthetic and natural product compounds as well as > 20,000 natural product extracts to affect growth and survival of VN-MCC and VP-MCC cell lines. Sixteen active compounds were identified that have mechanisms of action reported in the literature along with a number of compounds with unknown mechanisms. Screening results with pure compounds suggest a range of potential targets for MCC including DNA damage, inhibition of DNA or protein synthesis, reactive oxygen species, and proteasome inhibition as well as NFκB inhibition while also suggesting the importance of zinc and/or copper binding. Many of the active compounds, particularly some of the natural products, have multiple reported targets suggesting that this strategy might be a particularly fruitful approach. Processing of several active natural product extracts resulted in the identification of additional MCC-active compounds. Based on these results, further investigations focused on natural products sources, particularly of fungal origin, are expected to yield further potentially useful modulators of MCC.
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Affiliation(s)
- Emily A Smith
- Molecular Targets Program, National Cancer Institute, Frederick, MD, 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Natasha T Hill
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, 20891, USA
| | - Tara Gelb
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, 20891, USA
| | - Khalid A Garman
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, 20891, USA
| | - Ekaterina I Goncharova
- Molecular Targets Program, National Cancer Institute, Frederick, MD, 21702, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Heidi R Bokesch
- Molecular Targets Program, National Cancer Institute, Frederick, MD, 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Chang-Kwon Kim
- Molecular Targets Program, National Cancer Institute, Frederick, MD, 21702, USA
| | - Karen L Wendt
- Natural Products Discovery Group, Department of Chemistry & Biochemistry, Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, OK, 73019, USA
| | - Robert H Cichewicz
- Natural Products Discovery Group, Department of Chemistry & Biochemistry, Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, OK, 73019, USA
| | - Kirk R Gustafson
- Molecular Targets Program, National Cancer Institute, Frederick, MD, 21702, USA
| | - Isaac Brownell
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, 20891, USA
| | - Curtis J Henrich
- Molecular Targets Program, National Cancer Institute, Frederick, MD, 21702, USA.
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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13
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Wang L, Li S, Yao Y, Yin W, Ye T. The role of natural products in the prevention and treatment of pulmonary fibrosis: a review. Food Funct 2021; 12:990-1007. [PMID: 33459740 DOI: 10.1039/d0fo03001e] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pulmonary fibrosis is an incurable end-stage lung disease and remains a global public health problem. Although there have been some breakthroughs in understanding the pathogenesis of pulmonary fibrosis, effective intervention methods are still limited. Natural products have the advantages of multiple biological activities and high levels of safety, which are important factors for preventing and treating pulmonary fibrosis. In this review, we summarized the mechanisms and health benefits of natural products against pulmonary fibrosis. These natural products target oxidative stress, inflammatory injury, epithelial-mesenchymal transition (EMT), fibroblast activation, extracellular matrix accumulation and metabolic regulation, and the mechanisms involve the NF-κB, TGF-β1/Smad, PI3K/Akt, p38 MAPK, Nrf2-Nox4, and AMPK signaling pathways. We hope to provide new ideas for pulmonary fibrosis prevention and treatment strategies.
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Affiliation(s)
- Liqun Wang
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. and West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Sha Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Yuqin Yao
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Wenya Yin
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Tinghong Ye
- Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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14
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Subko K, Wang X, Nielsen FH, Isbrandt T, Gotfredsen CH, Ramos MC, Mackenzie T, Vicente F, Genilloud O, Frisvad JC, Larsen TO. Mass Spectrometry Guided Discovery and Design of Novel Asperphenamate Analogs From Penicillium astrolabium Reveals an Extraordinary NRPS Flexibility. Front Microbiol 2021; 11:618730. [PMID: 33519780 PMCID: PMC7843940 DOI: 10.3389/fmicb.2020.618730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Asperphenamate is a small peptide natural product that has gained much interest due to its antitumor activity. In the recent years numerous bioactive synthetic asperphenamate analogs have been reported, whereas only a handful of natural analogs either of microbial or plant origin has been discovered. Herein we describe a UHPLC-HRMS/MS and amino acid supplement approach for discovery and design of novel asperphenamate analogs. Chemical analysis of Penicillium astrolabium, a prolific producer of asperphenamate, revealed three previously described and two novel asperphenamate analogs produced in significant amounts, suggesting a potential for biosynthesis of further asperphenamate analogs by varying the amino acid availability. Subsequent growth on proteogenic and non-proteogenic amino acid enriched media, revealed a series of novel asperphenamate analogs, including single or double amino acid exchange, as well as benzoic acid exchange for nicotinic acid, with the latter observed from a natural source for the first time. In total, 22 new asperphenamate analogs were characterized by HRMS/MS, with one additionally confirmed by isolation and NMR structure elucidation. This study indicates an extraordinary nonribosomal peptide synthetase (NRPS) flexibility based on substrate availability, and therefore the potential for manipulating and designing novel peptide natural products in filamentous fungi.
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Affiliation(s)
- Karolina Subko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Xinhui Wang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Frederik H Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Isbrandt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | | | | | | | - Jens C Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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15
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Chakraborty C, Bhattacharya M, Mallick B, Sharma AR, Lee SS, Agoramoorthy G. SARS-CoV-2 protein drug targets landscape: a potential pharmacological insight view for the new drug development. Expert Rev Clin Pharmacol 2021; 14:225-238. [PMID: 33423554 DOI: 10.1080/17512433.2021.1874348] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Protein drug targets play a significant choice in different stages of the drug discovery process. There is an urgent need to understand the drug discovery approaches and protein drug targets (PDT) of SARS-CoV-2, with structural insights for the development of SARS-CoV-2 drugs through targeted therapeutic approach.Areas covered: We have described the protein as a drug target class and also discussed various drug discovery approaches for SARS-CoV-2 involving the protein drug targets such as drug repurposing study, designing of viral entry inhibitors, viral replication inhibitors, and different enzymes of the virus. We have performed comprehensive literature search from the popular databases such as PubMed Google scholar, Web of Science, and Scopus. Finally, we have illustrated the structural landscape of different significant viral proteins (3 CLpro or Mpro, PLpro, RdRp, helicase, S protein) and host proteins as drug targets (cathepsin L, furin, TMPRSS2, ACE2).Expert opinion: The structural landscape of PDT with their binding pockets, and significant residues involved in binding has been discussed further to better understand the PDT and the structure-based drug discovery for SARS-CoV-2. This attempt will increase more therapeutic options, and combination therapies with a multi-target strategy.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal India.,Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Republic of Korea
| | | | - Bidyut Mallick
- Department of Applied Science, Galgotias College of Engineering and Technology, Greater Noida, Uttar Pradesh, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Republic of Korea
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16
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Iverson E, Kaler L, Agostino EL, Song D, Duncan GA, Scull MA. Leveraging 3D Model Systems to Understand Viral Interactions with the Respiratory Mucosa. Viruses 2020; 12:E1425. [PMID: 33322395 PMCID: PMC7763686 DOI: 10.3390/v12121425] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Respiratory viruses remain a significant cause of morbidity and mortality in the human population, underscoring the importance of ongoing basic research into virus-host interactions. However, many critical aspects of infection are difficult, if not impossible, to probe using standard cell lines, 2D culture formats, or even animal models. In vitro systems such as airway epithelial cultures at air-liquid interface, organoids, or 'on-chip' technologies allow interrogation in human cells and recapitulate emergent properties of the airway epithelium-the primary target for respiratory virus infection. While some of these models have been used for over thirty years, ongoing advancements in both culture techniques and analytical tools continue to provide new opportunities to investigate airway epithelial biology and viral infection phenotypes in both normal and diseased host backgrounds. Here we review these models and their application to studying respiratory viruses. Furthermore, given the ability of these systems to recapitulate the extracellular microenvironment, we evaluate their potential to serve as a platform for studies specifically addressing viral interactions at the mucosal surface and detail techniques that can be employed to expand our understanding.
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Affiliation(s)
- Ethan Iverson
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (E.I.); (E.L.A.)
| | - Logan Kaler
- Biophysics Program, University of Maryland, College Park, MD 20742, USA; (L.K.); (G.A.D.)
| | - Eva L. Agostino
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (E.I.); (E.L.A.)
| | - Daniel Song
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA;
| | - Gregg A. Duncan
- Biophysics Program, University of Maryland, College Park, MD 20742, USA; (L.K.); (G.A.D.)
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA;
| | - Margaret A. Scull
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (E.I.); (E.L.A.)
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17
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Gil C, Ginex T, Maestro I, Nozal V, Barrado-Gil L, Cuesta-Geijo MÁ, Urquiza J, Ramírez D, Alonso C, Campillo NE, Martinez A. COVID-19: Drug Targets and Potential Treatments. J Med Chem 2020; 63:12359-12386. [PMID: 32511912 PMCID: PMC7323060 DOI: 10.1021/acs.jmedchem.0c00606] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 02/07/2023]
Abstract
Currently, humans are immersed in a pandemic caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which threatens public health worldwide. To date, no drug or vaccine has been approved to treat the severe disease caused by this coronavirus, COVID-19. In this paper, we will focus on the main virus-based and host-based targets that can guide efforts in medicinal chemistry to discover new drugs for this devastating disease. In principle, all CoV enzymes and proteins involved in viral replication and the control of host cellular machineries are potentially druggable targets in the search for therapeutic options for SARS-CoV-2. This Perspective provides an overview of the main targets from a structural point of view, together with reported therapeutic compounds with activity against SARS-CoV-2 and/or other CoVs. Also, the role of innate immune response to coronavirus infection and the related therapeutic options will be presented.
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Affiliation(s)
- Carmen Gil
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Tiziana Ginex
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Inés Maestro
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Vanesa Nozal
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Lucía Barrado-Gil
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Miguel Ángel Cuesta-Geijo
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Jesús Urquiza
- Department of Biotechnology,
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (INIA),
Ctra. de la Coruña km 7.5, 28040 Madrid,
Spain
| | - David Ramírez
- Instituto de Ciencias Biomédicas,
Universidad Autónoma de Chile,
Llano Subercaseaux 2801- piso 6, 7500912 Santiago,
Chile
| | - Covadonga Alonso
- Department of Biotechnology,
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (INIA),
Ctra. de la Coruña km 7.5, 28040 Madrid,
Spain
| | - Nuria E. Campillo
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
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18
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Kumar D, Chauhan G, Kalra S, Kumar B, Gill MS. A perspective on potential target proteins of COVID-19: Comparison with SARS-CoV for designing new small molecules. Bioorg Chem 2020; 104:104326. [PMID: 33142431 PMCID: PMC7524440 DOI: 10.1016/j.bioorg.2020.104326] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 (COVID-19) epidemic has created an unprecedented medical and economic crisis all over the world. SARS-CoV-2 is found to have more contagious character as compared to MERS-CoV and is spreading in a very fast manner all around the globe. It has affected over 31 million people all over the world till date. This virus shares around 80% of genome similarity with SARS-CoV. In this perspective, we have explored three major targets namely; SARS-CoV-2 spike (S) protein, RNA dependent RNA polymerase, and 3CL or Mpro Protease for the inhibition of SARS-CoV-2. These targets have attracted attention of the medicinal chemists working on computer-aided drug design in developing new small molecules that might inhibit these targets for combating COVID-19 disease. Moreover, we have compared the similarity of these target proteins with earlier reported coronavirus (SARS-CoV). We have observed that both the coronaviruses share around 80% similarity in their amino acid sequence. The key amino acid interactions which can play a crucial role in designing new small molecule inhibitors against COVID-19 have been reported in this perspective. Authors believe that this study will help the medicinal chemists to understand the key amino acids essential for interactions at the active site of target proteins in SARS-CoV-2, based on their similarity with earlier reported viruses. In this review, we have also described the lead molecules under various clinical trials for their efficacy against COVID-19.
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Affiliation(s)
- Devendra Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, G.T Road, Moga, Punjab 142001, India
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico
| | - Sourav Kalra
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, SAS Nagar, Sector 67, Mohali, Punjab 160062, India
| | - Bhupinder Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, G.T Road, Moga, Punjab 142001, India.
| | - Manjinder Singh Gill
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, SAS Nagar, Sector 67, Mohali, Punjab 160062, India.
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19
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Zhang J, Liu X, Zhou W, Cheng G, Wu J, Guo S, Jia S, Liu Y, Li B, Zhang X, Wang M. A bioinformatics investigation into molecular mechanism of Yinzhihuang granules for treating hepatitis B by network pharmacology and molecular docking verification. Sci Rep 2020; 10:11448. [PMID: 32651427 PMCID: PMC7351787 DOI: 10.1038/s41598-020-68224-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Yinzhihuang granules (YZHG) is a patented Chinese medicine for the treatment of hepatitis B. This study aimed to investigate the intrinsic mechanisms of YZHG in the treatment of hepatitis B and to provide new evidence and insights for its clinical application. The chemical compounds of YZHG were searched in the CNKI and PUBMED databases, and their putative targets were then predicted through a search of the SuperPred and Swiss Target Prediction databases. In addition, the targets of hepatitis B were obtained from TTD, PharmGKB and DisGeNET. The abovementioned data were visualized using Cytoscape 3.7.1, and network construction identified a total of 13 potential targets of YZHG in the treatment of hepatitis B. Molecular docking verification showed that CDK6, CDK2, TP53 and BRCA1 might be strongly correlated with hepatitis B treatment. Furthermore, GO and KEGG analyses indicated that the treatment of hepatitis B by YZHG might be related to positive regulation of transcription, positive regulation of gene expression, the hepatitis B pathway and the viral carcinogenesis pathway. Network pharmacology intuitively shows the multicomponent, multitarget and multichannel pharmacological effects of YZHG in the treatment of hepatitis B and provides a scientific basis for its mechanism of action.
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Affiliation(s)
- Jingyuan Zhang
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Xinkui Liu
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Wei Zhou
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Guoliang Cheng
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, 276000, China
| | - Jiarui Wu
- Beijing University of Chinese Medicine, Beijing, 100102, China.
| | - Siyu Guo
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Shanshan Jia
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Yingying Liu
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Bingbing Li
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, 276000, China
| | - Xiaomeng Zhang
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Miaomiao Wang
- Beijing University of Chinese Medicine, Beijing, 100102, China
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