1
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Lee SB, Gupta H, Min BH, Ganesan R, Sharma SP, Won SM, Jeong JJ, Cha MG, Kwon GH, Jeong MK, Hyun JY, Eom JA, Park HJ, Yoon SJ, Lee SY, Choi MR, Kim DJ, Oh KK, Suk KT. A consortium of Hordeum vulgare and gut microbiota against non-alcoholic fatty liver disease via data-driven analysis. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:250-260. [PMID: 38687561 DOI: 10.1080/21691401.2024.2347380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
Despite many recent studies on non-alcoholic fatty liver disease (NAFLD) therapeutics, the optimal treatment has yet to be determined. In this unfinished project, we combined secondary metabolites (SMs) from the gut microbiota (GM) and Hordeum vulgare (HV) to investigate their combinatorial effects via network pharmacology (NP). Additionally, we analyzed GM or barley - signalling pathways - targets - metabolites (GBSTMs) in combinatorial perspectives (HV, and GM). A total of 31 key targets were analysed via a protein-protein interaction (PPI) network, and JUN was identified as the uppermost target in NAFLD. On a bubble plot, we revealed that apelin signalling pathway, which had the lowest enrichment factor antagonize NAFLD. Holistically, we scrutinized GBSTM to identify key components (GM, signalling pathways, targets, and metabolites) associated with the Apelin signalling pathway. Consequently, we found that the primary GMs (Eubacterium limosum, Eggerthella sp. SDG-2, Alistipes indistinctus YIT 12060, Odoribacter laneus YIT 12061, Paraprevotella clara YIT 11840, Paraprevotella xylaniphila YIT 11841) to ameliorate NAFLD. The molecular docking test (MDT) suggested that tryptanthrin-JUN is an agonist, conversely, dihydroglycitein-HDAC5, 1,3-diphenylpropan-2-ol-NOS1, and (10[(Acetyloxy)methyl]-9-anthryl)methyl acetate-NOS2, which are antagonistic conformers in the apelin signalling pathway. Overall, these results suggest that combination therapy could be an effective strategy for treating NAFLD.
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Affiliation(s)
- Su-Been Lee
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Haripriya Gupta
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Byeong-Hyun Min
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Satya Priya Sharma
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Sung-Min Won
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Jin-Ju Jeong
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Min-Gi Cha
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Goo-Hyun Kwon
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Min-Kyo Jeong
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Ji-Ye Hyun
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Jung-A Eom
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Hee-Jin Park
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Sang-Jun Yoon
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Sang Youn Lee
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Mi-Ran Choi
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Dong Joon Kim
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Ki-Kwang Oh
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
| | - Ki-Tae Suk
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, Korea
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Zia S, Sumon MM, Ashik MA, Basar A, Lim S, Oh Y, Park Y, Rahman MM. Potential Inhibitors of Lumpy Skin Disease's Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches. Animals (Basel) 2024; 14:1283. [PMID: 38731287 PMCID: PMC11083254 DOI: 10.3390/ani14091283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 05/13/2024] Open
Abstract
Lumpy skin disease (LSD), caused by a virus within the Poxviridae family and Capripoxvirus genus, induces nodular skin lesions in cattle. This spreads through direct contact and insect vectors, significantly affecting global cattle farming. Despite the availability of vaccines, their efficacy is limited by poor prophylaxis and adverse effects. Our study aimed to identify the potential inhibitors targeting the LSDV-encoded DNA polymerase protein (gene LSDV039) for further investigation through comprehensive analysis and computational methods. Virtual screening revealed rhein and taxifolin as being potent binders among 380 phytocompounds, with respective affinities of -8.97 and -7.20 kcal/mol. Canagliflozin and tepotinib exhibited strong affinities (-9.86 and -8.86 kcal/mol) among 718 FDA-approved antiviral drugs. Simulating the molecular dynamics of canagliflozin, tepotinib, rhein, and taxifolin highlighted taxifolin's superior stability and binding energy. Rhein displayed compactness in RMSD and RMSF, but fluctuated in Rg and SASA, while canagliflozin demonstrated stability compared to tepotinib. This study highlights the promising potential of using repurposed drugs and phytocompounds as potential LSD therapeutics. However, extensive validation through in vitro and in vivo testing and clinical trials is crucial for their practical application.
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Affiliation(s)
- Sabbir Zia
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Md-Mehedi Sumon
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Md-Ashiqur Ashik
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Abul Basar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Sangjin Lim
- College of Forest & Environmental Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Yeonsu Oh
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Yungchul Park
- College of Forest & Environmental Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Md-Mafizur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
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Yan BH, Xu QX, Ge X, Gao MT, Li Y, Guo L, Hu P, Pan Y. Molecular mechanisms of Chengshi Beixie Fenqing Decoction based on network pharmacology: pivotal roles of relaxin signaling pathway and its associated target proteins against Benign prostatic hyperplasia. J Biomol Struct Dyn 2024; 42:2075-2093. [PMID: 37102991 DOI: 10.1080/07391102.2023.2203237] [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: 01/13/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023]
Abstract
Benign prostatic hyperplasia (BPH) is a common disease that affects the quality of life of middle-aged and older men. We investigated the therapeutical effects of Chengshi Beixie Fenqing Decoction (CBFD), a classic traditional Chinese medicine prescription, on BPH through in vivo model and network pharmacology. Bioactives in CBFD were detected through UPLC-Q-Tof-MS/MS and GC-MS, and filtered by the modified Lipinski's rule. Target proteins associated with the filtered compounds and BPH are selected from public databases. Venn diagram identified the overlapping target proteins between the bioactives-interacted target proteins and the BPH-targeted proteins. The bioactive-protein interactive networking of BPH was analyzed through the KEGG pathway on STRING to identify potential ligand-target and visualized the rich factors on the R packet. After that, the molecular docking test (MDT) was performed between bioactives and target proteins. It showed that the mechanism of CBFD against BPH was related to 104 signaling pathways of 42 compounds. AKT1, 6-demethyl-4'-methyl-N-methylcoclaurine and relaxin signaling pathways were selected as a hub target, key bioactivitie and hub signaling pathway, respectively. In addition, three major compounds, 6-demethyl-4'-methyl-N-methylcoclaurine, isoliensinine and liensinine, had the highest affinity on MDT for the three crucial target proteins, AKT1, JUN and MAPK1. These proteins were associated with the relaxin signaling pathway, which regulated the level of nitric oxide and is implicated in both BPH development and CBFD. We concluded that the three key bioactivities found in Plumula nelumbinis of CBFD may contribute to improving BPH condition by activating the relaxin signaling pathways.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bing-Hui Yan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Qi-Xuan Xu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xiao Ge
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Ming-Tong Gao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yun Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Liang Guo
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Po Hu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yang Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
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Saqib U, Demaree IS, Obukhov AG, Baig MS, Khan MS, Altwaijry N, Nasution MAF, Mizuguchi K, Hajela K. Structural and accessibility studies highlight the differential binding of clemizole to TRPC5 and TRPC6. J Biomol Struct Dyn 2024:1-14. [PMID: 38279926 DOI: 10.1080/07391102.2024.2306198] [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: 10/10/2023] [Accepted: 01/07/2024] [Indexed: 01/29/2024]
Abstract
Transient Receptor Potential Canonical 5 (T RP C5) and T RP C6 channels play critical physiological roles in various cell types. Their involvement in numerous disease progression mechanisms has led to extensive searches for their inhibitors. Although several potent T RP C inhibitors have been developed and the structure of their binding sites were mapped using cryo electron microscopy, a comprehensive understanding of the molecular interactions within the inhibitor binding site of T RP Cs remains elusive. This study aimed to decipher the structural determinants and molecular mechanisms contributing to the differential binding of clemizole to T RP C5 and T RP C6, with a particular focus on the accessibility of binding site residues. This information can help better understand what molecular features allow for selective binding, which is a key characteristic of clinically effective pharmacological agents. Using computational methodologies, we conducted an in-depth molecular docking analysis of clemizole with T RP C5 and T RP C6 channels. The protein structures were retrieved from publicly accessible protein databases. Discovery Studio 2020 Client Visualizer and Chimera software facilitated our in-silico mutation experiments and enabled us to identify the critical structural elements influencing clemizole binding. Our study reveals key molecular determinants at the clemizole binding site, specifically outlining the role of residues' Accessible Surface Area (ASA) and Relative Accessible Surface Area (RASA) in differential binding. We found that lower accessibility of T RP C6 binding site residues, compared to those in T RP C5, could account for the lower affinity binding of clemizole to T RP C6. This work illuminates the pivotal role of binding site residue accessibility in determining the affinity of clemizole to T RP C5 and T RP C6. A nuanced understanding of the distinct binding properties between these homologous proteins may pave the way for the development of more selective inhibitors, promising improved therapeutic efficacy and fewer off-target effects. By demystifying the structural and molecular subtleties of T RP C inhibitors, this research could significantly accelerate the drug discovery process, offering hope to patients afflicted with T RP C-related diseases.
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Affiliation(s)
- Uzma Saqib
- School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, MP, India
| | - Isaac S Demaree
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alexander G Obukhov
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mirza S Baig
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nojood Altwaijry
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mochammad Arfin Fardiansyah Nasution
- Institute for Protein Research, Osaka University, Osaka, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Kenji Mizuguchi
- Institute for Protein Research, Osaka University, Osaka, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Krishnan Hajela
- School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, MP, India
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5
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Sayin AZ, Abali Z, Senyuz S, Cankara F, Gursoy A, Keskin O. Conformational diversity and protein-protein interfaces in drug repurposing in Ras signaling pathway. Sci Rep 2024; 14:1239. [PMID: 38216592 PMCID: PMC10786864 DOI: 10.1038/s41598-023-50913-8] [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: 08/14/2023] [Accepted: 12/27/2023] [Indexed: 01/14/2024] Open
Abstract
We focus on drug repurposing in the Ras signaling pathway, considering structural similarities of protein-protein interfaces. The interfaces formed by physically interacting proteins are found from PDB if available and via PRISM (PRotein Interaction by Structural Matching) otherwise. The structural coverage of these interactions has been increased from 21 to 92% using PRISM. Multiple conformations of each protein are used to include protein dynamics and diversity. Next, we find FDA-approved drugs bound to structurally similar protein-protein interfaces. The results suggest that HIV protease inhibitors tipranavir, indinavir, and saquinavir may bind to EGFR and ERBB3/HER3 interface. Tipranavir and indinavir may also bind to EGFR and ERBB2/HER2 interface. Additionally, a drug used in Alzheimer's disease can bind to RAF1 and BRAF interface. Hence, we propose a methodology to find drugs to be potentially used for cancer using a dataset of structurally similar protein-protein interface clusters rather than pockets in a systematic way.
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Affiliation(s)
- Ahenk Zeynep Sayin
- Department of Chemical and Biological Engineering, College of Engineering, Koc University, Rumeli Feneri Yolu Sariyer, 34450, Istanbul, Turkey
| | - Zeynep Abali
- Graduate School of Science and Engineering, Computational Sciences and Engineering, Koc University, 34450, Istanbul, Turkey
| | - Simge Senyuz
- Graduate School of Science and Engineering, Computational Sciences and Engineering, Koc University, 34450, Istanbul, Turkey
| | - Fatma Cankara
- Graduate School of Science and Engineering, Computational Sciences and Engineering, Koc University, 34450, Istanbul, Turkey
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, 34450, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, College of Engineering, Koc University, Rumeli Feneri Yolu Sariyer, 34450, Istanbul, Turkey.
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Li C, Xu J, Abdurehim A, Sun Q, Xie J, Zhang Y. TRPA1: A promising target for pulmonary fibrosis? Eur J Pharmacol 2023; 959:176088. [PMID: 37777106 DOI: 10.1016/j.ejphar.2023.176088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023]
Abstract
Pulmonary fibrosis is a disease characterized by progressive scar formation and the ultimate manifestation of numerous lung diseases. It is known as "cancer that is not cancer" and has attracted widespread attention. However, its formation process is very complex, and the mechanism of occurrence has not been fully elucidated. Current research has found that TRPA1 may be a promising target in the pathogenesis of pulmonary fibrosis. The TRPA1 channel was first successfully isolated in human lung fibroblasts, and it was found to have a relatively concentrated distribution in the lungs and respiratory tract. It is also involved in various acute and chronic inflammatory processes of lung diseases and may even play a core role in the progression and/or prevention of pulmonary fibrosis. Natural ligands targeting TRPA1 could offer a promising alternative treatment for pulmonary diseases. Therefore, this review delves into the current understanding of pulmonary fibrogenesis, analyzes TRPA1 biological properties and regulation of lung disease with a focus on pulmonary fibrosis, summarizes the TRPA1 molecular structure and its biological function, and summarizes TRPA1 natural ligand sources, anti-pulmonary fibrosis activity and potential mechanisms. The aim is to decipher the exact role of TRPA1 channels in the pathophysiology of pulmonary fibrosis and to consider their potential in the development of new therapeutic strategies.
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Affiliation(s)
- Chao Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Jiawen Xu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Aliya Abdurehim
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Qing Sun
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Junbo Xie
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Yanqing Zhang
- Biotechnology & Food Science College, Tianjin University of Commerce, Tianjin, 300134, China.
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Rampogu S, Shaik MR, Khan M, Khan M, Oh TH, Shaik B. CBPDdb: a curated database of compounds derived from Coumarin-Benzothiazole-Pyrazole. Database (Oxford) 2023; 2023:baad062. [PMID: 37702993 PMCID: PMC10498939 DOI: 10.1093/database/baad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/01/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023]
Abstract
The present article describes the building of a small-molecule web server, CBPDdb, employing R-shiny. For the generation of the web server, three compounds were chosen, namely coumarin, benzothiazole and pyrazole, and their derivatives were curated from the literature. The two-dimensional (2D) structures were drawn using ChemDraw, and the .sdf file was created employing Discovery Studio Visualizer v2017. These compounds were read on the R-shiny app using ChemmineR, and the dataframe consisting of a total of 1146 compounds was generated and manipulated employing the dplyr package. The web server is provided with JSME 2D sketcher. The descriptors of the compounds are obtained using propOB with a filter. The users can download the filtered data in the .csv and .sdf formats, and the entire dataset of a compound can be downloaded in .sdf format. This web server facilitates the researchers to screen plausible inhibitors for different diseases. Additionally, the method used in building the web server can be adapted for developing other small-molecule databases (web servers) in RStudio. Database URL: https://srampogu.shinyapps.io/CBPDdb_Revised/.
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Affiliation(s)
| | - Mohammed Rafi Shaik
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Merajuddin Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mujeeb Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Tae Hwan Oh
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Baji Shaik
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
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8
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Alnammi M, Liu S, Ericksen SS, Ananiev GE, Voter AF, Guo S, Keck JL, Hoffmann FM, Wildman SA, Gitter A. Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries. J Chem Inf Model 2023; 63:5513-5528. [PMID: 37625010 PMCID: PMC10538940 DOI: 10.1021/acs.jcim.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 08/27/2023]
Abstract
Traditional small-molecule drug discovery is a time-consuming and costly endeavor. High-throughput chemical screening can only assess a tiny fraction of drug-like chemical space. The strong predictive power of modern machine-learning methods for virtual chemical screening enables training models on known active and inactive compounds and extrapolating to much larger chemical libraries. However, there has been limited experimental validation of these methods in practical applications on large commercially available or synthesize-on-demand chemical libraries. Through a prospective evaluation with the bacterial protein-protein interaction PriA-SSB, we demonstrate that ligand-based virtual screening can identify many active compounds in large commercial libraries. We use cross-validation to compare different types of supervised learning models and select a random forest (RF) classifier as the best model for this target. When predicting the activity of more than 8 million compounds from Aldrich Market Select, the RF substantially outperforms a naïve baseline based on chemical structure similarity. 48% of the RF's 701 selected compounds are active. The RF model easily scales to score one billion compounds from the synthesize-on-demand Enamine REAL database. We tested 68 chemically diverse top predictions from Enamine REAL and observed 31 hits (46%), including one with an IC50 value of 1.3 μM.
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Affiliation(s)
- Moayad Alnammi
- Department
of Computer Sciences, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
- Department
of Information and Computer Science, King
Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Shengchao Liu
- Department
of Computer Sciences, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
| | - Spencer S. Ericksen
- Small
Molecule Screening Facility, University
of Wisconsin−Madison, Madison, Wisconsin 53792, United States
| | - Gene E. Ananiev
- Small
Molecule Screening Facility, University
of Wisconsin−Madison, Madison, Wisconsin 53792, United States
| | - Andrew F. Voter
- Department
of Biomolecular Chemistry, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Song Guo
- Small
Molecule Screening Facility, University
of Wisconsin−Madison, Madison, Wisconsin 53792, United States
| | - James L. Keck
- Department
of Biomolecular Chemistry, University of
Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - F. Michael Hoffmann
- Small
Molecule Screening Facility, University
of Wisconsin−Madison, Madison, Wisconsin 53792, United States
- McArdle Laboratory
for Cancer Research, University of Wisconsin−Madison, Madison, Wisconsin 53705, United States
| | - Scott A. Wildman
- Small
Molecule Screening Facility, University
of Wisconsin−Madison, Madison, Wisconsin 53792, United States
| | - Anthony Gitter
- Department
of Computer Sciences, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
- Department
of Biostatistics and Medical Informatics, University of Wisconsin−Madison, Madison, Wisconsin 53792, United States
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9
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Krishna Swaroop A, Krishnan Namboori PK, Esakkimuthukumar M, Praveen TK, Nagarjuna P, Patnaik SK, Selvaraj J. Leveraging decagonal in-silico strategies for uncovering IL-6 inhibitors with precision. Comput Biol Med 2023; 163:107231. [PMID: 37421735 DOI: 10.1016/j.compbiomed.2023.107231] [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: 02/19/2023] [Revised: 06/27/2023] [Accepted: 07/01/2023] [Indexed: 07/10/2023]
Abstract
Interleukin-6 upregulation leads to various acute phase reactions such as local inflammation and systemic inflammation in many diseases like cancer, multiple sclerosis, rheumatoid arthritis, anemia, and Alzheimer's disease stimulating JAK/STAT3, Ras/MAPK, PI3K-PKB/Akt pathogenic pathways. Since no small molecules are available in the market against IL-6 till now, we have designed a class of small bioactive 1,3 - indanedione (IDC) molecules for inhibiting IL-6 using a decagonal approach computational studies. The IL-6 mutations were mapped in the IL-6 protein (PDB ID: 1ALU) from thorough pharmacogenomic and proteomics studies. The protein-drug interaction networking analysis for 2637 FFDA-approved drugs with IL-6 protein using Cytoscape software showed that 14 drugs have prominent interactions with IL-6. Molecular docking studies showed that the designed compound IDC-24 (-11.8 kcal/mol) and methotrexate (-5.20) bound most strongly to the 1ALU south asian population mutated protein. MMGBSA results indicated that IDC-24 (-41.78 kcal/mol) and methotrexate (-36.81 kcal/mol) had the highest binding energy when compared to the standard molecules LMT-28 (-35.87 kcal/mol) and MDL-A (-26.18 kcal/mol). These results we substantiated by the molecular dynamic studies in which the compound IDC-24 and the methotrexate had the highest stability. Further, the MMPBSA computations produced energies of -28 kcal/mol and -14.69 kcal/mol for IDC-24 and LMT-28. KDeep absolute binding affinity computations revealed energies of -5.81 kcal/mol and -4.74 kcal/mol for IDC-24 and LMT-28 respectively. Finally, our decagonal approach established the compound IDC-24 from the designed 1,3-indanedione library and methotrexate from protein drug interaction networking as suitable HITs against IL-6.
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Affiliation(s)
- Akey Krishna Swaroop
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - P K Krishnan Namboori
- Amrita Molecular Modeling and Synthesis (AMMAS) Research Lab, Amrita Vishwavidyapeetham, Amrita Nagar, Ettimadai, Coimbatore, Tamilnadu, India
| | - M Esakkimuthukumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - T K Praveen
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - Palathoti Nagarjuna
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - Sunil Kumar Patnaik
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - Jubie Selvaraj
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India.
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10
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Lamanna G, Delre P, Marcou G, Saviano M, Varnek A, Horvath D, Mangiatordi GF. GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design. J Chem Inf Model 2023; 63:5107-5119. [PMID: 37556857 PMCID: PMC10466378 DOI: 10.1021/acs.jcim.3c00963] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Indexed: 08/11/2023]
Abstract
This study introduces a new de novo design algorithm called GENERA that combines the capabilities of a deep-learning algorithm for automated drug-like analogue design, called DeLA-Drug, with a genetic algorithm for generating molecules with desired target-oriented properties. Specifically, GENERA was applied to the angiotensin-converting enzyme 2 (ACE2) target, which is implicated in many pathological conditions, including COVID-19. The ability of GENERA to de novo design promising candidates for a specific target was assessed using two docking programs, PLANTS and GLIDE. A fitness function based on the Pareto dominance resulting from computed PLANTS and GLIDE scores was applied to demonstrate the algorithm's ability to perform multiobjective optimizations effectively. GENERA can quickly generate focused libraries that produce better scores compared to a starting set of known ACE-2 binders. This study is the first to utilize a DL-based algorithm designed for analogue generation as a mutational operator within a GA framework, representing an innovative approach to target-oriented de novo design.
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Affiliation(s)
- Giuseppe Lamanna
- Chemistry
Department, University of Bari “Aldo
Moro”, Via E.
Orabona, 4, I-70125 Bari, Italy
- CNR
− Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
| | - Pietro Delre
- CNR
− Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
| | - Gilles Marcou
- Laboratoire
de Chémoinformatique UMR7140, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Michele Saviano
- CNR
− Institute of Crystallography, Via Vivaldi 43, 81100 Caserta, Italy
| | - Alexandre Varnek
- Laboratoire
de Chémoinformatique UMR7140, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Dragos Horvath
- Laboratoire
de Chémoinformatique UMR7140, 4 rue Blaise Pascal, 67000 Strasbourg, France
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11
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Venkatraman V. FP-MAP: an extensive library of fingerprint-based molecular activity prediction tools. Front Chem 2023; 11:1239467. [PMID: 37649967 PMCID: PMC10462816 DOI: 10.3389/fchem.2023.1239467] [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: 06/13/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023] Open
Abstract
Discovering new drugs for disease treatment is challenging, requiring a multidisciplinary effort as well as time, and resources. With a view to improving hit discovery and lead compound identification, machine learning (ML) approaches are being increasingly used in the decision-making process. Although a number of ML-based studies have been published, most studies only report fragments of the wider range of bioactivities wherein each model typically focuses on a particular disease. This study introduces FP-MAP, an extensive atlas of fingerprint-based prediction models that covers a diverse range of activities including neglected tropical diseases (caused by viral, bacterial and parasitic pathogens) as well as other targets implicated in diseases such as Alzheimer's. To arrive at the best predictive models, performance of ≈4,000 classification/regression models were evaluated on different bioactivity data sets using 12 different molecular fingerprints. The best performing models that achieved test set AUC values of 0.62-0.99 have been integrated into an easy-to-use graphical user interface that can be downloaded from https://gitlab.com/vishsoft/fpmap.
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Affiliation(s)
- Vishwesh Venkatraman
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
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12
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Huang Z, Liu H, Zhang X, Tang M, Lin Y, Feng L, Ye J, Zhou T, Chen L. Ceftazidime-Decorated Gold Nanoparticles: a Promising Strategy against Clinical Ceftazidime-Avibactam-Resistant Enterobacteriaceae with Different Resistance Mechanisms. Antimicrob Agents Chemother 2023; 67:e0026223. [PMID: 37358468 PMCID: PMC10353462 DOI: 10.1128/aac.00262-23] [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: 02/27/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023] Open
Abstract
Nanoparticle-based antibiotic delivery systems are essential in combating antibiotic-resistant bacterial infections arising from acquired resistance and/or biofilm formation. Here, we report that the ceftazidime-decorated gold nanoparticles (CAZ_Au NPs) can effectively kill clinical ceftazidime-avibactam-resistant Enterobacteriaceae with various resistance mechanisms. Further study of underlying antibacterial mechanisms suggests that CAZ_Au NPs can damage the bacterial cell membrane and increase the level of intracellular reactive oxygen species. Moreover, CAZ_Au NPs show great potential in inhibiting biofilm formation and eradicating mature biofilms via crystal violet and scanning electron microscope assays. In addition, CAZ_Au NPs demonstrate excellent performance in improving the survival rate in the mouse model of abdominal infection. In addition, CAZ_Au NPs show no significant toxicity at bactericidal concentrations in the cell viability assay. Thus, this strategy provides a simple way to drastically improve the potency of ceftazidime as an antibiotic and its use in further biomedical applications.
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Affiliation(s)
- Zeyu Huang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Haifeng Liu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaotuan Zhang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Miran Tang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuzhan Lin
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Luozhu Feng
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianzhong Ye
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lijiang Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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13
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Thomson TM. On the importance for drug discovery of a transnational Latin American database of natural compound structures. Front Pharmacol 2023; 14:1207559. [PMID: 37426821 PMCID: PMC10324963 DOI: 10.3389/fphar.2023.1207559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Affiliation(s)
- Timothy M. Thomson
- Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Universidad Peruana Cayetano Heredia, Lima, Peru
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14
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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: 0] [Impact Index Per Article: 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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15
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Oh KK, Yoon SJ, Lee SB, Lee SY, Gupta H, Ganesan R, Sharma SP, Won SM, Jeong JJ, Kim DJ, Suk KT. The convergent application of metabolites from Avena sativa and gut microbiota to ameliorate non-alcoholic fatty liver disease: a network pharmacology study. J Transl Med 2023; 21:263. [PMID: 37069607 PMCID: PMC10111676 DOI: 10.1186/s12967-023-04122-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a serious public health issue globally, currently, the treatment of NAFLD lies still in the labyrinth. In the inchoate stage, the combinatorial application of food regimen and favorable gut microbiota (GM) are considered as an alternative therapeutic. Accordingly, we integrated secondary metabolites (SMs) from GM and Avena sativa (AS) known as potent dietary grain to identify the combinatorial efficacy through network pharmacology. METHODS We browsed the SMs of AS via Natural Product Activity & Species Source (NPASS) database and SMs of GM were retrieved by gutMGene database. Then, specific intersecting targets were identified from targets related to SMs of AS and GM. The final targets were selected on NAFLD-related targets, which was considered as crucial targets. The protein-protein interaction (PPI) networks and bubble chart analysis to identify a hub target and a key signaling pathway were conducted, respectively. In parallel, we analyzed the relationship of GM or AS─a key signaling pathway─targets─SMs (GASTM) by merging the five components via RPackage. We identified key SMs on a key signaling pathway via molecular docking assay (MDA). Finally, the identified key SMs were verified the physicochemical properties and toxicity in silico platform. RESULTS The final 16 targets were regarded as critical proteins against NAFLD, and Vascular Endothelial Growth Factor A (VEGFA) was a key target in PPI network analysis. The PI3K-Akt signaling pathway was the uppermost mechanism associated with VEGFA as an antagonistic mode. GASTM networks represented 122 nodes (60 GM, AS, PI3K-Akt signaling pathway, 4 targets, and 56 SMs) and 154 edges. The VEGFA-myricetin, or quercetin, GSK3B-myricetin, IL2-diosgenin complexes formed the most stable conformation, the three ligands were derived from GM. Conversely, NR4A1-vestitol formed stable conformation with the highest affinity, and the vestitol was obtained from AS. The given four SMs were no hurdles to develop into drugs devoid of its toxicity. CONCLUSION In conclusion, we show that combinatorial application of AS and GM might be exerted to the potent synergistic effects against NAFLD, dampening PI3K-Akt signaling pathway. This work provides the importance of dietary strategy and beneficial GM on NAFLD, a data mining basis for further explicating the SMs and pharmacological mechanisms of combinatorial application (AS and GM) against NAFLD.
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Affiliation(s)
- Ki-Kwang Oh
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Sang-Jun Yoon
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Su-Been Lee
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Sang Youn Lee
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Haripriya Gupta
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Satya Priya Sharma
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Sung-Min Won
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Jin-Ju Jeong
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Dong Joon Kim
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea
| | - Ki-Tae Suk
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, 24252, Korea.
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16
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Current trends in natural products for the treatment and management of dementia: Computational to clinical studies. Neurosci Biobehav Rev 2023; 147:105106. [PMID: 36828163 DOI: 10.1016/j.neubiorev.2023.105106] [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: 06/07/2022] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023]
Abstract
The number of preclinical and clinical studies evaluating natural products-based management of dementia has gradually increased, with an exponential rise in 2020 and 2021. Keeping this in mind, we examined current trends from 2016 to 2021 in order to assess the growth potential of natural products in the treatment of dementia. Publicly available literature was collected from various databases like PubMed and Google Scholar. Oxidative stress-related targets, NF-κB pathway, anti-tau aggregation, anti-AChE, and A-β aggregation were found to be common targets and pathways. A retrospective analysis of 33 antidementia natural compounds identified 125 sustainable resources distributed among 65 families, 39 orders, and 7 classes. We found that families such as Berberidaceae, Zingiberaceae, and Fabaceae, as well as orders such as Lamiales, Sapindales, and Myrtales, appear to be important and should be researched further for antidementia compounds. Moreover, some natural products, such as quercetin, curcumin, icariside II, berberine, and resveratrol, have a wide range of applications. Clinical studies and patents support the importance of dietary supplements and natural products, which we will also discuss. Finally, we conclude with the broad scope, future challenges, and opportunities for field researchers.
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17
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Jung S, Vatheuer H, Czodrowski P. VSFlow: an open-source ligand-based virtual screening tool. J Cheminform 2023; 15:40. [PMID: 37004101 PMCID: PMC10064649 DOI: 10.1186/s13321-023-00703-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/18/2023] [Indexed: 04/03/2023] Open
Abstract
Ligand-based virtual screening is a widespread method in modern drug design. It allows for a rapid screening of large compound databases in order to identify similar structures. Here we report an open-source command line tool which includes a substructure-, fingerprint- and shape-based virtual screening. Most of the implemented features fully rely on the RDKit cheminformatics framework. VSFlow accepts a wide range of input file formats and is highly customizable. Additionally, a quick visualization of the screening results as pdf and/or pymol file is supported.
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Affiliation(s)
- Sascha Jung
- grid.5675.10000 0001 0416 9637Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Helge Vatheuer
- grid.5675.10000 0001 0416 9637Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Paul Czodrowski
- grid.5802.f0000 0001 1941 7111Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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18
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Li H, Zou L, Kowah JAH, He D, Liu Z, Ding X, Wen H, Wang L, Yuan M, Liu X. A compact review of progress and prospects of deep learning in drug discovery. J Mol Model 2023; 29:117. [PMID: 36976427 DOI: 10.1007/s00894-023-05492-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023]
Abstract
BACKGROUND Drug discovery processes, such as new drug development, drug synergy, and drug repurposing, consume significant yearly resources. Computer-aided drug discovery can effectively improve the efficiency of drug discovery. Traditional computer methods such as virtual screening and molecular docking have achieved many gratifying results in drug development. However, with the rapid growth of computer science, data structures have changed considerably; with more extensive and dimensional data and more significant amounts of data, traditional computer methods can no longer be applied well. Deep learning methods are based on deep neural network structures that can handle high-dimensional data very well, so they are used in current drug development. RESULTS This review summarized the applications of deep learning methods in drug discovery, such as drug target discovery, drug de novo design, drug recommendation, drug synergy, and drug response prediction. While applying deep learning methods to drug discovery suffers from a lack of data, transfer learning is an excellent solution to this problem. Furthermore, deep learning methods can extract deeper features and have higher predictive power than other machine learning methods. Deep learning methods have great potential in drug discovery and are expected to facilitate drug discovery development.
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Affiliation(s)
- Huijun Li
- College of Medicine, Guangxi University, Nanning, 530004, China
| | - Lin Zou
- College of Medicine, Guangxi University, Nanning, 530004, China
| | | | - Dongqiong He
- College of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Zifan Liu
- College of Medicine, Guangxi University, Nanning, 530004, China
| | - Xuejie Ding
- College of Medicine, Guangxi University, Nanning, 530004, China
| | - Hao Wen
- College of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Lisheng Wang
- College of Medicine, Guangxi University, Nanning, 530004, China
| | - Mingqing Yuan
- College of Medicine, Guangxi University, Nanning, 530004, China
| | - Xu Liu
- College of Medicine, Guangxi University, Nanning, 530004, China.
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19
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Zhang H, Zhang HR, Zhang J, Hu ML, Ren L, Luo QQ, Qi HZ. Discovery of novel S6K1 inhibitors by an ensemble-based virtual screening method and molecular dynamics simulation. J Mol Model 2023; 29:102. [PMID: 36933164 DOI: 10.1007/s00894-023-05504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/08/2023] [Indexed: 03/19/2023]
Abstract
Ribosomal protein S6 kinase beta-1 (S6K1) is considered a potential target for the treatment of various diseases, such as obesity, type II diabetes, and cancer. Development of novel S6K1 inhibitors is an urgent and important task for the medicinal chemists. In this research, an effective ensemble-based virtual screening method, including common feature pharmacophore model, 3D-QSAR pharmacophore model, naïve Bayes classifier model, and molecular docking, was applied to discover potential S6K1 inhibitors from BioDiversity database with 29,158 compounds. Finally, 7 hits displayed considerable properties and considered as potential inhibitors against S6K1. Further, carefully analyzing the interactions between these 7 hits and key residues in the S6K1 active site, and comparing them with the reference compound PF-4708671, it was found that 2 hits exhibited better binding patterns. In order to further investigate the mechanism of the interactions between 2 hits and S6K1 at simulated physiological conditions, the molecular dynamics simulation was performed. The ΔGbind energies for S6K1-Hit1 and S6K1-Hit2 were - 111.47 ± 1.29 and - 54.29 ± 1.19 kJ mol-1, respectively. Furthermore, deep analysis of these results revealed that Hit1 was the most stable complex, which can stably bind to S6K1 active site, interact with all of the key residues, and induce H1, H2, and M-loop regions changes. Therefore, the identified Hit1 may be a promising lead compound for developing new S6K1 inhibitor for various metabolic diseases treatment.
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Affiliation(s)
- Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, People's Republic of China.
| | - Hong-Rui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, People's Republic of China
| | - Jian Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, People's Republic of China
| | - Mei-Ling Hu
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, People's Republic of China
| | - Li Ren
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, People's Republic of China
| | - Qing-Qing Luo
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, People's Republic of China
| | - Hua-Zhao Qi
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, People's Republic of China
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20
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In silico approach of novel HPPD/PDS dual target inhibitors by pharmacophore, AILDE and molecular docking. J Taiwan Inst Chem Eng 2023. [DOI: 10.1016/j.jtice.2023.104711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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21
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Blanes-Mira C, Fernández-Aguado P, de Andrés-López J, Fernández-Carvajal A, Ferrer-Montiel A, Fernández-Ballester G. Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening. Molecules 2022; 28:molecules28010175. [PMID: 36615367 PMCID: PMC9821981 DOI: 10.3390/molecules28010175] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
The rapid advances of 3D techniques for the structural determination of proteins and the development of numerous computational methods and strategies have led to identifying highly active compounds in computer drug design. Molecular docking is a method widely used in high-throughput virtual screening campaigns to filter potential ligands targeted to proteins. A great variety of docking programs are currently available, which differ in the algorithms and approaches used to predict the binding mode and the affinity of the ligand. All programs heavily rely on scoring functions to accurately predict ligand binding affinity, and despite differences in performance, none of these docking programs is preferable to the others. To overcome this problem, consensus scoring methods improve the outcome of virtual screening by averaging the rank or score of individual molecules obtained from different docking programs. The successful application of consensus docking in high-throughput virtual screening highlights the need to optimize the predictive power of molecular docking methods.
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22
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Screening and Molecular Mechanisms of Novel ACE-Inhibitory Peptides from Gracilariopsis lemaneiformis. Int J Mol Sci 2022; 23:ijms232314850. [PMID: 36499176 PMCID: PMC9739792 DOI: 10.3390/ijms232314850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/10/2022] [Accepted: 11/19/2022] [Indexed: 12/05/2022] Open
Abstract
Candidate peptides with novel angiotensin-I-converting enzyme (ACE) inhibitor activity were obtained from hydrolysates of Gracilariopsis lemaneiformis by virtual screening method. Our results showed that G. lemaneiformis peptides (GLP) could significantly lower blood pressure in spontaneously hypertensive rats (SHR). At least 101 peptide sequences of GLP were identified by LC-MS/MS analysis and subjected to virtual screening. A total of 20 peptides with the highest docking score were selected and chemically synthesized in order to verify their ACE-inhibitory activities. Among them, SFYYGK, RLVPVPY, and YIGNNPAKG showed good effects with IC50 values of 6.45 ± 0.22, 9.18 ± 0.42, and 11.23 ± 0.23 µmoL/L, respectively. Molecular docking studies revealed that three peptides interacted with the active center of ACE by hydrogen bonding, hydrophobic interactions, and electrostatic forces. These peptides could form stable complexes with ACE. Furthermore, SFYYGK, RLVPVPY, and YIGNNPAKG significantly reduced systolic blood pressure (SBP) in SHR. YIGNNPAKG exhibited the highest antihypertensive effect, with the largest decrease in SBP (approximately 23 mmHg). In conclusion, SFYYGK, RLVPVPY, and YIGNNPAKG can function as potent therapeutic candidates for hypertension treatment.
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23
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Vivekanandan S, Vetrivel U, Hanna LE. Design of human immunodeficiency virus-1 neutralizing peptides targeting CD4-binding site: An integrative computational biologics approach. Front Med (Lausanne) 2022; 9:1036874. [DOI: 10.3389/fmed.2022.1036874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
Peptide therapeutics have recently gained momentum in antiviral therapy due to their increased potency and cost-effectiveness. Interaction of the HIV-1 envelope gp120 with the host CD4 receptor is a critical step for viral entry, and therefore the CD4-binding site (CD4bs) of gp120 is a potential hotspot for blocking HIV-1 infection. The present study aimed to design short peptides from well-characterized CD4bs targeting broadly neutralizing antibodies (bNAbs), which could be utilized as bNAb mimetics for viral neutralization. Co-crystallized structures of HIV-1 gp120 in complex with CD4bs-directed bNAbs were used to derive hexameric peptides using the Rosetta Peptiderive protocol. Based on empirical insights into co-crystallized structures, peptides derived from the heavy chain alone were considered. The peptides were docked with both HIV-1 subtype B and C gp120, and the stability of the peptide–antigen complexes was validated using extensive Molecular Dynamics (MD) simulations. Two peptides identified in the study demonstrated stable intermolecular interactions with SER365, GLY366, and GLY367 of the PHE43 cavity in the CD4 binding pocket, and with ASP368 of HIV-1 gp120, thereby mimicking the natural interaction between ASP368gp120 and ARG59CD4–RECEPTOR. Furthermore, the peptides featured favorable physico-chemical properties for virus neutralization suggesting that these peptides may be highly promising bNAb mimetic candidates that may be taken up for experimental validation.
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Elucidation of Prebiotics, Probiotics, Postbiotics, and Target from Gut Microbiota to Alleviate Obesity via Network Pharmacology Study. Cells 2022; 11:cells11182903. [PMID: 36139478 PMCID: PMC9496669 DOI: 10.3390/cells11182903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
The metabolites produced by the gut microbiota have been reported as crucial agents against obesity; however, their key targets have not been revealed completely in complex microbiome systems. Hence, the aim of this study was to decipher promising prebiotics, probiotics, postbiotics, and more importantly, key target(s) via a network pharmacology approach. First, we retrieved the metabolites related to gut microbes from the gutMGene database. Then, we performed a meta-analysis to identify metabolite-related targets via the similarity ensemble approach (SEA) and SwissTargetPrediction (STP), and obesity-related targets were identified by DisGeNET and OMIM databases. After selecting the overlapping targets, we adopted topological analysis to identify core targets against obesity. Furthermore, we employed the integrated networks to microbiota-substrate-metabolite-target (MSMT) via R Package. Finally, we performed a molecular docking test (MDT) to verify the binding affinity between metabolite(s) and target(s) with the Autodock 1.5.6 tool. Based on holistic viewpoints, we performed a filtering step to discover the core targets through topological analysis. Then, we implemented protein-protein interaction (PPI) networks with 342 overlapping target, another subnetwork was constructed with the top 30% degree centrality (DC), and the final core networks were obtained after screening the top 30% betweenness centrality (BC). The final core targets were IL6, AKT1, and ALB. We showed that the three core targets interacted with three other components via the MSMT network in alleviating obesity, i.e., four microbiota, two substrates, and six metabolites. The MDT confirmed that equol (postbiotics) converted from isoflavone (prebiotics) via Lactobacillus paracasei JS1 (probiotics) can bind the most stably on IL6 (target) compared with the other four metabolites (3-indolepropionic acid, trimethylamine oxide, butyrate, and acetate). In this study, we demonstrated that the promising substate (prebiotics), microbe (probiotics), metabolite (postbiotics), and target are suitable for obsesity treatment, providing a microbiome basis for further research.
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Sun Y, Jiao Y, Shi C, Zhang Y. Deep learning-based molecular dynamics simulation for structure-based drug design against SARS-CoV-2. Comput Struct Biotechnol J 2022; 20:5014-5027. [PMID: 36091720 PMCID: PMC9448712 DOI: 10.1016/j.csbj.2022.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/03/2022] [Accepted: 09/03/2022] [Indexed: 11/26/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has led to a global pandemic. Deep learning (DL) technology and molecular dynamics (MD) simulation are two mainstream computational approaches to investigate the geometric, chemical and structural features of protein and guide the relevant drug design. Despite a large amount of research papers focusing on drug design for SARS-COV-2 using DL architectures, it remains unclear how the binding energy of the protein-protein/ligand complex dynamically evolves which is also vital for drug development. In addition, traditional deep neural networks usually have obvious deficiencies in predicting the interaction sites as protein conformation changes. In this review, we introduce the latest progresses of the DL and DL-based MD simulation approaches in structure-based drug design (SBDD) for SARS-CoV-2 which could address the problems of protein structure and binding prediction, drug virtual screening, molecular docking and complex evolution. Furthermore, the current challenges and future directions of DL-based MD simulation for SBDD are also discussed.
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Affiliation(s)
- Yao Sun
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Yanqi Jiao
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Chengcheng Shi
- State Key Lab of Urban Water Resource and Environment, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Yang Zhang
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
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Bajusz D, Keserű GM. Maximizing the integration of virtual and experimental screening in hit discovery. Expert Opin Drug Discov 2022; 17:629-640. [PMID: 35671403 DOI: 10.1080/17460441.2022.2085685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Experimental and virtual screening contributes to the discovery of more than 50% of clinical candidates. Considering the similar concept and goals, early-phase drug discovery would benefit from the effective integration of these approaches. AREAS COVERED After reviewing the recent trends in both experimental and virtual screening, the authors discuss different integration strategies from parallel, focused, sequential, and iterative screening. Strategic considerations are demonstrated in a number of real-life case studies. EXPERT OPINION Experimental and virtual screening are complementary approaches that should be integrated in lead discovery settings. Virtual screening can access extremely large synthetically feasible chemical space that can be effectively searched on GPU clusters or cloud architectures. Experimental screening provides reliable datasets by quantitative HTS applications, and DNA-encoded libraries (DEL) have enlarged the chemical space covered by these technologies. These developments, together with the use of artificial intelligence methods, represent new options for their efficient integration. The case studies discussed here demonstrate the benefits of complementary strategies, such as focused and iterative screening.
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Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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Tanwar S, Auberger P, Gillet G, DiPaola M, Tsaioun K, Villoutreix BO. A new ChEMBL dataset for the similarity-based target fishing engine FastTargetPred: Annotation of an exhaustive list of linear tetrapeptides. Data Brief 2022; 42:108159. [PMID: 35496477 PMCID: PMC9046614 DOI: 10.1016/j.dib.2022.108159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022] Open
Abstract
Drug discovery often requires the identification of off-targets as the binding of a compound to targets other than the intended target(s) can be beneficial in some cases or detrimental in other situations (e.g., binding to anti-targets). Such investigations are also of importance during the early stage of a project, for example when the target is not known (e.g., phenotypic screening). Target identification can be performed in-vitro, but various in-silico methods have also been developed in recent years to facilitate target identification and help generate ideas. FastTargetPred is one such approach, it is a freely available Python/C program that attempts to predict putative macromolecular targets (i.e., target fishing) for a single input small molecule query or an entire compound collection using established chemical similarity search approaches. Indeed, the putative macromolecular target(s) of a small chemical compound can be predicted by identifying ligands that are known experimentally to bind to some targets and that are structurally similar to the input query chemical compound. Therefore, this type of target fishing approach relies on a large collection of experimentally validated macromolecule-chemical compound binding data. The small chemical compounds can be described as molecular fingerprints encoding their structural characteristics as a vector. The published version of FastTargetPred used ligand-target binding data extracted from the release 25 (2019) of the ChEMBL database. Here we provide a new dataset for FastTargetPred extracted from the last ChEMBL release, namely, at the time of writing, ChEMBL29 (2021). Four fingerprints were computed (ECFP4, ECFP6, MACCS and PL) for the extracted compound dataset (714,780 unique ChEMBL29 compounds while the entire ChEMBL29 database contained about 2.1 million compounds). However, it was not possible to compute fingerprints for 19 molecules because of their unusual chemistry (complex macrocycles). These data files were then prepared so as to be compatible with FastTargetPred requirements. The 714,761 ChEMBL chemical compounds with computed fingerprints hit 6,477 macromolecular targets based on the selected criteria. For these ChEMBL compounds a ChEMBL target ID is reported and these target IDs were matched with the corresponding UniProt IDs. Thus, when available, the UniProt ID is provided, the protein UniProt name, the gene name, the organism as well as annotated involvement in diseases, gene ontology data, and cross-references to the Reactome pathway database. As short peptides can be of interest for drug discovery and chemical biology endeavours, we were interested in attempting to predict putative macromolecular targets for a previously reported exhaustive combination of peptides containing four natural amino acids (i.e., 20 × 20 × 20 × 20 = 160,000 linear tetrapeptides) using FastTargetPred and the presently generated ChEMBL29 dataset. With the parameters used, putative targets are reported for 63,944 unique query peptides. These target predictions are provided in two different searchable files with hyperlinks to the ChEMBL, UniProt and Reactome databases.
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Du BX, Qin Y, Jiang YF, Xu Y, Yiu SM, Yu H, Shi JY. Compound–protein interaction prediction by deep learning: Databases, descriptors and models. Drug Discov Today 2022; 27:1350-1366. [DOI: 10.1016/j.drudis.2022.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/19/2021] [Accepted: 02/28/2022] [Indexed: 11/24/2022]
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Wu Z, Ma H, Liu Z, Zheng L, Yu Z, Cao S, Fang W, Wu L, Li W, Liu G, Huang J, Tang Y. wSDTNBI: a novel network-based inference method for virtual screening. Chem Sci 2022; 13:1060-1079. [PMID: 35211272 PMCID: PMC8790893 DOI: 10.1039/d1sc05613a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/15/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, the rapid development of network-based methods for the prediction of drug-target interactions (DTIs) provides an opportunity for the emergence of a new type of virtual screening (VS), namely, network-based VS. Herein, we reported a novel network-based inference method named wSDTNBI. Compared with previous network-based methods that use unweighted DTI networks, wSDTNBI uses weighted DTI networks whose edge weights are correlated with binding affinities. A two-pronged approach based on weighted DTI and drug-substructure association networks was employed to calculate prediction scores. To show the practical value of wSDTNBI, we performed network-based VS on retinoid-related orphan receptor γt (RORγt), and purchased 72 compounds for experimental validation. Seven of the purchased compounds were confirmed to be novel RORγt inverse agonists by in vitro experiments, including ursonic acid and oleanonic acid with IC50 values of 10 nM and 0.28 μM, respectively. Moreover, the direct contact between ursonic acid and RORγt was confirmed using the X-ray crystal structure, and in vivo experiments demonstrated that ursonic acid and oleanonic acid have therapeutic effects on multiple sclerosis. These results indicate that wSDTNBI might be a powerful tool for network-based VS in drug discovery.
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Affiliation(s)
- Zengrui Wu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Hui Ma
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Zehui Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Lulu Zheng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Zhuohang Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Shuying Cao
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Wenqing Fang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Lili Wu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Jin Huang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
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Azevedo TSM, Silva LKB, Lima ÁS, Pereira MM, Franceschi E, Faria Soares CM. In Silico Evaluation of Enzymatic Tunnels in the Biotransformation of α-Tocopherol Esters. Front Bioeng Biotechnol 2022; 9:805059. [PMID: 35127674 PMCID: PMC8814584 DOI: 10.3389/fbioe.2021.805059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Motivation: α-Tocopherol is a molecule obtained primarily from plant sources that are important for the pharmaceutical and cosmetics industry. However, this component has some limitations such as sensitivity to oxygen, presence of light, and high temperatures. For this molecule to become more widely used, it is important to carry out a structural modification so that there is better stability and thus it can carry out its activities. To carry out this structural modification, some modifications are carried out, including the application of biotransformation using enzymes as biocatalysts. Thus, the application of a computational tool that helps in understanding the transport mechanisms of molecules in the tunnels present in the enzymatic structures is of fundamental importance because it promotes a computational screening facilitating bench applications. Objective: The aim of this work was to perform a computational analysis of the biotransformation of α-tocopherol into tocopherol esters, observing the tunnels present in the enzymatic structures as well as the energies which correspond to the transport of molecules. Method: To carry out this work, 9 lipases from different organisms were selected; their structures were analyzed by identifying the tunnels (quantity, conformation, and possibility of transport) and later the calculations of substrate transport for the biotransformation reaction in the identified tunnels were carried out. Additionally, the transport of the product obtained in the reaction through the tunnels was also carried out. Results: In this work, the quantity of existing tunnels in the morphological conformational characteristics in the lipases was verified. Thus, the enzymes with fewer tunnels were RML (3 tunnels), LBC and RNL (4 tunnels), PBLL (5 tunnels), CALB (6 tunnels), HLG (7 tunnels), and LCR and LTL (8 tunnels) and followed by the enzyme LPP with the largest number of tunnels (39 tunnels). However, the enzyme that was most likely to transport substrates in terms of α-tocopherol biotransformation (in relation to the Emax and Ea energies of ligands and products) was CALB, as it obtains conformational and transport characteristics of molecules with a particularity. The most conditions of transport analysis were α-tocopherol tunnel 3 (Emax: −4.6 kcal/mol; Ea: 1.1 kcal/mol), vinyl acetate tunnel 1 (Emax: −2.4 kcal/mol; Ea: 0.1 kcal/mol), and tocopherol acetate tunnel 2 (Emax: −3.7 kcal/mol; Ea: 2 kcal/mol).
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Affiliation(s)
- Tamara Stela Mendonça Azevedo
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
| | - Lavínia Kelly Barros Silva
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
| | - Álvaro Silva Lima
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
| | - Matheus Mendonça Pereira
- Department of Materials and Ceramic Engineering, CICECO ‐ Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
| | - Elton Franceschi
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
| | - Cleide Mara Faria Soares
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
- *Correspondence: Cleide Mara Faria Soares,
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Singla RK, Joon S, Shen L, Shen B. Translational Informatics for Natural Products as Antidepressant Agents. Front Cell Dev Biol 2022; 9:738838. [PMID: 35127696 PMCID: PMC8811306 DOI: 10.3389/fcell.2021.738838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022] Open
Abstract
Depression, a neurological disorder, is a universally common and debilitating illness where social and economic issues could also become one of its etiologic factors. From a global perspective, it is the fourth leading cause of long-term disability in human beings. For centuries, natural products have proven their true potential to combat various diseases and disorders, including depression and its associated ailments. Translational informatics applies informatics models at molecular, imaging, individual, and population levels to promote the translation of basic research to clinical applications. The present review summarizes natural-antidepressant-based translational informatics studies and addresses challenges and opportunities for future research in the field.
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Affiliation(s)
- Rajeev K. Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Shikha Joon
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Li Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Bairong Shen,
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Mao J, Luo QQ, Zhang HR, Zheng XH, Shen C, Qi HZ, Hu ML, Zhang H. Discovery of microtubule stabilizers with novel scaffold structures based on virtual screening, biological evaluation, and molecular dynamics simulation. Chem Biol Interact 2021; 352:109784. [PMID: 34932952 DOI: 10.1016/j.cbi.2021.109784] [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: 08/05/2021] [Revised: 11/20/2021] [Accepted: 12/16/2021] [Indexed: 02/08/2023]
Abstract
Disrupting the dynamics and structures of microtubules can perturb mitotic spindle formation, cause cell cycle arrest in G2/M phase, and subsequently lead to cellular death via apoptosis. In this investigation, the structure-based virtual screening methods, including molecular docking and rescoring, and similarity analysis of interaction molecular fingerprints, were developed to discover novel tubulin inhibitors from ChemDiv database with 1,601,806 compounds. The screened compounds were further filtered by PAINS, ADME/T, Toxscore, SAscore, and Drug-likeness analysis. Finally, 17 hit compounds were selected, and then submitted to the biologic evaluation. Among these hits, the P2 exhibited the strongest antiproliferative activity against four tumor cells including HeLa, HepG2, MCF-7, and A549. The in vitro tubulin polymerization assay revealed P2 could promote tubulin polymerization in a dose dependent manner. Finally, in order to analyze the interaction modes of complexes, the molecular dynamics simulation was performed to investigate the interactions between P2 and tubulin. The molecular dynamics simulation analysis showed that P2 could stably bind to taxane site, induced H6-H7, B9-B10, and M-loop regions changes. The ΔGbind energies of tubulin-P2 and tubulin-paclitaxel were -68.25 ± 12.98 and -146.05 ± 16.17 kJ mol-1, respectively, which were in line with the results of the experimental test. Therefore, P2 has been well characterized as lead compounds for developing new tubulin inhibitors with potential anticancer activity.
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Affiliation(s)
- Jun Mao
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Qing-Qing Luo
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hong-Rui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Xiu-He Zheng
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Chen Shen
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hua-Zhao Qi
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Mei-Ling Hu
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, PR China.
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Abstract
Stochastic computing is an emerging scientific field pushed by the need for developing high-performance artificial intelligence systems in hardware to quickly solve complex data processing problems. This is the case of virtual screening, a computational task aimed at searching across huge molecular databases for new drug leads. In this work, we show a classification framework in which molecules are described by an energy-based vector. This vector is then processed by an ultra-fast artificial neural network implemented through FPGA by using stochastic computing techniques. Compared to other previously published virtual screening methods, this proposal provides similar or higher accuracy, while it improves processing speed by about two or three orders of magnitude.
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Oh KK, Adnan M, Cho DH. Elucidating Drug-Like Compounds and Potential Mechanisms of Corn Silk ( Stigma Maydis) against Obesity: A Network Pharmacology Study. Curr Issues Mol Biol 2021; 43:1906-1936. [PMID: 34889899 PMCID: PMC8929052 DOI: 10.3390/cimb43030133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Corn silk (Stigma Maydis) has been utilized as an important herb against obesity by Chinese, Korean, and Native Americans, but its phytochemicals and mechanisms(s) against obesity have not been deciphered completely. This study aimed to identify promising bioactive constituents and mechanism of action(s) of corn silk (CS) against obesity via network pharmacology. The compounds from CS were identified using Gas Chromatography Mass Spectrometry (GC-MS) and were confirmed ultimately by Lipinski’s rule via SwissADME. The relationships of the compound-targets or obesity-related targets were confirmed by public bioinformatics. The signaling pathways related to obesity, protein-protein interaction (PPI), and signaling pathways-targets-bioactives (STB) were constructed, visualized, and analyzed by RPackage. Lastly, Molecular Docking Test (MDT) was performed to validate affinity between ligand(s) and protein(s) on key signaling pathway(s). We identified a total of 36 compounds from CS via GC-MS, all accepted by Lipinski’s rule. The number of 36 compounds linked to 154 targets, 85 among 154 targets related directly to obesity-targets (3028 targets). Of the final 85 targets, we showed that the PPI network (79 edges, 357 edges), 12 signaling pathways on a bubble chart, and STB network (67 edges, 239 edges) are considered as therapeutic components. The MDT confirmed that two key activators (β-Amyrone, β-Stigmasterol) bound most stably to PPARA, PPARD, PPARG, FABP3, FABP4, and NR1H3 on the PPAR signaling pathway, also, three key inhibitors (Neotocopherol, Xanthosine, and β-Amyrone) bound most tightly to AKT1, IL6, FGF2, and PHLPP1 on the PI3K-Akt signaling pathway. Overall, we provided promising key signaling pathways, targets, and bioactives of CS against obesity, suggesting crucial pharmacological evidence for further clinical testing.
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Oh KK, Adnan M, Cho DH. Network Pharmacology Study on Morus alba L. Leaves: Pivotal Functions of Bioactives on RAS Signaling Pathway and Its Associated Target Proteins against Gout. Int J Mol Sci 2021; 22:9372. [PMID: 34502281 PMCID: PMC8431517 DOI: 10.3390/ijms22179372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/27/2022] Open
Abstract
M. alba L. is a valuable nutraceutical plant rich in potential bioactive compounds with promising anti-gouty arthritis. Here, we have explored bioactives, signaling pathways, and key proteins underlying the anti-gout activity of M. alba L. leaves for the first-time utilizing network pharmacology. Bioactives in M. alba L. leaves were detected through GC-MS (Gas Chromatography-Mass Spectrum) analysis and filtered by Lipinski's rule. Target proteins connected to the filtered compounds and gout were selected from public databases. The overlapping target proteins between bioactives-interacted target proteins and gout-targeted proteins were identified using a Venn diagram. Bioactives-Proteins interactive networking for gout was analyzed to identify potential ligand-target and visualized the rich factor on the R package via the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway on STRING. Finally, a molecular docking test (MDT) between bioactives and target proteins was analyzed via AutoDock Vina. Gene Set Enrichment Analysis (GSEA) demonstrated that mechanisms of M. alba L. leaves against gout were connected to 17 signaling pathways on 26 compounds. AKT1 (AKT Serine/Threonine Kinase 1), γ-Tocopherol, and RAS signaling pathway were selected as a hub target, a key bioactive, and a hub signaling pathway, respectively. Furthermore, three main compounds (γ-Tocopherol, 4-Dehydroxy-N-(4,5-methylenedioxy-2-nitrobenzylidene) tyramine, and Lanosterol acetate) and three key target proteins-AKT1, PRKCA, and PLA2G2A associated with the RAS signaling pathway were noted for their highest affinity on MDT. The identified three key bioactives in M. alba L. leaves might contribute to recovering gouty condition by inactivating the RAS signaling pathway.
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Affiliation(s)
| | | | - Dong Ha Cho
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (K.K.O.); (M.A.)
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Recent Advances in In Silico Target Fishing. Molecules 2021; 26:molecules26175124. [PMID: 34500568 PMCID: PMC8433825 DOI: 10.3390/molecules26175124] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/24/2022] Open
Abstract
In silico target fishing, whose aim is to identify possible protein targets for a query molecule, is an emerging approach used in drug discovery due its wide variety of applications. This strategy allows the clarification of mechanism of action and biological activities of compounds whose target is still unknown. Moreover, target fishing can be employed for the identification of off targets of drug candidates, thus recognizing and preventing their possible adverse effects. For these reasons, target fishing has increasingly become a key approach for polypharmacology, drug repurposing, and the identification of new drug targets. While experimental target fishing can be lengthy and difficult to implement, due to the plethora of interactions that may occur for a single small-molecule with different protein targets, an in silico approach can be quicker, less expensive, more efficient for specific protein structures, and thus easier to employ. Moreover, the possibility to use it in combination with docking and virtual screening studies, as well as the increasing number of web-based tools that have been recently developed, make target fishing a more appealing method for drug discovery. It is especially worth underlining the increasing implementation of machine learning in this field, both as a main target fishing approach and as a further development of already applied strategies. This review reports on the main in silico target fishing strategies, belonging to both ligand-based and receptor-based approaches, developed and applied in the last years, with a particular attention to the different web tools freely accessible by the scientific community for performing target fishing studies.
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Sabe VT, Ntombela T, Jhamba LA, Maguire GEM, Govender T, Naicker T, Kruger HG. Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review. Eur J Med Chem 2021; 224:113705. [PMID: 34303871 DOI: 10.1016/j.ejmech.2021.113705] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-clinical drug discovery, and various computational techniques and software programs are typically used in combination, in a bid to achieve the desired outcome. Several approved drugs have been developed with the aid of CADD. On SciFinder®, we evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD. The primary focus of this review was on the databases screened, virtual screening and/or molecular docking software program used. Furthermore, we evaluated the studies that subsequently performed molecular dynamics (MD) simulations and we reviewed the software programs applied, the application of density functional theory (DFT) calculations and experimental assays. To represent the latest trends, the most recent data obtained was between 2015 and 2020, consequently the most frequently employed techniques and software programs were recorded. Among these, the ZINC database was the most widely preferred with an average use of 31.2%. Structure-based virtual screening (SBVS) was the most prominently used type of virtual screening and it accounted for an average of 57.6%, with AutoDock being the preferred virtual screening/molecular docking program with 41.8% usage. Following the screening process, 38.5% of the studies performed MD simulations to complement the virtual screening and GROMACS with 39.3% usage, was the popular MD software program. Among the computational techniques, DFT was the least applied whereby it only accounts for 0.02% average use. An average of 36.5% of the studies included reports on experimental evaluations following virtual screening. Ultimately, since the inception and application of CADD in pre-clinical drug discovery, more than 70 approved drugs have been discovered, and this number is steadily increasing over time.
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Affiliation(s)
- Victor T Sabe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Lindiwe A Jhamba
- HIV Pathogenesis Program, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Faculty of Science and Agriculture, Department of Chemistry, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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Medina-Franco JL, Sánchez-Cruz N, López-López E, Díaz-Eufracio BI. Progress on open chemoinformatic tools for expanding and exploring the chemical space. J Comput Aided Mol Des 2021; 36:341-354. [PMID: 34143323 PMCID: PMC8211976 DOI: 10.1007/s10822-021-00399-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 01/10/2023]
Abstract
The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure-property relationships where the property can be a biological activity or any other characteristic of interest to a particular chemistry discipline. The chemical space is highly dependent on the molecular representation that is also a cornerstone concept in computational chemistry. Herein, we discuss the recent progress on chemoinformatic tools developed to expand and characterize the chemical space of compound data sets using different types of molecular representations, generate visual representations of such spaces, and explore structure-property relationships in the context of chemical spaces. We emphasize the development of methods and freely available tools focusing on drug discovery applications. We also comment on the general advantages and shortcomings of using freely available and easy-to-use tools and discuss the value of using such open resources for research, education, and scientific dissemination.
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Affiliation(s)
- José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
| | - Norberto Sánchez-Cruz
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Edgar López-López
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.,Departamento de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, 07000, Mexico City, Mexico
| | - Bárbara I Díaz-Eufracio
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
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Aguero S, Megy S, Eremina VV, Kalashnikov AI, Krylova SG, Kulagina DA, Lopatina KA, Fournier M, Povetyeva TN, Vorozhtsov AB, Sysolyatin SV, Zhdanov VV, Terreux R. Discovery of a Novel Non-Narcotic Analgesic Derived from the CL-20 Explosive: Synthesis, Pharmacology, and Target Identification of Thiowurtzine, a Potent Inhibitor of the Opioid Receptors and the Ion Channels. ACS OMEGA 2021; 6:15400-15411. [PMID: 34151118 PMCID: PMC8210403 DOI: 10.1021/acsomega.1c01786] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
The number of candidate molecules for new non-narcotic analgesics is extremely limited. Here, we report the identification of thiowurtzine, a new potent analgesic molecule with promising application in chronic pain treatment. We describe the chemical synthesis of this unique compound derived from the hexaazaisowurtzitane (CL-20) explosive molecule. Then, we use animal experiments to assess its analgesic activity in vivo upon chemical, thermal, and mechanical exposures, compared to the effect of several reference drugs. Finally, we investigate the potential receptors of thiowurtzine in order to better understand its complex mechanism of action. We use docking, molecular modeling, and molecular dynamics simulations to identify and characterize the potential targets of the drug and confirm the results of the animal experiments. Our findings finally indicate that thiowurtzine may have a complex mechanism of action by essentially targeting the mu opioid receptor, the TRPA1 ion channel, and the Cav voltage-gated calcium channel.
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Affiliation(s)
- Stephanie Aguero
- Équipe
ECMO, Laboratoire de Biologie Tissulaire et d’Ingénierie
(LBTI), UMR5305, Université Lyon 1, Lyon 69367, France
| | - Simon Megy
- Équipe
ECMO, Laboratoire de Biologie Tissulaire et d’Ingénierie
(LBTI), UMR5305, Université Lyon 1, Lyon 69367, France
| | - Valeria V. Eremina
- Institute
for Problems of Chemical and Energetic Technologies, Siberian Branch of the Russian Academy of Sciences (IPCET SB RAS), Biysk 659322, Altai Krai, Russia
| | - Alexander I. Kalashnikov
- Institute
for Problems of Chemical and Energetic Technologies, Siberian Branch of the Russian Academy of Sciences (IPCET SB RAS), Biysk 659322, Altai Krai, Russia
| | - Svetlana G. Krylova
- Goldberg
Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center of the Russian
Academy of Sciences, Tomsk 634028, Russia
| | - Daria A. Kulagina
- Institute
for Problems of Chemical and Energetic Technologies, Siberian Branch of the Russian Academy of Sciences (IPCET SB RAS), Biysk 659322, Altai Krai, Russia
| | - Ksenia A. Lopatina
- Goldberg
Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center of the Russian
Academy of Sciences, Tomsk 634028, Russia
| | - Mailys Fournier
- Équipe
ECMO, Laboratoire de Biologie Tissulaire et d’Ingénierie
(LBTI), UMR5305, Université Lyon 1, Lyon 69367, France
| | - Tatyana N. Povetyeva
- Goldberg
Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center of the Russian
Academy of Sciences, Tomsk 634028, Russia
| | | | - Sergey V. Sysolyatin
- Institute
for Problems of Chemical and Energetic Technologies, Siberian Branch of the Russian Academy of Sciences (IPCET SB RAS), Biysk 659322, Altai Krai, Russia
| | - Vadim V. Zhdanov
- Goldberg
Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center of the Russian
Academy of Sciences, Tomsk 634028, Russia
| | - Raphael Terreux
- Équipe
ECMO, Laboratoire de Biologie Tissulaire et d’Ingénierie
(LBTI), UMR5305, Université Lyon 1, Lyon 69367, France
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Medina-Franco JL, Martinez-Mayorga K, Fernández-de Gortari E, Kirchmair J, Bajorath J. Rationality over fashion and hype in drug design. F1000Res 2021; 10. [PMID: 34164109 PMCID: PMC8201421 DOI: 10.12688/f1000research.52676.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 01/05/2023] Open
Abstract
The current hype associated with machine learning and artificial intelligence often confuses scientists and students and may lead to uncritical or inappropriate applications of computational approaches. Even the field of computer-aided drug design (CADD) is not an exception. The situation is ambivalent. On one hand, more scientists are becoming aware of the benefits of learning from available data and are beginning to derive predictive models before designing experiments. However, on the other hand, easy accessibility of in silico tools comes at the risk of using them as "black boxes" without sufficient expert knowledge, leading to widespread misconceptions and problems. For example, results of computations may be taken at face value as "nothing but the truth" and data visualization may be used only to generate "pretty and colorful pictures". Computational experts might come to the rescue and help to re-direct such efforts, for example, by guiding interested novices to conduct meaningful data analysis, make scientifically sound predictions, and communicate the findings in a rigorous manner. However, this is not always ensured. This contribution aims to encourage investigators entering the CADD arena to obtain adequate computational training, communicate or collaborate with experts, and become aware of the fundamentals of computational methods and their given limitations, beyond the hype. By its very nature, this Opinion is partly subjective and we do not attempt to provide a comprehensive guide to the best practices of CADD; instead, we wish to stimulate an open discussion within the scientific community and advocate rational rather than fashion-driven use of computational methods. We take advantage of the open peer-review culture of F1000Research such that reviewers and interested readers may engage in this discussion and obtain credits for their candid personal views and comments. We hope that this open discussion forum will contribute to shaping the future practice of CADD.
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Affiliation(s)
- José L Medina-Franco
- DIFACQUIM research group, Department of Pharmacy, School of Pharmacy, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | | | - Eli Fernández-de Gortari
- Nanosafety Laboratory, International Iberian Nanotechnology Laboratory, Braga, 4715-330, Portugal
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53115, Germany
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Singh N, Villoutreix BO. Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. Comput Struct Biotechnol J 2021; 19:2537-2548. [PMID: 33936562 PMCID: PMC8074526 DOI: 10.1016/j.csbj.2021.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
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Affiliation(s)
- Natesh Singh
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Bruno O. Villoutreix
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
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Villoutreix BO, Krishnamoorthy R, Tamouza R, Leboyer M, Beaune P. Chemoinformatic Analysis of Psychotropic and Antihistaminic Drugs in the Light of Experimental Anti-SARS-CoV-2 Activities. Adv Appl Bioinform Chem 2021; 14:71-85. [PMID: 33880039 PMCID: PMC8051956 DOI: 10.2147/aabc.s304649] [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: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction There is an urgent need to identify therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. Objective Based upon clinical observations, we proposed that some psychotropic and antihistaminic drugs could protect psychiatric patients from SARS-CoV-2 infection. This observation is investigated in the light of experimental in vitro data on SARS-CoV-2. Methods SARS-CoV-2 high-throughput screening results are available at the NCATS COVID-19 portal. We investigated the in vitro anti-viral activity of many psychotropic and antihistaminic drugs using chemoinformatics approaches. Results and Discussion We analyze our clinical observations in the light of SARS-CoV-2 experimental screening results and propose that several cationic amphiphilic psychotropic and antihistaminic drugs could protect people from SARS-CoV-2 infection; some of these molecules have very limited adverse effects and could be used as prophylactic drugs. Other cationic amphiphilic drugs used in other disease areas are also highlighted. Recent analyses of patient electronic health records reported by several research groups indicate that some of these molecules could be of interest at different stages of the disease progression. In addition, recently reported drug combination studies further suggest that it might be valuable to associate several cationic amphiphilic drugs. Taken together, these observations underline the need for clinical trials to fully evaluate the potentials of these molecules, some fitting in the so-called category of broad-spectrum antiviral agents. Repositioning orally available drugs that have moderate side effects and should act on molecular mechanisms less prone to drug resistance would indeed be of utmost importance to deal with COVID-19.
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Affiliation(s)
- Bruno O Villoutreix
- INSERM U1141, NeuroDiderot, Université de Paris, Hôpital Robert-Debré, Paris, F-75019, France
| | - Rajagopal Krishnamoorthy
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuropsychiatrie Translationnelle, AP-HP, Département Medico-Universitaire de Psychiatrie et d'Addictologie (DMU ADAPT), Hôpital Henri Mondor, Fondation FondaMental, Créteil, F-94010, France
| | - Ryad Tamouza
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuropsychiatrie Translationnelle, AP-HP, Département Medico-Universitaire de Psychiatrie et d'Addictologie (DMU ADAPT), Hôpital Henri Mondor, Fondation FondaMental, Créteil, F-94010, France
| | - Marion Leboyer
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuropsychiatrie Translationnelle, AP-HP, Département Medico-Universitaire de Psychiatrie et d'Addictologie (DMU ADAPT), Hôpital Henri Mondor, Fondation FondaMental, Créteil, F-94010, France
| | - Philippe Beaune
- INSERM U1138, Centre de Recherche des Cordeliers, Université de Paris, Paris, 75006, France
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Sánchez-Cruz N, Medina-Franco JL. Epigenetic Target Profiler: A Web Server to Predict Epigenetic Targets of Small Molecules. J Chem Inf Model 2021; 61:1550-1554. [PMID: 33729791 DOI: 10.1021/acs.jcim.1c00045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The identification of protein targets of small molecules is essential for drug discovery. With the increasing amount of chemogenomic data in the public domain, multiple ligand-based models for target prediction have emerged. However, these models are generally biased by the number of known ligands for different targets, which involves an under-representation of epigenetic targets, and despite the increasing importance of epigenetic targets in drug discovery, there are no open tools for epigenetic target prediction. In this work, we introduce Epigenetic Target Profiler (ETP), a freely accessible and easy-to-use web application for the prediction of epigenetic targets of small molecules. For a query compound, ETP predicts its bioactivity profile over a panel of 55 different epigenetic targets. To that aim, ETP uses a consensus model based on two binary classification models for each target, relying on support vector machines and built on molecular fingerprints of different design. A distance-to-model parameter related to the reliability of the predictions is included to facilitate their interpretability and assist in the identification of small molecules with potential epigenetic activity. Epigenetic Target Profiler is freely available at http://www.epigenetictargetprofiler.com.
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Affiliation(s)
- Norberto Sánchez-Cruz
- DIFACQUIM research group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - José L Medina-Franco
- DIFACQUIM research group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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Sang Y, Mejuto JC, Xiao J, Simal-Gandara J. Assessment of Glyphosate Impact on the Agrofood Ecosystem. PLANTS (BASEL, SWITZERLAND) 2021; 10:405. [PMID: 33672572 PMCID: PMC7924050 DOI: 10.3390/plants10020405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
Agro-industries should adopt effective strategies to use agrochemicals such as glyphosate herbicides cautiously in order to protect public health. This entails careful testing and risk assessment of available choices, and also educating farmers and users with mitigation strategies in ecosystem protection and sustainable development. The key to success in this endeavour is using scientific research on biological pest control, organic farming and regulatory control, etc., for new developments in food production and safety, and for environmental protection. Education and research is of paramount importance for food and nutrition security in the shadow of climate change, and their consequences in food production and consumption safety and sustainability. This review, therefore, diagnoses on the use of glyphosate and the associated development of glyphosate-resistant weeds. It also deals with the risk assessment on human health of glyphosate formulations through environment and dietary exposures based on the impact of glyphosate and its metabolite AMPA-(aminomethyl)phosphonic acid-on water and food. All this to setup further conclusions and recommendations on the regulated use of glyphosate and how to mitigate the adverse effects.
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Affiliation(s)
- Yaxin Sang
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China;
| | - Juan-Carlos Mejuto
- Department of Physical Chemistry, Faculty of Science, University of Vigo—Ourense Campus, E32004 Ourense, Spain;
| | - Jianbo Xiao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo—Ourense Campus, E32004 Ourense, Spain
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo—Ourense Campus, E32004 Ourense, Spain
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Villoutreix BO, Calvez V, Marcelin AG, Khatib AM. In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Int J Mol Sci 2021; 22:1695. [PMID: 33567580 PMCID: PMC7915722 DOI: 10.3390/ijms22041695] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells. It has been reported that the UK and South African strains may have higher transmission capabilities, eventually in part due to amino acid substitutions on the SARS-CoV-2 Spike protein. The pathogenicity seems modified but is still under investigation. Here we used the experimental structure of the Spike RBD domain co-crystallized with part of the ACE2 receptor, several in silico methods and numerous experimental data reported recently to analyze the possible impacts of three amino acid replacements (Spike K417N, E484K, N501Y) with regard to ACE2 binding. We found that the N501Y replacement in this region of the interface (present in both the UK and South African strains) should be favorable for the interaction with ACE2, while the K417N and E484K substitutions (South African strain) would seem neutral or even unfavorable. It is unclear if the N501Y substitution in the South African strain could counterbalance the K417N and E484K Spike replacements with regard to ACE2 binding. Our finding suggests that the UK strain should have higher affinity toward ACE2 and therefore likely increased transmissibility and possibly pathogenicity. If indeed the South African strain has a high transmission level, this could be due to the N501Y replacement and/or to substitutions in regions located outside the direct Spike-ACE2 interface but not so much to the K417N and E484K replacements. Yet, it should be noted that amino acid changes at Spike position 484 can lead to viral escape from neutralizing antibodies. Further, these amino acid substitutions do not seem to induce major structural changes in this region of the Spike protein. This structure-function study allows us to rationalize some observations made for the UK strain but raises questions for the South African strain.
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Affiliation(s)
- Bruno O. Villoutreix
- Integrative Computational Pharmacology and Data Mining, INSERM UMR 1141, NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de Virologie, F75013 Paris, France; (V.C.); (A.-G.M.)
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM 1136, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de Virologie, F75013 Paris, France; (V.C.); (A.-G.M.)
| | - Abdel-Majid Khatib
- Université de Bordeaux, INSERM, LAMC, U1029, F-33600 Pessac, France
- Institut Bergonié, 33000 Bordeaux, France
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Shen C, Weng G, Zhang X, Leung ELH, Yao X, Pang J, Chai X, Li D, Wang E, Cao D, Hou T. Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening? Brief Bioinform 2021; 22:6070382. [PMID: 33418562 DOI: 10.1093/bib/bbaa410] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/26/2020] [Accepted: 12/12/2020] [Indexed: 12/13/2022] Open
Abstract
Machine-learning (ML)-based scoring functions (MLSFs) have gradually emerged as a promising alternative for protein-ligand binding affinity prediction and structure-based virtual screening. However, clouds of doubts have still been raised against the benefits of this novel type of scoring functions (SFs). In this study, to benchmark the performance of target-specific MLSFs on a relatively unbiased dataset, the MLSFs trained from three representative protein-ligand interaction representations were assessed on the LIT-PCBA dataset, and the classical Glide SP SF and three types of ligand-based quantitative structure-activity relationship (QSAR) models were also utilized for comparison. Two major aspects in virtual screening campaigns, including prediction accuracy and hit novelty, were systematically explored. The calculation results illustrate that the tested target-specific MLSFs yielded generally superior performance over the classical Glide SP SF, but they could hardly outperform the 2D fingerprint-based QSAR models. Although substantial improvements could be achieved by integrating multiple types of protein-ligand interaction features, the MLSFs were still not sufficient to exceed MACCS-based QSAR models. In terms of the correlations between the hit ranks or the structures of the top-ranked hits, the MLSFs developed by different featurization strategies would have the ability to identify quite different hits. Nevertheless, it seems that target-specific MLSFs do not have the intrinsic attributes of a traditional SF and may not be a substitute for classical SFs. In contrast, MLSFs can be regarded as a new derivative of ligand-based QSAR models. It is expected that our study may provide valuable guidance for the assessment and further development of target-specific MLSFs.
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Affiliation(s)
- Chao Shen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Gaoqi Weng
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Xujun Zhang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China
| | - Jinping Pang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Xin Chai
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dan Li
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
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47
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Radan M, Bošković J, Dobričić V, Čudina O, Nikolić K. Current computer-aided drug design methodologies in discovery of novel drug candidates for neuropsychiatric and inflammatory diseases. ARHIV ZA FARMACIJU 2021. [DOI: 10.5937/arhfarm71-32523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Drug discovery and development is a very challenging, expensive and time-consuming process. Impressive technological advances in computer sciences and molecular biology have made it possible to use computer-aided drug design (CADD) methods in various stages of the drug discovery and development pipeline. Nowadays, CADD presents an efficacious and indispensable tool, widely used in medicinal chemistry, to lead rational drug design and synthesis of novel compounds. In this article, an overview of commonly used CADD approaches from hit identification to lead optimization was presented. Moreover, different aspects of design of multitarget ligands for neuropsychiatric and anti-inflammatory diseases were summarized. Apparently, designing multi-target directed ligands for treatment of various complex diseases may offer better efficacy, and fewer side effects. Antipsychotics that act through aminergic G protein-coupled receptors (GPCRs), especially Dopamine D2 and serotonin 5-HT2A receptors, are the best option for treatment of various symptoms associated with neuropsychiatric disorders. Furthermore, multi-target directed cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) inhibitors are also a successful approach to aid the discovery of new anti-inflammatory drugs with fewer side effects. Overall, employing CADD approaches in the process of rational drug design provides a great opportunity for future development, allowing rapid identification of compounds with the optimal polypharmacological profile.
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48
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Menduti G, Rasà DM, Stanga S, Boido M. Drug Screening and Drug Repositioning as Promising Therapeutic Approaches for Spinal Muscular Atrophy Treatment. Front Pharmacol 2020; 11:592234. [PMID: 33281605 PMCID: PMC7689316 DOI: 10.3389/fphar.2020.592234] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the most common genetic disease affecting infants and young adults. Due to mutation/deletion of the survival motor neuron (SMN) gene, SMA is characterized by the SMN protein lack, resulting in motor neuron impairment, skeletal muscle atrophy and premature death. Even if the genetic causes of SMA are well known, many aspects of its pathogenesis remain unclear and only three drugs have been recently approved by the Food and Drug Administration (Nusinersen-Spinraza; Onasemnogene abeparvovec or AVXS-101-Zolgensma; Risdiplam-Evrysdi): although assuring remarkable results, the therapies show some important limits including high costs, still unknown long-term effects, side effects and disregarding of SMN-independent targets. Therefore, the research of new therapeutic strategies is still a hot topic in the SMA field and many efforts are spent in drug discovery. In this review, we describe two promising strategies to select effective molecules: drug screening (DS) and drug repositioning (DR). By using compounds libraries of chemical/natural compounds and/or Food and Drug Administration-approved substances, DS aims at identifying new potentially effective compounds, whereas DR at testing drugs originally designed for the treatment of other pathologies. The drastic reduction in risks, costs and time expenditure assured by these strategies make them particularly interesting, especially for those diseases for which the canonical drug discovery process would be long and expensive. Interestingly, among the identified molecules by DS/DR in the context of SMA, besides the modulators of SMN2 transcription, we highlighted a convergence of some targeted molecular cascades contributing to SMA pathology, including cell death related-pathways, mitochondria and cytoskeleton dynamics, neurotransmitter and hormone modulation.
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Affiliation(s)
| | | | | | - Marina Boido
- Department of Neuroscience Rita Levi Montalcini, Neuroscience Institute Cavalieri Ottolenghi, University of Turin, Turin, Italy
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49
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Singh N, Villoutreix BO. Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABA A Receptor by Molecular Modeling. Front Pharmacol 2020; 11:561834. [PMID: 33041802 PMCID: PMC7518038 DOI: 10.3389/fphar.2020.561834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
GABAA receptors are pentameric ligand-gated ion channels that serve as major inhibitory neurotransmitter receptors in the mammalian brain and the target of numerous clinically relevant drugs interacting with different ligand binding sites. Here, we report an in silico approach to investigate the binding of pyrazoloquinolinones (PQs) that mediate allosteric effects through the extracellular α+/β- interface of GABAA receptors. First, we docked a potent prototype of PQs into the α1+/β3- site of a homology model of the human α1β3γ2 subtype of the GABAA receptor. Next, for each docking pose, we computationally derived protein-ligand complexes for 18 PQ analogs with known experimental potency. Subsequently, binding energy was calculated for all complexes using the molecular mechanics-generalized Born surface area method. Finally, docking poses were quantitatively assessed in the light of experimental data to derive a binding hypothesis. Collectively, the results indicate that PQs at the α1+/β3- site likely exhibit a common binding mode that can be characterized by a hydrogen bond interaction with β3Q64 and hydrophobic interactions involving residues α1F99, β3Y62, β3M115, α1Y159, and α1Y209. Importantly, our results are in good agreement with the recently resolved cryo-Electron Microscopy structures of the human α1β3γ2 and α1β2γ2 subtypes of GABAA receptors.
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Affiliation(s)
- Natesh Singh
- Univ. Lille, INSERM, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, Lille, France.,Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Bruno O Villoutreix
- Univ. Lille, INSERM, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, Lille, France
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50
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Domenico A, Nicola G, Daniela T, Fulvio C, Nicola A, Orazio N. De Novo Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization. J Chem Inf Model 2020; 60:4582-4593. [PMID: 32845150 DOI: 10.1021/acs.jcim.0c00517] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Artificial intelligence and multiobjective optimization represent promising solutions to bridge chemical and biological landscapes by addressing the automated de novo design of compounds as a result of a humanlike creative process. In the present study, we conceived a novel pair-based multiobjective approach implemented in an adapted SMILES generative algorithm based on recurrent neural networks for the automated de novo design of new molecules whose overall features are optimized by finding the best trade-offs among relevant physicochemical properties (MW, logP, HBA, HBD) and additional similarity-based constraints biasing specific biological targets. In this respect, we carried out the de novo design of chemical libraries targeting neuraminidase, acetylcholinesterase, and the main protease of severe acute respiratory syndrome coronavirus 2. Several quality metrics were employed to assess drug-likeness, chemical feasibility, diversity content, and validity. Molecular docking was finally carried out to better evaluate the scoring and posing of the de novo generated molecules with respect to X-ray cognate ligands of the corresponding molecular counterparts. Our results indicate that artificial intelligence and multiobjective optimization allow us to capture the latent links joining chemical and biological aspects, thus providing easy-to-use options for customizable design strategies, which are especially effective for both lead generation and lead optimization. The algorithm is freely downloadable at https://github.com/alberdom88/moo-denovo and all of the data are available as Supporting Information.
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Affiliation(s)
- Alberga Domenico
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
| | - Gambacorta Nicola
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
| | - Trisciuzzi Daniela
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy.,Molecular Horizon srl, Via Montelino 32, 06084 Bettona, Italy
| | - Ciriaco Fulvio
- Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
| | - Amoroso Nicola
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
| | - Nicolotti Orazio
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
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