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Li Z, Fang F, Li Y, Lv X, Zheng R, Jiao P, Wang Y, Zhu G, Jin Z, Xu X, Qiu Y, Zhang G, Li Z, Liu Z, Zhang L. Carbazole and tetrahydro-carboline derivatives as dopamine D 3 receptor antagonists with the multiple antipsychotic-like properties. Acta Pharm Sin B 2023; 13:4553-4577. [PMID: 37969740 PMCID: PMC10638516 DOI: 10.1016/j.apsb.2023.07.024] [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: 03/17/2023] [Revised: 06/28/2023] [Accepted: 07/19/2023] [Indexed: 11/17/2023] Open
Abstract
Dopamine D3 receptor (D3R) is implicated in multiple psychotic symptoms. Increasing the D3R selectivity over dopamine D2 receptor (D2R) would facilitate the antipsychotic treatments. Herein, novel carbazole and tetrahydro-carboline derivatives were reported as D3R selective ligands. Through a structure-based virtual screen, ZLG-25 (D3R Ki = 685 nmol/L; D2R Ki > 10,000 nmol/L) was identified as a novel D3R selective bitopic ligand with a carbazole scaffold. Scaffolds hopping led to the discovery of novel D3R-selective analogs with tetrahydro-β-carboline or tetrahydro-γ-carboline core. Further functional studies showed that most derivatives acted as hD3R-selective antagonists. Several lead compounds could dose-dependently inhibit the MK-801-induced hyperactivity. Additional investigation revealed that 23j and 36b could decrease the apomorphine-induced climbing without cataleptic reaction. Furthermore, 36b demonstrated unusual antidepressant-like activity in the forced swimming tests and the tail suspension tests, and alleviated the MK-801-induced disruption of novel object recognition in mice. Additionally, preliminary studies confirmed the favorable PK/PD profiles, no weight gain and limited serum prolactin levels in mice. These results revealed that 36b provided potential opportunities to new antipsychotic drugs with the multiple antipsychotic-like properties.
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Affiliation(s)
- Zhongtang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Fan Fang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yiyan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xuehui Lv
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ruqiu Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Peili Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuxi Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Guiwang Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zefang Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiangqing Xu
- Jiangsu Nhwa Pharmaceutical Co., Ltd., Xuzhou 221116, China
| | - Yinli Qiu
- Jiangsu Nhwa Pharmaceutical Co., Ltd., Xuzhou 221116, China
| | - Guisen Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhongjun Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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2
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Jana A, Naga R, Saha S, Banerjee DR. 3D QSAR pharmacophore based lead identification of G9a lysine methyltransferase towards epigenetic therapeutics. J Biomol Struct Dyn 2023; 41:8635-8653. [PMID: 36264111 DOI: 10.1080/07391102.2022.2135600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/08/2022] [Indexed: 10/24/2022]
Abstract
The G9a, Lysine Methyltransferase that methylates the histone 3 lysine 9 (H3K9) of the nucleosome, is an excellent epigenetic target having no clinically passed inhibitor currently owing to adverse in vivo ADMET toxicities. In this work, we have carried out detailed computational investigations to find novel and safer lead against the target using advanced 3 D QSAR pharmacophore screening of databases containing more than 400000 entrees of natural compounds. The screening was conducted at different levels at increasing stringencies by employing pharmacophore mapping, druglikenesses and interaction profiles of the selected to identify potential hit compounds. The potential hits were further screened by advanced flexible docking, ADME and toxicity analysis to eight hit compounds. Based on the comparative analysis of the hits with the reference inhibitor, we identified one lead inhibitor against the G9a, having better binding efficacy and a safer ADMET profile than the reference inhibitor. Finally, the results were further verified using robust molecular dynamics simulation and MM-GBSA binding energy calculation. The natural compounds are generally considered benign due to their long human uses and this is the first attempt of in silico screening of a large natural compound library against G9a to our best knowledge. Therefore, the finding of this study may add value towards the development of epigenetic therapeutics against the G9a.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhisek Jana
- Department of Chemistry, National Institute of technology Durgapur, Durgapur, India
| | - Rahul Naga
- Department of Biotechnology, National Institute of technology Durgapur, Durgapur, India
| | - Sougata Saha
- Department of Biotechnology, National Institute of technology Durgapur, Durgapur, India
| | - Deb Ranjan Banerjee
- Department of Chemistry, National Institute of technology Durgapur, Durgapur, India
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3
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Bellver-Sanchis A, Choudhary BS, Companys-Alemany J, Sukanya S, A Ávila-López P, Martínez Rodríguez AL, Brea Floriani JM, Malik R, Pérez B, Pallàs M, Griñán-Ferré C. Structure based virtual screening, in vitro and in vivo analysis revealed novel potent methyltransferase G9a inhibitors as prospective anti-Alzheimer's agents. ChemMedChem 2022; 17:e202200002. [PMID: 35413149 PMCID: PMC9401600 DOI: 10.1002/cmdc.202200002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 04/11/2022] [Indexed: 11/20/2022]
Abstract
G9a is a lysine methyltransferase able to di‐methylate lysine 9 of histone H3, promoting the repression of genes involved in learning and memory. Novel strategies based on synthesizing epigenetic drugs could regulate gene expression through histone post‐translational modifications and effectively treat neurodegenerative diseases, like Alzheimer's disease (AD). Here, potential G9a inhibitors were identified using a structure‐based virtual screening against G9a, followed by in vitro and in vivo screenings. First, screening methods with the AD transgenic Caenorhabditis elegans strain CL2006, showed that the toxicity/function range was safe and recovered age‐dependent paralysis. Likewise, we demonstrated that the best candidates direct target G9a by reducing H3 K9me2 in the CL2006 strain. Further characterization of these compounds involved the assessment of the blood‐brain barrier‐permeability and impact on amyloid‐β aggregation, showing promising results. Thus, we present a G9a inhibitor candidate, F, with a novel and potent structure, providing both leads in G9a inhibitor design and demonstrating their participation in reducing AD pathology.
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Affiliation(s)
- Aina Bellver-Sanchis
- University of Barcelona: Universitat de Barcelona, Faculty of Pharmacy and Food Science, Av. Joan XXIII 27-31, 08028, Barcelona, SPAIN
| | - Bhanwar Singh Choudhary
- Shree SK Patel College of Pharmaceutical Education and Research, Pharmaceutical Chemistry, Ganpat University, Kherva, Ajmr, 384012, Mehsana, INDIA
| | - Júlia Companys-Alemany
- University of Barcelona: Universitat de Barcelona, Faculty of Pharmacy and Food Science, Av. Joan XXIII 27-31, 08028, Barcelona, SPAIN
| | - Sukanya Sukanya
- Central University of Rajasthan, Department of Pharmacy, Bandarsindri, Kishangarh, Ajmer, 304817, Ajmer, INDIA
| | - Pedro A Ávila-López
- Northwestern University, Feinberg School of Medicine, Chicago, UNITED STATES
| | - Antón Leandro Martínez Rodríguez
- Universidad de Santiago de Compostela: Universidade de Santiago de Compostela, Pharmacology, Pharmacy and Pharmaceutical Technology, SPAIN
| | - Jose Manuel Brea Floriani
- Universidad de Santiago de Compostela: Universidade de Santiago de Compostela, Pharmacology, Pharmacy and Pharmaceutical Technology, SPAIN
| | - Ruchi Malik
- Central University of Rajasthan, Department of Pharmacy, Bandarsindri, Kishangarh, 304817, Ajmer, INDIA
| | - Belén Pérez
- Universitat Autònoma de Barcelona: Universitat Autonoma de Barcelona, Department of Pharmacology, Therapeutic and Toxicology, Barcelona, SPAIN
| | - Mercè Pallàs
- University of Barcelona: Universitat de Barcelona, Faculty of Pharmacy and Food Science, 08028, Barcelona, SPAIN
| | - Christian Griñán-Ferré
- University of Barcelona: Universitat de Barcelona, Pharmacology, Toxicology and Therapeutic Chemistry, Joan XXIII, 27-31, 08028, Barcelona, SPAIN
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4
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EHMT2/G9a as an Epigenetic Target in Pediatric and Adult Brain Tumors. Int J Mol Sci 2021; 22:ijms222011292. [PMID: 34681949 PMCID: PMC8539543 DOI: 10.3390/ijms222011292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/09/2021] [Indexed: 02/08/2023] Open
Abstract
Epigenetic mechanisms, including post-translational modifications of DNA and histones that influence chromatin structure, regulate gene expression during normal development and are also involved in carcinogenesis and cancer progression. The histone methyltransferase G9a (euchromatic histone lysine methyltransferase 2, EHMT2), which mostly mediates mono- and dimethylation by histone H3 lysine 9 (H3K9), influences gene expression involved in embryonic development and tissue differentiation. Overexpression of G9a has been observed in several cancer types, and different classes of G9a inhibitors have been developed as potential anticancer agents. Here, we review the emerging evidence suggesting the involvement of changes in G9a activity in brain tumors, namely glioblastoma (GBM), the main type of primary malignant brain cancer in adults, and medulloblastoma (MB), the most common type of malignant brain cancer in children. We also discuss the role of G9a in neuroblastoma (NB) and the drug development of G9a inhibitors.
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5
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A facile access to 2-substituted naphtho[2,3-g]quinoline-3-carboxylic acid esters via intramolecular cyclization and PyBOP-promoted functionalization. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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6
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Cao H, Li L, Yang D, Zeng L, Yewei X, Yu B, Liao G, Chen J. Recent progress in histone methyltransferase (G9a) inhibitors as anticancer agents. Eur J Med Chem 2019; 179:537-546. [PMID: 31276898 DOI: 10.1016/j.ejmech.2019.06.072] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/26/2019] [Accepted: 06/26/2019] [Indexed: 12/30/2022]
Abstract
Epigenetics is the study of heritable changes in gene expression without changing the DNA sequence - a change in phenotype without a change in genotype. Epigenetic abnormalities can lead to serious diseases such as cancer in organisms. Histone methylation is one of the several manifestations of epigenetics, and requires specific enzymes to catalyze, for example, G9a, which is a histone methyl transferase. G9a catalyzes the methylation of histone 3 lysine 9 (H3K9) and histone 3 lysine 27 (H3K27). In addition, G9a also plays an essential role in DNA replication, damage and repair, and gene expression by regulating DNA methylation. Moreover, G9a has been found to be overexpressed in many tumor cells and is associated with the occurrence and development of tumors. Because of its unique characteristics, G9a has become a very promising target for anti-cancer agents. Over the last decade, dozens of G9a inhibitors have been discovered as potential anticancer therapeutic agents. In this review, we summarize and classify current G9a inhibitors, the challenges and future direction are also discussed in detail.
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Affiliation(s)
- Hao Cao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
| | - Ling Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
| | - Deying Yang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Liming Zeng
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xie Yewei
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Guochao Liao
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Jianjun Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China.
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7
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Abstract
The epigenetic control of gene expression could be affected by addition and/or removal of post-translational modifications such as phosphorylation, acetylation and methylation of histone proteins, as well as methylation of DNA (5-methylation on cytosines). Misregulation of these modifications is associated with altered gene expression, resulting in various disease conditions. G9a belongs to the protein lysine methyltransferases that specifically methylates the K9 residue of histone H3, leading to suppression of several tumor suppressor genes. In this review, G9a functions, role in various diseases, structural biology aspects for inhibitor design, structure-activity relationship among the reported inhibitors are discussed which could aid in the design and development of potent G9a inhibitors for cancer treatment in the future.
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8
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Ye Q, Li Q, Gao A, Ying H, Cheng G, Chen J, Che J, Li J, Dong X, Zhou Y. Discovery of novel indoleaminopyrimidine NIK inhibitors based on molecular docking-based support vector regression (SVR) model. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.01.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Milite C, Feoli A, Horton JR, Rescigno D, Cipriano A, Pisapia V, Viviano M, Pepe G, Amendola G, Novellino E, Cosconati S, Cheng X, Castellano S, Sbardella G. Discovery of a Novel Chemotype of Histone Lysine Methyltransferase EHMT1/2 (GLP/G9a) Inhibitors: Rational Design, Synthesis, Biological Evaluation, and Co-crystal Structure. J Med Chem 2019; 62:2666-2689. [PMID: 30753076 DOI: 10.1021/acs.jmedchem.8b02008] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since the discovery of compound BIX01294 over 10 years ago, only a very limited number of nonquinazoline inhibitors of H3K9-specific methyltransferases G9a and G9a-like protein (GLP) have been reported. Herein, we report the identification of a novel chemotype for G9a/GLP inhibitors, based on the underinvestigated 2-alkyl-5-amino- and 2-aryl-5-amino-substituted 3 H-benzo[ e][1,4]diazepine scaffold. Our research efforts resulted in the identification 12a (EML741), which not only maintained the high in vitro and cellular potency of its quinazoline counterpart, but also displayed improved inhibitory potency against DNA methyltransferase 1, improved selectivity against other methyltransferases, low cell toxicity, and improved apparent permeability values in both parallel artificial membrane permeability assay (PAMPA) and blood-brain barrier-specific PAMPA, and therefore might potentially be a better candidate for animal studies. Finally, the co-crystal structure of GLP in complex with 12a provides the basis for the further development of benzodiazepine-based G9a/GLP inhibitors.
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Affiliation(s)
| | | | - John R Horton
- Department of Molecular and Cellular Oncology , The University of Texas MD Anderson Cancer Center , Houston , Texas 77030 , United States
| | | | | | | | | | | | - Giorgio Amendola
- DiSTABiF , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - Ettore Novellino
- Department of Pharmacy , University Federico II of Naples , Via D. Montesano 49 , 80131 Naples , Italy
| | - Sandro Cosconati
- DiSTABiF , University of Campania "Luigi Vanvitelli" , Via Vivaldi 43 , 81100 Caserta , Italy
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology , The University of Texas MD Anderson Cancer Center , Houston , Texas 77030 , United States
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10
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The Distribution of Standard Deviations Applied to High Throughput Screening. Sci Rep 2019; 9:1268. [PMID: 30718587 PMCID: PMC6361996 DOI: 10.1038/s41598-018-36722-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/24/2018] [Indexed: 12/14/2022] Open
Abstract
High throughput screening (HTS) assesses compound libraries for “activity” using target assays. A subset of HTS data contains a large number of sample measurements replicated a small number of times providing an opportunity to introduce the distribution of standard deviations (DSD). Applying the DSD to some HTS data sets revealed signs of bias in some of the data and discovered a sub-population of compounds exhibiting high variability which may be difficult to screen. In the data examined, 21% of 1189 such compounds were pan-assay interference compounds. This proportion reached 57% for the most closely related compounds within the sub-population. Using the DSD, large HTS data sets can be modelled in many cases as two distributions: a large group of nearly normally distributed “inactive” compounds and a residual distribution of “active” compounds. The latter were not normally distributed, overlapped inactive distributions – on both sides –, and were larger than typically assumed. As such, a large number of compounds are being misclassified as “inactive” or are invisible to current methods which could become the next generation of drugs. Although applied here to HTS, it is applicable to data sets with a large number of samples measured a small number of times.
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11
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Kumar A, Zhang KYJ. Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3. J Comput Aided Mol Des 2018; 33:47-59. [PMID: 30084081 DOI: 10.1007/s10822-018-0142-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/01/2018] [Indexed: 12/15/2022]
Abstract
To extend the utility of ligand 3D shape similarity into pose prediction and virtual screening, we have previously developed CDVS and PoPSS methods. Both of them utilize ligand 3D shape similarity with the crystallographic ligands to improve pose prediction. While CDVS utilizes shape similarity to select suitable receptor structures for molecular docking, PoPSS places a ligand conformation of the highest shape similarity with crystal ligands into the target protein binding pocket which is then refined by side-chain repacking and Monte Carlo energy minimization. Analyses of PoPSS revealed some drawbacks in ligand conformation generation and the scoring scheme used. Moreover, as PoPSS does not sample the ligand conformation after placing it in the binding pocket, it relies solely on conformation generation methods to produce native like conformations. To address these limitations of PoPSS method, we report here a modified approach named as PoPSS-Lite, where side-chain repacking was replaced by a simple grid-based energy minimization. This modification also allowed the sampling of terminal functional groups while keeping the core scaffold fixed. Furthermore, shape similarity calculations were improved by increasing the number of ligand conformations and using a different similarity metric. The performance of PoPSS-Lite was prospectively evaluated in D3R GC3. Comparison of PoPSS-Lite demonstrated superior performance over PoPSS and CDVS with lower mean and median RMSDs. Furthermore, comparison with other D3R GC3 pose prediction submissions revealed top performance for PoPSS-Lite. Our D3R GC3 result extends our perspective that ligand 3D shape similarity with known crystallographic information can be successfully used to predict the binding pose of ligands with unknown binding modes. Our D3R GC3 results further highlight the necessity for improvement in conformer generation methods in order to improve shape similarity guided pose prediction.
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Affiliation(s)
- Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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12
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Kumar A, Zhang KYJ. Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Front Chem 2018; 6:315. [PMID: 30090808 PMCID: PMC6068280 DOI: 10.3389/fchem.2018.00315] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Affiliation(s)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
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13
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Rabal O, San José-Enériz E, Agirre X, Sánchez-Arias JA, Vilas-Zornoza A, Ugarte A, de Miguel I, Miranda E, Garate L, Fraga M, Santamarina P, Fernandez Perez R, Ordoñez R, Sáez E, Roa S, García-Barchino MJ, Martínez-Climent JA, Liu Y, Wu W, Xu M, Prosper F, Oyarzabal J. Discovery of Reversible DNA Methyltransferase and Lysine Methyltransferase G9a Inhibitors with Antitumoral in Vivo Efficacy. J Med Chem 2018; 61:6518-6545. [PMID: 29953809 DOI: 10.1021/acs.jmedchem.7b01926] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using knowledge- and structure-based approaches, we designed and synthesized reversible chemical probes that simultaneously inhibit the activity of two epigenetic targets, histone 3 lysine 9 methyltransferase (G9a) and DNA methyltransferases (DNMT), at nanomolar ranges. Enzymatic competition assays confirmed our design strategy: substrate competitive inhibitors. Next, an initial exploration around our hit 11 was pursued to identify an adequate tool compound for in vivo testing. In vitro treatment of different hematological neoplasia cell lines led to the identification of molecules with clear antiproliferative efficacies (GI50 values in the nanomolar range). On the basis of epigenetic functional cellular responses (levels of lysine 9 methylation and 5-methylcytosine), an acceptable therapeutic window (around 1 log unit) and a suitable pharmacokinetic profile, 12 was selected for in vivo proof-of-concept ( Nat. Commun. 2017 , 8 , 15424 ). Herein, 12 achieved a significant in vivo efficacy: 70% overall tumor growth inhibition of a human acute myeloid leukemia (AML) xenograft in a mouse model.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mario Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC) , Universidad de Oviedo-Principado de Asturias , Avenida de la Vega, 4-6 , 33940 El Entrego , Spain
| | - Pablo Santamarina
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC) , Universidad de Oviedo-Principado de Asturias , Avenida de la Vega, 4-6 , 33940 El Entrego , Spain
| | - Raul Fernandez Perez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC) , Universidad de Oviedo-Principado de Asturias , Avenida de la Vega, 4-6 , 33940 El Entrego , Spain
| | | | | | | | | | | | - Yingying Liu
- WuXi Apptec (Tianjin) Co. Ltd., TEDA , No. 111 HuangHai Road, Fourth Avenue , Tianjin 300456 , PR China
| | - Wei Wu
- WuXi Apptec (Tianjin) Co. Ltd., TEDA , No. 111 HuangHai Road, Fourth Avenue , Tianjin 300456 , PR China
| | - Musheng Xu
- WuXi Apptec (Tianjin) Co. Ltd., TEDA , No. 111 HuangHai Road, Fourth Avenue , Tianjin 300456 , PR China
| | - Felipe Prosper
- Departmento de Hematología, Clinica Universidad de Navarra , University of Navarra , Avenida Pio XII 36 , E-31008 Pamplona , Spain
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14
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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15
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Tikhomirov AS, Lin CY, Volodina YL, Dezhenkova LG, Tatarskiy VV, Schols D, Shtil AA, Kaur P, Chueh PJ, Shchekotikhin AE. New antitumor anthra[2,3-b]furan-3-carboxamides: Synthesis and structure-activity relationship. Eur J Med Chem 2018; 148:128-139. [DOI: 10.1016/j.ejmech.2018.02.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 02/06/2018] [Accepted: 02/09/2018] [Indexed: 11/16/2022]
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16
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Heterocyclic Analogs of 5,12-Naphthacenequinone 14*. Synthesis of naphtho[2,3-f]indole-3-carboxylic Acid Derivatives. Chem Heterocycl Compd (N Y) 2017. [DOI: 10.1007/s10593-017-2173-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Treshalina HM, Romanenko VI, Kaluzhny DN, Treshalin MI, Nikitin AA, Tikhomirov AS, Shchekotikhin AE. Development and pharmaceutical evaluation of the anticancer Anthrafuran/Cavitron complex, a prototypic parenteral drug formulation. Eur J Pharm Sci 2017; 109:631-637. [DOI: 10.1016/j.ejps.2017.09.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/24/2017] [Accepted: 09/15/2017] [Indexed: 12/27/2022]
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18
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Xiong Y, Li F, Babault N, Wu H, Dong A, Zeng H, Chen X, Arrowsmith CH, Brown PJ, Liu J, Vedadi M, Jin J. Structure-activity relationship studies of G9a-like protein (GLP) inhibitors. Bioorg Med Chem 2017; 25:4414-4423. [PMID: 28662962 DOI: 10.1016/j.bmc.2017.06.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/10/2017] [Accepted: 06/13/2017] [Indexed: 02/01/2023]
Abstract
Given the high homology between the protein lysine methyltransferases G9a-like protein (GLP) and G9a, it has been challenging to develop potent and selective inhibitors for either enzyme. Recently, we reported two quinazoline compounds, MS0124 and MS012, as GLP selective inhibitors. To further investigate the structure-activity relationships (SAR) of the quinazoline scaffold, we designed and synthesized a range of analogs bearing different 2-amino substitutions and evaluated their inhibition potencies against both GLP and G9a. These studies led to the identification of two new GLP selective inhibitors, 13 (MS3748) and 17 (MS3745), with 59- and 65-fold higher potency for GLP over G9a, which were confirmed by isothermal titration calorimetry (ITC). Crystal structures of GLP and G9a in complex with 13 and 17 provide insight into the interactions of the inhibitors with both proteins. In addition, we generated GLP selective inhibitors bearing a quinoline core instead of the quinazoline core.
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Affiliation(s)
- Yan Xiong
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Nicolas Babault
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Xin Chen
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jing Liu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | - Jian Jin
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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19
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Leite FHA, Froes TQ, da Silva SG, de Souza EIM, Vital-Fujii DG, Trossini GHG, Pita SSDR, Castilho MS. An integrated approach towards the discovery of novel non-nucleoside Leishmania major pteridine reductase 1 inhibitors. Eur J Med Chem 2017; 132:322-332. [DOI: 10.1016/j.ejmech.2017.03.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/18/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
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20
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Xiong Y, Li F, Babault N, Dong A, Zeng H, Wu H, Chen X, Arrowsmith CH, Brown PJ, Liu J, Vedadi M, Jin J. Discovery of Potent and Selective Inhibitors for G9a-Like Protein (GLP) Lysine Methyltransferase. J Med Chem 2017; 60:1876-1891. [PMID: 28135087 DOI: 10.1021/acs.jmedchem.6b01645] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
G9a-like protein (GLP) and G9a are highly homologous protein lysine methyltransferases (PKMTs) sharing approximately 80% sequence identity in their catalytic domains. GLP and G9a form a heterodimer complex and catalyze mono- and dimethylation of histone H3 lysine 9 and nonhistone substrates. Although they are closely related, GLP and G9a possess distinct physiological and pathophysiological functions. Thus, GLP or G9a selective small-molecule inhibitors are useful tools to dissect their distinct biological functions. We previously reported potent and selective G9a/GLP dual inhibitors including UNC0638 and UNC0642. Here we report the discovery of potent and selective GLP inhibitors including 4 (MS0124) and 18 (MS012), which are >30-fold and 140-fold selective for GLP over G9a and other methyltransferases, respectively. The cocrystal structures of GLP and G9a in the complex with either 4 or 18 displayed virtually identical binding modes and interactions, highlighting the challenges in structure-based design of selective inhibitors for either enzyme.
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Affiliation(s)
- Yan Xiong
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Nicolas Babault
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Xin Chen
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G 2M9, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Jing Liu
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Jian Jin
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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21
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Sunke R, Nallapati SB, Kumar JS, Shiva Kumar K, Pal M. Use of AlCl3 in Friedel Crafts arylation type reactions and beyond: an overview on the development of unique methodologies leading to N-heteroarenes. Org Biomol Chem 2017; 15:4042-4057. [DOI: 10.1039/c7ob00468k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
An overview on the development of unique methodologies that highlight the use of AlCl3 in reactions leading to new N-heteroarenes of biological significance is presented.
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Affiliation(s)
- Rajnikanth Sunke
- Dr Reddy's Institute of Life Sciences
- Hyderabad Central University
- Hyderabad-500 046
- India
| | - Suresh Babu Nallapati
- Dr Reddy's Institute of Life Sciences
- Hyderabad Central University
- Hyderabad-500 046
- India
| | - Jetta Sandeep Kumar
- Dr Reddy's Institute of Life Sciences
- Hyderabad Central University
- Hyderabad-500 046
- India
| | - K. Shiva Kumar
- Department of Chemistry
- Osmania University
- Hyderabad-500 007
- India
| | - Manojit Pal
- Dr Reddy's Institute of Life Sciences
- Hyderabad Central University
- Hyderabad-500 046
- India
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