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Radwan AA, Alanazi F, Al-Dhfyan A. Bioinformatics-driven discovery of novel EGFR kinase inhibitors as anti-cancer therapeutics: In silico screening and in vitro evaluation. PLoS One 2024; 19:e0298326. [PMID: 38625872 PMCID: PMC11020408 DOI: 10.1371/journal.pone.0298326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/18/2024] [Indexed: 04/18/2024] Open
Abstract
Epidermal growth factor receptor EGFR inhibitors are widely used as first line therapy for the treatment of non-small-cell lung cancer (NSCLC) in patients harboring EGFR mutation. However, the acquisition of a second-site mutation (T790 M) limited the efficacy and developed resistance. Therefore, discovery and development of specific drug target for this mutation is of urgent needs. In our study we used the ChemDiv diversity database for receptor-based virtual screening to secure EGFR-TK inhibitors chemotherapeutics. We identified four compounds that bind to the ATP-binding region of the EGFR-TK using AutoDock 4.0 and AutoDock Vina1.1.2 and post-docking investigations. The ligand showed hydrophobic interactions to the hydrophobic region of the binding site and engaged in hydrogen bonding with Met793. The ligands also explored π-cation interactions between the π-system of the ligand-phenyl ring and the positive amino group of Lys745. Molecular mechanics Poisson-Boltzmann surface area MM/PBSA per-residue energy decomposition analyses revealed that Val726, Leu792, Met793, Gly796, Cys797, Leu798, and Thr844 contributed the most to the binding energy. Biological evaluation of the retrieved hit compounds showed suppressing activity against EGFR auto phosphorylation and selective apoptosis-induced effects toward lung cancer cells harboring the EGFR L858R/T790M double mutation. Our work anticipated into novel and specific EGFR-TKIs and identified new compounds with therapeutic potential against lung cancer.
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Affiliation(s)
- Awwad A. Radwan
- Department of Pharmaceutics, Kayyli Chair for Pharmaceutical Industries, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department King Faisal Specialized Hospital and Research Center, Cell Therapy & Immunobiology, Riyadh, Saudi Arabia
| | - Fars Alanazi
- Department of Pharmaceutics, Kayyli Chair for Pharmaceutical Industries, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Al-Dhfyan
- Department King Faisal Specialized Hospital and Research Center, Cell Therapy & Immunobiology, Riyadh, Saudi Arabia
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2
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Kelam LM, Chhabra V, Dhiman S, Kumari D, Sobhia ME. Protein tyrosine phosphatase inhibitors: a patent review and update (2012-2023). Expert Opin Ther Pat 2024; 34:187-209. [PMID: 38920057 DOI: 10.1080/13543776.2024.2362203] [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: 03/28/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Protein tyrosine phosphatases (PTPs), essential and evolutionarily highly conserved enzymes, govern cellular functions by modulating tyrosine phosphorylation, a pivotal post-translational modification for signal transduction. The recent strides in phosphatase drug discovery, leading to the identification of selective modulators for enzymes, restoring interest in the therapeutic targeting of protein phosphatases. AREAS COVERED The compilation of patents up to the year 2023 focuses on the efficacy of various classes of Tyrosine phosphatases and their inhibitors, detailing their chemical structure and biochemical characteristics. These findings have broad implications, as they can be applied to treating diverse conditions like cancer, diabetes, autoimmune disorders, and neurological diseases. The search for scientific articles and patent literature was conducted using well known different platforms to gather information up to 2023. EXPERT OPINION The latest improvements in protein tyrosine phosphatase (PTP) research include the discovery of new inhibitors targeting specific PTP enzymes, with a focus on developing allosteric site covalent inhibitors for enhanced efficacy and specificity. These advancements have not only opened up new possibilities for therapeutic interventions in various disease conditions but also hold the potential for innovative treatments. PTPs offer promising avenues for drug discovery efforts and innovative treatments across a spectrum of health conditions.
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Affiliation(s)
- Lakshmi Mounika Kelam
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, India
| | - Vaishnavi Chhabra
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, India
| | - Sarika Dhiman
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, India
| | - Deevena Kumari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, India
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3
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Qiu X, Hou X, Yang Y, Fang H, Cui F, Yang X. An in-line method for high-throughput screening of protein tyrosine phosphatase receptor type O inhibitors by capillary electrophoresis based on electrophoretically mediated microanalysis. J Chromatogr A 2024; 1713:464511. [PMID: 38007841 DOI: 10.1016/j.chroma.2023.464511] [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: 09/18/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
Protein tyrosine phosphatase receptor type O (PTPRO) plays an important role in inflammation-related pathways and has become an emerging drug target. In this study, we developed an in-line capillary electrophoresis (CE) method for the investigation of the enzymatic activity of PTPRO, which was based on electrophoretically mediated microanalysis (EMMA). After a thorough method validation of the optimized conditions, this protocol was successfully employed to determine the kinetics of PTPRO as well as the half-maximal inhibitory concentration (IC50) of two typical PTPRO inhibitors. The final results were consistent with the values obtained through classical ultraviolet-visible (UV-vis) spectrophotometry. Our new method exhibited improved accuracy and reduced consumption, avoiding the disadvantages of traditional methods. This work provides a new strategy for PTPRO enzyme kinetic studies as well as inhibitory activity determination through capillary electrophoresis for the first time.
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Affiliation(s)
- Xueting Qiu
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Yue Yang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Fei Cui
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Xinying Yang
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China.
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Haq KU, Sa'adah NL, Siswanto I, Suwito H. Bioactivity of dihydropyrimidinone derivatives as inhibitors of cyclooxygenase-2 (COX-2): an in silico approach. RSC Adv 2023; 13:34348-34357. [PMID: 38024961 PMCID: PMC10665647 DOI: 10.1039/d3ra05942a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/29/2023] [Indexed: 12/01/2023] Open
Abstract
Cyclooxygenase-2 (COX-2) is an enzyme involved in inflammation. The overexpression of COX-2 causes chronic inflammation, which can be prevented by COX-2 inhibitors. Generally, COX-2 inhibitors possess a carboxyl group and an aromatic ring in their molecular structure. These moieties are involved in the interaction with the active site of COX-2, thus playing a pivotal role in the inhibitory activity. Regarding the requisite molecular structure of COX-2 inhibitors, derivatives of dihydropyrimidinone (DHPM) are ideal candidates to be explored as COX-2 inhibitors, due to the ease of synthesis and their versatility to be transformed chemically. In this study, we prepared a novel small library consisting of 288 designed DHPM derivatives by varying the constituent components. The selection criteria of potential candidates for the COX-2 inhibitor of the data bank involve in silico studies via molecular docking investigations, prediction of ADMET and druglikeness, as well as molecular dynamics (MD) simulations. Molecular docking served as the initial step of selection, based on the comparison of grid score, docking pose, and interactions with those of lumiracoxib (LUR) as the original ligand of COX-2. The next criteria of selection were scores obtained from the ADMET and druglikeness by comparing the designed candidates with COX-2 inhibitors that were already marketed. Compound RDUE2 and SDT29 were the most potential candidates, which were further analyzed using the MD simulation. The results of the MD simulation indicated that RDUE2 and SDT29 interacted stably with amino acid residues on the active site of COX-2. The estimation of binding free energy indicated that SDT29 exhibited an inhibitory activity comparable to that of LUR, whereas RDUE2 showed a lower inhibitory activity than that of SDT29 and LUR.
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Affiliation(s)
- Kautsar Ul Haq
- Bioinformatic Division, University CoE-Research Center for Bio-Molecule Engineering (BIOME), Airlangga University Surabaya 60115 Indonesia
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Surabaya 60115 Indonesia
| | - Nur Lailatus Sa'adah
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Surabaya 60115 Indonesia
| | - Imam Siswanto
- Bioinformatic Division, University CoE-Research Center for Bio-Molecule Engineering (BIOME), Airlangga University Surabaya 60115 Indonesia
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Surabaya 60115 Indonesia
| | - Hery Suwito
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Surabaya 60115 Indonesia
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McKay K, Hamilton NB, Remington JM, Schneebeli ST, Li J. Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery. Front Mol Biosci 2022; 9:879212. [PMID: 35847975 PMCID: PMC9277106 DOI: 10.3389/fmolb.2022.879212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/18/2022] [Indexed: 11/23/2022] Open
Abstract
The lack of biologically relevant protein structures can hinder rational design of small molecules to target G protein-coupled receptors (GPCRs). While ensemble docking using multiple models of the protein target is a promising technique for structure-based drug discovery, model clustering and selection still need further investigations to achieve both high accuracy and efficiency. In this work, we have developed an original ensemble docking approach, which identifies the most relevant conformations based on the essential dynamics of the protein pocket. This approach is applied to the study of small-molecule antagonists for the PAC1 receptor, a class B GPCR and a regulator of stress. As few as four representative PAC1 models are selected from simulations of a homology model and then used to screen three million compounds from the ZINC database and 23 experimentally validated compounds for PAC1 targeting. Our essential dynamics ensemble docking (EDED) approach can effectively reduce the number of false negatives in virtual screening and improve the accuracy to seek potent compounds. Given the cost and difficulties to determine membrane protein structures for all the relevant states, our methodology can be useful for future discovery of small molecules to target more other GPCRs, either with or without experimental structures.
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Hou X, Du J, Fang H. PTPRO is a therapeutic target and correlated with immune infiltrates in pancreatic cancer. J Cancer 2022; 12:7445-7453. [PMID: 35003364 PMCID: PMC8734421 DOI: 10.7150/jca.64661] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/04/2021] [Indexed: 11/17/2022] Open
Abstract
As a member of protein tyrosine phosphatases (PTPs), the protein tyrosine phosphatase receptor type O (PTPRO) has attracted increasing attention for its important roles in cell signaling. Currently, the roles of PTPRO in human cancers remain elusive. Herein, we performed bioinformatic analyses and revealed the potential oncogenic role of PTPRO in specific cancer types. Further in vitro experiments indicated that inhibition of PTPRO suppresses the proliferative abilities of tumor cells in pancreatic cancer, blood cancer, and breast cancer. Moreover, small molecular PTPRO inhibitor could induce cell apoptosis and affect the cell cycle in pancreatic cancer. In addition, PTPRO expression promoted the infiltration of CD8+ T, macrophages, dendritic cells, and neutrophils, in pancreatic cancers. Our findings suggested PTPRO may serve as a potential drug target for pancreatic cancer.
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Affiliation(s)
- Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), Cheeloo College of Medicine, School of Pharmaeutical Science, Shandong University, Jinan, Shandong, 250012, China
| | - Jintong Du
- Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, Shandong, 250117, China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), Cheeloo College of Medicine, School of Pharmaeutical Science, Shandong University, Jinan, Shandong, 250012, China
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7
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Rallabandi HR, Ganesan P, Kim YJ. Targeting the C-Terminal Domain Small Phosphatase 1. Life (Basel) 2020; 10:life10050057. [PMID: 32397221 PMCID: PMC7281111 DOI: 10.3390/life10050057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
The human C-terminal domain small phosphatase 1 (CTDSP1/SCP1) is a protein phosphatase with a conserved catalytic site of DXDXT/V. CTDSP1’s major activity has been identified as dephosphorylation of the 5th Ser residue of the tandem heptad repeat of the RNA polymerase II C-terminal domain (RNAP II CTD). It is also implicated in various pivotal biological activities, such as acting as a driving factor in repressor element 1 (RE-1)-silencing transcription factor (REST) complex, which silences the neuronal genes in non-neuronal cells, G1/S phase transition, and osteoblast differentiation. Recent findings have denoted that negative regulation of CTDSP1 results in suppression of cancer invasion in neuroglioma cells. Several researchers have focused on the development of regulating materials of CTDSP1, due to the significant roles it has in various biological activities. In this review, we focused on this emerging target and explored the biological significance, challenges, and opportunities in targeting CTDSP1 from a drug designing perspective.
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8
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Katigbak J, Li H, Rooklin D, Zhang Y. AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters. J Chem Inf Model 2020; 60:1494-1508. [PMID: 31995373 PMCID: PMC7093224 DOI: 10.1021/acs.jcim.9b00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Modern rational modulator design and structure-function characterization often concentrate on concave regions of biomolecular surfaces, ranging from well-defined small-molecule binding sites to large protein-protein interaction interfaces. Here, we introduce a β-cluster as a pseudomolecular representation of fragment-centric pockets detected by AlphaSpace [J. Chem. Inf. Model. 2015, 55, 1585], a recently developed computational analysis tool for topographical mapping of biomolecular concavities. By mimicking the shape as well as atomic details of potential molecular binders, this new β-cluster representation allows direct pocket-to-ligand shape comparison and can be used to guide ligand optimization. Furthermore, we defined the β-score, the optimal Vina score of the β-cluster, as an indicator of pocket ligandability and developed an ensemble β-cluster approach, which allows one-to-one pocket mapping and comparison among aligned protein structures. We demonstrated the utility of β-cluster representation by applying the approach to a wide variety of problems including binding site detection and comparison, characterization of protein-protein interactions, and fragment-based ligand optimization. These new β-cluster functionalities have been implemented in AlphaSpace 2.0, which is freely available on the web at http://www.nyu.edu/projects/yzhang/AlphaSpace2.
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Affiliation(s)
- Joseph Katigbak
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Haotian Li
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - David Rooklin
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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9
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Zhu Y, Gao Y, Sun X, Wang C, Rui X, Si D, Zhu J, Li W, Liu J. Discovery of novel serine/threonine protein phosphatase 1 inhibitors from traditional Chinese medicine through virtual screening and biological assays. J Biomol Struct Dyn 2019; 38:5464-5473. [PMID: 31820681 DOI: 10.1080/07391102.2019.1702588] [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] [Indexed: 02/07/2023]
Abstract
Protein phosphatase 1 (PP1) is a critical regulator of several processes, such as muscle contraction, neuronal signaling, glycogen synthesis, and cell proliferation. Dysregulation of PP1 has recently been found to be implicated in cardiac dysfunctions, which indicates that PP1 could be an attractive therapeutic target. However, discovery of PP1 inhibitors with satisfied safety and efficiency is still a challenge. Here, in order to discover potential PP1 inhibitors, compounds extracted from traditional Chinese medicine (TCM) were screened by a novel integrated virtual screening protocol including pharmacophore modeling and docking approaches. Combined with protein phosphatase inhibition assay, ZINC43060554 showed strongly inhibitory activity with IC50 values of 26.78 μM. Furthermore, molecular dynamics simulation and Molecular Mechanics/Generalized Born Surface Area binding free-energy analysis were performed to examine the stability of ligand binding modes. These novel scaffolds discovered in the present study can be used for rational design of PP1 inhibitors with high affinity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yehua Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Research Institute, Nanjing Tongrentang Pharmaceutical Co. Ltd, Nanjing, China
| | - Yi Gao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinjie Sun
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chao Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiyan Rui
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Dongjuan Si
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junru Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jian Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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10
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Lu J, Hou X, Wang C, Zhang Y. Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions. J Chem Inf Model 2019; 59:4540-4549. [PMID: 31638801 PMCID: PMC6878146 DOI: 10.1021/acs.jcim.9b00645] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Structure-based drug design is critically dependent on accuracy of molecular docking scoring functions, and there is of significant interest to advance scoring functions with machine learning approaches. In this work, by judiciously expanding the training set, exploring new features related to explicit mediating water molecules as well as ligand conformation stability, and applying extreme gradient boosting (XGBoost) with Δ-Vina parametrization, we have improved robustness and applicability of machine-learning scoring functions. The new scoring function ΔvinaXGB can not only perform consistently among the top compared to classical scoring functions for the CASF-2016 benchmark but also achieves significantly better prediction accuracy in different types of structures that mimic real docking applications.
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Affiliation(s)
- Jianing Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xuben Hou
- Department of Chemistry, New York University, New York, New York 10003, United States
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Science, Shandong University, Jinan, Shandong 250012, China
| | - Cheng Wang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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