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Duan H, Lou C, Gu Y, Wang Y, Li W, Liu G, Tang Y. In Silico prediction of inhibitors for multiple transporters via machine learning methods. Mol Inform 2024; 43:e202300270. [PMID: 38235949 DOI: 10.1002/minf.202300270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
Transporters play an indispensable role in facilitating the transport of nutrients, signaling molecules and the elimination of metabolites and toxins in human cells. Contemporary computational methods have been employed in the prediction of transporter inhibitors. However, these methods often focus on isolated endpoints, overlooking the interactions between transporters and lacking good interpretation. In this study, we integrated a comprehensive dataset and constructed models to assess the inhibitory effects on seven transporters. Both conventional machine learning and multi-task deep learning methods were employed. The results demonstrated that the MLT-GAT model achieved superior performance with an average AUC value of 0.882. It is noteworthy that our model excels not only in prediction performance but also in achieving robust interpretability, aided by GNN-Explainer. It provided valuable insights into transporter inhibition. The reliability of our model's predictions positioned it as a promising and valuable tool in the field of transporter inhibition research. Related data and code are available at https://gitee.com/wutiantian99/transporter_code.git.
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Affiliation(s)
- Hao Duan
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Chaofeng Lou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yaxin Gu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yimeng Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
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2
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Banerjee S, Kejriwal S, Ghosh B, Lanka G, Jha T, Adhikari N. Fragment-based investigation of thiourea derivatives as VEGFR-2 inhibitors: a cross-validated approach of ligand-based and structure-based molecular modeling studies. J Biomol Struct Dyn 2024; 42:1047-1063. [PMID: 37029768 DOI: 10.1080/07391102.2023.2198039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/26/2023] [Indexed: 04/09/2023]
Abstract
Angiogenesis is mediated by the vascular endothelial growth factor (VEGF) that plays a key role in the modulation of progression, invasion and metastasis, related to solid tumors and hematological malignancies. Several small-molecule VEGFR-2 inhibitors are marketed, but their usage is restricted to specific cancers due to severe toxicities. Therefore, cost-effective novel small molecule VEGFR-2 inhibitors may be an alternative to overcome these adverse effects. Here, a set of thiourea-based VEGFR-2 inhibitors were considered for a combined fragment-based QSAR technique, structure-based molecular docking followed by molecular dynamics simulation studies to acquire insights into the key structural attributes and the binding pattern of enzyme-ligand interactions. Noticeably, amine-substituted quinazoline phenyl ring and a higher number of nitrogen atoms, and the hydrazide function in the molecular structure are crucial for VEGFR-2 inhibition whereas methoxy groups are detrimental to VEGFR-2 inhibition. The MD simulation study of sorafenib and thiourea derivatives explored the significance of urea and thiourea moiety binding at VEGFR-2 active site that can be utilized further in the future to design molecules for greater binding stability and better VEGFR-2 selectivity. Therefore, such findings can be beneficial for the development of newer VEGFR-2 inhibitors for further refinement to acquire better therapeutic efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Shristi Kejriwal
- Indian Institute of Science Education and Research (IISER) Kolkata, Nadia, West Bengal, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Goverdhan Lanka
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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3
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Baidya SK, Banerjee S, Ghosh B, Jha T, Adhikari N. A fragment-based exploration of diverse MMP-9 inhibitors through classification-dependent structural assessment. J Mol Graph Model 2024; 126:108671. [PMID: 37976979 DOI: 10.1016/j.jmgm.2023.108671] [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: 03/01/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Matrix metalloproteinases (MMPs) are belonging to the Zn2+-dependent metalloenzymes. These can degenerate the extracellular matrix (ECM) that is entailed with various biological processes. Among the MMP family members, MMP-9 is associated with several pathophysiological circumstances. Apart from wound healing, remodeling of bone, inflammatory mechanisms, and rheumatoid arthritis, MMP-9 has also significant roles in tumor invasion and metastasis. Therefore, MMP-9 has been in the spotlight of anticancer drug discovery programs for more than a decade. In this present study, classification-based QSAR techniques along with fragment-based data mining have been carried out on divergent MMP-9 inhibitors to point out the important structural attributes. This current study may be able to elucidate the importance of several pivotal molecular fragments such as sulfonamide, hydroxamate, i-butyl, and ethoxy functions for imparting potential MMP-9 inhibition. These observations are in correlation with the ligand-bound co-crystal structures of MMP-9. Therefore, these findings are beneficial for the design and discovery of effective MMP-9 inhibitors in the future.
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Affiliation(s)
- Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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4
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Raza A, Chohan TA, Buabeid M, Arafa ESA, Chohan TA, Fatima B, Sultana K, Ullah MS, Murtaza G. Deep learning in drug discovery: a futuristic modality to materialize the large datasets for cheminformatics. J Biomol Struct Dyn 2023; 41:9177-9192. [PMID: 36305195 DOI: 10.1080/07391102.2022.2136244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
Artificial intelligence (AI) development imitates the workings of the human brain to comprehend modern problems. The traditional approaches such as high throughput screening (HTS) and combinatorial chemistry are lengthy and expensive to the pharmaceutical industry as they can only handle a smaller dataset. Deep learning (DL) is a sophisticated AI method that uses a thorough comprehension of particular systems. The pharmaceutical industry is now adopting DL techniques to enhance the research and development process. Multi-oriented algorithms play a crucial role in the processing of QSAR analysis, de novo drug design, ADME evaluation, physicochemical analysis, preclinical development, followed by clinical trial data precision. In this study, we investigated the performance of several algorithms, including deep neural networks (DNN), convolutional neural networks (CNN) and multi-task learning (MTL), with the aim of generating high-quality, interpretable big and diverse databases for drug design and development. Studies have demonstrated that CNN, recurrent neural network and deep belief network are compatible, accurate and effective for the molecular description of pharmacodynamic properties. In Covid-19, existing pharmacological compounds has also been repurposed using DL models. In the absence of the Covid-19 vaccine, remdesivir and oseltamivir have been widely employed to treat severe SARS-CoV-2 infections. In conclusion, the results indicate the potential benefits of employing the DL strategies in the drug discovery process.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali Raza
- Department of pharmaceutical chemistry, Faculty of Pharmacy, The University of Lahore, Pakistan
- Institute of Molecular Biology and Biochemistry, The University of Lahore, Pakistan
| | - Talha Ali Chohan
- Institute of Molecular Biology and Biochemistry, The University of Lahore, Pakistan
- Institute of Pharmaceutical Science, UVAS, Lahore, Pakistan
| | - Manal Buabeid
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
| | - El-Shaima A Arafa
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | | | - Batool Fatima
- Department of biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Kishwar Sultana
- Department of pharmaceutical chemistry, Faculty of Pharmacy, The University of Lahore, Pakistan
| | - Malik Saad Ullah
- Department of Pharmacy, Government College University, Faisalabad, Pakistan
| | - Ghulam Murtaza
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus, Pakistan
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Sardar S, Bhattacharya A, Amin SA, Jha T, Gayen S. Exploring molecular fingerprints of different drugs having bile interaction: a stepping stone towards better drug delivery. Mol Divers 2023:10.1007/s11030-023-10670-2. [PMID: 37369957 DOI: 10.1007/s11030-023-10670-2] [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: 01/20/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023]
Abstract
Bile acids are amphiphilic substances produced naturally in humans. In the context of drug delivery and dosage form design, it is critical to understand whether a drug interacts with bile inside the gastrointestinal (GI) tract or not. This study focuses on the identification of structural fingerprints/features important for bile interaction. Molecular modelling methods such as Bayesian classification and recursive partitioning (RP) studies are executed to find important fingerprints/features for the bile interaction. For the Bayesian classification study, the ROC score of 0.837 and 0.950 are found for the training set and the test set compounds, respectively. The fluorine-containing aliphatic/aromatic group, the branched chain of the alkyl group containing hydroxyl moiety and the phenothiazine ring etc. are identified as good fingerprints having a positive contribution towards bile interactions, whereas, the bad fingerprints such as free carboxylate group, purine, and pyrimidine ring etc. have a negative contribution towards bile interactions. The best tree (tree ID: 1) from the RP study classifies the bile interacting or non-interacting compounds with a ROC score of 0.941 for the training and 0.875 for the test set. Additionally, SARpy and QSAR-Co analyses are also been performed to classify compounds as bile interacting/non-interacting. Moreover, forty-six recently FDA-approved drugs have been screened by the developed SARpy and QSAR-Co models to assess their bile interaction properties. Overall, this attempt may facilitate the researchers to identify bile interacting/non-interacting molecules in a faster way and help in the design of formulations and target-specific drug development.
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Affiliation(s)
- Sourav Sardar
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Arijit Bhattacharya
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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Escobedo-González RG, Moyers-Montoya ED, Martínez-Pérez CA, García-Casillas PE, Miranda-Ruvalcaba R, Nicolás-Vázquez MIN. In Silico Study of Novel Cyclodextrin Inclusion Complexes of Polycaprolactone and Its Correlation with Skin Regeneration. Int J Mol Sci 2023; 24:ijms24108932. [PMID: 37240276 DOI: 10.3390/ijms24108932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Three novel biomaterials obtained via inclusion complexes of β-cyclodextrin, 6-deoxi-6-amino-β-cyclodextrin and epithelial growth factor grafted to 6-deoxi-6-amino-β-cyclodextrin with polycaprolactone. Furthermore, some physicochemical, toxicological and absorption properties were predicted using bioinformatics tools. The electronic, geometrical and spectroscopical calculated properties agree with the properties obtained via experimental methods, explaining the behaviors observed in each case. The interaction energy was obtained, and its values were -60.6, -20.9 and -17.1 kcal/mol for β-cyclodextrin/polycaprolactone followed by the 6-amino-β-cyclodextrin-polycaprolactone complex and finally the complex of epithelial growth factor anchored to 6-deoxy-6-amino-β-cyclodextrin/polycaprolactone. Additionally, the dipolar moments were calculated, achieving values of 3.2688, 5.9249 and 5.0998 Debye, respectively, and in addition the experimental wettability behavior of the studied materials has also been explained. It is important to note that the toxicological predictions suggested no mutagenic, tumorigenic or reproductive effects; moreover, an anti-inflammatory effect has been shown. Finally, the improvement in the cicatricial effect of the novel materials has been conveniently explained by comparing the poly-caprolactone data obtained in the experimental assessments.
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Affiliation(s)
- René Gerardo Escobedo-González
- Department of Industrial Maintenance, Technological University of the City of Juárez, Av. Universidad Tecnológica No. 3051, Col. Lote Bravo II, Ciudad Juárez 32695, Mexico
| | - Edgar Daniel Moyers-Montoya
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
| | - Carlos Alberto Martínez-Pérez
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
| | - Perla Elvia García-Casillas
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
- Applied Chemistry Research Center, Blvd. Enrique Reyna Hermosillo No. 140, Saltillo 25294, Mexico
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Bhattacharya A, Amin SA, Kumar P, Jha T, Gayen S. Exploring structural requirements of HDAC10 inhibitors through comparative machine learning approaches. J Mol Graph Model 2023; 123:108510. [PMID: 37216830 DOI: 10.1016/j.jmgm.2023.108510] [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: 02/24/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are in the limelight of anticancer drug development and research. HDAC10 is one of the class-IIb HDACs, responsible for cancer progression. The search for potent and effective HDAC10 selective inhibitors is going on. However, the absence of human HDAC10 crystal/NMR structure hampers the structure-based drug design of HDAC10 inhibitors. Different ligand-based modeling techniques are the only hope to speed up the inhibitor design. In this study, we applied different ligand-based modeling techniques on a diverse set of HDAC10 inhibitors (n = 484). Machine learning (ML) models were developed that could be used to screen unknown compounds as HDAC10 inhibitors from a large chemical database. Moreover, Bayesian classification and Recursive partitioning models were used to identify the structural fingerprints regulating the HDAC10 inhibitory activity. Additionally, a molecular docking study was performed to understand the binding pattern of the identified structural fingerprints towards the active site of HDAC10. Overall, the modeling insight might offer helpful information for medicinal chemists to design and develop efficient HDAC10 inhibitors.
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Affiliation(s)
- Arijit Bhattacharya
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India; Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Prabhat Kumar
- Department of Computer Science, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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Tamaian R, Porozov Y, Shityakov S. Exhaustive in silico design and screening of novel antipsychotic compounds with improved pharmacodynamics and blood-brain barrier permeation properties. J Biomol Struct Dyn 2023; 41:14849-14870. [PMID: 36927517 DOI: 10.1080/07391102.2023.2184179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/18/2023] [Indexed: 03/18/2023]
Abstract
Antipsychotic drugs or neuroleptics are widely used in the treatment of psychosis as a manifestation of schizophrenia and bipolar disorder. However, their effectiveness largely depends on the blood-brain barrier (BBB) permeation (pharmacokinetics) and drug-receptor pharmacodynamics. Therefore, in this study, we developed and implemented the in silico pipeline to design novel compounds (n = 260) as leads using the standard drug scaffolds with improved PK/PD properties from the standard scaffolds. As a result, the best candidates (n = 3) were evaluated in molecular docking to interact with serotonin and dopamine receptors. Finally, haloperidol (HAL) derivative (1-(4-fluorophenyl)-4-(4-hydroxy-4-{4-[(2-phenyl-1,3-thiazol-4-yl)methyl]phenyl}piperidin-1-yl)butan-1-one) was identified as a "magic shotgun" lead compound with better affinity to the 5-HT2A, 5-HT1D, D2, D3, and 5-HT1B receptors than the control molecule. Additionally, this hit substance was predicted to possess similar BBB permeation properties and much lower toxicological profiles in comparison to HAL. Overall, the proposed rational drug design platform for novel antipsychotic drugs based on the BBB permeation and receptor binding might be an invaluable asset for a medicinal chemist or translational pharmacologist.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Radu Tamaian
- ICSI Analytics, National Research and Development Institute for Cryogenics and Isotopic Technologies - ICSI Rm. Vâlcea, Râmnicu Vâlcea, Romania
| | - Yuri Porozov
- Center of Bio- and Chemoinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
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Tan S, Lu R, Yao D, Wang J, Gao P, Xie G, Liu H, Yao X. Identification of LRRK2 Inhibitors through Computational Drug Repurposing. ACS Chem Neurosci 2023; 14:481-493. [PMID: 36649061 DOI: 10.1021/acschemneuro.2c00672] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder that affects more than ten million people worldwide. However, the current PD treatments are still limited and alternative treatment strategies are urgently required. Leucine-rich repeat kinase 2 (LRRK2) has been recognized as a promising target for PD treatment. However, there are no approved LRRK2 inhibitors on the market. To rapidly identify potential drug repurposing candidates that inhibit LRRK2 kinase, we report a structure-based drug repurposing workflow that combines molecular docking, recursive partitioning model, molecular dynamics (MD) simulation, and molecular mechanics-generalized Born surface area (MM-GBSA) calculation. Thirteen compounds screened from our drug repurposing workflow were further evaluated through the experiment. The experimental results showed six drugs (Abivertinib, Aumolertinib, Encorafenib, Bosutinib, Rilzabrutinib, and Mobocertinib) with IC50 less than 5 μM that were identified as potential LRRK2 kinase inhibitors. The most potent compound Abivertinib showed potent inhibitions with IC50 toward G2019S mutation and wild-type LRRK2 of 410.3 nM and 177.0 nM, respectively. Our combination screening strategy had a 53% hit rate in this repurposing task. MD simulations and MM-GBSA free energy analysis further revealed the atomic binding mechanism between the identified drugs and G2019S LRRK2. In summary, the results showed that our drug repurposing workflow could be used to identify potent compounds for LRRK2. The potent inhibitors discovered in our work can be a starting point to develop more effective LRRK2 inhibitors.
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Affiliation(s)
- Shuoyan Tan
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou730000, China
| | - Ruiqiang Lu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou730000, China
| | - Dahong Yao
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen518060, China
| | - Jun Wang
- Ping An Healthcare Technology, Beijing100000, China
| | - Peng Gao
- Ping An Healthcare Technology, Beijing100000, China
| | - Guotong Xie
- Ping An Healthcare Technology, Beijing100000, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou730000, China.,State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China
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10
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Sun L, Zhang M, Xie L, Gao Q, Xu X, Xu L. In silico prediction of boiling point, octanol-water partition coefficient, and retention time index of polycyclic aromatic hydrocarbons through machine learning. Chem Biol Drug Des 2023; 101:52-68. [PMID: 35852446 DOI: 10.1111/cbdd.14121] [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: 06/23/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 12/15/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), a special class of persistent organic pollutants (POPs) with two or more aromatic rings, have received extensive attention owing to their carcinogenic, mutagenic, and teratogenic effects. Quantitative structure-property relationship (QSPR) is powerful chemometric method to correlate structural descriptors of PAHs with their physicochemical properties. In this manuscript, a QSPR study of PAHs was performed to predict their boiling point (bp), octanol-water partition coefficient (LogKow ), and retention time index (RI). In addition to traditional molecular descriptors, structural fingerprints play an important role in the correlation of the above properties. Three regression methods, partial least squares (PLS), multiple linear regression (MLR), and genetic function approximation (GFA), were used to establish QSPR models for each property of PAHs. The correlation coefficient (R2 test ) and root mean square error (RMSE) of best model were 0.980 and 24.39% (PLS), 0.979 and 35.80% (GFA), 0.926 and 22.90% (MLR) for bp, LogKow, and RI, respectively. The model proposed here can be used to estimate physicochemical properties and inform toxicity prediction of environmental chemicals.
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Affiliation(s)
- Linkang Sun
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Min Zhang
- School of Computer Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Qian Gao
- School of Computer Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
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11
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Pradhan S, Prasad R, Sinha C, Sen P. Molecular modeling of potent novel sulfonamide derivatives as non-peptide small molecule anti-COVID 19 agents. J Biomol Struct Dyn 2022; 40:7129-7142. [PMID: 34060418 PMCID: PMC8171005 DOI: 10.1080/07391102.2021.1897043] [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: 07/29/2020] [Accepted: 02/19/2021] [Indexed: 11/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19. The Sulfonamides groups have been widely introduced in several drugs, especially for their antibacterial activities and generally prescribed for respiratory infections. On the other hand, imidazole groups have the multipotency to act as drugs, including antiviral activity. We have used a structure-based drug design approach to design some imidazole derivatives of sulfonamide, which can efficiently bind to the active site of SARS-CoV-2 main protease and thus may have the potential to inhibit its proteases activity. We conducted molecular docking and molecular dynamics simulation to observe the stability and flexibility of inhibitor complexes. We have checked ADMET (absorption, distribution, metabolism, excretion and toxicity) and drug-likeness rules to scrutinize toxicity and then designed the most potent compound based on computational chemistry. Our small predicted molecule non-peptide protease inhibitors could provide a useful model in the further search for novel compounds since it has many advantages over peptidic drugs, like lower side effects, toxicity and less chance of drug resistance. Further, we confirmed the stability of our inhibitor-complex and interaction profile through the Molecular dynamics simulation study. Our small predicted moleculeCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayantan Pradhan
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Prosenjit Sen
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
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12
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Liu Z, Du J, Lin Z, Li Z, Liu B, Cui Z, Fang J, Xie L. DenovoProfiling: A webserver for de novo generated molecule library profiling. Comput Struct Biotechnol J 2022; 20:4082-4097. [PMID: 36016718 PMCID: PMC9379519 DOI: 10.1016/j.csbj.2022.07.045] [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: 03/03/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 01/10/2023] Open
Abstract
Various deep learning-based architectures for molecular generation have been proposed for de novo drug design. The flourish of the de novo molecular generation methods and applications has created a great demand for the visualization and functional profiling for the de novo generated molecules. An increasing number of publicly available chemogenomic databases sets good foundations and creates good opportunities for comprehensive profiling of the de novo library. In this paper, we present DenovoProfiling, a webserver dedicated to de novo library visualization and functional profiling. Currently, DenovoProfiling contains six modules: (1) identification & visualization module for chemical structure visualization and identify the reported structures, (2) chemical space module for chemical space exploration using similarity maps, principal components analysis (PCA), drug-like properties distribution, and scaffold-based clustering, (3) ADMET prediction module for predicting the ADMET properties of the de novo molecules, (4) molecular alignment module for three dimensional molecular shape analysis, (5) drugs mapping module for identifying structural similar drugs, and (6) target & pathway module for identifying the reported targets and corresponding functional pathways. DenovoProfiling could provide structural identification, chemical space exploration, drug mapping, and target & pathway information. The comprehensive annotated information could give users a clear picture of their de novo library and could guide the further selection of candidates for chemical synthesis and biological confirmation. DenovoProfiling is freely available at http://denovoprofiling.xielab.net.
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Key Words
- DDR1, Discovered potent discoidin domain receptor 1
- De novo drug design
- De novo molecule library
- Deep learning
- FBDD, Fragment-based drug design
- FDR, False discovery rate
- GAN, Generative adversarial networks
- HTS, High throughput screening
- LSTM, Long short-term memory
- Library profiling
- PCA, Principal components analysis
- RNN, Recurrent neural networks
- SCA, Scaffold-based classification approach
- VAE, Variational autoencoders
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Affiliation(s)
- Zhihong Liu
- School of Public Health, Xinxiang Medical University, Xinxiang, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jiewen Du
- Beijing Jingpai Technology Co., Ltd., 1500-1, Hailong Building Z-Park, Beijing 100090, China
| | - Ziying Lin
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Ze Li
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Bingdong Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zongbin Cui
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jiansong Fang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- Corresponding authors at: School of Public Health, Xinxiang Medical University, Xinxiang, China (L. Xie). Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China (J. Fang).
| | - Liwei Xie
- School of Public Health, Xinxiang Medical University, Xinxiang, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Corresponding authors at: School of Public Health, Xinxiang Medical University, Xinxiang, China (L. Xie). Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China (J. Fang).
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13
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Folate-Targeted Curcumin-Loaded Niosomes for Site-Specific Delivery in Breast Cancer Treatment: In Silico and In Vitro Study. Molecules 2022; 27:molecules27144634. [PMID: 35889513 PMCID: PMC9322601 DOI: 10.3390/molecules27144634] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 12/21/2022] Open
Abstract
As the most common cancer in women, efforts have been made to develop novel nanomedicine-based therapeutics for breast cancer. In the present study, the in silico curcumin (Cur) properties were investigated, and we found some important drawbacks of Cur. To enhance cancer therapeutics of Cur, three different nonionic surfactants (span 20, 60, and 80) were used to prepare various Cur-loaded niosomes (Nio-Cur). Then, fabricated Nio-Cur were decorated with folic acid (FA) and polyethylene glycol (PEG) for breast cancer suppression. For PEG-FA@Nio-Cur, the gene expression levels of Bax and p53 were higher compared to free drug and Nio-Cur. With PEG-FA-decorated Nio-Cur, levels of Bcl2 were lower than the free drug and Nio-Cur. When MCF7 and 4T1 cell uptake tests of PEG-FA@Nio-Cur and Nio-Cur were investigated, the results showed that the PEG-FA-modified niosomes exhibited the most preponderant endocytosis. In vitro experiments demonstrate that PEG-FA@Nio-Cur is a promising strategy for the delivery of Cur in breast cancer therapy. Breast cancer cells absorbed the prepared nanoformulations and exhibited sustained drug release characteristics.
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14
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A fragment-based structural analysis of MMP-2 inhibitors in search of meaningful structural fragments. Comput Biol Med 2022; 144:105360. [DOI: 10.1016/j.compbiomed.2022.105360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 11/21/2022]
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15
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Moshawih S, Goh HP, Kifli N, Idris AC, Yassin H, Kotra V, Goh KW, Liew KB, Ming LC. Synergy between machine learning and natural products cheminformatics: Application to the lead discovery of anthraquinone derivatives. Chem Biol Drug Des 2022; 100:185-217. [PMID: 35490393 DOI: 10.1111/cbdd.14062] [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: 01/18/2022] [Revised: 04/15/2022] [Accepted: 04/23/2022] [Indexed: 11/28/2022]
Abstract
Cheminformatics utilizing machine learning (ML) techniques have opened up a new horizon in drug discovery. This is owing to vast chemical space expansion with rocketing numbers of expected hits and lead compounds that match druggable macromolecular targets, in particular from natural compounds. Due to the natural products' (NP) structural complexity, uniqueness, and diversity, they could occupy a bigger space in pharmaceuticals, allowing the industry to pursue more selective leads in the nanomolar range of binding affinity. ML is an essential part of each step of the drug design pipeline, such as target prediction, compound library preparation, and lead optimization. Notably, molecular mechanic and dynamic simulations, induced docking, and free energy perturbations are essential in predicting best binding poses, binding free energy values, and molecular mechanics force fields. Those applications have leveraged from artificial intelligence (AI), which decreases the computational costs required for such costly simulations. This review aimed to describe chemical space and compound libraries related to NPs. High-throughput screening utilized for fractionating NPs and high-throughput virtual screening and their strategies, and significance, are reviewed. Particular emphasis was given to AI approaches, ML tools, algorithms, and techniques, especially in drug discovery of macrocyclic compounds and approaches in computer-aided and ML-based drug discovery. Anthraquinone derivatives were discussed as a source of new lead compounds that can be developed using ML tools for diverse medicinal uses such as cancer, infectious diseases, and metabolic disorders. Furthermore, the power of principal component analysis in understanding relevant protein conformations, and molecular modeling of protein-ligand interaction were also presented. Apart from being a concise reference for cheminformatics, this review is a useful text to understand the application of ML-based algorithms to molecular dynamics simulation and in silico absorption, distribution, metabolism, excretion, and toxicity prediction.
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Affiliation(s)
- Said Moshawih
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Hui Poh Goh
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Nurolaini Kifli
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Azam Che Idris
- Faculty of Integrated Technologies, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Hayati Yassin
- Faculty of Integrated Technologies, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Vijay Kotra
- Faculty of Pharmacy, Quest International University, Perak, Malaysia
| | - Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, Nilai, Malaysia
| | - Kai Bin Liew
- Faculty of Pharmacy, University of Cyberjaya, Cyberjaya, Malaysia
| | - Long Chiau Ming
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
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16
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Dey V, Machiraju R, Ning X. Improving Compound Activity Classification via Deep Transfer and Representation Learning. ACS OMEGA 2022; 7:9465-9483. [PMID: 35350358 PMCID: PMC8945064 DOI: 10.1021/acsomega.1c06805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Recent advances in molecular machine learning, especially deep neural networks such as graph neural networks (GNNs), for predicting structure-activity relationships (SAR) have shown tremendous potential in computer-aided drug discovery. However, the applicability of such deep neural networks is limited by the requirement of large amounts of training data. In order to cope with limited training data for a target task, transfer learning for SAR modeling has been recently adopted to leverage information from data of related tasks. In this work, in contrast to the popular parameter-based transfer learning such as pretraining, we develop novel deep transfer learning methods TAc and TAc-fc to leverage source domain data and transfer useful information to the target domain. TAc learns to generate effective molecular features that can generalize well from one domain to another and increase the classification performance in the target domain. Additionally, TAc-fc extends TAc by incorporating novel components to selectively learn feature-wise and compound-wise transferability. We used the bioassay screening data from PubChem and identified 120 pairs of bioassays such that the active compounds in each pair are more similar to each other compared to their inactive compounds. Overall, TAc achieves the best performance with an average ROC-AUC of 0.801; it significantly improves the ROC-AUC of 83% of target tasks with an average task-wise performance improvement of 7.102%, compared to the best baseline dmpna. Our experiments clearly demonstrate that TAc achieves significant improvement over all baselines across a large number of target tasks. Furthermore, although TAc-fc achieves slightly worse ROC-AUC on average compared to TAc (0.798 vs 0.801), TAc-fc still achieves the best performance on more tasks in terms of PR-AUC and F1 compared to other methods. In summary, TAc-fc is also found to be a strong model with competitive or even better performance than TAc on a notable number of target tasks.
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Affiliation(s)
- Vishal Dey
- Department
of Computer Science and Engineering, The
Ohio State University, Columbus, Ohio 43210, United States
| | - Raghu Machiraju
- Department
of Computer Science and Engineering, The
Ohio State University, Columbus, Ohio 43210, United States
- Biomedical
Informatics, The Ohio State University, Columbus, Ohio 43210, United States
- Translational
Data Analytics Institute, The Ohio State
University, Columbus, Ohio 43210, United
States
| | - Xia Ning
- Department
of Computer Science and Engineering, The
Ohio State University, Columbus, Ohio 43210, United States
- Biomedical
Informatics, The Ohio State University, Columbus, Ohio 43210, United States
- Translational
Data Analytics Institute, The Ohio State
University, Columbus, Ohio 43210, United
States
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17
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Das S, Amin SA, Gayen S, Jha T. Insight into the structural requirements of gelatinases (MMP-2 and MMP-9) inhibitors by multiple validated molecular modelling approaches: Part II. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:167-192. [PMID: 35301933 DOI: 10.1080/1062936x.2022.2041722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Inhibition of the matrix metalloproteinases (MMPs) is effective against metastasis of secondary tumours. Previous MMP inhibitors have failed in clinical trials due to their off-target toxicity in solid tumours. Thus, newer MMP inhibitors now have paramount importance. Here, different molecular modelling techniques were applied on a dataset of 110 gelatinase (MMP-2 and MMP-9) inhibitors. The objectives of the present study were to identify structural fingerprints for gelatinase inhibition and also to develop statistically validated QSAR models for the screening and prediction of different derivatives as MMP-2 (gelatinase A) and MMP-9 (gelatinase B) inhibitors. The Bayesian classification study provided the ROC values for the training set of 0.837 and 0.815 for MMP-2 and MMP-9, respectively. The linear model also produced the leave-one-out cross-validated Q2 of 0.805 (eq. 1, MMP-2) and 0.724 (eq. 2, MMP-9), an r2 of 0.845 (eq. 1, MMP-2) and 0.782 (eq. 2, MMP-9), an r2Pred of 0.806 (eq. 1, MMP-2) and 0.732 (eq. 2, MMP-9). Similarly, non-linear learning models were also statistically significant and reliable. Overall, this study may help in the rational design of newer compounds with higher gelatinase inhibition to fight against both primary and secondary cancers in future.
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Affiliation(s)
- S Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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18
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Mora Lagares L, Pérez-Castillo Y, Minovski N, Novič M. Structure-Function Relationships in the Human P-Glycoprotein (ABCB1): Insights from Molecular Dynamics Simulations. Int J Mol Sci 2021; 23:ijms23010362. [PMID: 35008783 PMCID: PMC8745603 DOI: 10.3390/ijms23010362] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 12/24/2022] Open
Abstract
P-Glycoprotein (P-gp) is a transmembrane protein belonging to the ATP binding cassette superfamily of transporters, and it is a xenobiotic efflux pump that limits intracellular drug accumulation by pumping compounds out of cells. P-gp contributes to a reduction in toxicity, and has broad substrate specificity. It is involved in the failure of many cancer and antiviral chemotherapies due to the phenomenon of multidrug resistance (MDR), in which the membrane transporter removes chemotherapeutic drugs from target cells. Understanding the details of the ligand–P-gp interaction is therefore critical for the development of drugs that can overcome the MDR phenomenon, for the early identification of P-gp substrates that will help us to obtain a more effective prediction of toxicity, and for the subsequent outdesign of substrate properties if needed. In this work, a series of molecular dynamics (MD) simulations of human P-gp (hP-gp) in an explicit membrane-and-water environment were performed to investigate the effects of binding different compounds on the conformational dynamics of P-gp. The results revealed significant differences in the behaviour of P-gp in the presence of active and non-active compounds within the binding pocket, as different patterns of movement were identified that could be correlated with conformational changes leading to the activation of the translocation mechanism. The predicted ligand–P-gp interactions are in good agreement with the available experimental data, as well as the estimation of the binding-free energies of the studied complexes, demonstrating the validity of the results derived from the MD simulations.
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Affiliation(s)
- Liadys Mora Lagares
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-1-4760-438 (L.M.L.); +386-1-4760-253 (M.N.)
| | - Yunierkis Pérez-Castillo
- Bio-Cheminformatics Research Group and Escuela de Ciencias Físicas y Matemáticas, Universidad de Las Américas, Quito 170513, Ecuador;
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
| | - Marjana Novič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-1-4760-438 (L.M.L.); +386-1-4760-253 (M.N.)
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19
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Moinul M, Amin SA, Kumar P, Patil UK, Gajbhiye A, Jha T, Gayen S. Exploring sodium glucose cotransporter (SGLT2) inhibitors with machine learning approach: A novel hope in anti-diabetes drug discovery. J Mol Graph Model 2021; 111:108106. [PMID: 34923429 DOI: 10.1016/j.jmgm.2021.108106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022]
Abstract
Conventional anti-diabetes agents exhibit some undesirable side effects. Recently, lactic acidosis and/or bladder cancer were also reported with the use of these agents. Hence, there is an urgent need for alternative anti-diabetes in order to reduce/avoid the unwanted effects. In this scenario sodium glucose cotransporter 2 (SGLT2) inhibitors has already been established as an important class of anti-diabetic drug. The search for new generation SGLT2 inhibitors with high affinity is still an ongoing process. Here, we aim to develop computational models to predict the SGLT2 inhibitory activity of small molecules based on chemical structures. This work provides in-silico analysis to propose possible fragment/fingerprint identification recommended for SGLT2 inhibitors. Up-to-our knowledge, this study is an initiative to propose fingerprints responsible for SGLT2 inhibition. Furthermore, we used nine different algorithms to build machine learning (ML) models that could be used to prioritize compounds as SGLT2 inhibitors from large libraries. The best performing ML models were applied to virtually screen a large collection of FDA approved drugs. The best predicted compounds have been recommended to be biologically investigated in future in order to identify next generation SGLT2 inhibitors with different chemical structure.
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Affiliation(s)
- Md Moinul
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, 470003, India
| | - Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Prabhat Kumar
- Department of Computer Science, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Umesh Kumar Patil
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, 470003, India
| | - Asmita Gajbhiye
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, 470003, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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20
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Nandi S, Kumar P, Amin SA, Jha T, Gayen S. First molecular modelling report on tri-substituted pyrazolines as phosphodiesterase 5 (PDE5) inhibitors through classical and machine learning based multi-QSAR analysis. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:917-939. [PMID: 34727793 DOI: 10.1080/1062936x.2021.1989721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
Phosphodiesterase 5 (PDE5) falls under a broad category of metallohydrolase enzymes responsible for the catalysis of the phosphodiesterase bond, and thus it can terminate the action of cyclic guanosine monophosphate (cGMP). Overexpression of this enzyme leads to development of a number of pathological conditions. Thus, targeting the enzyme to develop inhibitors could be useful for the treatment of erectile dysfunction as well as pulmonary hypertension. In the current study, several molecular modelling techniques were utilized including Bayesian classification, single tree and forest tree recursive partitioning, and genetic function approximation to identify crucial structural fingerprints important for optimization of tri-substituted pyrazoline derivatives as PDE5 inhibitors. Later, various machine learning models were also developed that could be utilized to predict and screen PDE5 inhibitors in the future.
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Affiliation(s)
- S Nandi
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, India
| | - P Kumar
- Department of Computer Science, Institute of Science, Banaras Hindu University, Varanasi, India
| | - S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Gayen
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, India
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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21
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Abstract
MMP2, a Zn2+-dependent metalloproteinase, is related to cancer and angiogenesis. Inhibition of this enzyme might result in a potential antimetastatic drug to leverage the anticancer drug armory. In silico or computer-aided ligand-based drug design is a method of rational drug design that takes multiple chemometrics (i.e., multi-quantitative structure-activity relationship methods) into account for virtually selecting or developing a series of probable selective MMP2 inhibitors. Though existing matrix metalloproteinase inhibitors have shown plausible pan-matrix metalloproteinase (MMP) activity, they have resulted in various adverse effects leading to their being rescinded in later phases of clinical trials. Therefore a review of the ligand-based designing methods of MMP2 inhibitors would result in an explicit route map toward successfully designing and synthesizing novel and selective MMP2 inhibitors.
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22
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Chu CSM, Simpson JD, O'Neill PM, Berry NG. Machine learning - Predicting Ames mutagenicity of small molecules. J Mol Graph Model 2021; 109:108011. [PMID: 34555723 DOI: 10.1016/j.jmgm.2021.108011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/29/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
In modern drug discovery, detection of a compound's potential mutagenicity is crucial. However, the traditional method of mutagenicity detection using the Ames test is costly and time consuming as the compounds need to be synthesised and then tested and the results are not always accurate and reproducible. Therefore, it would be advantageous to develop robust in silico models which can accurately predict the mutagenicity of a compound prior to synthesis to overcome the inadequacies of the Ames test. After curation of a previously defined compound mutagenicity library, over 5000 molecules had their chemical fingerprints and molecular properties calculated. Using 8 classification modelling algorithms, including support vector machine (SVM), random forest (RF) and extreme gradient boosting (XGB), a total of 112 predictive models have been constructed. Their performance has been assessed using 10-fold cross validation and a hold-out test set and some of the top performing models have been assessed using the y-randomisation approach. As a result, we have found SVM and XGB models to have good performance during the 10-fold cross validation (AUROC >0.90, sensitivity >0.85, specificity >0.75, balanced accuracy >0.80, Kappa >0.65) and on the test set (AUROC >0.65, sensitivity >0.65, specificity >0.60, balanced accuracy >0.65, Kappa >0.30). We have also identified molecular properties that are the most influential for mutagenicity prediction when combined with chemical molecular fingerprints. Using the Class A mutagenic compounds from the Ames/QSAR International Challenge Project, we were able to verify our models perform better, predicting more mutagens correctly then the StarDrop Ames mutagenicity prediction and TEST mutagenicity prediction.
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Affiliation(s)
- Charmaine S M Chu
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK.
| | - Jack D Simpson
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | - Paul M O'Neill
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | - Neil G Berry
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK.
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23
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Das S, Amin SA, Jha T. Insight into the structural requirement of aryl sulphonamide based gelatinases (MMP-2 and MMP-9) inhibitors - Part I: 2D-QSAR, 3D-QSAR topomer CoMFA and Naïve Bayes studies - First report of 3D-QSAR Topomer CoMFA analysis for MMP-9 inhibitors and jointly inhibitors of gelatinases together. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:655-687. [PMID: 34355614 DOI: 10.1080/1062936x.2021.1955414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Gelatinases [gelatinase A - matrix metalloproteinase-2 (MMP-2), gelatinase B - matrix metalloproteinase-9 (MMP-9)] play key roles in many disease conditions including cancer. Despite some research work on gelatinases inhibitors both jointly and individually had been reported, challenges still exist in achieving potency as well as selectivity. Here in part I of a series of work, we have reported the structural requirement of some arylsulfonamides. In particular, regression-based 2D-QSARs, topomer CoMFA (comparative molecular field analysis) and Bayesian classification models were constructed to refine structural features for attaining better gelatinase inhibitory activity. The 2D-QSAR models exhibited good statistical significance. The descriptors nsssN, SHBint6, SHBint7, PubchemFP629 were directly correlated with the MMP-2 binding affinities whereas nsssN, SHBint10 and AATS2i were directly proportional to MMP-9 binding affinities. The topomer CoMFA results indicated that the steric and electrostatic fields play key roles in gelatinase inhibition. The established Naïve Bayes prediction models were evaluated by fivefold cross validation and an external test set. Furthermore, important molecular descriptors related to MMP-2 and MMP-9 binding affinities and some active/inactive fragments were identified. Thus, these observations may be helpful for further work of aryl sulphonamide based gelatinase inhibitors in future.
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Affiliation(s)
- S Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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24
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Olasupo SB, Uzairu A, Shallangwa GA, Uba S. Computer-aided drug design and in silico pharmacokinetics predictions of some potential antipsychotic agents. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Zhao J, Xu P, Liu X, Ji X, Li M, Dev S, Qu X, Lu W, Niu B. Application of machine learning methods for the development of antidiabetic drugs. Curr Pharm Des 2021; 28:260-271. [PMID: 34161205 DOI: 10.2174/1381612827666210622104428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/10/2021] [Indexed: 11/22/2022]
Abstract
Diabetes is a chronic non-communicable disease caused by several different routes, which has attracted increasing attention. In order to speed up the development of new selective drugs, machine learning (ML) technology has been applied in the process of diabetes drug development, which opens up a new blueprint for drug design. This review provides a comprehensive portrayal of the application of ML in antidiabetic drug use.
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Affiliation(s)
- Juanjuan Zhao
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Pengcheng Xu
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Xiujuan Liu
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Xiaobo Ji
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Minjie Li
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Sooranna Dev
- Department of Obstetrics and Gynaecology, Imperial College London, Fulham Road, London SW10 9 NH, United Kingdom
| | - Xiaosheng Qu
- National Engineering Laboratory of Southwest Endangered Medicinal Resources Development, Guangxi Botanical Garden of Medicinal Plants, No. 189, Changgang Road, 530023, Nanning, China
| | - Wencong Lu
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Bing Niu
- School of Life Sciences, Shanghai University, 200444, China
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Adhikari N, Banerjee S, Baidya SK, Ghosh B, Jha T. Robust classification-based molecular modelling of diverse chemical entities as potential SARS-CoV-2 3CL pro inhibitors: theoretical justification in light of experimental evidences. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:473-493. [PMID: 34011224 DOI: 10.1080/1062936x.2021.1914721] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
COVID-19 is the most unanticipated incidence of 2020 affecting the human population worldwide. Currently, it is utmost important to produce novel small molecule anti-SARS-CoV-2 drugs urgently that can save human lives globally. Based on the earlier SARS-CoV and MERS-CoV infection along with the general characters of coronaviral replication, a number of drug molecules have been proposed. However, one of the major limitations is the lack of experimental observations with different drug molecules. In this article, 70 diverse chemicals having experimental SARS-CoV-2 3CLproinhibitory activity were accounted for robust classification-based QSAR analysis statistically validated with 4 different methodologies to recognize the crucial structural features responsible for imparting the activity. Results obtained from all these methodologies supported and validated each other. Important observations obtained from these analyses were also justified with the ligand-bound crystal structure of SARS-CoV-2 3CLpro enzyme. Our results suggest that molecules should contain a 2-oxopyrrolidine scaffold as well as a methylene (hydroxy) sulphonic acid warhead in proper orientation to achieve higher inhibitory potency against SARS-CoV-2 3CLpro. Outcomes of our study may be able to design and discover highly effective SARS-CoV-2 3CLpro inhibitors as potential anticoronaviral therapy to crusade against COVID-19.
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Affiliation(s)
- N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - B Ghosh
- Department of Pharmacy, BITS-Pilani, Hyderabad, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Classification and Design of HIV-1 Integrase Inhibitors Based on Machine Learning. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5559338. [PMID: 33868450 PMCID: PMC8035010 DOI: 10.1155/2021/5559338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 11/17/2022]
Abstract
A key enzyme in human immunodeficiency virus type 1 (HIV-1) life cycle, integrase (IN) aids the integration of viral DNA into the host DNA, which has become an ideal target for the development of anti-HIV drugs. A total of 1785 potential HIV-1 IN inhibitors were collected from the databases of ChEMBL, Binding Database, DrugBank, and PubMed, as well as from 40 references. The database was divided into the training set and test set by random sampling. By exploring the correlation between molecular descriptors and inhibitory activity, it is found that the classification and specific activity data of inhibitors can be more accurately predicted by the combination of molecular descriptors and molecular fingerprints. The calculation of molecular fingerprint descriptor provides the additional substructure information to improve the prediction ability. Based on the training set, two machine learning methods, the recursive partition (RP) and naive Bayes (NB) models, were used to build the classifiers of HIV-1 IN inhibitors. Through the test set verification, the RP technique accurately predicted 82.5% inhibitors and 86.3% noninhibitors. The NB model predicted 88.3% inhibitors and 87.2% noninhibitors with correlation coefficient of 85.2%. The results show that the prediction performance of NB model is slightly better than that of RP, and the key molecular segments are also obtained. Additionally, CoMFA and CoMSIA models with good activity prediction ability both were constructed by exploring the structure-activity relationship, which is helpful for the design and optimization of HIV-1 IN inhibitors.
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Jiang D, Wu Z, Hsieh CY, Chen G, Liao B, Wang Z, Shen C, Cao D, Wu J, Hou T. Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models. J Cheminform 2021; 13:12. [PMID: 33597034 PMCID: PMC7888189 DOI: 10.1186/s13321-020-00479-8] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/26/2020] [Indexed: 12/31/2022] Open
Abstract
Graph neural networks (GNN) has been considered as an attractive modelling method for molecular property prediction, and numerous studies have shown that GNN could yield more promising results than traditional descriptor-based methods. In this study, based on 11 public datasets covering various property endpoints, the predictive capacity and computational efficiency of the prediction models developed by eight machine learning (ML) algorithms, including four descriptor-based models (SVM, XGBoost, RF and DNN) and four graph-based models (GCN, GAT, MPNN and Attentive FP), were extensively tested and compared. The results demonstrate that on average the descriptor-based models outperform the graph-based models in terms of prediction accuracy and computational efficiency. SVM generally achieves the best predictions for the regression tasks. Both RF and XGBoost can achieve reliable predictions for the classification tasks, and some of the graph-based models, such as Attentive FP and GCN, can yield outstanding performance for a fraction of larger or multi-task datasets. In terms of computational cost, XGBoost and RF are the two most efficient algorithms and only need a few seconds to train a model even for a large dataset. The model interpretations by the SHAP method can effectively explore the established domain knowledge for the descriptor-based models. Finally, we explored use of these models for virtual screening (VS) towards HIV and demonstrated that different ML algorithms offer diverse VS profiles. All in all, we believe that the off-the-shelf descriptor-based models still can be directly employed to accurately predict various chemical endpoints with excellent computability and interpretability.![]()
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Affiliation(s)
- Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.,State Key Lab of CAD & CG, Zhejiang University, Hangzhou, 310058, Zhejiang, China.,College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Zhenxing Wu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Chang-Yu Hsieh
- Tencent Quantum Laboratory Tencent, Shenzhen, 518057, Guangdong, China
| | - Guangyong Chen
- Shenzhen Institutes of Advanced Technology, Shenzhen, 518055, Guangdong, China
| | - Ben Liao
- Tencent Quantum Laboratory Tencent, Shenzhen, 518057, Guangdong, China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410004, Hunan, China.
| | - Jian Wu
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China.
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China. .,State Key Lab of CAD & CG, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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Fu L, Yang ZY, Yang ZJ, Yin MZ, Lu AP, Chen X, Liu S, Hou TJ, Cao DS. QSAR-assisted-MMPA to expand chemical transformation space for lead optimization. Brief Bioinform 2021; 22:6071857. [PMID: 33418563 DOI: 10.1093/bib/bbaa374] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 11/13/2022] Open
Abstract
Matched molecular pairs analysis (MMPA) has become a powerful tool for automatically and systematically identifying medicinal chemistry transformations from compound/property datasets. However, accurate determination of matched molecular pair (MMP) transformations largely depend on the size and quality of existing experimental data. Lack of high-quality experimental data heavily hampers the extraction of more effective medicinal chemistry knowledge. Here, we developed a new strategy called quantitative structure-activity relationship (QSAR)-assisted-MMPA to expand the number of chemical transformations and took the logD7.4 property endpoint as an example to demonstrate the reliability of the new method. A reliable logD7.4 consensus prediction model was firstly established, and its applicability domain was strictly assessed. By applying the reliable logD7.4 prediction model to screen two chemical databases, we obtained more high-quality logD7.4 data by defining a strict applicability domain threshold. Then, MMPA was performed on the predicted data and experimental data to derive more chemical rules. To validate the reliability of the chemical rules, we compared the magnitude and directionality of the property changes of the predicted rules with those of the measured rules. Then, we compared the novel chemical rules generated by our proposed approach with the published chemical rules, and found that the magnitude and directionality of the property changes were consistent, indicating that the proposed QSAR-assisted-MMPA approach has the potential to enrich the collection of rule types or even identify completely novel rules. Finally, we found that the number of the MMP rules derived from the experimental data could be amplified by the predicted data, which is helpful for us to analyze the medicinal chemical rules in local chemical environment. In summary, the proposed QSAR-assisted-MMPA approach could be regarded as a very promising strategy to expand the chemical transformation space for lead optimization, especially when no enough experimental data can support MMPA.
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Affiliation(s)
- Li Fu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China.,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Zi-Yi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Zhi-Jiang Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Ming-Zhu Yin
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, P. R China
| | - Xiang Chen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China.,Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China.,Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, P. R China
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30
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Artificial intelligence in the early stages of drug discovery. Arch Biochem Biophys 2020; 698:108730. [PMID: 33347838 DOI: 10.1016/j.abb.2020.108730] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Although the use of computational methods within the pharmaceutical industry is well established, there is an urgent need for new approaches that can improve and optimize the pipeline of drug discovery and development. In spite of the fact that there is no unique solution for this need for innovation, there has recently been a strong interest in the use of Artificial Intelligence for this purpose. As a matter of fact, not only there have been major contributions from the scientific community in this respect, but there has also been a growing partnership between the pharmaceutical industry and Artificial Intelligence companies. Beyond these contributions and efforts there is an underlying question, which we intend to discuss in this review: can the intrinsic difficulties within the drug discovery process be overcome with the implementation of Artificial Intelligence? While this is an open question, in this work we will focus on the advantages that these algorithms provide over the traditional methods in the context of early drug discovery.
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Zhu J, Wu Y, Wang M, Li K, Xu L, Chen Y, Cai Y, Jin J. Integrating Machine Learning-Based Virtual Screening With Multiple Protein Structures and Bio-Assay Evaluation for Discovery of Novel GSK3β Inhibitors. Front Pharmacol 2020; 11:566058. [PMID: 33041806 PMCID: PMC7517831 DOI: 10.3389/fphar.2020.566058] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/14/2020] [Indexed: 02/04/2023] Open
Abstract
Glycogen synthase kinase-3β (GSK3β) is associated with various key biological processes, and it has been considered as a critical therapeutic target for the treatment of many diseases. However, it is a big challenge to develop ATP-competition GSK3β inhibitors because of the high sequence homology with other kinases. In this work, a novel parallel virtual screening strategy based on multiple GSK3β protein structures, integrating molecular docking, complex-based pharmacophore, and naive Bayesian classification, was developed to screen a large chemical database, the 50 compounds with top-scores then underwent a luminescent kinase assay, which led to the discovery of two GSK3β inhibitor hits. The high screening enrichment rate indicates the reliability and practicability of the integrated protocol. Finally, molecular docking and molecular dynamics simulation were employed to investigate the binding modes of the GSK3β inhibitors, and some “hot residues” critical to GSK3β affinity were highlighted. The present study may provide some valuable guidance for the development of novel GSK3β inhibitors.
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Affiliation(s)
- Jingyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Yuanqing Wu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Man Wang
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Kan Li
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Lei Xu
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Yun Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Yanfei Cai
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
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Structural analysis of arylsulfonamide-based carboxylic acid derivatives: a QSAR study to identify the structural contributors toward their MMP-9 inhibition. Struct Chem 2020. [DOI: 10.1007/s11224-020-01635-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Discovering novel P38α inhibitors for the treatment of prostate cancer through virtual screening methods. Future Med Chem 2020; 11:3125-3137. [PMID: 31838901 DOI: 10.4155/fmc-2019-0223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: P38α plays a crucial role in the development of castration-resistant prostate cancer. Discovering novel inhibitors of P38α offers potential for the development of new anticancer drugs. Methods & results: Compounds from the Chemdiv and Enamine virtual libraries were filtered to construct the P38α inhibitor-like library. A total of 58 new P38α inhibitors were discovered via virtual screening; these included three compounds (compound 1, 5, 9) with kinase IC50 of below 10 μM. In vitro, these three compounds have the potential to suppress the viabilities of prostate cancer cell lines, however, only compound 9 can inhibit the proliferation and migration of prostate cancer cells. Conclusion: The potent compounds discovered in this study demonstrate anticancer functions by targeting the P38α mitogen-activated protein kinases signaling pathway and are worthy of further investigation.
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34
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Jiang D, Lei T, Wang Z, Shen C, Cao D, Hou T. ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning. J Cheminform 2020; 12:16. [PMID: 33430990 PMCID: PMC7059329 DOI: 10.1186/s13321-020-00421-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/20/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer resistance protein (BCRP/ABCG2), an ATP-binding cassette (ABC) efflux transporter, plays a critical role in multi-drug resistance (MDR) to anti-cancer drugs and drug–drug interactions. The prediction of BCRP inhibition can facilitate evaluating potential drug resistance and drug–drug interactions in early stage of drug discovery. Here we reported a structurally diverse dataset consisting of 1098 BCRP inhibitors and 1701 non-inhibitors. Analysis of various physicochemical properties illustrates that BCRP inhibitors are more hydrophobic and aromatic than non-inhibitors. We then developed a series of quantitative structure–activity relationship (QSAR) models to discriminate between BCRP inhibitors and non-inhibitors. The optimal feature subset was determined by a wrapper feature selection method named rfSA (simulated annealing algorithm coupled with random forest), and the classification models were established by using seven machine learning approaches based on the optimal feature subset, including a deep learning method, two ensemble learning methods, and four classical machine learning methods. The statistical results demonstrated that three methods, including support vector machine (SVM), deep neural networks (DNN) and extreme gradient boosting (XGBoost), outperformed the others, and the SVM classifier yielded the best predictions (MCC = 0.812 and AUC = 0.958 for the test set). Then, a perturbation-based model-agnostic method was used to interpret our models and analyze the representative features for different models. The application domain analysis demonstrated the prediction reliability of our models. Moreover, the important structural fragments related to BCRP inhibition were identified by the information gain (IG) method along with the frequency analysis. In conclusion, we believe that the classification models developed in this study can be regarded as simple and accurate tools to distinguish BCRP inhibitors from non-inhibitors in drug design and discovery pipelines.![]()
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Affiliation(s)
- Dejun Jiang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Tailong Lei
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Chao Shen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410004, Hunan, People's Republic of China.
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
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36
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Xu L, Jiang W, Jia H, Zheng L, Xing J, Liu A, Du G. Discovery of Multitarget-Directed Ligands Against Influenza A Virus From Compound Yizhihao Through a Predictive System for Compound-Protein Interactions. Front Cell Infect Microbiol 2020; 10:16. [PMID: 32117796 PMCID: PMC7026480 DOI: 10.3389/fcimb.2020.00016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/14/2020] [Indexed: 12/27/2022] Open
Abstract
Influenza A virus (IAV) is a threat to public health due to its high mutation rate and resistance to existing drugs. In this investigation, 15 targets selected from an influenza virus–host interaction network were successfully constructed as a multitarget virtual screening system for new drug discovery against IAV using Naïve Bayesian, recursive partitioning, and CDOCKER methods. The predictive accuracies of the models were evaluated using training sets and test sets. The system was then used to predict active constituents of Compound Yizhihao (CYZH), a Chinese medicinal compound used to treat influenza. Twenty-eight compounds with multitarget activities were selected for subsequent in vitro evaluation. Of the four compounds predicted to be active on neuraminidase (NA), chlorogenic acid, and orientin showed inhibitory activity in vitro. Linarin, sinensetin, cedar acid, isoliquiritigenin, sinigrin, luteolin, chlorogenic acid, orientin, epigoitrin, and rupestonic acid exhibited significant effects on TNF-α expression, which is almost consistent with predicted results. Results from a cytopathic effect (CPE) reduction assay revealed acacetin, indirubin, tryptanthrin, quercetin, luteolin, emodin, and apigenin had protective effects against wild-type strains of IAV. Quercetin, luteolin, and apigenin had good efficacy against resistant IAV strains in CPE reduction assays. Finally, with the aid of Gene Ontology biological process analysis, the potential mechanisms of CYZH action were revealed. In conclusion, a compound-protein interaction-prediction system was an efficient tool for the discovery of novel compounds against influenza, and the findings from CYZH provide important information for its usage and development.
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Affiliation(s)
- Lvjie Xu
- Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Wen Jiang
- The Sixth Clinical Hospital of Xinjiang Medical University, Ürümqi, China
| | - Hao Jia
- Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lishu Zheng
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Jianguo Xing
- Xinjiang Institute of Materia Medica, Ürümqi, China
| | - Ailin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Guanhua Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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37
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Amin SA, Ghosh K, Mondal D, Jha T, Gayen S. Exploring indole derivatives as myeloid cell leukaemia-1 (Mcl-1) inhibitors with multi-QSAR approach: a novel hope in anti-cancer drug discovery. NEW J CHEM 2020. [DOI: 10.1039/d0nj03863f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In humans, the over-expression of Mcl-1 protein causes different cancers and it is also responsible for cancer resistance to different cytotoxic agents.
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Affiliation(s)
- Sk. Abdul Amin
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata
| | - Kalyan Ghosh
- Laboratory of Drug Design and Discovery
- Department of Pharmaceutical Sciences
- Dr Harisingh Gour University
- Sagar
- India
| | - Dipayan Mondal
- Laboratory of Drug Design and Discovery
- Department of Pharmaceutical Sciences
- Dr Harisingh Gour University
- Sagar
- India
| | - Tarun Jha
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery
- Department of Pharmaceutical Sciences
- Dr Harisingh Gour University
- Sagar
- India
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38
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Banerjee S, Amin SA, Adhikari N, Jha T. Essential elements regulating HDAC8 inhibition: a classification based structural analysis and enzyme-inhibitor interaction study of hydroxamate based HDAC8 inhibitors. J Biomol Struct Dyn 2019; 38:5513-5525. [DOI: 10.1080/07391102.2019.1704881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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39
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Fu L, Liu L, Yang ZJ, Li P, Ding JJ, Yun YH, Lu AP, Hou TJ, Cao DS. Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis. J Chem Inf Model 2019; 60:63-76. [DOI: 10.1021/acs.jcim.9b00718] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Li Fu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Lu Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Zhi-Jiang Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Pan Li
- Beijing Institute of Pharmaceutical Chemistry, Beijing 102205, P. R. China
| | - Jun-Jie Ding
- Beijing Institute of Pharmaceutical Chemistry, Beijing 102205, P. R. China
| | - Yong-Huan Yun
- College of Food Science and Engineering, Hainan University, Haikou 570228, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, P. R. China
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, P. R. China
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40
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Ye N, Xu Q, Li W, Wang P, Zhou J. Recent Advances in Developing K-Ras Plasma Membrane Localization Inhibitors. Curr Top Med Chem 2019; 19:2114-2127. [PMID: 31475899 DOI: 10.2174/1568026619666190902145116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
The Ras proteins play an important role in cell growth, differentiation, proliferation and survival by regulating diverse signaling pathways. Oncogenic mutant K-Ras is the most frequently mutated class of Ras superfamily that is highly prevalent in many human cancers. Despite intensive efforts to combat various K-Ras-mutant-driven cancers, no effective K-Ras-specific inhibitors have yet been approved for clinical use to date. Since K-Ras proteins must be associated to the plasma membrane for their function, targeting K-Ras plasma membrane localization represents a logical and potentially tractable therapeutic approach. Here, we summarize the recent advances in the development of K-Ras plasma membrane localization inhibitors including natural product-based inhibitors achieved from high throughput screening, fragment-based drug design, virtual screening, and drug repurposing as well as hit-to-lead optimizations.
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Affiliation(s)
- Na Ye
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.,Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.,Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Qingfeng Xu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Wanwan Li
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Pingyuan Wang
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, United States
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41
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Hinge VK, Roy D, Kovalenko A. Prediction of P-glycoprotein inhibitors with machine learning classification models and 3D-RISM-KH theory based solvation energy descriptors. J Comput Aided Mol Des 2019; 33:965-971. [PMID: 31745705 DOI: 10.1007/s10822-019-00253-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/14/2019] [Indexed: 11/24/2022]
Abstract
Development of novel in silico methods for questing novel PgP inhibitors is crucial for the reversal of multi-drug resistance in cancer therapy. Here, we report machine learning based binary classification schemes to identify the PgP inhibitors from non-inhibitors using molecular solvation theory with excellent accuracy and precision. The excess chemical potential and partial molar volume in various solvents are calculated for PgP± (PgP inhibitors and non-inhibitors) compounds with the statistical-mechanical based three-dimensional reference interaction site model with the Kovalenko-Hirata closure approximation (3D-RISM-KH molecular theory of solvation). The statistical importance analysis of descriptors identified the 3D-RISM-KH based descriptors as top molecular descriptors for classification. Among the constructed classification models, the support vector machine predicted the test set of Pgp± compounds with highest accuracy and precision of ~ 97% for test set. The validation of models confirms the robustness of state-of-the-art molecular solvation theory based descriptors in identification of the Pgp± compounds.
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Affiliation(s)
- Vijaya Kumar Hinge
- Department of Mechanical Engineering, 10-203 Donadeo Innovation Centre for Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB, T6G 1H9, Canada
| | - Dipankar Roy
- Department of Mechanical Engineering, 10-203 Donadeo Innovation Centre for Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB, T6G 1H9, Canada
| | - Andriy Kovalenko
- Department of Mechanical Engineering, 10-203 Donadeo Innovation Centre for Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB, T6G 1H9, Canada. .,Nanotechnology Research Centre, 11421 Saskatchewan Drive, Edmonton, AB, T6G 2M9, Canada.
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42
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Amin SA, Adhikari N, Jha T. Development of decision trees to discriminate HDAC8 inhibitors and non-inhibitors using recursive partitioning. J Biomol Struct Dyn 2019; 39:1-8. [DOI: 10.1080/07391102.2019.1661876] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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43
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Carboranylanilinoquinazoline EGFR-inhibitors: toward ‘lead-to-candidate’ stage in the drug-development pipeline. Future Med Chem 2019; 11:2273-2285. [DOI: 10.4155/fmc-2019-0060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: Carboranylanilinoquinazoline-hybrids, developed for boron neutron capture therapy, have demonstrated cytotoxicity against murine-glioma cells with EGFR-inhibition ability. In addition, their adequate aqueous/metabolic stabilities and ability to cross blood–brain barrier make them good leads as to become antiglioma drugs. Aim: Analyze drug-like properties of representative carboranylanilinoquinazolines. Materials & methods: To expand carboranylanilinoquinazolines therapeutic spectrum, we studied their ability to act against glioma-mammal cells, U-87 MG and other tyrosine kinase-overexpress cells, HT-29. Additionally, we predicted theoretically and studied experimentally drug-like properties, in other words, organization for economic cooperation and development-recommended toxicity-studies and, due to some aqueous-solubility problems, and vehicularization for oral and intravenous administrations. Conclusion: We have identified a promising drug-candidate with broad activity spectrum, appropriate drug-like properties, adequate toxicological behavior and able ability to be loaded in suitable vehicles.
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Dávila B, Sánchez C, Fernández M, Cerecetto H, Lecot N, Cabral P, Glisoni R, González M. Selective Hypoxia‐Cytotoxin 7‐Fluoro‐2‐Aminophenazine 5,10‐Dioxide: Toward “Candidate‐to‐Drug” Stage in the Drug‐Development Pipeline. ChemistrySelect 2019. [DOI: 10.1002/slct.201902601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Belén Dávila
- Laboratorio de Química Orgánica MedicinalInstituto de Química Biológica. Facultad de CienciasUniversidad de la República. Iguá 4225 Montevideo 11400 Uruguay
| | - Carina Sánchez
- Laboratorio de Química Orgánica MedicinalInstituto de Química Biológica. Facultad de CienciasUniversidad de la República. Iguá 4225 Montevideo 11400 Uruguay
| | - Marcelo Fernández
- Laboratorio de Experimentación AnimalCentro de Investigaciones Nucleares. Facultad de CienciasUniversidad de la República. Mataojo 2055 Montevideo 11400 Uruguay
| | - Hugo Cerecetto
- Laboratorio de Química Orgánica MedicinalInstituto de Química Biológica. Facultad de CienciasUniversidad de la República. Iguá 4225 Montevideo 11400 Uruguay
- Área de RadiofarmaciaCentro de Investigaciones Nucleares. Facultad de CienciasUniversidad de la República. Mataojo 2055 Montevideo 11400 Uruguay
| | - Nicole Lecot
- Laboratorio de Química Orgánica MedicinalInstituto de Química Biológica. Facultad de CienciasUniversidad de la República. Iguá 4225 Montevideo 11400 Uruguay
- Laboratorio de Técnicas Nucleareas Aplicadas a Bioquímica y BiotecnologíaCentro de Investigaciones Nucleares. Facultad de CienciasUniversidad de la República. Mataojo 2055 Montevideo 11400 Uruguay
| | - Pablo Cabral
- Área de RadiofarmaciaCentro de Investigaciones Nucleares. Facultad de CienciasUniversidad de la República. Mataojo 2055 Montevideo 11400 Uruguay
| | - Romina Glisoni
- Departamento de Tecnología FarmacéuticaCátedra de Tecnología Farmacéutica II. CONICETInstituto de Nanobiotecnología (NANOBIOTEC). Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires
| | - Mercedes González
- Laboratorio de Química Orgánica MedicinalInstituto de Química Biológica. Facultad de CienciasUniversidad de la República. Iguá 4225 Montevideo 11400 Uruguay
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Mora Lagares L, Minovski N, Novič M. Multiclass Classifier for P-Glycoprotein Substrates, Inhibitors, and Non-Active Compounds. Molecules 2019; 24:molecules24102006. [PMID: 31130601 PMCID: PMC6571636 DOI: 10.3390/molecules24102006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 12/14/2022] Open
Abstract
P-glycoprotein (P-gp) is a transmembrane protein that actively transports a wide variety of chemically diverse compounds out of the cell. It is highly associated with the ADMET (absorption, distribution, metabolism, excretion and toxicity) properties of drugs/drug candidates and contributes to decreasing toxicity by eliminating compounds from cells, thereby preventing intracellular accumulation. Therefore, in the drug discovery and toxicological assessment process it is advisable to pay attention to whether a compound under development could be transported by P-gp or not. In this study, an in silico multiclass classification model capable of predicting the probability of a compound to interact with P-gp was developed using a counter-propagation artificial neural network (CP ANN) based on a set of 2D molecular descriptors, as well as an extensive dataset of 2512 compounds (1178 P-gp inhibitors, 477 P-gp substrates and 857 P-gp non-active compounds). The model provided a good classification performance, producing non error rate (NER) values of 0.93 for the training set and 0.85 for the test set, while the average precision (AvPr) was 0.93 for the training set and 0.87 for the test set. An external validation set of 385 compounds was used to challenge the model’s performance. On the external validation set the NER and AvPr values were 0.70 for both indices. We believe that this in silico classifier could be effectively used as a reliable virtual screening tool for identifying potential P-gp ligands.
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Affiliation(s)
- Liadys Mora Lagares
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia.
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia.
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia.
| | - Marjana Novič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia.
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46
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Zheng S, Wang Y, Liu H, Chang W, Xu Y, Lin F. Prediction of Hemolytic Toxicity for Saponins by Machine-Learning Methods. Chem Res Toxicol 2019; 32:1014-1026. [DOI: 10.1021/acs.chemrestox.8b00347] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P. R. China
- Chemical Biology Research Center, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P. R. China
| | - Yibing Wang
- Genetic Screening Center, National Institute of Biological Sciences, Beijing 102206, P. R. China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, P. R. China
| | - Hongmei Liu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P. R. China
| | - Wenping Chang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P. R. China
| | - Yong Xu
- Center of Chemical Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangdong, P. R. China
| | - Fu Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P. R. China
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47
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Zheng S, Chang W, Xu W, Xu Y, Lin F. e-Sweet: A Machine-Learning Based Platform for the Prediction of Sweetener and Its Relative Sweetness. Front Chem 2019; 7:35. [PMID: 30761295 PMCID: PMC6363693 DOI: 10.3389/fchem.2019.00035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/14/2019] [Indexed: 11/23/2022] Open
Abstract
Artificial sweeteners (AS) can elicit the strong sweet sensation with the low or zero calorie, and are widely used to replace the nutritive sugar in the food and beverage industry. However, the safety issue of current AS is still controversial. Thus, it is imperative to develop more safe and potent AS. Due to the costly and laborious experimental-screening of AS, in-silico sweetener/sweetness prediction could provide a good avenue to identify the potential sweetener candidates before experiment. In this work, we curate the largest dataset of 530 sweeteners and 850 non-sweeteners, and collect the second largest dataset of 352 sweeteners with the relative sweetness (RS) from the literature. In light of these experimental datasets, we adopt five machine-learning methods and conformational-independent molecular fingerprints to derive the classification and regression models for the prediction of sweetener and its RS, respectively via the consensus strategy. Our best classification model achieves the 95% confidence intervals for the accuracy (0.91 ± 0.01), precision (0.90 ± 0.01), specificity (0.94 ± 0.01), sensitivity (0.86 ± 0.01), F1-score (0.88 ± 0.01), and NER (Non-error Rate: 0.90 ± 0.01) on the test set, which outperforms the model (NER = 0.85) of Rojas et al. in terms of NER, and our best regression model gives the 95% confidence intervals for the R2(test set) and ΔR2 [referring to |R2(test set)- R2(cross-validation)|] of 0.77 ± 0.01 and 0.03 ± 0.01, respectively, which is also better than the other works based on the conformation-independent 2D descriptors (e.g., 2D Dragon) according to R2(test set) and ΔR2. Our models are obtained by averaging over nineteen data-splitting schemes, and fully comply with the guidelines of Organization for Economic Cooperation and Development (OECD), which are not completely followed by the previous relevant works that are all on the basis of only one random data-splitting scheme for the cross-validation set and test set. Finally, we develop a user-friendly platform “e-Sweet” for the automatic prediction of sweetener and its corresponding RS. To our best knowledge, it is a first and free platform that can enable the experimental food scientists to exploit the current machine-learning methods to boost the discovery of more AS with the low or zero calorie content.
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Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China.,Chemical Biology Research Center, Wenzhou Medical University, Wenzhou, China
| | - Wenping Chang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wenxin Xu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yong Xu
- Center of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Fu Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
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48
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Ye Z, Yang Y, Li X, Cao D, Ouyang D. An Integrated Transfer Learning and Multitask Learning Approach for Pharmacokinetic Parameter Prediction. Mol Pharm 2019; 16:533-541. [PMID: 30571137 DOI: 10.1021/acs.molpharmaceut.8b00816] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Pharmacokinetic evaluation is one of the key processes in drug discovery and development. However, current absorption, distribution, metabolism, and excretion prediction models still have limited accuracy. AIM This study aims to construct an integrated transfer learning and multitask learning approach for developing quantitative structure-activity relationship models to predict four human pharmacokinetic parameters. METHODS A pharmacokinetic data set included 1104 U.S. FDA approved small molecule drugs. The data set included four human pharmacokinetic parameter subsets (oral bioavailability, plasma protein binding rate, apparent volume of distribution at steady-state, and elimination half-life). The pretrained model was trained on over 30 million bioactivity data entries. An integrated transfer learning and multitask learning approach was established to enhance the model generalization. RESULTS The pharmacokinetic data set was split into three parts (60:20:20) for training, validation, and testing by the improved maximum dissimilarity algorithm with the representative initial set selection algorithm and the weighted distance function. The multitask learning techniques enhanced the model predictive ability. The integrated transfer learning and multitask learning model demonstrated the best accuracies, because deep neural networks have the general feature extraction ability; transfer learning and multitask learning improve the model generalization. CONCLUSIONS The integrated transfer learning and multitask learning approach with the improved data set splitting algorithm was first introduced to predict the pharmacokinetic parameters. This method can be further employed in drug discovery and development.
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Affiliation(s)
- Zhuyifan Ye
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences (ICMS) , University of Macau , Macau , China
| | - Yilong Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences (ICMS) , University of Macau , Macau , China.,Department of Computer and Information Science, Faculty of Science and Technology , University of Macau , Macau , China
| | - Xiaoshan Li
- Department of Computer and Information Science, Faculty of Science and Technology , University of Macau , Macau , China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences , Central South University , No. 172, Tongzipo Road , Yuelu District, Changsha 410083 , People's Republic of China
| | - Defang Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences (ICMS) , University of Macau , Macau , China
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49
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Luo Y, Zeng R, Guo Q, Xu J, Sun X, Wang L. Identifying a novel anticancer agent with microtubule-stabilizing effects through computational cell-based bioactivity prediction models and bioassays. Org Biomol Chem 2019; 17:1519-1530. [DOI: 10.1039/c8ob02193g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G03 is a novel anticancer agent with unusual microtubule-stabilizing effects.
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Affiliation(s)
- Yao Luo
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
| | - Ranran Zeng
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
| | - Qingqing Guo
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
| | - Jianrong Xu
- Department of Pharmacology
- Institute of Medical Sciences
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai 200025
| | - Xiaoou Sun
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
| | - Ling Wang
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
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50
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Zheng S, Chang W, Liu W, Liang G, Xu Y, Lin F. Computational Prediction of a New ADMET Endpoint for Small Molecules: Anticommensal Effect on Human Gut Microbiota. J Chem Inf Model 2018; 59:1215-1220. [PMID: 30352151 DOI: 10.1021/acs.jcim.8b00600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human gut microbiota (HGM), which are evolutionarily commensal in the human gastrointestinal system, are crucial to our health. However, HGM can be broadly shaped by multifaceted factors such as intake of drugs. About one-quarter of the existing drugs for humans, which are designed to target human cells rather than HGM, can notably alter the composition of HGM. Therefore, the anticommensal effect of human drugs should be avoided to the maximum extent possible in the drug discovery and development process. Nevertheless, the anticommensal effect of small molecules is a new ADMET (absorption, distribution, metabolism, excretion, and toxicity) end point, which was never predicted with the computational method before. In this work, we present the first machine-learning based consensus classification model with the accuracy (0.811 ± 0.012), precision (0.759 ± 0.032), specificity (0.901 ± 0.019), sensitivity (0.628 ± 0.036), F1-score (0.687 ± 0.023), and AUC (0.814 ± 0.030) respectively on the test set. Furthermore, we develop an easy-to-use "e-Commensal" program for the automatic prediction. Based on this program, virtual-screening of the food-constituent database (FooDB) indicates that 5888 of 23 202 food-relevant compounds are forecasted to possess an anticommensal effect on HGM. Several top-ranked anticommensal compounds in our prediction are further scrutinized and confirmed by experiments in the existing literature. To the best of our knowledge, this is the first classification model and stand-alone software for the prediction of commensal or anticommensal compounds impacting HGM.
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Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , P. R. China.,Chemical Biology Research Center , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , P. R. China
| | - Wenping Chang
- School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , P. R. China
| | - Wenxin Liu
- School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , P. R. China
| | - Guang Liang
- School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , P. R. China.,Chemical Biology Research Center , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , P. R. China
| | - Yong Xu
- Center of Chemical Biology , Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou , Guangdong 510530 , P. R. China
| | - Fu Lin
- School of Pharmaceutical Sciences , Wenzhou Medical University , Wenzhou , Zhejiang 325035 , P. R. China
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