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Ng MSY, Kaur G, Francis RS, Hawley CM, Johnson DW. Drug repurposing for glomerular diseases: an underutilized resource. Nat Rev Nephrol 2024:10.1038/s41581-024-00864-8. [PMID: 39085415 DOI: 10.1038/s41581-024-00864-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2024] [Indexed: 08/02/2024]
Abstract
Drug repurposing in glomerular disease can deliver opportunities for steroid-free regimens, enable personalized multi-target options for resistant or relapsing disease and enhance treatment options for understudied populations (for example, children) and in resource-limited settings. Identification of drug-repurposing candidates can be data driven, which utilizes existing data on disease pathobiology, drug features and clinical outcomes, or experimental, which involves high-throughput drug screens. Information from databases of approved drugs, clinical trials and PubMed registries suggests that at least 96 drugs on the market cover 49 targets with immunosuppressive potential that could be candidates for drug repurposing in glomerular disease. Furthermore, evidence to support drug repurposing is available for 191 immune drug target-glomerular disease pairs. Non-immunological drug repurposing includes strategies to reduce haemodynamic overload, podocyte injury and kidney fibrosis. Recommended strategies to expand drug-repurposing capacity in glomerular disease include enriching drug databases with glomeruli-specific information, enhancing the accessibility of primary clinical trial data, biomarker discovery to improve participant selection into clinical trials and improve surrogate outcomes and initiatives to reduce patent, regulatory and organizational hurdles.
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Affiliation(s)
- Monica Suet Ying Ng
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia.
| | - Gursimran Kaur
- Department of Rheumatology, Saint Vincent's Hospital, Sydney, New South Wales, Australia
- Saint Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Rheumatology Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Ross S Francis
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Carmel M Hawley
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Centre for Kidney Disease Research, University of Queensland, Brisbane, Queensland, Australia
| | - David W Johnson
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Centre for Kidney Disease Research, University of Queensland, Brisbane, Queensland, Australia
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2
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Chen L, Gu R, Li Y, Liu H, Han W, Yan Y, Chen Y, Zhang Y, Jiang Y. Epigenetic target identification strategy based on multi-feature learning. J Biomol Struct Dyn 2024; 42:5946-5962. [PMID: 37827992 DOI: 10.1080/07391102.2023.2259511] [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: 01/16/2023] [Accepted: 06/20/2023] [Indexed: 10/14/2023]
Abstract
The identification of potential epigenetic targets for a known bioactive compound is essential and promising as more and more epigenetic drugs are used in cancer clinical treatment and the availability of chemogenomic data related to epigenetics increases. In this study, we introduce a novel epigenetic target identification strategy (ETI-Strategy) that integrates a multi-task graph convolutional neural network prior model and a protein-ligand interaction classification discriminating model using large-scale bioactivity data for a panel of 55 epigenetic targets. Our approach utilizes machine learning techniques to achieve an AUC value of 0.934 for the prior model and 0.830 for the discriminating model, outperforming inverse docking in predicting protein-ligand interactions. When comparing with other open-source target identification tools, it was found that only our tool was able to accurately predict all the targets corresponding to each compound. This further demonstrates the ability of our strategy to take full advantage of molecular-level information as well as protein-level information in molecular activity prediction. Our work highlights the contribution of machine learning in the identification of potential epigenetic targets and offers a novel approach for epigenetic drug discovery and development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lingfeng Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
| | - Rui Gu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
| | - Yuanyuan Li
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
| | - Weijie Han
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
| | - Yingchao Yan
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
| | - Yulei Jiang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, China
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3
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Santos-Júnior PFDS, Batista VDM, Nascimento IJDS, Nunes IC, Silva LR, Costa CACB, Freitas JDD, Quintans-Júnior LJ, Araújo-Júnior JXD, Freitas MEGD, Zhan P, Green KD, Garneau-Tsodikova S, Mendonça-Júnior FJB, Rodrigues-Junior VS, Silva-Júnior EFD. A consensus reverse docking approach for identification of a competitive inhibitor of acetyltransferase enhanced intracellular survival protein from Mycobacterium tuberculosis. Bioorg Med Chem 2024; 108:117774. [PMID: 38833750 DOI: 10.1016/j.bmc.2024.117774] [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: 01/24/2024] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), which remains a significant global health challenge. The emergence of multidrug-resistant (MDR) Mtb strains imposes the development of new therapeutic strategies. This study focuses on the identification and evaluation of potential inhibitors against Mtb H37Ra through a comprehensive screening of an in-house chemolibrary. Subsequently, a promising pyrimidine derivative (LQM495) was identified as promising and then further investigated by experimental and in silico approaches. In this context, computational techniques were used to elucidate the potential molecular target underlying the inhibitory action of LQM495. Then, a consensus reverse docking (CRD) protocol was used to investigate the interactions between this compound and several Mtb targets. Out of 98 Mtb targets investigated, the enhanced intracellular survival (Eis) protein emerged as a target for LQM495. To gain insights into the stability of the LQM495-Eis complex, molecular dynamics (MD) simulations were conducted over a 400 ns trajectory. Further insights into its binding modes within the Eis binding site were obtained through a Quantum mechanics (QM) approach, using density functional theory (DFT), with B3LYP/D3 basis set. These calculations shed light on the electronic properties and reactivity of LQM495. Subsequently, inhibition assays and kinetic studies of the Eis activity were used to investigate the activity of LQM495. Then, an IC50 value of 11.0 ± 1.4 µM was found for LQM495 upon Eis protein. Additionally, its Vmax, Km, and Ki parameters indicated that it is a competitive inhibitor. Lastly, this study presents LQM495 as a promising inhibitor of Mtb Eis protein, which could be further explored for developing novel anti-TB drugs in the future.
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Affiliation(s)
| | - Vitoria de Melo Batista
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | - Igor José Dos Santos Nascimento
- Post-Graduation Program of Pharmaceutical Sciences, Pharmacy Department, State University of Paraíba, Campina Grande, Brazil
| | - Isabelle Cavalcante Nunes
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | - Leandro Rocha Silva
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | | | - Johnnatan Duarte de Freitas
- Department of Chemistry, Federal Institute of Alagoas, Maceió campus, Mizael Domingues Street, 57020-600 Maceió, Alagoas, Brazil
| | - Lucindo José Quintans-Júnior
- Pharmaceutical Sciences Graduate Program (PPGCS), Federal University of Sergipe, São Cristóvão, Sergipe 49100-001, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | | | - 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 Jinan, Shandong, PR China
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536-0596, United States
| | | | - Valnês S Rodrigues-Junior
- Department of Pharmaceutical Sciences, Federal University of Paraíba, João Pessoa, Brazil; Post-Graduation Program in Natural Products and Bioactive Synthetics, Federal University of Paraíba, João Pessoa, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil.
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4
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Verma C, Jain K, Saini A, Mani I, Singh V. Exploring the potential of drug repurposing for treating depression. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:79-105. [PMID: 38942546 DOI: 10.1016/bs.pmbts.2024.03.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Researchers are interested in drug repurposing or drug repositioning of existing pharmaceuticals because of rising costs and slower rates of new medication development. Other investigations that authorized these treatments used data from experimental research and off-label drug use. More research into the causes of depression could lead to more effective pharmaceutical repurposing efforts. In addition to the loss of neurotransmitters like serotonin and adrenaline, inflammation, inadequate blood flow, and neurotoxins are now thought to be plausible mechanisms. Because of these other mechanisms, repurposing drugs has resulted for treatment-resistant depression. This chapter focuses on therapeutic alternatives and their effectiveness in drug repositioning. Atypical antipsychotics, central nervous system stimulants, and neurotransmitter antagonists have investigated for possible repurposing. Nonetheless, extensive research is required to ensure their formulation, effectiveness, and regulatory compliance.
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Affiliation(s)
- Chaitenya Verma
- Department of Pathology, Ohio State University, Columbus, OH, United States
| | - Kritika Jain
- Department of Microbiology, Institute of Home Economics, University of Delhi, New Delhi, India
| | - Ashok Saini
- Department of Microbiology, Institute of Home Economics, University of Delhi, New Delhi, India
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, India.
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5
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Sahu M, Vashishth S, Kukreti N, Gulia A, Russell A, Ambasta RK, Kumar P. Synergizing drug repurposing and target identification for neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:111-169. [PMID: 38789177 DOI: 10.1016/bs.pmbts.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Despite dedicated research efforts, the absence of disease-curing remedies for neurodegenerative diseases (NDDs) continues to jeopardize human society and stands as a challenge. Drug repurposing is an attempt to find new functionality of existing drugs and take it as an opportunity to discourse the clinically unmet need to treat neurodegeneration. However, despite applying this approach to rediscover a drug, it can also be used to identify the target on which a drug could work. The primary objective of target identification is to unravel all the possibilities of detecting a new drug or repurposing an existing drug. Lately, scientists and researchers have been focusing on specific genes, a particular site in DNA, a protein, or a molecule that might be involved in the pathogenesis of the disease. However, the new era discusses directing the signaling mechanism involved in the disease progression, where receptors, ion channels, enzymes, and other carrier molecules play a huge role. This review aims to highlight how target identification can expedite the whole process of drug repurposing. Here, we first spot various target-identification methods and drug-repositioning studies, including drug-target and structure-based identification studies. Moreover, we emphasize various drug repurposing approaches in NDDs, namely, experimental-based, mechanism-based, and in silico approaches. Later, we draw attention to validation techniques and stress on drugs that are currently undergoing clinical trials in NDDs. Lastly, we underscore the future perspective of synergizing drug repurposing and target identification in NDDs and present an unresolved question to address the issue.
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Affiliation(s)
- Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Shrutikirti Vashishth
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Neha Kukreti
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ashima Gulia
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ashish Russell
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India.
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Wang Q, Fu X, Yan Y, Liu T, Xie Y, Song X, Zhou Y, Xu M, Wang P, Fu P, Huang J, Huang N. Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors. J Chem Inf Model 2024; 64:761-774. [PMID: 38215394 DOI: 10.1021/acs.jcim.3c01282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Metal complexes exhibit a diverse range of coordination geometries, representing novel privileged scaffolds with convenient click types of preparation inaccessible for typical carbon-centered organic compounds. Herein, we explored the opportunity to identify biologically active organometallic complexes by reverse docking of a rigid, minimum-size octahedral organoruthenium scaffold against thousands of protein-binding pockets. Interestingly, cannabinoid receptor type 1 (CB1) was identified based on the docking scores and the degree of overlap between the docked organoruthenium scaffold and the hydrophobic scaffold of the cocrystallized ligand. Further structure-based optimization led to the discovery of organoruthenium complexes with nanomolar binding affinities and high selectivity toward CB2. Our work indicates that octahedral organoruthenium scaffolds may be advantageous for targeting the large and hydrophobic binding pockets and that the reverse docking approach may facilitate the discovery of novel privileged scaffolds, such as organometallic complexes, for exploring chemical space in lead discovery.
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Affiliation(s)
- Qing Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xuegang Fu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yuting Yan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Tao Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yuting Xie
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xiaoqing Song
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yu Zhou
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Min Xu
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Ping Wang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Peng Fu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jianhui Huang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Niu Huang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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7
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Zhu L, Wang Y, Huang X, Liu X, Ye B, He Y, Yu H, Lv W, Wang L, Hu J. Schizandrin A induces non-small cell lung cancer apoptosis by suppressing the epidermal growth factor receptor activation. Cancer Med 2024; 13:e6942. [PMID: 38376003 PMCID: PMC10877655 DOI: 10.1002/cam4.6942] [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: 10/18/2023] [Revised: 12/29/2023] [Accepted: 01/06/2024] [Indexed: 02/21/2024] Open
Abstract
OBJECTIVE The purpose of this study is to explore the biological mechanism of Schizandrin A (SchA) inducing non-small cell lung cancer (NSCLC) apoptosis. METHODS The reverse molecular docking tool "Swiss Target Prediction" was used to predict the targets of SchA. Protein-protein interaction analysis was performed on potential targets using the String database. Functional enrichment analyses of potential targets were performed with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. The conformation of SchA binding to target was simulated by chemical-protein interactomics and molecular docking. The effect of SchA on the expression and phosphorylation level of EGFR was detected by Western blot. Lipofectamine 3000 and EGFR plasmids were used to overexpress EGFR. Apoptosis was tested with Annexin V-FITC and propidium iodide staining, and cell cycle was detected by propidium iodide staining. RESULTS The "Swiss Target Prediction" database predicted 112 and 111 targets based on the 2D and 3D structures of SchA, respectively, of which kinases accounted for the most, accounting for 24%. Protein interaction network analyses showed that molecular targets such as ERBB family and SRC were at the center of the network. Functional enrichment analyses indicated that ERBB-related signaling pathways were enriched. Compound-protein interactomics and molecular docking revealed that SchA could bind to the ATP-active pocket of the EGFR tyrosine kinase domain. Laboratory results showed that SchA inhibited the phosphorylation of EGFR. Insulin could counteract the cytotoxic effect of SchA. EGFR overexpression and excess EGF or IGF-1 had limited impacts on the cytotoxicity of SchA. CONCLUSIONS Network pharmacology analyses suggested that ERBB family members may be the targets of SchA. SchA can inhibit NSCLC at least in part by inhibiting EGFR phosphorylation, and activating the EGFR bypass can neutralize the cytotoxicity of SchA.
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Affiliation(s)
- Linhai Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanye Wang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuhua Huang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xide Liu
- Department of Arthropathy, Zhejiang University of Traditional Chinese Medicine Affiliated Integrated Chinese and Western Medicine Hospital, Hangzhou, China
| | - Bo Ye
- Department of Thoracic Surgery, Hangzhou Red Cross Hospital, Hangzhou, China
| | - Yi He
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Haojie Yu
- State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Wang Lv
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Luming Wang
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Hu
- Department of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical Evaluation Technology for Medical device of Zhejiang Province, Hangzhou, China
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8
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Hou Y, Bai Y, Lu C, Wang Q, Wang Z, Gao J, Xu H. Applying molecular docking to pesticides. PEST MANAGEMENT SCIENCE 2023; 79:4140-4152. [PMID: 37547967 DOI: 10.1002/ps.7700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/17/2023] [Accepted: 08/05/2023] [Indexed: 08/08/2023]
Abstract
Pesticide creation is related to the development of sustainable agricultural and ecological safety, and molecular docking technology can effectively help in pesticide innovation. This paper introduces the basic theory behind molecular docking, pesticide databases, and docking software. It also summarizes the application of molecular docking in the pesticide field, including the virtual screening of lead compounds, detection of pesticides and their metabolites in the environment, reverse screening of pesticide targets, and the study of resistance mechanisms. Finally, problems with the use of molecular docking technology in pesticide creation are discussed, and prospects for the future use of molecular docking technology in new pesticide development are discussed. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yang Hou
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Yuqian Bai
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Chang Lu
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Qiuchan Wang
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Zishi Wang
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Jinsheng Gao
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Hongliang Xu
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
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9
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Yu S, Zhong ZP, Fang Y, Patel RB, Li QP, Liu W, Li Z, Xu L, Sagona-Stophel S, Mer E, Thomas SE, Meng Y, Li ZP, Yang YZ, Wang ZA, Guo NJ, Zhang WH, Tranmer GK, Dong Y, Wang YT, Tang JS, Li CF, Walmsley IA, Guo GC. A universal programmable Gaussian boson sampler for drug discovery. NATURE COMPUTATIONAL SCIENCE 2023; 3:839-848. [PMID: 38177757 PMCID: PMC10768638 DOI: 10.1038/s43588-023-00526-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 09/01/2023] [Indexed: 01/06/2024]
Abstract
Gaussian boson sampling (GBS) has the potential to solve complex graph problems, such as clique finding, which is relevant to drug discovery tasks. However, realizing the full benefits of quantum enhancements requires large-scale quantum hardware with universal programmability. Here we have developed a time-bin-encoded GBS photonic quantum processor that is universal, programmable and software-scalable. Our processor features freely adjustable squeezing parameters and can implement arbitrary unitary operations with a programmable interferometer. Leveraging our processor, we successfully executed clique finding on a 32-node graph, achieving approximately twice the success probability compared to classical sampling. As proof of concept, we implemented a versatile quantum drug discovery platform using this GBS processor, enabling molecular docking and RNA-folding prediction tasks. Our work achieves GBS circuitry with its universal and programmable architecture, advancing GBS toward use in real-world applications.
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Affiliation(s)
- Shang Yu
- Research Center for Quantum Sensing, Zhejiang Lab, Hangzhou, People's Republic of China.
- Quantum Optics and Laser Science, Blackett Laboratory, Imperial College London, London, UK.
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China.
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China.
| | - Zhi-Peng Zhong
- Research Center for Quantum Sensing, Zhejiang Lab, Hangzhou, People's Republic of China
| | - Yuhua Fang
- College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Raj B Patel
- Quantum Optics and Laser Science, Blackett Laboratory, Imperial College London, London, UK.
| | - Qing-Peng Li
- Research Center for Quantum Sensing, Zhejiang Lab, Hangzhou, People's Republic of China
| | - Wei Liu
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Zhenghao Li
- Quantum Optics and Laser Science, Blackett Laboratory, Imperial College London, London, UK
| | - Liang Xu
- Research Center for Quantum Sensing, Zhejiang Lab, Hangzhou, People's Republic of China
| | - Steven Sagona-Stophel
- Quantum Optics and Laser Science, Blackett Laboratory, Imperial College London, London, UK
| | - Ewan Mer
- Quantum Optics and Laser Science, Blackett Laboratory, Imperial College London, London, UK
| | - Sarah E Thomas
- Quantum Optics and Laser Science, Blackett Laboratory, Imperial College London, London, UK
| | - Yu Meng
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Zhi-Peng Li
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Yuan-Ze Yang
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Zhao-An Wang
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Nai-Jie Guo
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Wen-Hao Zhang
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | - Geoffrey K Tranmer
- College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ying Dong
- Research Center for Quantum Sensing, Zhejiang Lab, Hangzhou, People's Republic of China
| | - Yi-Tao Wang
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China.
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China.
| | - Jian-Shun Tang
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China.
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China.
- Hefei National Laboratory, University of Science and Technology of China, Hefei, China.
| | - Chuan-Feng Li
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China.
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China.
- Hefei National Laboratory, University of Science and Technology of China, Hefei, China.
| | - Ian A Walmsley
- Quantum Optics and Laser Science, Blackett Laboratory, Imperial College London, London, UK
| | - Guang-Can Guo
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, China
- CAS Center For Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, China
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10
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Zhang J, Li F, Shen S, Yang Z, Ji X, Wang X, Liao X, Zhang Y. More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review. Food Chem 2023; 416:135726. [PMID: 36893635 DOI: 10.1016/j.foodchem.2023.135726] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
The investigation of intermolecular interactions has become increasingly important in many studies, mainly by combining different analytical approaches to reveal the molecular mechanisms behind specific experimental phenomena. From spectroscopic analysis to sophisticated molecular simulation techniques like molecular docking, molecular dynamics (MD) simulation, and quantum chemical calculations (QCC), the mechanisms of intermolecular interactions are gradually being characterized more clearly and accurately, leading to revolutionary advances. This article aims to review the progression in the main techniques involving intermolecular interactions in food research and the corresponding experimental results. Finally, we discuss the significant impact that cutting-edge molecular simulation technologies may have on the future of conducting deeper exploration. Applications of molecular simulation technology may revolutionize the food research, making it possible to design new future foods with precise nutrition and desired properties.
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Affiliation(s)
- Jinghao Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Fangwei Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China; College of Food Science and Engineering, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Suxia Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Zhaotian Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xingyu Ji
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xiao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China
| | - Yan Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China; National Engineering Research Center for Fruit and Vegetable Processing, Ministry of Science and Technology, Beijing 100083, People's Republic of China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China; Beijing Key Laboratory of Food Non-Thermal Processing, Beijing 100083, People's Republic of China.
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11
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McChord J, Pereyra VM, Froebel S, Bekeredjian R, Schwab M, Ong P. Drug repurposing-a promising approach for patients with angina but non-obstructive coronary artery disease (ANOCA). Front Cardiovasc Med 2023; 10:1156456. [PMID: 37396593 PMCID: PMC10313125 DOI: 10.3389/fcvm.2023.1156456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
In today's era of individualized precision medicine drug repurposing represents a promising approach to offer patients fast access to novel treatments. Apart from drug repurposing in cancer treatments, cardiovascular pharmacology is another attractive field for this approach. Patients with angina pectoris without obstructive coronary artery disease (ANOCA) report refractory angina despite standard medications in up to 40% of cases. Drug repurposing also appears to be an auspicious option for this indication. From a pathophysiological point of view ANOCA patients frequently suffer from vasomotor disorders such as coronary spasm and/or impaired microvascular vasodilatation. Consequently, we carefully screened the literature and identified two potential therapeutic targets: the blockade of the endothelin-1 (ET-1) receptor and the stimulation of soluble guanylate cyclase (sGC). Genetically increased endothelin expression results in elevated levels of ET-1, justifying ET-1 receptor blockers as drug candidates to treat coronary spasm. sGC stimulators may be beneficial as they stimulate the NO-sGC-cGMP pathway leading to GMP-mediated vasodilatation.
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Affiliation(s)
- Johanna McChord
- Department of Cardiology and Angiology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | | | - Sarah Froebel
- Department of Cardiology and Angiology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - Raffi Bekeredjian
- Department of Cardiology and Angiology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- Departments of Clinical Pharmacology, and Biochemistry and Pharmacy, University Tübingen, Tübingen, Germany
| | - Peter Ong
- Department of Cardiology and Angiology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
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12
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Azad I, Khan T, Ahmad N, Khan AR, Akhter Y. Updates on drug designing approach through computational strategies: a review. Future Sci OA 2023; 9:FSO862. [PMID: 37180609 PMCID: PMC10167725 DOI: 10.2144/fsoa-2022-0085] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
The drug discovery and development (DDD) process in pursuit of novel drug candidates is a challenging procedure requiring lots of time and resources. Therefore, computer-aided drug design (CADD) methodologies are used extensively to promote proficiency in drug development in a systematic and time-effective manner. The point in reference is SARS-CoV-2 which has emerged as a global pandemic. In the absence of any confirmed drug moiety to treat the infection, the science fraternity adopted hit and trial methods to come up with a lead drug compound. This article is an overview of the virtual methodologies, which assist in finding novel hits and help in the progression of drug development in a short period with a specific medicinal solution.
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Affiliation(s)
- Iqbal Azad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Tahmeena Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Naseem Ahmad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, UP, 2260025, India
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13
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Li XY, Luo YT, Wang YH, Yang ZX, Shang YZ, Guan QX. Anti-inflammatory effect and antihepatoma mechanism of carrimycin. World J Gastroenterol 2023; 29:2134-2152. [PMID: 37122599 PMCID: PMC10130968 DOI: 10.3748/wjg.v29.i14.2134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/29/2022] [Accepted: 03/13/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND New drugs are urgently needed for the treatment of liver cancer, a feat that could be feasibly accomplished by finding new therapeutic purposes for marketed drugs to save time and costs. As a new class of national anti-infective drugs, carrimycin (CAM) has strong activity against gram-positive bacteria and no cross resistance with similar drugs. Studies have shown that the components of CAM have anticancer effects.
AIM To obtain a deeper understanding of CAM, its distribution, metabolism and anti-inflammatory effects were assessed in the organs of mice, and its mechanism of action against liver cancer was predicted by a network pharmacology method.
METHODS In this paper, the content of isovaleryl spiramycin III was used as an index to assess the distribution and metabolism of CAM and its effect on inflammatory factors in various mouse tissues and organs. Reverse molecular docking technology was utilized to determine the target of CAM, identify each target protein based on disease type, and establish a target protein-disease type network to ascertain the effect of CAM in liver cancer. Then, the key action targets of CAM in liver cancer were screened by a network pharmacology method, and the core targets were verified by molecular docking and visual analyses.
RESULTS The maximum CAM concentration was reached in the liver, kidney, lung and spleen 2.5 h after intragastric administration. In the intestine, the maximum drug concentration was reached 0.5 h after administration. In addition, CAM significantly reduced the interleukin-4 (IL-4) levels in the lung and kidney and especially the liver and spleen; moreover, CAM significantly reduced the IL-1β levels in the spleen, liver, and kidney and particularly the small intestine and lung. CAM is predicted to regulate related pathways by acting on many targets, such as albumin, estrogen receptor 1, epidermal growth factor receptor and caspase 3, to treat cancer, inflammation and other diseases.
CONCLUSION We determined that CAM inhibited inflammation. We also predicted the complex multitargeted effects of CAM that involve multiple pathways and the diversity of these effects in the treatment of liver cancer, which provides a basis and direction for further clinical research.
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Affiliation(s)
- Xiu-Yan Li
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Yu-Ting Luo
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Yan-Hong Wang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Zhi-Xin Yang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Yu-Zhou Shang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Qing-Xia Guan
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
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14
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Masters MR, Mahmoud AH, Wei Y, Lill MA. Deep Learning Model for Efficient Protein-Ligand Docking with Implicit Side-Chain Flexibility. J Chem Inf Model 2023; 63:1695-1707. [PMID: 36916514 DOI: 10.1021/acs.jcim.2c01436] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Protein-ligand docking is an essential tool in structure-based drug design with applications ranging from virtual high-throughput screening to pose prediction for lead optimization. Most docking programs for pose prediction are optimized for redocking to an existing cocrystallized protein structure, ignoring protein flexibility. In real-world drug design applications, however, protein flexibility is an essential feature of the ligand-binding process. Flexible protein-ligand docking still remains a significant challenge to computational drug design. To target this challenge, we present a deep learning (DL) model for flexible protein-ligand docking based on the prediction of an intermolecular Euclidean distance matrix (EDM), making the typical use of iterative search algorithms obsolete. The model was trained on a large-scale data set of protein-ligand complexes and evaluated on independent test sets. Our model generates high quality poses for a diverse set of protein and ligand structures and outperforms comparable docking methods.
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Affiliation(s)
- Matthew R Masters
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Amr H Mahmoud
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Yao Wei
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Markus A Lill
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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15
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Rodrigues Garcia T, Freire PDTC, da Silva AW, Ferreira MKA, Rebouças EDL, Mendes FRS, Marinho EM, Marinho MM, Teixeira AMR, Marinho ES, Bandeira PN, de Menezes JESA, Dos Santos HS. Anxiolytic and anticonvulsant effect of Ibuprofen derivative through GABAergic neuromodulation in adult Zebrafish. J Biomol Struct Dyn 2023; 41:12055-12062. [PMID: 36695084 DOI: 10.1080/07391102.2023.2170915] [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: 09/14/2022] [Accepted: 12/27/2022] [Indexed: 01/26/2023]
Abstract
Anxiety and epilepsy affect millions of people worldwide, and the treatment of these pathologies involves the use of Benzodiazepines, drugs that have serious adverse effects such as dependence and sedation, so the discovery of new anxiolytic and antiepileptic drugs are necessary. Many routes for synthesizing ibuprofen derivatives have been developed, and these derivatives have shown promising pharmacological effects. Therefore, this study aims to evaluate its anxiolytic and anticonvulsant effect against the adult Zebrafish animal model of Ibuprofen (IBUACT) and its interaction with the GABAergic receptor through in silico studies. The light/dark preference test (Scototaxis test) was used to evaluate the anxiolytic behavior of adult Zebrafish acutely treated with IBUACT and Diazepam, and their anticonvulsant effects were investigated through the pentylenetetrazol (PTZ)-induced seizure model. Animals treated with IBUACT showed anxiolytic behavior similar to Diazepam, and pretreatment with flumazenil reversed this behavior. PTZ-induced seizures were delayed by IBUACT in all three stages and were shown to bind strongly in the Diazepam region of GABAA. In addition, this work presents evidence of new pharmacological applications of ibuprofen derivative in pathologies of the central nervous system (CNS), opening the horizon for new studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Antonio Wlisses da Silva
- Postgraduate Program in Biotechnology, RENORBIO, State University of Ceara, Fortaleza, CE, Brazil
| | | | | | | | | | | | - Alexandre Magno Rodrigues Teixeira
- Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
- Postgraduate Program in Biotechnology, RENORBIO, State University of Ceara, Fortaleza, CE, Brazil
| | - Emmanuel Silva Marinho
- Department of Chemistry, State University of Ceara, Limoeiro do Norte, CE, Brazil
- State University of Ceara, Graduate Program in Natural Sciences, Fortaleza, CE, Brazil
| | | | | | - Helcio Silva Dos Santos
- Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
- Postgraduate Program in Biotechnology, RENORBIO, State University of Ceara, Fortaleza, CE, Brazil
- State University of Vale do Acaraú, Chemistry Course, Sobral, CE, Brazil
- State University of Ceara, Graduate Program in Natural Sciences, Fortaleza, CE, Brazil
- Department of Analytical Chemistry and Physical Chemistry, Federal University of Ceara, Fortaleza, CE, Brazil
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16
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Wong F, Krishnan A, Zheng EJ, Stärk H, Manson AL, Earl AM, Jaakkola T, Collins JJ. Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery. Mol Syst Biol 2022; 18:e11081. [PMID: 36065847 PMCID: PMC9446081 DOI: 10.15252/msb.202211081] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/12/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Efficient identification of drug mechanisms of action remains a challenge. Computational docking approaches have been widely used to predict drug binding targets; yet, such approaches depend on existing protein structures, and accurate structural predictions have only recently become available from AlphaFold2. Here, we combine AlphaFold2 with molecular docking simulations to predict protein‐ligand interactions between 296 proteins spanning Escherichia coli's essential proteome, and 218 active antibacterial compounds and 100 inactive compounds, respectively, pointing to widespread compound and protein promiscuity. We benchmark model performance by measuring enzymatic activity for 12 essential proteins treated with each antibacterial compound. We confirm extensive promiscuity, but find that the average area under the receiver operating characteristic curve (auROC) is 0.48, indicating weak model performance. We demonstrate that rescoring of docking poses using machine learning‐based approaches improves model performance, resulting in average auROCs as large as 0.63, and that ensembles of rescoring functions improve prediction accuracy and the ratio of true‐positive rate to false‐positive rate. This work indicates that advances in modeling protein‐ligand interactions, particularly using machine learning‐based approaches, are needed to better harness AlphaFold2 for drug discovery.
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Affiliation(s)
- Felix Wong
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aarti Krishnan
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erica J Zheng
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hannes Stärk
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tommi Jaakkola
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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17
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Yuan H, Xu Y, Luo Y, Zhang J, Zhu X, Xiao J. Ganoderic acid D prevents oxidative stress-induced senescence by targeting 14-3-3ε to activate CaM/CaMKII/NRF2 signaling pathway in mesenchymal stem cells. Aging Cell 2022; 21:e13686. [PMID: 35929187 PMCID: PMC9470892 DOI: 10.1111/acel.13686] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 01/25/2023] Open
Abstract
Stem cell senescence is an important cause of aging. Delaying senescence may present a novel way to combat aging and age-associated diseases. This study provided a mechanistic insight into the protective effect of ganoderic acid D (GA-D) against human amniotic mesenchymal stem cell (hAMSCs) senescence. GA-D, a Ganoderma lucidum-derived triterpenoid, markedly prevented hAMSCs senescence via activating the Ca2+ calmodulin (CaM)/CaM-dependent protein kinase II (CaMKII)/nuclear erythroid 2-related factor 2 (Nrf2) axis, and 14-3-3ε was identified as a target of GA-D. 14-3-3ε-encoding gene (YWHAE) knockdown in hAMSCs reversed the activation of the CaM/CaMKII/Nrf2 signals to attenuate the GA-D anti-aging effect and increase senescence-associated β-galactosidase (SA-β-gal), p16 and p21 expression levels, including reactive oxygen species (ROS) production, thereby promoting cell cycle arrest and decreasing differentiation potential. YWHAE overexpression maintained or slightly enhanced the GA-D anti-aging effect. GA-D prevented d-galactose-caused aging in mice by significantly increasing the total antioxidant capacity, as well as superoxide dismutase and glutathione peroxidase activity, and reducing the formation of malondialdehyde, advanced glycation end products, and receptor of advanced glycation end products. Consistent with the protective mechanism of GA-D against hAMSCs senescence, GA-D delayed the senescence of bone-marrow mesenchymal stem cells in this aging model in vivo, reduced SA-β-gal and ROS production, alleviated cell cycle arrest, and enhanced cell viability and differentiation via regulating 14-3-3ε and CaM/CaMKII/Nrf2 axis. Therefore, GA-D retards hAMSCs senescence by targeting 14-3-3ε to activate the CaM/CaMKII/Nrf2 signaling pathway. Furthermore, the in vivo GA-D anti-aging effect may involve the regulation of stem cell senescence via the same signal axis.
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Affiliation(s)
- Huan Yuan
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina,Zunyi Municiptal Key Laboratory of Medicinal Biotechnology and Guizhou Provincial Research Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Yan Xu
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina,Zunyi Municiptal Key Laboratory of Medicinal Biotechnology and Guizhou Provincial Research Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Yi Luo
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina,Zunyi Municiptal Key Laboratory of Medicinal Biotechnology and Guizhou Provincial Research Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Jia‐Rong Zhang
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Xin‐Xin Zhu
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Jian‐Hui Xiao
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina,Zunyi Municiptal Key Laboratory of Medicinal Biotechnology and Guizhou Provincial Research Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyiChina
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18
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Jing D, Wu W, Chen X, Xiao H, Zhang Z, Chen F, Zhang Z, Liu J, Shao Z, Pu F. Quercetin encapsulated in Folic Acid-Modified Liposomes is therapeutic against osteosarcoma by non-Covalent binding to the JH2 Domain of JAK2 Via the JAK2-STAT3-PDL1. Pharmacol Res 2022; 182:106287. [PMID: 35671921 DOI: 10.1016/j.phrs.2022.106287] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/19/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022]
Abstract
Osteosarcoma (OS) is a malignant solid tumor prone to lung metastasis that occurs in adolescents aged 15-19 years. Neoadjuvant chemotherapy and surgical treatment aimed at curing OS have gained limited progress over the last 30 years. Exploring new effective second-line therapies for OS patients is a serious challenge for researchers. Quercetin, a multiple biologically active polyphenolic flavonoid, has been used in tumor therapy. However, the exact mechanism of quercetin is still unknown, which limits the application of quercetin. In the current study, we found that quercetin could inhibit JAK2 through the JH2 domain in a non-covalent manner, resulting in the inhibition of OS proliferation and immune escape via the JAK2-STAT3-PD-L1 signaling axis. More importantly, to overcome the shortcomings of quercetin, including low water solubility and low oral availability, we encapsulated it with folic acid-modified liposomes. The transportation of quercetin by folic acid-modified liposomes may provide a feasible strategy to cure OS.
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Affiliation(s)
- Doudou Jing
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
| | - Wei Wu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
| | - Xuanzuo Chen
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
| | - Hongwei Xiao
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, P.R. China.
| | - Zhenhao Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
| | - Fengxia Chen
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, P.R. China.
| | - Zhicai Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
| | - Jianxiang Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
| | - Zengwu Shao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
| | - Feifei Pu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
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19
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Kores K, Kolenc Z, Furlan V, Bren U. Inverse Molecular Docking Elucidating the Anticarcinogenic Potential of the Hop Natural Product Xanthohumol and Its Metabolites. Foods 2022; 11:foods11091253. [PMID: 35563976 PMCID: PMC9104229 DOI: 10.3390/foods11091253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
Natural products from plants exert a promising potential to act as antioxidants, antimicrobials, anti-inflammatory, and anticarcinogenic agents. Xanthohumol, a natural compound from hops, is indeed known for its anticarcinogenic properties. Xanthohumol is converted into three metabolites: isoxanthohumol (non-enzymatically) as well as 8- and 6-prenylnaringenin (enzymatically). An inverse molecular docking approach was applied to xanthohumol and its three metabolites to discern their potential protein targets. The aim of our study was to disclose the potential protein targets of xanthohumol and its metabolites in order to expound on the potential anticarcinogenic mechanisms of xanthohumol based on the found target proteins. The investigated compounds were docked into the predicted binding sites of all human protein structures from the Protein Data Bank, and the best docking poses were examined. Top scoring human protein targets with successfully docked compounds were identified, and their experimental connection with the anticarcinogenic function or cancer was investigated. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using retrospective metrics. More than half of the human protein targets of xanthohumol with the highest docking scores have already been connected with the anticarcinogenic function, and four of them (including two important representatives of the matrix metalloproteinase family, MMP-2 and MMP-9) also have a known experimental correlation with xanthohumol. Another important protein target is acyl-protein thioesterase 2, to which xanthohumol, isoxanthohumol, and 6-prenylnaringenin were successfully docked with the lowest docking scores. Moreover, the results for the metabolites show that their most promising protein targets are connected with the anticarcinogenic function as well. We firmly believe that our study can help to elucidate the anticarcinogenic mechanisms of xanthohumol and its metabolites as after consumption, all four compounds can be simultaneously present in the organism.
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Affiliation(s)
- Katarina Kores
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (Z.K.); (V.F.)
| | - Zala Kolenc
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (Z.K.); (V.F.)
| | - Veronika Furlan
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (Z.K.); (V.F.)
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (Z.K.); (V.F.)
- Department of Applied Natural Sciences, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
- Correspondence: ; Tel.: +386-2-229-4421
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20
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Yu P, Chen Z, Liu Y, Gu Z, Wang X, Zhang Y, Ma Y, Dong M, Tian Z. Bioactivity-Guided Separation of Anti-Cholinesterase Alkaloids from Uncaria rhynchophlly (Miq.) Miq. Ex Havil Based on HSCCC Coupled with Molecular Docking. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27062013. [PMID: 35335376 PMCID: PMC8949104 DOI: 10.3390/molecules27062013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/14/2022] [Accepted: 03/18/2022] [Indexed: 11/29/2022]
Abstract
As an important source of cholinesterase inhibitors, alkaloids in natural products have high potential value in terms of exerting pharmacological activities. In this study, a strategy for targeted preparation of cholinesterase inhibitors in Uncaria rhynchophlly (Miq.) Miq. ex Havil (UR) by high-speed counter-current chromatography was provided. In the method, a two-phase polar solvent system composed of ethyl acetate/n-butanol/water (1:4:5, v/v/v) was used, which isolated five alkaloids from the UR extract for the first time. All alkaloids were identified by HR-ESI-MS and NMR as 7-epi-javaniside (1), vincosamide (2), strictosamide (3), cadambine (4), and 3α-dihydrocadambine (5). The poorly resolved compounds 2 and 3 were separated by preparative HPLC (prep-HPLC). Among them, compounds 1, 4, and 5 were firstly obtained from UR. The purity of these plant isolates was 98.8%, 98.7%, 99.2%, 95.7%, and 98.5%, respectively. Compounds 1–5 exhibited an inhibitory effect on acetyl-cholinesterase and butyryl-cholinesterase with an IC50 from 1.47 to 23.24 µg/mL and 1.01 to 18.24 µg/mL. Molecular docking and inhibitory activities indicated that compound 1 showed stronger inhibitory activity on acetyl-cholinesterase and butyryl-cholinesterase.
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Affiliation(s)
- Pengfei Yu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (P.Y.); (Z.C.); (Y.Z.); (M.D.)
- Inner MenGolia Mengqi Pharmaceutical Co. Ltd., Huhhot 011700, China
| | - Zhenshan Chen
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (P.Y.); (Z.C.); (Y.Z.); (M.D.)
| | - Yuecheng Liu
- Shandong Academy of Traditional Chinese Medicine, Jinan 250014, China;
| | - Zhengwei Gu
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (Z.G.); (X.W.); (Y.M.)
| | - Xiaoming Wang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (Z.G.); (X.W.); (Y.M.)
| | - Yaowen Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (P.Y.); (Z.C.); (Y.Z.); (M.D.)
| | - Yanni Ma
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (Z.G.); (X.W.); (Y.M.)
| | - Meiyue Dong
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (P.Y.); (Z.C.); (Y.Z.); (M.D.)
| | - Zhenhua Tian
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (Z.G.); (X.W.); (Y.M.)
- Correspondence: ; Tel.: +86-0531-89628192
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21
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Zheng L, Meng J, Jiang K, Lan H, Wang Z, Lin M, Li W, Guo H, Wei Y, Mu Y. Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term. Brief Bioinform 2022; 23:6548372. [PMID: 35289359 PMCID: PMC9116214 DOI: 10.1093/bib/bbac051] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022] Open
Abstract
Scoring functions are important components in molecular docking for structure-based drug discovery. Traditional scoring functions, generally empirical- or force field-based, are robust and have proven to be useful for identifying hits and lead optimizations. Although multiple highly accurate deep learning- or machine learning-based scoring functions have been developed, their direct applications for docking and screening are limited. We describe a novel strategy to develop a reliable protein–ligand scoring function by augmenting the traditional scoring function Vina score using a correction term (OnionNet-SFCT). The correction term is developed based on an AdaBoost random forest model, utilizing multiple layers of contacts formed between protein residues and ligand atoms. In addition to the Vina score, the model considerably enhances the AutoDock Vina prediction abilities for docking and screening tasks based on different benchmarks (such as cross-docking dataset, CASF-2016, DUD-E and DUD-AD). Furthermore, our model could be combined with multiple docking applications to increase pose selection accuracies and screening abilities, indicating its wide usage for structure-based drug discoveries. Furthermore, in a reverse practice, the combined scoring strategy successfully identified multiple known receptors of a plant hormone. To summarize, the results show that the combination of data-driven model (OnionNet-SFCT) and empirical scoring function (Vina score) is a good scoring strategy that could be useful for structure-based drug discoveries and potentially target fishing in future.
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Affiliation(s)
- Liangzhen Zheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Jintao Meng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,National Supercomputer Center in Shenzhen, Shenzhen, 518000, China
| | - Kai Jiang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Haidong Lan
- Tencent AI Lab, Shenzhen, Guangdong 518000, China
| | - Zechen Wang
- School of Physics, Shandong University, Jinan, Shandong 250101, China
| | - Mingzhi Lin
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, Shandong 250101, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Yanjie Wei
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
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22
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Jukič M, Kores K, Janežič D, Bren U. Repurposing of Drugs for SARS-CoV-2 Using Inverse Docking Fingerprints. Front Chem 2021; 9:757826. [PMID: 35028304 PMCID: PMC8748264 DOI: 10.3389/fchem.2021.757826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/12/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 is a virus that belongs to the Coronaviridae family. This group of viruses commonly causes colds but possesses a tremendous pathogenic potential. In humans, an outbreak of SARS caused by the SARS-CoV virus was first reported in 2003, followed by 2012 when the Middle East respiratory syndrome coronavirus (MERS-CoV) led to an outbreak of Middle East respiratory syndrome (MERS). Moreover, COVID-19 represents a serious socioeconomic and global health problem that has already claimed more than four million lives. To date, there are only a handful of therapeutic options to combat this disease, and only a single direct-acting antiviral, the conditionally approved remdesivir. Since there is an urgent need for active drugs against SARS-CoV-2, the strategy of drug repurposing represents one of the fastest ways to achieve this goal. An in silico drug repurposing study using two methods was conducted. A structure-based virtual screening of the FDA-approved drug database on SARS-CoV-2 main protease was performed, and the 11 highest-scoring compounds with known 3CLpro activity were identified while the methodology was used to report further 11 potential and completely novel 3CLpro inhibitors. Then, inverse molecular docking was performed on the entire viral protein database as well as on the Coronaviridae family protein subset to examine the hit compounds in detail. Instead of target fishing, inverse docking fingerprints were generated for each hit compound as well as for the five most frequently reported and direct-acting repurposed drugs that served as controls. In this way, the target-hitting space was examined and compared and we can support the further biological evaluation of all 11 newly reported hits on SARS-CoV-2 3CLpro as well as recommend further in-depth studies on antihelminthic class member compounds. The authors acknowledge the general usefulness of this approach for a full-fledged inverse docking fingerprint screening in the future.
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Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Katarina Kores
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
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23
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Dey S, Samadder A, Nandi S. Current Role of Nanotechnology Used in Food Processing Industry to Control Food Additives and Exploring Their Biochemical Mechanisms. Curr Drug Targets 2021; 23:513-539. [PMID: 34915833 DOI: 10.2174/1389450123666211216150355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/25/2021] [Accepted: 09/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND With the advent of food additives centuries ago, the human race has found ways to improve and maintain the safety of utility, augment the taste, color, texture, nutritional value, and appearance of the food. Since the 19th century, when the science behind food spoilage was discerned, the use of food additives in food preservation has been increasing worldwide and at a fast pace to get along with modern lifestyles. Although food additives are thought to be used to benefit the food market, some of them are found to be associated with several health issues at an alarming rate. Studies are still going on regarding the mechanisms by which food additives affect public health. Therefore, an attempt has been made to find out the remedies by exploiting technologies that may convey new properties of food additives that can only enhance the quality of food without having any systemic side effects. Thus, this review focuses on the applications of nanotechnology in the production of nano-food additives and evaluates its success regarding reduction in the health-related hazards collaterally maintaining the food nutrient value. METHODOLOGY A thorough literature study was performed using scientific databases like PubMed, Science Direct, Scopus, Web of Science for determining the design of the study, and each article was checked for citation and referred to formulate the present review article. CONCLUSION Nanotechnology can be applied in the food processing industry to control the unregulated use of food additives and to intervene in the biochemical mechanisms at a cellular and physiological level for the ensuring safety of food products. The prospective of nano-additive of chemical origin could be useful to reduce risks of hazards related to human health that are caused majorly due to the invasion of food contaminants (either intentional or non-intentional) into food, though this area still needs scientific validation. Therefore, this review provides comprehensive knowledge on different facets of food contaminants and also serves as a platform of ideas for encountering health risk problems about the design of improved versions of nano-additives.
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Affiliation(s)
- Sudatta Dey
- Cytogenetics and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia-741235. India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia-741235. India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (GIPER) (Affiliated to Uttarakhand Technical University). Kashipur-244713. India
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24
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Ribone SR, Paz SA, Abrams CF, Villarreal MA. Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking. J Comput Aided Mol Des 2021; 36:25-37. [PMID: 34825285 PMCID: PMC8616721 DOI: 10.1007/s10822-021-00432-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022]
Abstract
Screening already approved drugs for activity against a novel pathogen can be an important part of global rapid-response strategies in pandemics. Such high-throughput repurposing screens have already identified several existing drugs with potential to combat SARS-CoV-2. However, moving these hits forward for possible development into drugs specifically against this pathogen requires unambiguous identification of their corresponding targets, something the high-throughput screens are not typically designed to reveal. We present here a new computational inverse-docking protocol that uses all-atom protein structures and a combination of docking methods to rank-order targets for each of several existing drugs for which a plurality of recent high-throughput screens detected anti-SARS-CoV-2 activity. We demonstrate validation of this method with known drug-target pairs, including both non-antiviral and antiviral compounds. We subjected 152 distinct drugs potentially suitable for repurposing to the inverse docking procedure. The most common preferential targets were the human enzymes TMPRSS2 and PIKfyve, followed by the viral enzymes Helicase and PLpro. All compounds that selected TMPRSS2 are known serine protease inhibitors, and those that selected PIKfyve are known tyrosine kinase inhibitors. Detailed structural analysis of the docking poses revealed important insights into why these selections arose, and could potentially lead to more rational design of new drugs against these targets.
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Affiliation(s)
- Sergio R Ribone
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), X5000HUA, Córdoba, Argentina
| | - S Alexis Paz
- Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba , X5000HUA, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Instituto de Fisicoquímica de Córdoba (INFIQC), X5000HUA, Córdoba, Argentina
| | - Cameron F Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Marcos A Villarreal
- Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba , X5000HUA, Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Instituto de Fisicoquímica de Córdoba (INFIQC), X5000HUA, Córdoba, Argentina.
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25
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Wang H, He H, Zhang T, Jiang J. Application of Reverse Docking in the Research of Small Molecule Drugs and Traditional Chinese Medicine. Biol Pharm Bull 2021; 45:19-26. [PMID: 34719576 DOI: 10.1248/bpb.b21-00324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With the development of structural biology and data mining, computer-aided drug design (CADD) has been playing an important role in all aspects of new drug development. Reverse docking, a method of virtual screening based on molecular docking in CADD, is widely used in drug repositioning, drug rescue, and traditional Chinese medicine (TCM) research, for it can search for macromolecular targets that can bind to a given ligand molecule. This review revealed the principle of reverse docking, summarized common target protein databases and docking procedures, and enumerated the applications of reverse docking in drug repositioning, adverse drug reactions, traditional Chinese medicine, and COVID-19 treatment. Hope our work can give some inspiration to researchers engaged in drug development.
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Affiliation(s)
- Hongxu Wang
- Jiangsu key lab of Drug Screening, China Pharmaceutical University
| | - Huiqin He
- Jiangsu key lab of Drug Screening, China Pharmaceutical University
| | - Tingting Zhang
- Jiangsu key lab of Drug Screening, China Pharmaceutical University
| | - Jingwei Jiang
- Jiangsu key lab of Drug Screening, China Pharmaceutical University
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26
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Prieto Santamaría L, Ugarte Carro E, Díaz Uzquiano M, Menasalvas Ruiz E, Pérez Gallardo Y, Rodríguez-González A. A data-driven methodology towards evaluating the potential of drug repurposing hypotheses. Comput Struct Biotechnol J 2021; 19:4559-4573. [PMID: 34471499 PMCID: PMC8387760 DOI: 10.1016/j.csbj.2021.08.003] [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: 05/20/2021] [Revised: 07/08/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022] Open
Abstract
Drug repurposing has become a widely used strategy to accelerate the process of finding treatments. While classical de novo drug development involves high costs, risks, and time-consuming paths, drug repurposing allows to reuse already-existing and approved drugs for new indications. Numerous research has been carried out in this field, both in vitro and in silico. Computational drug repurposing methods make use of modern heterogeneous biomedical data to identify and prioritize new indications for old drugs. In the current paper, we present a new complete methodology to evaluate new potentially repurposable drugs based on disease-gene and disease-phenotype associations, identifying significant differences between repurposing and non-repurposing data. We have collected a set of known successful drug repurposing case studies from the literature and we have analysed their dissimilarities with other biomedical data not necessarily participating in repurposing processes. The information used has been obtained from the DISNET platform. We have performed three analyses (at the genetical, phenotypical, and categorization levels), to conclude that there is a statistically significant difference between actual repurposing-related information and non-repurposing data. The insights obtained could be relevant when suggesting new potential drug repurposing hypotheses.
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Key Words
- ACE, Angiotensin I Converting Enzyme
- AHR, Aryl Hydrocarbon Receptor
- ALK, Anaplastic Lymphoma Kinase
- API, Application Programming Interface
- CMap, Connectivity Map
- COX-2, Cyclooxygenase 2
- CUI, Concept Unique Identifier
- DISNET knowledge base
- DR, Drug Repurposing or Drug Repositioning
- DRD3, Dopamine Receptor D3
- Data integration
- Disease understanding
- Drug repositioning
- Drug repurposing
- Drug-disease validation
- ESR1, Estrogen Receptor 1
- ESR2, Estrogen Receptor 2
- FCGR2A, Fc Fragment Of IgG Receptor IIa
- FCGR3A, Fc Fragment Of IgG Receptor IIIa
- FCGR3B, Fc Fragment Of IgG Receptor IIIb
- GDA, Gene Disease Association
- ICD-10-CM, International Classification of Diseases, 10th revision, Clinical Modification
- ID, Identifier
- KDR, Kinase insert Domain Receptor
- LTα, Lymphotoxin alpha
- MeSH-PA, Medical Subject Headings – Pharmacological Action
- ND, New Disease
- NLM, National Library of Medicine
- OD, Original Disease
- PTGS2, Prostaglandin-endoperoxidase synthase 2
- SM, Supplementary Material
- SRD5A1, Steroid 5 Alpha-Reductase 1
- SRD5A2, Steroid 5 Alpha-Reductase 2
- TNFα, Tumour Necrosis Factor alpha
- UMLS, Unified Medical Language System
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Affiliation(s)
- Lucía Prieto Santamaría
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain.,ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain.,Ezeris Networks Global Services S.L., 28028 Madrid, Spain
| | - Esther Ugarte Carro
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain
| | - Marina Díaz Uzquiano
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain
| | - Ernestina Menasalvas Ruiz
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain.,ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain
| | | | - Alejandro Rodríguez-González
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain.,ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, 28660 Boadilla del Monte, Madrid, Spain
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Meireles PW, de Souza DPB, Rezende MG, Borsodi MPG, de Oliveira DE, da Silva LCRP, de Souza AMT, Viana GM, Rodrigues CR, do Carmo FA, de Sousa VP, Rossi-Bergmann B, Cabral LM. Nanoparticles Loaded with a New Thiourea Derivative: Development and In vitro Evaluation Against Leishmania amazonensis. Curr Drug Deliv 2021; 17:694-702. [PMID: 32621717 DOI: 10.2174/1567201817666200704132348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/27/2019] [Accepted: 02/13/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Leishmaniasis is a neglected tropical disease caused by protozoa of the genus Leishmania. Current treatments are restricted to a small number of drugs that display both severe side effects and a potential for parasites to develop resistance. A new N-(3,4-methylenedioxyphenyl)-N'- (2-phenethyl) thiourea compound (thiourea 1) has shown promising in vitro activity against Leishmania amazonensis with an IC50 of 54.14 μM for promastigotes and an IC50 of 70 μM for amastigotes. OBJECTIVE To develop a formulation of thiourea 1 as an oral treatment for leishmaniasis, it was incorporated into Nanoparticles (NPs), a proven approach to provide long-acting drug delivery systems. METHODS Poly (D,L-Lactic-co-Glycolic Acid) (PLGA) polymeric NPs containing thiourea 1 were obtained through a nanoprecipitation methodology associated with solvent evaporation. The NPs containing thiourea 1 were characterized for Encapsulation Efficiency (EE%), reaction yield (% w/w), surface charge, particle size and morphology by Transmission Electron Microscopy (TEM). RESULTS NPs with thiourea 1 showed an improved in vitro leishmanicidal activity with a reduction in its cytotoxicity against macrophages (CC50>100 μg/mL) while preserving its IC50 against intracellular amastigotes (1.46 ± 0.09 μg/mL). This represents a parasite Selectivity Index (SI) of 68.49, which is a marked advancement from the reference drug pentamidine (SI = 30.14). CONCLUSION The results suggest that the incorporation into NPs potentiated the therapeutic effect of thiourea 1, most likely by improving the selective delivery of the drug to the phagocytic cells that are targeted for infection by L. amazonensis. This work reinforces the importance of nanotechnology in the acquisition of new therapeutic alternatives for oral treatments.
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Affiliation(s)
- Paloma Wetler Meireles
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dandara Paiva Barroso de Souza
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marianne Grilo Rezende
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | - Gil Mendes Viana
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos Rangel Rodrigues
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flavia Almada do Carmo
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valeria Pereira de Sousa
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bartira Rossi-Bergmann
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucio Mendes Cabral
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Lu X, Yan G, Dawood M, Klauck SM, Sugimoto Y, Klinger A, Fleischer E, Shan L, Efferth T. A novel moniliformin derivative as pan-inhibitor of histone deacetylases triggering apoptosis of leukemia cells. Biochem Pharmacol 2021; 194:114677. [PMID: 34265280 DOI: 10.1016/j.bcp.2021.114677] [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] [Received: 05/05/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022]
Abstract
New and potent agents that evade multidrug resistance (MDR) and inhibit epigenetic modifications are of great interest in cancer drug development. Here, we describe that a moniliformin derivative (IUPAC name: 3-(naphthalen-2-ylsulfanyl)-4-{[(2Z)-1,3,3-trimethyl-2,3-dihydro-1H-indol-2-ylidene]methyl}cyclobut-3-ene-1,2-dione; code: MCC1381) bypasses P-gp-mediated MDR. Using transcriptomics, we identified a large number of genes significantly regulated in response to MCC1381, which affected the cell cycle and disturbed cellular death and survival. The potential targets of MCC1381 might be histone deacetylases (HDACs) as predicted by SwissTargetPrediction. In silico studies confirmed that MCC1381 presented comparable affinity with HDAC1, 2, 3, 6, 8 and 11. Besides, the inhibition activity of HDACs was dose-dependently inhibited by MCC1381. Particularly, a strong binding affinity was observed between MCC1381 and HDAC6 by microscale thermophoresis analysis. MCC1381 decreased the expression of HDAC6, inversely correlated with the increase of acetylated HDAC6 substrates, acetylation p53 and α-tubulin. Furthermore, MCC1381 arrested the cell cycle at the G2/M phase, induced the generation of reactive oxygen species and collapse of the mitochondrial membrane potential. MCC1381 exhibited in vivo anti-cancer activity in xenografted zebrafish. Collectively, MCC1381 extended cytotoxicity towards P-gp-resistant leukemia cancer cells and may act as a pan-HDACs inhibitor, indicating that MCC1381 is a novel candidate for cancer therapy.
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Affiliation(s)
- Xiaohua Lu
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ge Yan
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Mona Dawood
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany; Department of Molecular Biology, Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan
| | - Sabine M Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Yoshikazu Sugimoto
- Division of Chemotherapy, Faculty of Pharmacy, Keio University, Tokyo, Japan
| | | | | | - Letian Shan
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany.
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Sharma S, Bhatia V. Appraisal of the Role of In silico Methods in Pyrazole Based Drug Design. Mini Rev Med Chem 2021; 21:204-216. [PMID: 32875985 DOI: 10.2174/1389557520666200901184146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/19/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022]
Abstract
Pyrazole and its derivatives are a pharmacologically and significantly active scaffolds that have innumerable physiological and pharmacological activities. They can be very good targets for the discovery of novel anti-bacterial, anti-cancer, anti-inflammatory, anti-fungal, anti-tubercular, antiviral, antioxidant, antidepressant, anti-convulsant and neuroprotective drugs. This review focuses on the importance of in silico manipulations of pyrazole and its derivatives for medicinal chemistry. The authors have discussed currently available information on the use of computational techniques like molecular docking, structure-based virtual screening (SBVS), molecular dynamics (MD) simulations, quantitative structure activity relationship (QSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) to drug design using pyrazole moieties. Pyrazole based drug design is mainly dependent on the integration of experimental and computational approaches. The authors feel that more studies need to be done to fully explore the pharmacological potential of the pyrazole moiety and in silico method can be of great help.
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Affiliation(s)
- Smriti Sharma
- Department of Chemistry, Miranda House, University of Delhi, India
| | - Vinayak Bhatia
- ICARE Eye Hospital and Postgraduate Institute, U.P., Noida, India
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Stanzione F, Giangreco I, Cole JC. Use of molecular docking computational tools in drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:273-343. [PMID: 34147204 DOI: 10.1016/bs.pmch.2021.01.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular docking has become an important component of the drug discovery process. Since first being developed in the 1980s, advancements in the power of computer hardware and the increasing number of and ease of access to small molecule and protein structures have contributed to the development of improved methods, making docking more popular in both industrial and academic settings. Over the years, the modalities by which docking is used to assist the different tasks of drug discovery have changed. Although initially developed and used as a standalone method, docking is now mostly employed in combination with other computational approaches within integrated workflows. Despite its invaluable contribution to the drug discovery process, molecular docking is still far from perfect. In this chapter we will provide an introduction to molecular docking and to the different docking procedures with a focus on several considerations and protocols, including protonation states, active site waters and consensus, that can greatly improve the docking results.
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Affiliation(s)
| | - Ilenia Giangreco
- Cambridge Crystallographic Data Centre, Cambridge, United Kingdom
| | - Jason C Cole
- Cambridge Crystallographic Data Centre, Cambridge, United Kingdom
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Kharkar PS. Computational Approaches for the Design of (Mutant-)Selective Tyrosine Kinase Inhibitors: State-of-the-Art and Future Prospects. Curr Top Med Chem 2021; 20:1564-1575. [PMID: 32357816 DOI: 10.2174/1568026620666200502005853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 03/26/2020] [Indexed: 02/08/2023]
Abstract
Kinases remain one of the major attractive therapeutic targets for a large number of indications such as cancer, rheumatoid arthritis, cardiac failure and many others. Design and development of kinase inhibitors (ATP-competitive, allosteric or covalent) is a clinically validated and successful strategy in the pharmaceutical industry. The perks come with limitations, particularly the development of resistance to highly potent and selective inhibitors. When this happens, the cycle needs to be repeated, i.e., the design and development of kinase inhibitors active against the mutated forms. The complexity of tumor milieu makes it awfully difficult for these molecularly-targeted therapies to work. Every year newer and better versions of these agents are introduced in the clinic. Several computational approaches such as structure-, ligand-based or hybrid ones continue to live up to their potential in discovering novel kinase inhibitors. New schools of thought in this area continue to emerge, e.g., development of dual-target kinase inhibitors. But there are fundamental issues with this approach. It is indeed difficult to selectively optimize binding at two entirely different or related kinases. In addition to the conventional strategies, modern technologies (machine learning, deep learning, artificial intelligence, etc.) started yielding the results and building success stories. Computational tools invariably played a critical role in catalysing the phenomenal progress in kinase drug discovery field. The present review summarized the progress in utilizing computational methods and tools for discovering (mutant-)selective tyrosine kinase inhibitor drugs in the last three years (2017-2019). Representative investigations have been discussed, while others are merely listed. The author believes that the enthusiastic reader will be inspired to dig out the cited literature extensively to appreciate the progress made so far and the future prospects of the field.
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Affiliation(s)
- Prashant S Kharkar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400 019, India
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Al-Soud YA, Al-Ahmad AH, Abu-Qatouseh L, Shtaiwi A, Alhelal KAS, Al-Suod HH, Alsawakhneh SO, Al-Qawasmeh RA. Nitroimidazoles Part 9. Synthesis, molecular docking, and anticancer evaluations of piperazine-tagged imidazole derivatives. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2021. [DOI: 10.1515/znb-2020-0200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
New piperazine-tagged imidazole derivatives were synthesized via reaction of 1-alkyl/aryl-5-bromo-2-alkyl-4-nitro-1H-imidazoles 1–3 with piperazine nucleophiles. Nine selected compounds were assessed for their antiproliferative inhibition potency against five human cancer cell lines (MCF-7, PC3, Du145, HepG2 and Dermal/Fibroblast). Compounds 7 and 10 are the most potent anticancer agents on HepG2 cell line with IC50 values of (5.6 ± 0.5 µm) and (29.6 ± 7.6 µm) respectively, and on MCF-7 with IC50 values of (32.1 ± 5.6 µm) and (46.2 ± 8.2 µm) respectively. The molecular docking of compounds 7 and 10 has been studied, and the results reveal that the newly designed piperazine-tagged imidazole derivatives bind to the hydrophobic pocket and polar contact with high affinity.
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Affiliation(s)
- Yaseen A. Al-Soud
- Department of Chemistry, Faculty of Science , Al al-Bayt University , Al-Mafraq 25113 , Jordan
| | - Ala’a H. Al-Ahmad
- Department of Chemistry, Faculty of Science , Al al-Bayt University , Al-Mafraq 25113 , Jordan
| | | | - Amneh Shtaiwi
- School of Pharmacy , Middle East University , Queen Alia Airport Street , Amman 11118 , Jordan
| | - Kafa’ A. S. Alhelal
- Department of Chemistry, Faculty of Science , Al al-Bayt University , Al-Mafraq 25113 , Jordan
| | - Hossam H. Al-Suod
- Department of Chemistry, Faculty of Science , Al al-Bayt University , Al-Mafraq 25113 , Jordan
| | - Sondos O. Alsawakhneh
- Department of Chemistry, Faculty of Science , Al al-Bayt University , Al-Mafraq 25113 , Jordan
| | - Raed A. Al-Qawasmeh
- Department of Chemistry, College of Sciences , University of Sharjah , Sharjah 27272 , UAE
- Department of Chemistry , The University of Jordan , Amman 11942 , Jordan
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Zhu C, Niu H, Nie A, Bian M. Bioactivity-guided separation of potential α-glycosidase inhibitor from clerodendranthus spicatus based on HSCCC coupled with molecular docking. Sci Rep 2021; 11:6914. [PMID: 33767281 PMCID: PMC7994796 DOI: 10.1038/s41598-021-86379-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/12/2021] [Indexed: 11/15/2022] Open
Abstract
Clerodendranthus Spicatus is a traditional Dais medi-edible plant and it has been proven to have good blood glucose-lowering efficacy. However, the material basis of Clerodendranthus Spicatus has not been clarified yet and therefore needs to be determined. In this paper, the effective ingredients of this medicine were purified by high-speed counter-current chromatography. Alongside, their potential hypoglycemic activity was determined by α-glucosidase inhibitory activities in vitro and molecular docking. Finally, five compounds were purified and identified as 2-caffeoyl-L-tartaric acid (1), N-(E)-caffeoyldopamine (2), rosmarinc acid (3), methyl rosmarinate (4), 6,7,8,3',4'-Pentamethoxyflavone (5). Examination of α-glucosidase inhibitory activity in vitro showed that 2-caffeoyl-L-tartaric acid and rosmarinic acid had a higher inhibitory activity than acarbose. Molecular docking indicated that the affinity energy of the identified compounds ranged from - 7.6 to - 8.6 kcal/mol, a more desirable result than acarbose (- 6.6 kcal/mol). Particularly, rosmarinc acid with the lowest affinity energy of - 8.6 kcal/mol was wrapped with 6 hydrogen bonds. Overall, α-glucosidase inhibitory activities and molecular docking suggested that rosmarinc acid was likely to be a promising hypoglycemic drug.
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Affiliation(s)
- Chunsheng Zhu
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hongjuan Niu
- School of Pharmacy in Minzu University of China, Beijing, 100081, China
| | - Anzheng Nie
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Meng Bian
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Abstract
INTRODUCTION Molecular docking has been consolidated as one of the most important methods in the molecular modeling field. It has been recognized as a prominent tool in the study of protein-ligand complexes, to describe intermolecular interactions, to accurately predict poses of multiple ligands, to discover novel promising bioactive compounds. Molecular docking methods have evolved in terms of their accuracy and reliability; but there are pending issues to solve for improving the connection between the docking results and the experimental evidence. AREAS COVERED In this article, the author reviews very recent innovative molecular docking applications with special emphasis on reverse docking, treatment of protein flexibility, the use of experimental data to guide the selection of docking poses, the application of Quantum mechanics(QM) in docking, and covalent docking. EXPERT OPINION There are several issues being worked on in recent years that will lead to important breakthroughs in molecular docking methods in the near future These developments are related to more efficient exploration of large datasets and receptor conformations, advances in electronic description, and the use of structural information for guiding the selection of results.
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Affiliation(s)
- Julio Caballero
- Departamento De Bioinformática, Centro De Bioinformática, Simulación Y Modelado (CBSM), Facultad De Ingeniería, Universidad De Talca, Talca, Chile
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Liu C, Yin J, Hu W, Zhang H. Glycogen Phosphorylase: A Drug Target of Amino Alcohols in Echinococcus granulosus, Predicted by a Computer-Aided Method. Front Microbiol 2020; 11:557039. [PMID: 33329421 PMCID: PMC7719768 DOI: 10.3389/fmicb.2020.557039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022] Open
Abstract
Echinococcosis is an important parasitic disease that threats human health and animal husbandry worldwide. However, the low cure rate of clinical drugs for this disease is a challenge. Hence, novel compounds and specific drug targets are urgently needed. In this study, we identified drug targets of amino alcohols with effects on Echinococcus species. The drug targets were predicted with the idTarget web server. Corresponding three-dimensional structures of the drug targets were built after sequence BLAST analysis and homology modeling. After further screening by molecular docking, the activities of the candidate targets were validated in vitro. We ultimately identified glycogen phosphorylase as a potential drug target for amino alcohols. There are two genes coding glycogen phosphorylase in Echinococcus granulosus (EgGp1 and EgGp2). EgGp1 was abundant in E. granulosus PSCs, while EgGp2 was abundant in the cysts. These proteins were located at suckers and somas of E. granulosus PSCs and near the rostellum of cysts developed from PSCs. The effective compounds docked into a pocket consisting of E124, K543 and K654 and affected (either inhibited or enhanced) the activity of E. granulosus glycogen phosphorylase. In this study, we designed a method to predict drug targets for echinococcosis treatment based on inverse docking. The candidate targets found by this method can contribute not only to understanding of the modes of action of amino alcohols but also to modeling-aided drug design based on targets.
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Affiliation(s)
- Congshan Liu
- Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Ministry of Health (MOH), National Center for International Research on Tropical Diseases, World Health Organization (WHO) Collaborating Centre for Tropical Diseases, Shanghai, China
| | - Jianhai Yin
- Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Ministry of Health (MOH), National Center for International Research on Tropical Diseases, World Health Organization (WHO) Collaborating Centre for Tropical Diseases, Shanghai, China
| | - Wei Hu
- Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Ministry of Health (MOH), National Center for International Research on Tropical Diseases, World Health Organization (WHO) Collaborating Centre for Tropical Diseases, Shanghai, China.,Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Haobing Zhang
- Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Ministry of Health (MOH), National Center for International Research on Tropical Diseases, World Health Organization (WHO) Collaborating Centre for Tropical Diseases, Shanghai, China
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Aventurado CA, Billones JB, Vasquez RD, Castillo AL. In Ovo and In Silico Evaluation of the Anti-Angiogenic Potential of Syringin. Drug Des Devel Ther 2020; 14:5189-5204. [PMID: 33268982 PMCID: PMC7701684 DOI: 10.2147/dddt.s271952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/08/2020] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Cancer is considered as one of the deadliest human diseases today. Angiogenesis, the propagation of new blood vessels from pre-existing vasculature, is a critical step in the progression of cancer as it is essential in the growth and metastasis of tumors. Hence, suppression of angiogenesis is a promising approach in cancer therapy. Syringin, a phenylpropanoid glycoside with a molecular formula of C17H24O9, has been found to exhibit chemopreventive effects. However, its anti-angiogenic activity and the underlying mechanism of action are still unknown. METHODS In this work, in ovo chorioallantoic membrane (CAM) assay has been conducted to evaluate the effect of syringin on neovascularization. Additionally, reverse molecular docking studies have been performed in order to identify the probable enzyme targets in the angiogenesis pathway. RESULTS Treatment with syringin showed significant dose-dependent inhibition of blood vessel length and junctions in the CAM of duck eggs; the anti-angiogenic activity of syringin at 100 µM and 200 µM is comparable with 200 µM of the positive control celecoxib. The results of reverse docking studies indicate that syringin binds the strongest to dihydrofolate reductase (DHFR) and, to some extent, with transforming growth factor-beta receptor type 1 (TGF-βR1), vascular endothelial growth factor receptor 2 (VEGFR2), and matrix metalloproteinase-2 (MMP-2). Furthermore, ADMET models revealed that syringin potentially possesses excellent pharmacokinetic and toxicity profiles. CONCLUSION This study demonstrates the potential of syringin as an anti-angiogenic agent and elicits further investigations to establish its application in cancer suppression.
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Affiliation(s)
| | - Junie B Billones
- Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila, Philippines
| | - Ross D Vasquez
- The Graduate School, University of Santo Tomas, Manila1015, Philippines
- Faculty of Pharmacy, University of Santo Tomas, Manila1015, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila1015, Philippines
| | - Agnes L Castillo
- The Graduate School, University of Santo Tomas, Manila1015, Philippines
- Faculty of Pharmacy, University of Santo Tomas, Manila1015, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila1015, Philippines
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Chen G, Seukep AJ, Guo M. Recent Advances in Molecular Docking for the Research and Discovery of Potential Marine Drugs. Mar Drugs 2020; 18:md18110545. [PMID: 33143025 PMCID: PMC7692358 DOI: 10.3390/md18110545] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/28/2022] Open
Abstract
Marine drugs have long been used and exhibit unique advantages in clinical practices. Among the marine drugs that have been approved by the Food and Drug Administration (FDA), the protein–ligand interactions, such as cytarabine–DNA polymerase, vidarabine–adenylyl cyclase, and eribulin–tubulin complexes, are the important mechanisms of action for their efficacy. However, the complex and multi-targeted components in marine medicinal resources, their bio-active chemical basis, and mechanisms of action have posed huge challenges in the discovery and development of marine drugs so far, which need to be systematically investigated in-depth. Molecular docking could effectively predict the binding mode and binding energy of the protein–ligand complexes and has become a major method of computer-aided drug design (CADD), hence this powerful tool has been widely used in many aspects of the research on marine drugs. This review introduces the basic principles and software of the molecular docking and further summarizes the applications of this method in marine drug discovery and design, including the early virtual screening in the drug discovery stage, drug target discovery, potential mechanisms of action, and the prediction of drug metabolism. In addition, this review would also discuss and prospect the problems of molecular docking, in order to provide more theoretical basis for clinical practices and new marine drug research and development.
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Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement & Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (G.C.); (A.J.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
| | - Armel Jackson Seukep
- Key Laboratory of Plant Germplasm Enhancement & Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (G.C.); (A.J.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, P.O. Box 63 Buea, Cameroon
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement & Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (G.C.); (A.J.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
- Correspondence: ; Tel.: +86-27-8770-0850
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Deshapriya US, Dinuka DLS, Ratnaweera PB, Ratnaweera CN. In silico study for prediction of novel bioactivities of the endophytic fungal alkaloid, mycoleptodiscin B for human targets. J Mol Graph Model 2020; 102:107767. [PMID: 33130394 DOI: 10.1016/j.jmgm.2020.107767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 11/28/2022]
Abstract
Mycoleptodiscin B is a natural product extracted from the endophytic fungus Mycoleptodiscus sp. found in Sri Lanka and Panama with experimentally unexplored activities for human targets. In this study, a computational methodology was applied to determine druggable targets of mycoleptodiscin B. According to the computational toxicity and pharmacokinetics assessment, mycoleptodiscin B was proven to be a suitable drug candidate. Druggable targets for this compound, aromatase, acidic plasma glycoprotein and androgen receptor, were predicted using reverse docking. A two-step validation of those targets was performed using conventional molecular docking and molecular dynamic (MD) simulations, resulting in aromatase being determined as the potential therapeutic target. Based on molecular mechanics/Generalized Born Surface Area (GBSA) free energies and ligand stability inside the active site cavity during its 120 ns MD run, it can be concluded that mycoleptodiscin B is a potent aromatase inhibitor and could be subjected to further in vitro and in vivo experiments in the drug development pipeline. Consequently, natural product chemists can quickly identify the hidden medicinal properties of their miracle compounds using the computational approach applied in this research.
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Affiliation(s)
- Uthpala S Deshapriya
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya, Sri Lanka; Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - D L Senal Dinuka
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya, Sri Lanka; Department of Chemistry, Mississippi State University, Mississippi State, USA
| | - Pamoda B Ratnaweera
- Department of Science and Technology, Faculty of Applied Sciences, Uva Wellassa University, Badulla, Sri Lanka
| | - Chinthaka N Ratnaweera
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya, Sri Lanka; Department of Chemistry, University of Ruhuna, Matara, Sri Lanka.
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Agamah FE, Mazandu GK, Hassan R, Bope CD, Thomford NE, Ghansah A, Chimusa ER. Computational/in silico methods in drug target and lead prediction. Brief Bioinform 2020; 21:1663-1675. [PMID: 31711157 PMCID: PMC7673338 DOI: 10.1093/bib/bbz103] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/10/2023] Open
Abstract
Drug-like compounds are most of the time denied approval and use owing to the unexpected clinical side effects and cross-reactivity observed during clinical trials. These unexpected outcomes resulting in significant increase in attrition rate centralizes on the selected drug targets. These targets may be disease candidate proteins or genes, biological pathways, disease-associated microRNAs, disease-related biomarkers, abnormal molecular phenotypes, crucial nodes of biological network or molecular functions. This is generally linked to several factors, including incomplete knowledge on the drug targets and unpredicted pharmacokinetic expressions upon target interaction or off-target effects. A method used to identify targets, especially for polygenic diseases, is essential and constitutes a major bottleneck in drug development with the fundamental stage being the identification and validation of drug targets of interest for further downstream processes. Thus, various computational methods have been developed to complement experimental approaches in drug discovery. Here, we present an overview of various computational methods and tools applied in predicting or validating drug targets and drug-like molecules. We provide an overview on their advantages and compare these methods to identify effective methods which likely lead to optimal results. We also explore major sources of drug failure considering the challenges and opportunities involved. This review might guide researchers on selecting the most efficient approach or technique during the computational drug discovery process.
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Affiliation(s)
- Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Gaston K Mazandu
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- African Institute for Mathematical Sciences, Muizenberg, Cape Town 7945, South Africa
| | - Radia Hassan
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Christian D Bope
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Nicholas E Thomford
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, PO Box LG 581, Legon, Ghana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
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Dinić J, Efferth T, García-Sosa AT, Grahovac J, Padrón JM, Pajeva I, Rizzolio F, Saponara S, Spengler G, Tsakovska I. Repurposing old drugs to fight multidrug resistant cancers. Drug Resist Updat 2020; 52:100713. [PMID: 32615525 DOI: 10.1016/j.drup.2020.100713] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 02/08/2023]
Abstract
Overcoming multidrug resistance represents a major challenge for cancer treatment. In the search for new chemotherapeutics to treat malignant diseases, drug repurposing gained a tremendous interest during the past years. Repositioning candidates have often emerged through several stages of clinical drug development, and may even be marketed, thus attracting the attention and interest of pharmaceutical companies as well as regulatory agencies. Typically, drug repositioning has been serendipitous, using undesired side effects of small molecule drugs to exploit new disease indications. As bioinformatics gain increasing popularity as an integral component of drug discovery, more rational approaches are needed. Herein, we show some practical examples of in silico approaches such as pharmacophore modelling, as well as pharmacophore- and docking-based virtual screening for a fast and cost-effective repurposing of small molecule drugs against multidrug resistant cancers. We provide a timely and comprehensive overview of compounds with considerable potential to be repositioned for cancer therapeutics. These drugs are from diverse chemotherapeutic classes. We emphasize the scope and limitations of anthelmintics, antibiotics, antifungals, antivirals, antimalarials, antihypertensives, psychopharmaceuticals and antidiabetics that have shown extensive immunomodulatory, antiproliferative, pro-apoptotic, and antimetastatic potential. These drugs, either used alone or in combination with existing anticancer chemotherapeutics, represent strong candidates to prevent or overcome drug resistance. We particularly focus on outcomes and future perspectives of drug repositioning for the treatment of multidrug resistant tumors and discuss current possibilities and limitations of preclinical and clinical investigations.
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Affiliation(s)
- Jelena Dinić
- Department of Neurobiology, Institute for Biological Research "Siniša Stanković" - National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | | | - Jelena Grahovac
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - José M Padrón
- BioLab, Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, E-38071 La Laguna, Spain.
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Flavio Rizzolio
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, 301724 Venezia-Mestre, Italy; Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy
| | - Simona Saponara
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Gabriella Spengler
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, H-6720 Szeged, Dóm tér 10, Hungary
| | - Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
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41
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Radaeva M, Dong X, Cherkasov A. The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. J Chem Inf Model 2020; 60:3703-3721. [DOI: 10.1021/acs.jcim.0c00325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
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Shi Y, Zhang X, Mu K, Peng C, Zhu Z, Wang X, Yang Y, Xu Z, Zhu W. D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19. Acta Pharm Sin B 2020; 10:1239-1248. [PMID: 32318328 PMCID: PMC7169934 DOI: 10.1016/j.apsb.2020.04.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 01/16/2023] Open
Abstract
A highly effective medicine is urgently required to cure coronavirus disease 2019 (COVID-19). For the purpose, we developed a molecular docking based webserver, namely D3Targets-2019-nCoV, with two functions, one is for predicting drug targets for drugs or active compounds observed from clinic or in vitro/in vivo studies, the other is for identifying lead compounds against potential drug targets via docking. This server has its unique features, (1) the potential target proteins and their different conformations involving in the whole process from virus infection to replication and release were included as many as possible; (2) all the potential ligand-binding sites with volume larger than 200 Å3 on a protein structure were identified for docking; (3) correlation information among some conformations or binding sites was annotated; (4) it is easy to be updated, and is accessible freely to public (https://www.d3pharma.com/D3Targets-2019-nCoV/index.php). Currently, the webserver contains 42 proteins [20 severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) encoded proteins and 22 human proteins involved in virus infection, replication and release] with 69 different conformations/structures and 557 potential ligand-binding pockets in total. With 6 examples, we demonstrated that the webserver should be useful to medicinal chemists, pharmacologists and clinicians for efficiently discovering or developing effective drugs against the SARS-CoV-2 to cure COVID-19.
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Affiliation(s)
- Yulong Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinben Zhang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kaijie Mu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou 215123, China
| | - Cheng Peng
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanqing Yang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
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43
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Tortosa V, Pietropaolo V, Brandi V, Macari G, Pasquadibisceglie A, Polticelli F. Computational Methods for the Identification of Molecular Targets of Toxic Food Additives. Butylated Hydroxytoluene as a Case Study. Molecules 2020; 25:E2229. [PMID: 32397407 PMCID: PMC7248939 DOI: 10.3390/molecules25092229] [Citation(s) in RCA: 4] [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: 03/09/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 11/24/2022] Open
Abstract
Butylated hydroxytoluene (BHT) is one of the most commonly used synthetic antioxidants in food, cosmetic, pharmaceutical and petrochemical products. BHT is considered safe for human health; however, its widespread use together with the potential toxicological effects have increased consumers concern about the use of this synthetic food additive. In addition, the estimated daily intake of BHT has been demonstrated to exceed the recommended acceptable threshold. In the present work, using BHT as a case study, the usefulness of computational techniques, such as reverse screening and molecular docking, in identifying protein-ligand interactions of food additives at the bases of their toxicological effects has been probed. The computational methods here employed have been useful for the identification of several potential unknown targets of BHT, suggesting a possible explanation for its toxic effects. In silico analyses can be employed to identify new macromolecular targets of synthetic food additives and to explore their functional mechanisms or side effects. Noteworthy, this could be important for the cases in which there is an evident lack of experimental studies, as is the case for BHT.
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Affiliation(s)
- Valentina Tortosa
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (V.T.); (V.P.); (V.B.); (G.M.); (A.P.)
| | - Valentina Pietropaolo
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (V.T.); (V.P.); (V.B.); (G.M.); (A.P.)
| | - Valentina Brandi
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (V.T.); (V.P.); (V.B.); (G.M.); (A.P.)
| | - Gabriele Macari
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (V.T.); (V.P.); (V.B.); (G.M.); (A.P.)
| | - Andrea Pasquadibisceglie
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (V.T.); (V.P.); (V.B.); (G.M.); (A.P.)
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (V.T.); (V.P.); (V.B.); (G.M.); (A.P.)
- National Institute of Nuclear Physics, Roma Tre University, 00146 Rome, Italy
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44
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Novel pyrazine based anti-tubercular agents: Design, synthesis, biological evaluation and in silico studies. Bioorg Chem 2020; 96:103610. [DOI: 10.1016/j.bioorg.2020.103610] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 12/02/2019] [Accepted: 01/20/2020] [Indexed: 12/31/2022]
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45
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Liu Y, Grimm M, Dai WT, Hou MC, Xiao ZX, Cao Y. CB-Dock: a web server for cavity detection-guided protein-ligand blind docking. Acta Pharmacol Sin 2020; 41:138-144. [PMID: 31263275 PMCID: PMC7471403 DOI: 10.1038/s41401-019-0228-6] [Citation(s) in RCA: 319] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/14/2019] [Indexed: 12/19/2022] Open
Abstract
As the number of elucidated protein structures is rapidly increasing, the growing data call for methods to efficiently exploit the structural information for biological and pharmaceutical purposes. Given the three-dimensional (3D) structure of a protein and a ligand, predicting their binding sites and affinity are a key task for computer-aided drug discovery. To address this task, a variety of docking tools have been developed. Most of them focus on docking in the preset binding sites given by users. To automatically predict binding modes without information about binding sites, we developed a user-friendly blind docking web server, named CB-Dock, which predicts binding sites of a given protein and calculates the centers and sizes with a novel curvature-based cavity detection approach, and performs docking with a popular docking program, Autodock Vina. This method was carefully optimized and achieved ~70% success rate for the top-ranking poses whose root mean square deviation (RMSD) were within 2 Å from the X-ray pose, which outperformed the state-of-the-art blind docking tools in our benchmark tests. CB-Dock offers an interactive 3D visualization of results, and is freely available at http://cao.labshare.cn/cb-dock/.
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Affiliation(s)
- Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Maximilian Grimm
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wen-Tao Dai
- Shanghai Center for Bioinformation Technology & Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Mu-Chun Hou
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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46
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Wang F, Wu FX, Li CZ, Jia CY, Su SW, Hao GF, Yang GF. ACID: a free tool for drug repurposing using consensus inverse docking strategy. J Cheminform 2019; 11:73. [PMID: 33430982 PMCID: PMC6882193 DOI: 10.1186/s13321-019-0394-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/09/2019] [Indexed: 12/15/2022] Open
Abstract
Drug repurposing offers a promising alternative to dramatically shorten the process of traditional de novo development of a drug. These efforts leverage the fact that a single molecule can act on multiple targets and could be beneficial to indications where the additional targets are relevant. Hence, extensive research efforts have been directed toward developing drug based computational approaches. However, many drug based approaches are known to incur low successful rates, due to incomplete modeling of drug-target interactions. There are also many technical limitations to transform theoretical computational models into practical use. Drug based approaches may, thus, still face challenges for drug repurposing task. Upon this challenge, we developed a consensus inverse docking (CID) workflow, which has a ~ 10% enhancement in success rate compared with current best method. Besides, an easily accessible web server named auto in silico consensus inverse docking (ACID) was designed based on this workflow (http://chemyang.ccnu.edu.cn/ccb/server/ACID).
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Affiliation(s)
- Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Feng-Xu Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Cheng-Zhang Li
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Chen-Yang Jia
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Sun-Wen Su
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, 550025, People's Republic of China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China. .,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjing, 300072, People's Republic of China.
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47
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Winkler DA, Warden AC, Prangé T, Colloc'h N, Thornton AW, Ramirez-Gil JF, Farjot G, Katz I. Massive in Silico Study of Noble Gas Binding to the Structural Proteome. J Chem Inf Model 2019; 59:4844-4854. [PMID: 31613613 DOI: 10.1021/acs.jcim.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Noble gases are chemically inert, and it was therefore thought they would have little effect on biology. Paradoxically, it was found that they do exhibit a wide range of biological effects, many of which are target-specific and potentially useful and some of which have been demonstrated in vivo. The underlying mechanisms by which useful pharmacology, such as tissue and neuroprotection, anti-addiction effects, and analgesia, is elicited are relatively unexplored. Experiments to probe the interactions of noble gases with specific proteins are more difficult with gases than those with other chemicals. It is clearly impractical to conduct the large number of gas-protein experiments required to gain a complete picture of noble gas biology. Given the simplicity of atoms as ligands, in silico methods provide an opportunity to gain insight into which noble gas-protein interactions are worthy of further experimental or advanced computational investigation. Our previous validation studies showed that in silico methods can accurately predict experimentally determined noble gas binding sites in X-ray structures of proteins. Here, we summarize the largest reported in silico reverse docking study involving 127 854 protein structures and the five nonradioactive noble gases. We describe how these computational screening methods are implemented, summarize the main types of interactions that occur between noble gases and target proteins, describe how the massive data set that this study generated can be analyzed (freely available at group18.csiro.au), and provide the NDMA receptor as an example of how these data can be used to understand the molecular pharmacology underlying the biology of the noble gases. We encourage chemical biologists to access the data and use them to expand the knowledge base of noble gas pharmacology, and to use this information, together with more efficient delivery systems, to develop "atomic drugs" that can fully exploit their considerable and relatively unexplored potential in medicine.
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Affiliation(s)
- D A Winkler
- CSIRO Future Industries , Bayview Avenue , Clayton , Victoria 3168 , Australia.,Monash Institute of Pharmaceutical Sciences , Monash University , 392 Royal Parade , Parkville 3052 , Australia.,La Trobe Institute for Molecular Science , La Trobe University , Kingsbury Drive , Bundoora 3086 , Australia.,School of Pharmacy , University of Nottingham , Nottingham NG7 2QL , U.K
| | - A C Warden
- CSIRO Land and Water , Clunies Ross Street , Acton , New South Wales 2601 , Australia
| | - T Prangé
- CiTeCoM UMR 8038 CNRS University Paris Descartes , Paris 75006 , France
| | - N Colloc'h
- ISTCT UMR 6030 CNRS Université de Caen-Normandie CEA, CERVOxy Team, Centre Cyceron , Caen 14032 , France
| | - A W Thornton
- CSIRO Future Industries , Bayview Avenue , Clayton , Victoria 3168 , Australia
| | - J-F Ramirez-Gil
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
| | - G Farjot
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
| | - I Katz
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
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48
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Andrade CH, Neves BJ, Melo-Filho CC, Rodrigues J, Silva DC, Braga RC, Cravo PVL. In Silico Chemogenomics Drug Repositioning Strategies for Neglected Tropical Diseases. Curr Med Chem 2019. [DOI: 10.2174/0929867325666180309114824] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Only ~1% of all drug candidates against Neglected Tropical Diseases (NTDs)
have reached clinical trials in the last decades, underscoring the need for new, safe and effective
treatments. In such context, drug repositioning, which allows finding novel indications
for approved drugs whose pharmacokinetic and safety profiles are already known,
emerging as a promising strategy for tackling NTDs. Chemogenomics is a direct descendent
of the typical drug discovery process that involves the systematic screening of chemical
compounds against drug targets in high-throughput screening (HTS) efforts, for the identification
of lead compounds. However, different to the one-drug-one-target paradigm, chemogenomics
attempts to identify all potential ligands for all possible targets and diseases. In
this review, we summarize current methodological development efforts in drug repositioning
that use state-of-the-art computational ligand- and structure-based chemogenomics approaches.
Furthermore, we highlighted the recent progress in computational drug repositioning
for some NTDs, based on curation and modeling of genomic, biological, and chemical data.
Additionally, we also present in-house and other successful examples and suggest possible solutions
to existing pitfalls.
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Affiliation(s)
- Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Bruno Junior Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Cleber Camilo Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Juliana Rodrigues
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Diego Cabral Silva
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Rodolpho Campos Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Pedro Vitor Lemos Cravo
- Laboratory of Cheminformatics, Centro Universitario de Anapolis (UniEVANGELICA), Anapolis, GO, 75083-515, Brazil
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49
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Molecular Docking: Shifting Paradigms in Drug Discovery. Int J Mol Sci 2019; 20:ijms20184331. [PMID: 31487867 PMCID: PMC6769923 DOI: 10.3390/ijms20184331] [Citation(s) in RCA: 777] [Impact Index Per Article: 155.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022] Open
Abstract
Molecular docking is an established in silico structure-based method widely used in drug discovery. Docking enables the identification of novel compounds of therapeutic interest, predicting ligand-target interactions at a molecular level, or delineating structure-activity relationships (SAR), without knowing a priori the chemical structure of other target modulators. Although it was originally developed to help understanding the mechanisms of molecular recognition between small and large molecules, uses and applications of docking in drug discovery have heavily changed over the last years. In this review, we describe how molecular docking was firstly applied to assist in drug discovery tasks. Then, we illustrate newer and emergent uses and applications of docking, including prediction of adverse effects, polypharmacology, drug repurposing, and target fishing and profiling, discussing also future applications and further potential of this technique when combined with emergent techniques, such as artificial intelligence.
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50
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Negi A, Reilly CO, Jarikote DV, Zhou J, Murphy PV. Multi-targeting protein-protein interaction inhibitors: Evolution of macrocyclic ligands with embedded carbohydrates (MECs) to improve selectivity. Eur J Med Chem 2019; 176:292-309. [PMID: 31112891 DOI: 10.1016/j.ejmech.2019.04.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/01/2019] [Accepted: 04/24/2019] [Indexed: 10/26/2022]
Abstract
Compounds targeting multiple proteins can have synergistic effects and are therefore of interest in medicinal chemistry. At the same time, inhibiting protein-protein interactions (PPI) is increasingly desired in the treatment of disorders or diseases. The development of non-peptidomimetic inhibitors is still a challenge. Herein we investigate macrocyclic scaffolds with one or two embedded carbohydrates (MECs) that present amino acid side chains, or related isosteres, as pharmacophoric groups. Firstly, retroscreening of the previously reported eannaphane-40 (E40, 40), a MEC presenting two pharmacophoric groups, against a set of 55 receptor-subtypes led to a finding of sub-micromolar inhibitory activity for E40 against three serotonergic isoforms (5HT1A/2A/2B) as well as the Na+ channel and the NK-2 receptor. We synthesised MECs with an additional pharmacophoric group compared to E40, with a view to identifying compounds where the selectivity profile was altered among the protein hits from the retroscreening. MECs were produced based on scaffolds with two monosaccharide residues, leading to the incorporation of a third pharmacophoric group. Later, homology models were prepared for four proteins (5HT1A, 5HT2A, NK2 and site-2 of the sodium channel) whose 3D structure is unknown. Inverse docking of the synthesised compounds led to the selection of a new MEC (MEC-B) for protein binding assays. MEC-B was found to have its selectivity profile modulated, in line with docking prediction, compared to E40. MEC-B is dual inhibitor of both 5-HT1A and the sodium channel with improved selectivity for these proteins compared to 5-HT2A/2B/2C, 5-HT transporter and NK2 receptor. Thus, a new multitargeting compound, with an improved selectivity profile was identified, based on a MEC peptidomimetic scaffold.
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Affiliation(s)
- Arvind Negi
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Ciaran O Reilly
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Dilip V Jarikote
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Jian Zhou
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Paul V Murphy
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
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