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Cho AYH, Chung H, Romero-Parra J, Kumar P, Allarà M, Ligresti A, Gallardo-Garrido C, Pessoa-Mahana H, Faúndez M, Pessoa-Mahana CD. Motifs in Natural Products as Useful Scaffolds to Obtain Novel Benzo[ d]imidazole-Based Cannabinoid Type 2 (CB2) Receptor Agonists. Int J Mol Sci 2023; 24:10918. [PMID: 37446093 DOI: 10.3390/ijms241310918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/02/2023] [Accepted: 05/11/2023] [Indexed: 07/15/2023] Open
Abstract
The endocannabinoid system (ECS) constitutes a broad-spectrum modulator of homeostasis in mammals, providing therapeutic opportunities for several pathologies. Its two main receptors, cannabinoid type 1 (CB1) and type 2 (CB2) receptors, mediate anti-inflammatory responses; however, their differing patterns of expression make the development of CB2-selective ligands therapeutically more attractive. The benzo[d]imidazole ring is considered to be a privileged scaffold in drug discovery and has demonstrated its versatility in the development of molecules with varied pharmacologic properties. On the other hand, the main psychoactive component of Cannabis sativa, delta-9-tetrahydrocannabinol (THC), can be structurally described as an aliphatic terpenoid motif fused to an aromatic polyphenolic (resorcinol) structure. Inspired by the structure of this phytocannabinoid, we combined different natural product motifs with a benzo[d]imidazole scaffold to obtain a new library of compounds targeting the CB2 receptor. Here, we synthesized 26 new compounds, out of which 15 presented CB2 binding and 3 showed potent agonist activity. SAR analysis indicated that the presence of bulky aliphatic or aromatic natural product motifs at position 2 of the benzo[d]imidazoles ring linked by an electronegative atom is essential for receptor recognition, while substituents with moderate bulkiness at position 1 of the heterocyclic core also participate in receptor recognition. Compounds 5, 6, and 16 were further characterized through in vitro cAMP functional assay, showing potent EC50 values between 20 and 3 nM, and compound 6 presented a significant difference between the EC50 of pharmacologic activity (3.36 nM) and IC50 of toxicity (30-38 µM).
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Affiliation(s)
- Analia Young Hwa Cho
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Hery Chung
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Javier Romero-Parra
- Organic Chemistry and Physical Chemistry Department, Faculty of Chemical and Pharmaceutical Sciences, Universidad de Chile, Olivos 1007, Santiago 7820436, Chile
| | - Poulami Kumar
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Marco Allarà
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Alessia Ligresti
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Carlos Gallardo-Garrido
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Hernán Pessoa-Mahana
- Organic Chemistry and Physical Chemistry Department, Faculty of Chemical and Pharmaceutical Sciences, Universidad de Chile, Olivos 1007, Santiago 7820436, Chile
| | - Mario Faúndez
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Carlos David Pessoa-Mahana
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile
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Ma C, Liu WG, Liu WD, Xi CC, Xiong F, Zhang SP. Molecular Docking and 3D-QSAR Studies on a Series of Benzenesulfonamide Derivatives as a Hepatitis B Virus Capsid Assembly Inhibitor. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2020.1871038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Chao Ma
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, China
| | - Wen-guang Liu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, China
| | - Wen-ding Liu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, China
| | - Chang-cheng Xi
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, China
| | - Shu-ping Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, China
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Song X, Cai X, Zhang X, Fan X. Synthesis of N-acylbenzimidazoles through [4 + 1] annulation of N-arylpivalimidamides with dioxazolones. Org Chem Front 2021. [DOI: 10.1039/d1qo01137e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Presented herein is a novel and efficient synthesis of N-acylbenzimidazoles through an unprecedented [4 + 1] annulation of N-arylpivalimidamides with dioxazolones.
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Affiliation(s)
- Xia Song
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xinyuan Cai
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xinying Zhang
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xuesen Fan
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
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4
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Zhao J, Zang J, Yang J, Gao QB, Yan Y, Ma C, Chen Y, Ding L, Liu HM. Investigating the binding mechanism of piperidinyl ureas inhibitors based on the UBC12-DCN1 interaction by 3D-QSAR, molecular docking and molecular dynamics simulations. J Biomol Struct Dyn 2020; 40:2674-2688. [PMID: 33183176 DOI: 10.1080/07391102.2020.1841678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Neddylation regulates a variety of biological processes by modulating Cullin-RING E3 ubiquitin ligases (CRLs) which is considered to be an important target for human diseases. The activation of CRLs required Cullins Neddylation, which regulated by the interaction of UBC12-DCN1 complex. Here, to investigate the structure-activity relationship and binding mechanism of 41 piperidinyl ureas inhibitors based on the UBC12-DCN1 protein-protein interaction, we carried out molecular modeling studies using three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations.Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to generate 3D-QSAR models. The results show that the best CoMFA model has q2=0.736, r2ncv=0.978, r2pred=0.78 (CoMFA), and the best CoMSIA model has q2=0.761, r2ncv=0.987, r2pred=0.86. The electrostatic, hydrophobic and H-bond donor fields play important roles in the models. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. Molecular dynamics simulations results reveal that the complex of the ligand and the receptor protein are stable at 300 K. The results of MM-GBSA indicated the residues of Ile1083, Ile1086, Ala1098, Val1102, Ile1105, Gln1114, Phe1164 and Leu1184 might be the key residues during the process of inhibitors bound to DCN1. This study could provide an important theoretical basis for further developing novel inhibitors design based on UBC12-DCN1 protein-protein interaction. All the results can provide us more useful information for our further drug design. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiangheng Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Jieying Zang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Jing Yang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Qi-Bing Gao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Ying Yan
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Chaoya Ma
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Yujie Chen
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Hong-Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
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Virtual Screening of C. Sativa Constituents for the Identification of Selective Ligands for Cannabinoid Receptor 2. Int J Mol Sci 2020; 21:ijms21155308. [PMID: 32722631 PMCID: PMC7432466 DOI: 10.3390/ijms21155308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 12/18/2022] Open
Abstract
The selective targeting of the cannabinoid receptor 2 (CB2) is crucial for the development of peripheral system-acting cannabinoid analgesics. This work aimed at computer-assisted identification of prospective CB2-selective compounds among the constituents of Cannabis Sativa. The molecular structures and corresponding binding affinities to CB1 and CB2 receptors were collected from ChEMBL. The molecular structures of Cannabis Sativa constituents were collected from a phytochemical database. The collected records were curated and applied for the development of quantitative structure-activity relationship (QSAR) models with a machine learning approach. The validated models predicted the affinities of Cannabis Sativa constituents. Four structures of CB2 were acquired from the Protein Data Bank (PDB) and the discriminatory ability of CB2-selective ligands and two sets of decoys were tested. We succeeded in developing the QSAR model by achieving Q2 5-CV > 0.62. The QSAR models helped to identify three prospective CB2-selective molecules that are dissimilar to already tested compounds. In a complementary structure-based virtual screening study that used available PDB structures of CB2, the agonist-bound, Cryogenic Electron Microscopy structure of CB2 showed the best statistical performance in discriminating between CB2-active and non-active ligands. The same structure also performed best in discriminating between CB2-selective ligands from non-selective ligands.
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Ul-Haq Z, Khan A, Ashraf S, Morales-Bayuelo A. Quantum mechanics and 3D-QSAR studies on thienopyridine analogues: inhibitors of IKKβ. Heliyon 2020; 6:e04125. [PMID: 32566780 PMCID: PMC7298411 DOI: 10.1016/j.heliyon.2020.e04125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/11/2020] [Accepted: 05/29/2020] [Indexed: 01/23/2023] Open
Abstract
Inhibitor of kappa B kinase subunit β (IKKβ) is a main regulator of nuclear factor kappa B (NF-κB) and has received considerable attention as an attractive therapeutic target for the treatment of lung cancer or other inflammatory disease. A group of diversified thienopyridine derivatives exhibited a wide range of biological activity was used to investigate its structural requirements by using DFT and 3D-Quantitative structure activity relationship. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were established using the experimental activity of thienopyridine derivatives. The cross-validation coefficient (q2) values for CoMFA and CoMSIA are 0.671 and 0.647 respectively, were achieved, demonstrating high predictive capability of the model. The contour analysis indicate that presence of hydrophobic and electrostatic field is highly desirable for biological activity. The results indicate that substitution of hydrophobic group with electron withdrawing effect at R4 and R6 position have more possibility to increase the biological activity of thienopyridine derivatives. Subsequently molecular docking and DFT calculation were performed to assess the potency of the compounds.
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Affiliation(s)
- Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Alamgir Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Alejandro Morales-Bayuelo
- Grupo de Investigaciones Básicas y Clínicas de la Universidad del Sinú (GIBACUS), Escuela de Medicina, Universidad del Sinú, Seccional Cartagena de Indias, Colombia
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7
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Zhang C, Li Q, Ren Y, Liu F. Molecular modeling studies of benzothiophene-containing derivatives as promising selective estrogen receptor downregulators: a combination of 3D-QSAR, molecular docking and molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:2702-2723. [PMID: 32249694 DOI: 10.1080/07391102.2020.1751717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Selective estrogen receptor downregulators (SERDs) for the treatment of positive breast cancer can act both as estrogen alpha receptor (ERα) antagonists and degraders. In this study, the optimal antagonist models (CoMFA-A, q2 = 0.660, r2 = 0.996; CoMSIA-A, q2 = 0.728, r2 = 0.992) and degrader models (CoMFA-D, q2 = 0.850, r2 = 0.996; CoMSIA-D, q2 = 0.719, r2 = 0.995) of a series of potent benzothiophene-containing SERDs were constructed to explore the three-dimensional quantitative structure-activity relationship. Internal and external validation indicated that all models exhibited good applicability, high predictive ability and robustness. Contour maps revealed the relationships between the essential structural features and antagonistic and degradation activities. Additionally, molecular docking, molecular dynamics and free energy calculation studies were further performed to investigate the detailed binding mode. Results indicated that several key residues, ARG394, GLU353, PHE404 and ILE424, were crucial for the stability of the ligand binding domain. The hydrophobic, electrostatic and Van der Waals interactions played significant effect on the binding affinity. Finally, ten novel compounds were designed based on above findings, where the predicted activity of compound D8 was equivalent to that of the compound LSZ102. 3D-QSAR, ADMET and bioavailability predictions indicated that all designed compounds with good predicted activity, good physicochemical and bioavailability could be potential candidates for SERDs. These results and combinations of computational methods provided guidance for the rational drug design of novel potential SERDs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cuihua Zhang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Qunlin Li
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Yujie Ren
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Fei Liu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
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Wang Y, Guo H, Tang G, He Q, Zhang Y, Hu Y, Wang Y, Lin Z. A selectivity study of benzenesulfonamide derivatives on human carbonic anhydrase II/IX by 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation. Comput Biol Chem 2019; 80:234-243. [DOI: 10.1016/j.compbiolchem.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 02/14/2019] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
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Lorca M, Valdes Y, Chung H, Romero-Parra J, Pessoa-Mahana CD, Mella J. Three-Dimensional Quantitative Structure-Activity Relationships (3D-QSAR) on a Series of Piperazine-Carboxamides Fatty Acid Amide Hydrolase (FAAH) Inhibitors as a Useful Tool for the Design of New Cannabinoid Ligands. Int J Mol Sci 2019; 20:ijms20102510. [PMID: 31117309 PMCID: PMC6566251 DOI: 10.3390/ijms20102510] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/27/2019] [Accepted: 05/07/2019] [Indexed: 11/16/2022] Open
Abstract
Fatty Acid Amide Hydrolase (FAAH) is one of the main enzymes responsible for endocannabinoid metabolism. Inhibition of FAAH increases endogenous levels of fatty acid ethanolamides such as anandamide (AEA) and thus consitutes an indirect strategy that can be used to modulate endocannabinoid tone. In the present work, we present a three-dimensional quantitative structure-activity relationships/comparative molecular similarity indices analysis (3D-QSAR/CoMSIA) study on a series of 90 reported irreversible inhibitors of FAAH sharing a piperazine-carboxamide scaffold. The model obtained was extensively validated (q2 = 0.734; r2 = 0.966; r2m = 0.723). Finally, based on the information derived from the contour maps we designed a series of 10 new compounds with high predicted FAAH inhibition (predicted pIC50 of the best-proposed compounds = 12.196; 12.416).
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Affiliation(s)
- Marcos Lorca
- Escuela de Quimica y Farmacia, Facultad de Medicina, Universidad Andres Bello, Quillota 980, Viña del Mar 2531015, Chile.
| | - Yudisladys Valdes
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile.
| | - Hery Chung
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile.
| | - Javier Romero-Parra
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Avenida Angamos 0610, Antofagasta 1270709, Chile.
| | - C David Pessoa-Mahana
- Pharmacy Department, Faculty of Chemistry, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile.
| | - Jaime Mella
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Av. Gran Bretaña 1111, Valparaíso 2360102, Chile.
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Santa Marta 183, Valparaíso 2360134, Chile.
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Wang L, Zhang Y, Wang X, Ye Z. Electroacupuncture-induced cannabinoid receptor expression in repair of abducens nerve. Int J Neurosci 2019; 129:923-929. [PMID: 30889365 DOI: 10.1080/00207454.2019.1593980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Objective: Through the development of beagle abducens nerve injury model, taking electroacupuncture as the core and microglia as the starting point, the author investigated whether electroacupuncture can promote the repair of injured abducens nerve by cannabinoid receptor-mediated regulation of microglia activation. Methods: Healthy beagle dogs were randomly divided into five groups: sham operation group (A), injury group (B), electroacupuncture pretreatment group (C), antagonist group (D) and solvent group (E). After stimulation with electroacupuncture, the expression of cannabinoid 1 receptor (CB1R) and cannabinoid 2 receptor (CB2R) in A, B and C microglia cells was detected by Western Bolt analysis, and further the expression of CB2R in five groups was further analyzed by immunofluorescence, thereby statistical differences were analyzed. Results: Among group A, group B and group C, Western Blot analysis showed that there were no significant changes in the expression of CB1R protein after electroacupuncture [F (2, 12)=1.75, p = 0.215]. After electroacupuncture preconditioning for 15 min for 2 weeks, group C was compared with group A and group B, which showed CB2 was affected. The expression of CB2R protein was significantly increased among groups A, B and C [F (2, 12)=5189.57, p < 0.001], but there was no significant difference in the expression of CB2R protein between group A and group B (p > 0.05). The results of immunofluorescence showed that Arginse/CD11b was significantly increased in group C comparing to group A (*p < 0.001), while there was a significant increase in group E comparing to group A about Arginse/CD11b [F (4, 20)=4345.44, p < 0.001]. Conclusions: The CB2R in the cannabinoid receptor is mainly involved in the electro-acupuncture-induced neuroprotection. Electroacupuncture can promote the repair of injured abducens nerve by CB2R-mediated activation of microglia.
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Affiliation(s)
- Lei Wang
- a Department of Emergency Center , Affiliated Hospital 2 of Nantong University , Nantong , Jiangsu , China
| | - Yi Zhang
- b Department of Neurosurgery , Affiliated Hospital 2 of Nantong University , Nantong , Jiangsu , China
| | - Xudong Wang
- c Department of Chinese Traditional Medicine , Affiliated Hospital 2 of Nantong University , Nantong , Jiangsu , China
| | - Zi Ye
- b Department of Neurosurgery , Affiliated Hospital 2 of Nantong University , Nantong , Jiangsu , China
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Wang ZZ, Ma CY, Yang J, Gao QB, Sun XD, Ding L, Liu HM. Investigating the binding mechanism of (4-Cyanophenyl)glycine derivatives as reversible LSD1 by 3D-QSAR, molecular docking and molecular dynamics simulations. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Zhang G, Ren Y. Molecular Modeling and Design Studies of Purine Derivatives as Novel CDK2 Inhibitors. Molecules 2018; 23:molecules23112924. [PMID: 30423939 PMCID: PMC6278423 DOI: 10.3390/molecules23112924] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/29/2018] [Accepted: 11/06/2018] [Indexed: 11/16/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is a potential target for treating cancer. Purine heterocycles have attracted particular attention as the scaffolds for the development of CDK2 inhibitors. To explore the interaction mechanism and the structure–activity relationship (SAR) and to design novel candidate compounds as potential CDK2 inhibitors, a systematic molecular modeling study was conducted on 35 purine derivatives as CDK2 inhibitors by combining three-dimensional quantitative SAR (3D-QSAR), virtual screening, molecular docking, and molecular dynamics (MD) simulations. The predictive CoMFA model (q2 = 0.743, rpred2 = 0.991), the CoMSIA model (q2 = 0.808, rpred2 = 0.990), and the Topomer CoMFA model (q2 = 0.779, rpred2 = 0.962) were obtained. Contour maps revealed that the electrostatic, hydrophobic, hydrogen bond donor and steric fields played key roles in the QSAR models. Thirty-one novel candidate compounds with suitable predicted activity (predicted pIC50 > 8) were designed by using the results of virtual screening. Molecular docking indicated that residues Asp86, Glu81, Leu83, Lys89, Lys33, and Gln131 formed hydrogen bonds with the ligand, which affected activity of the ligand. Based on the QSAR model prediction and molecular docking, two candidate compounds, I13 and I60 (predicted pIC50 > 8, docking score > 10), with the most potential research value were further screened out. MD simulations of the corresponding complexes of these two candidate compounds further verified their stability. This study provided valuable information for the development of new potential CDK2 inhibitors.
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Affiliation(s)
- Gaomin Zhang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Yujie Ren
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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13
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Design, synthesis and biological evaluation of novel zanamivir derivatives as potent neuraminidase inhibitors. Bioorg Med Chem Lett 2018; 28:3622-3629. [PMID: 30389293 DOI: 10.1016/j.bmcl.2018.10.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/25/2018] [Indexed: 01/22/2023]
Abstract
Neuraminidase (NA) is an important antiviral drug target. Zanamivir is one of the most potent NA inhibitors. In this paper, a series of zanamivir derivatives as potential NA inhibitors were studied by combination of molecular modeling techniques including 3D-QSAR, molecular docking, and molecular dynamics (MD) simulation. The results show that the best CoMFA (comparative molecular field analysis) model has q2 = 0.728 and r2 = 0.988, and the best CoMSIA (comparative molecular similarity indices analysis) model has q2 = 0.750 and r2 = 0.981, respectively. The built 3D-QSAR models show significant statistical quality and excellent predictive ability. Seven new NA inhibitors were designed and predicted. 20 ns of MD simulations were carried out and their binding free energies were calculated. Two designed compounds were selected to be synthesized and biologically evaluated by NA inhibition and virus inhibition assays. One compound (IC50 = 0.670 µM, SI > 149) exhibits excellent antiviral activity against A/WSN/33 H1N1, which is superior to the reference drug zanamivir (IC50 = 0.873 µM, SI > 115). The theoretical and experimental results may provide reference for development of new anti-influenza drugs.
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14
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Meng L, Feng K, Ren Y. Molecular modelling studies of tricyclic triazinone analogues as potential PKC-θ inhibitors through combined QSAR, molecular docking and molecular dynamics simulations techniques. J Taiwan Inst Chem Eng 2018. [DOI: 10.1016/j.jtice.2018.06.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Floresta G, Apirakkan O, Rescifina A, Abbate V. Discovery of High-Affinity Cannabinoid Receptors Ligands through a 3D-QSAR Ushered by Scaffold-Hopping Analysis. Molecules 2018; 23:molecules23092183. [PMID: 30200181 PMCID: PMC6225167 DOI: 10.3390/molecules23092183] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 01/08/2023] Open
Abstract
Two 3D quantitative structure–activity relationships (3D-QSAR) models for predicting Cannabinoid receptor 1 and 2 (CB1 and CB2) ligands have been produced by way of creating a practical tool for the drug-design and optimization of CB1 and CB2 ligands. A set of 312 molecules have been used to build the model for the CB1 receptor, and a set of 187 molecules for the CB2 receptor. All of the molecules were recovered from the literature among those possessing measured Ki values, and Forge was used as software. The present model shows high and robust predictive potential, confirmed by the quality of the statistical analysis, and an adequate descriptive capability. A visual understanding of the hydrophobic, electrostatic, and shaping features highlighting the principal interactions for the CB1 and CB2 ligands was achieved with the construction of 3D maps. The predictive capabilities of the model were then used for a scaffold-hopping study of two selected compounds, with the generation of a library of new compounds with high affinity for the two receptors. Herein, we report two new 3D-QSAR models that comprehend a large number of chemically different CB1 and CB2 ligands and well account for the individual ligand affinities. These features will facilitate the recognition of new potent and selective molecules for CB1 and CB2 receptors.
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MESH Headings
- Cannabinoid Receptor Agonists/chemistry
- Cannabinoid Receptor Agonists/metabolism
- Cannabinoid Receptor Antagonists/chemistry
- Cannabinoid Receptor Antagonists/metabolism
- Drug Design
- Hydrophobic and Hydrophilic Interactions
- Ligands
- Models, Molecular
- Molecular Conformation
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Molecular Structure
- Protein Binding
- Quantitative Structure-Activity Relationship
- Receptor, Cannabinoid, CB1/chemistry
- Receptor, Cannabinoid, CB1/metabolism
- Receptor, Cannabinoid, CB2/chemistry
- Receptor, Cannabinoid, CB2/metabolism
- Receptors, Cannabinoid/chemistry
- Receptors, Cannabinoid/metabolism
- Software
- Static Electricity
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Affiliation(s)
- Giuseppe Floresta
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
- Department of Chemical Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
- Institute of Pharmaceutical Science, King's College London, Stamford Street, London SE1 9NH, UK.
| | - Orapan Apirakkan
- King's Forensics, School of Population Health & Environmental Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
| | - Antonio Rescifina
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Vincenzo Abbate
- King's Forensics, School of Population Health & Environmental Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
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Liu G, Wan Y, Wang W, Fang S, Gu S, Ju X. Docking-based 3D-QSAR and pharmacophore studies on diarylpyrimidines as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Mol Divers 2018; 23:107-121. [PMID: 30051344 DOI: 10.1007/s11030-018-9860-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/13/2018] [Indexed: 11/30/2022]
Abstract
Diarylpyrimidines (DAPYs), a type of effective HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), have been considered as one of the most successful agents for treating AIDS. A number of structurally diverse DAPYs have been designed and synthesized in the past decade, and most of them exhibited potent anti-HIV-1 activities; however, the structure-activity relationships of recently reported DAPYs and their pharmacophore features that interacted with HIV-1 reverse transcriptase (RT) remain to be studied. In the present study, molecular docking studies were first performed on three novel classes of DAPYs to study their binding pattern in the HIV-1 RT. Based on the docking conformations of these DAPYs, 3D-QSAR models were constructed using CoMSIA and Topomer CoMFA methods, and pharmacophore models were also built using distance comparison technique. All selected DAPYs presented preferred U- or L-shaped conformations while being docked into the non-nucleoside inhibitor-binding pocket of the HIV-1 RT. The best CoMSIA model exhibited powerful predictivity, with satisfactory statistical parameters such as a q2 of 0.572, an r2 of 0.952, and an [Formula: see text] of 0.728. Contour maps of the best CoMSIA model were in accordance with those of the Topomer CoMFA model, giving the insight into the feature requirements of DAPYs for the anti-HIV-1 activity. Three potential pharmacophore models were constructed, and each of them was consisted of five hypothesis features. All results suggested that the aromatic ring on the left wing of DAPYs and the central pyrimidine ring contained key pharmacophore features for the anti-HIV-1 activity, and also indicated that the right wing of DAPYs had potential for further structural modification to improve activity. Eight novel DAPY molecules with potential anti-HIV-1 activities were designed on the basis of the obtained results. The findings in this study might provide important information for further design and development of novel HIV-1 NNRTIs.
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Affiliation(s)
- Genyan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China.
| | - Youlan Wan
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Wenjie Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Sai Fang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Shuangxi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China.
| | - Xiulian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
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Design, synthesis and biological evaluation of novel oseltamivir derivatives as potent neuraminidase inhibitors. Bioorg Med Chem Lett 2017; 27:5429-5435. [DOI: 10.1016/j.bmcl.2017.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 11/19/2022]
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18
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Rescifina A, Floresta G, Marrazzo A, Parenti C, Prezzavento O, Nastasi G, Dichiara M, Amata E. Development of a Sigma-2 Receptor affinity filter through a Monte Carlo based QSAR analysis. Eur J Pharm Sci 2017; 106:94-101. [DOI: 10.1016/j.ejps.2017.05.061] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/26/2017] [Accepted: 05/27/2017] [Indexed: 10/19/2022]
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19
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Peng XX, Feng KR, Ren YJ. Molecular modeling studies of quinazolinone derivatives as novel PI3Kδ selective inhibitors. RSC Adv 2017. [DOI: 10.1039/c7ra10870b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The main molecular modeling method, the docking results of newly designed compoundD04and the best pharmacophore model are reported herein.
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Affiliation(s)
- Xiu Xiu Peng
- School of Chemical and Environmental Engineering
- Shanghai Institute of Technology
- Shanghai 201418
- China
| | - Kai Rui Feng
- School of Chemical and Environmental Engineering
- Shanghai Institute of Technology
- Shanghai 201418
- China
| | - Yu Jie Ren
- School of Chemical and Environmental Engineering
- Shanghai Institute of Technology
- Shanghai 201418
- China
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