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Kalsoom I, Shehzadi K, Li HS, Wen HL, Yu MJ. Unraveling the Mechanisms of Cannabidiol's Pharmacological Actions: A Comprehensive Research Overview. Top Curr Chem (Cham) 2024; 382:20. [PMID: 38829467 DOI: 10.1007/s41061-024-00465-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/05/2024] [Indexed: 06/05/2024]
Abstract
Cannabis sativa has long been used for neurological and psychological healing. Recently, cannabidiol (CBD) extracted from cannabis sativa has gained prominence in the medical field due to its non-psychotropic therapeutic effects on the central and peripheral nervous systems. CBD, also acting as a potent antioxidant, displays diverse clinical properties such as anticancer, antiinflammatory, antidepressant, antioxidant, antiemetic, anxiolytic, antiepileptic, and antipsychotic effects. In this review, we summarized the structural activity relationship of CBD with different receptors by both experimental and computational techniques and investigated the mechanism of interaction between related receptors and CBD. The discovery of structural activity relationship between CBD and target receptors would provide a direction to optimize the scaffold of CBD and its derivatives, which would give potential medical applications on CBD-based therapies in various illnesses.
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Affiliation(s)
- Iqra Kalsoom
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Han-Sheng Li
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Hong-Liang Wen
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Ming-Jia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
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2
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Wang R, Duan L, Zhao B, Zheng Y, Chen L. Molecular recognition between volatile molecules and odorant binding proteins 7 by homology modeling, molecular docking and molecular dynamics simulation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38767431 DOI: 10.1002/jsfa.13595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/01/2024] [Accepted: 05/04/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Odorant-binding proteins (OBPs) in insects are key to detection and recognition of external chemical signals associated with survival. OBP7 in Spodoptera frugiperda's larval stage (SfruOBP7) may search for host plants by sensing plant volatiles, which are important sources of pest attractants and repellents. However, the atomic-level basis of binding modes remains elusive. RESULTS SfruOBP7 structure was constructed through homology modeling, and complex models of six plant volatiles ((E)-2-hexenol, α-pinene, (Z)-3-hexenyl acetate, lauric acid, O-cymene and 1-octanol) and SfruOBP7 were obtained through molecular docking. To study the detailed interactions between the six plant volatile molecules and SfruOBP7, we conducted three 300 ns molecular dynamics simulations for each study object. The correlation coefficients between binding free energy obtained by molecular mechanics/generalized Born surface area together with solvated interaction energy methods and experimental values are 0.90 and 0.88, respectively, showing a good correlation. By comparing binding free energy along with interaction patterns between SfruOBP7 and the six volatile molecules, hotspot residues of SfruOBP7 when binding with different volatile molecules were determined. Hydrophobic interactions stemming from van der Waals interactions play a significant role in SfruOBP7 and these plant volatile systems. CONCLUSION The optimized three-dimensional structure of SfruOBP7 and its binding modes with six plant volatiles revealed their interactions, thus providing a means for estimating the binding energies of other plant volatiles. Our study will help to guide the rational design of effective and selective insect attractants. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
| | - Lixin Duan
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
| | - Bing Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar University, Qiqihar, China
| | - Yongjie Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
| | - Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
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3
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Chen G, Niu X, Chen Y, Wang M, Bi Y, Gao Y, Ji Y, An T. Estrogenic disruption effects and formation mechanisms of transformation products during photolysis of preservative parabens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171608. [PMID: 38492588 DOI: 10.1016/j.scitotenv.2024.171608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
The ubiquitous presence of emerging contaminants (ECs) in the environment and their associated adverse effects has raised concerns about their potential risks. The increased toxicity observed during the environmental transformation of ECs is often linked to the formation of their transformation products (TPs). However, comprehension of their formation mechanisms and contribution to the increased toxicity remains an unresolved challenge. To address this gap, by combining quantum chemical and molecular simulations with photochemical experiments in water, this study investigated the formation of TPs and their molecular interactions related to estrogenic effect using the photochemical degradation of benzylparaben (BZP) preservative as a representative example. A non-targeted analysis was carried out and three previously unknown TPs were identified during the transformation of BZP. Noteworthy, two of these novel TPs, namely oligomers BZP-o-phenol and BZP-m-phenol, exhibited higher estrogenic activities compared to the parent BZP. Their IC50 values of 0.26 and 0.50 μM, respectively, were found to be lower than that of the parent BZP (6.42 μM). The binding free energies (ΔGbind) of BZP-o-phenol and BZP-m-phenol (-29.71 to -23.28 kcal·mol-1) were lower than that of the parent BZP (-20.86 kcal·mol-1), confirming their stronger binding affinities toward the estrogen receptor (ER) α-ligand binding domain. Subsequent analysis unveiled that these hydrophobic residues contributed most favorably to ER binding, with van der Waals interactions playing a significant role. In-depth examination of the formation mechanisms indicated that these toxic TPs primarily originated from the successive cleavage of ester bonds (OCH2C6H5 and COO group), followed by their combination with BZP*. This study provides valuable insight into the mechanisms underlying the formation of toxic TPs and their binding interactions causing the endocrine-disrupting effects. It offers a crucial framework for elucidating the toxicological patterns of ECs with similar structures.
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Affiliation(s)
- Guanhui Chen
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiaolin Niu
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yi Chen
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Mei Wang
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yashi Bi
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yanpeng Gao
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Yuemeng Ji
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Taicheng An
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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Doganc F, Ozkan T, Farhangzad N, Mavideniz A, Celik I, Sunguroglu A, Göker H. Synthesis of novel indol-3-acetamido analogues as potent anticancer agents, biological evaluation and molecular modeling studies. Bioorg Chem 2024; 148:107429. [PMID: 38728910 DOI: 10.1016/j.bioorg.2024.107429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/21/2024] [Accepted: 05/04/2024] [Indexed: 05/12/2024]
Abstract
Cannabinoids bind to cannabinoid receptors CB1 and CB2 and their antitumoral activity has been reported against some various cancer cell lines. Some synthetic cannabinoids possessing indole rings such as JWH-015 and JWH-133 particularly bind to the cannabinoid CB2 receptor and it was reported that they inhibit the proliferation and growth of various cancer cells without their psychoactive effects. However, the pharmacological action mechanisms of the cannabinoids are completely unknown. In this study, we report the synthesis of some new cannabinoidic novel indoles and evaluate their anticancer activity on various cancerous and normal cell lines (U87, RPMI 8226, HL60 and L929) using several cellular and molecular assays including MTT assay, real-time q-PCR, scratch assay, DAPI assay, Annexin V-PE/7AAD staining, caspase3/7 activity tests. Our findings indicated that compounds 7, 10, 13, 16, and 17 could reduce cell viability effectively. Compound 17 markedly increased proapoptotic genes (BAX, BAD, and BIM), tumor suppressor gene (p53) expression levels as well as the BAX/BCL-2 ratio in U87 cells. In addition, 17 inhibited cell migration. Based on these results, 17 was chosen for determining the mechanism of cell death in U87 cells. DAPI and Annexin V-7AAD staining results showed that 17 induced apoptosis, moreover activated caspase 3/7 significantly. Hence, compound 17, was selected as a lead compound for further pharmacomodulation. To rationalize the observed biological activities of 17, our study also included a comprehensive analysis using molecular docking and MD simulations. This integrative approach revealed that 17 fits tightly into the active site of the CB2 receptor and is involved in key interactions that may be responsible for its anti-proliferative effects.
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Affiliation(s)
- Fatima Doganc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey
| | - Tulin Ozkan
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Nazila Farhangzad
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey; Graduate School of Health Sciences, Ankara University, Dışkapı, Ankara, Turkey
| | - Acelya Mavideniz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; Graduate School of Health Sciences, Ankara University, Dışkapı, Ankara, Turkey
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38280, Turkey
| | - Asuman Sunguroglu
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Hakan Göker
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey.
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5
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Long Q, Li T, Zhu Q, He L, Zhao B. SuanZaoRen decoction alleviates neuronal loss, synaptic damage and ferroptosis of AD via activating DJ-1/Nrf2 signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 323:117679. [PMID: 38160863 DOI: 10.1016/j.jep.2023.117679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/03/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE SuanZaoRen Decoction (SZRD), a famous herbal prescription, and has been widely proven to have positive therapeutic effects on insomnia, depression and Alzheimer's disease (AD). However, the anti-AD molecular mechanism of SZRD remains to be further investigated. AIM OF THE STUDY To elucidate the molecular mechanism of SZRD's improvement in AD's neuronal loss, synaptic damage and ferroptosis by regulating DJ-1/Nrf2 signaling pathway. MATERIALS AND METHODS LC-MS/MS was used to detect the active ingredients from SZRD. APP/PS1 mice was treated with SZRD and a ferroptosis inhibitor (Liproxstatin-1), respectively. Upon the completion of behavioral tests, Nissl staining, FJB staining, Golgi staining, immunofluorescence, immunohistochemistry, and transmission electron microscopy were preformed to evaluate the effects of SZRD on neuronal loss, synaptic damage, Aβ deposition. Iron staining, transmission electron microscopy, and iron assay kit was performed to estimate the effects of SZRD on ferroptosis. SOD kit, MDA kit, GSH kit, and GSH/GSSG kit were utilized to measure the oxidative stress levels in the hippocampus. The protein expression of TfR1, FTH1, FTL, FPN1, DJ-1, Nrf2, GPX4, SLC7A11, and ACSL4 were detected by Western blot. RESULTS A total of 16 active ingredients were identified from SZRD extract. SZRD SZRD significantly alleviated learning and memory impairment in APP/PS1 mice. SZRD improved the hippocampal neuronal loss and degenerated neurons in APP/PS1 mice via inhibiting the Aβ deposit. SZRD mitigated the hippocampal synaptic damage in APP/PS1 mice. SZRD inhibited iron accumulation, and alleviated the oxidative stress level in the hippocampus of APP/PS1 mice. Meanwhile, SZRD could up-regulate the protein expression level of FPN1, DJ-1, Nrf2, GPX4 and SLC7A11 in the hippocampus, and inhibit TfR1, FTH1, FTL, and ACSL4 protein expression. CONCLUSION SZRD alleviated neuronal loss, synaptic damage and ferroptosis in AD via activating DJ-1/Nrf2 signaling pathway.
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Affiliation(s)
- Qinghua Long
- Health Medical Center, Hubei Minzu University, Enshi, 445000, China; Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Hubei Minzu University, Enshi, 445000, China
| | - Tong Li
- Health Medical Center, Hubei Minzu University, Enshi, 445000, China
| | - Qihang Zhu
- Health Medical Center, Hubei Minzu University, Enshi, 445000, China; Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Hubei Minzu University, Enshi, 445000, China
| | - Liling He
- Health Medical Center, Hubei Minzu University, Enshi, 445000, China.
| | - Binbin Zhao
- Basic Medicine College, Hubei University of Chinese Medicine, Wuhan, 430065, China; Engineering Research Center of TCM Protection Technology and New Product Development for the Elderly Brain Health, Ministry of Education, Hubei University of Chinese Medicine, Wuhan, 430065, China; Hubei Shizhen Laboratory, Wuhan, 430065, China.
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6
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Sahu S, Ghosh S, Sinha SK, Datta S, Sengupta N. Thermal Sensitivity of the Enzymatic Activity of β-Glucosidase: Simulations Lend Mechanistic Insights into Experimental Observations. Biochemistry 2023; 62:3440-3452. [PMID: 37997958 DOI: 10.1021/acs.biochem.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
A crucial prerequisite for industrial applications of enzymes is the maintenance of specific activity across wide thermal ranges. β-Glucosidase (EC 3.2.1.21) is an essential enzyme for converting cellulose in biomass to glucose. While the reaction mechanisms of β-glucosidases from various thermal ranges (hyperthermophilic, thermophilic, and mesophilic) are similar, the factors underlying their thermal sensitivity remain obscure. The work presented here aims to unravel the molecular mechanisms underlying the thermal sensitivity of the enzymatic activity of the β-glucosidase BglB from the bacterium Paenibacillus polymyxa. Experiments reveal a maximum enzymatic activity at 315 K, with a marked decrease in the activity below and above this temperature. Employing in silico simulations, we identified the crucial role of the active site tunnel residues in the thermal sensitivity. Specific tunnel residues were identified via energetic decomposition and protein-substrate hydrogen bond analyses. The experimentally observed trends in specific activity with temperature coincide with variations in overall binding free energy changes, showcasing a predominantly electrostatic effect that is consistent with enhanced catalytic pocket-substrate hydrogen bonding (HB) at Topt. The entropic advantage owing to the HB substate reorganization was found to facilitate better substrate binding at 315 K. This study elicits molecular-level insights into the associative mechanisms between thermally enabled fluctuations and enzymatic activity. Crucial differences emerge between molecular mechanisms involving the actual substrate (cellobiose) and a commonly employed chemical analogue. We posit that leveraging the role of fluctuations may reveal unexpected insights into enzyme behavior and offer novel paradigms for enzyme engineering.
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Affiliation(s)
- Sneha Sahu
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sayani Ghosh
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sushant K Sinha
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Supratim Datta
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
- Center for the Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
- Center for the Climate and Environmental Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
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7
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Ge H, Ji B, Fang J, Wang J, Li J, Wang J. Discovery of Potent and Selective CB2 Agonists Utilizing a Function-Based Computational Screening Protocol. ACS Chem Neurosci 2023; 14:3941-3958. [PMID: 37823773 PMCID: PMC10623575 DOI: 10.1021/acschemneuro.3c00580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/13/2023] Open
Abstract
Nowadays, the identification of agonists and antagonists represents a great challenge in computer-aided drug design. In this work, we developed a computational protocol enabling us to design/screen novel chemicals that are likely to serve as selective CB2 agonists. The principle of this protocol is that by calculating the ligand-residue interaction profile (LRIP) of a ligand binding to a specific target, the agonist-antagonist function of a compound is then able to be determined after statistical analysis and free energy calculations. This computational protocol was successfully applied in CB2 agonist development starting from a lead compound, and a success rate of 70% was achieved. The functions of the synthesized derivatives were determined by in vitro functional assays. Moreover, the identified potent CB2 agonists and antagonists strongly interact with the key residues identified using the already known potent CB2 agonists/antagonists. The analysis of the interaction profile of compound 6, a potent agonist, showed strong interactions with F2.61, I186, and F2.64, while compound 39, a potent antagonist, showed strong interactions with L17, W6.48, V6.51, and C7.42. Still, some residues including V3.32, T3.33, S7.39, F183, W5.43, and I3.29 are hotspots for both CB2 agonists and antagonists. More significantly, we identified three hotspot residues in the loop, including I186 for agonists, L17 for antagonists, and F183 for both. These hotspot residues are typically not considered in CB1/CB2 rational ligand design. In conclusion, LRIP is a useful concept in rationally designing a compound to possess a certain function.
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Affiliation(s)
- Haixia Ge
- School
of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Beihong Ji
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Jiahui Fang
- Chinese
Academy of Sciences Key Laboratory of Receptor Research, National
Center for Drug Screening, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiayang Wang
- School
of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Jing Li
- Chinese
Academy of Sciences Key Laboratory of Receptor Research, National
Center for Drug Screening, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Junmei Wang
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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Agarwal D, Malik J, Bhanwala N, Ambatwar R, Kumar S, Chandrakar L, Datusalia AK, Khatik GL. Networkodynamic approach to perceive the key phytoconstituents of E. officinalis (Amla) as natural BACE1 inhibitors: an in-silico study. J Biomol Struct Dyn 2023:1-13. [PMID: 37861402 DOI: 10.1080/07391102.2023.2269260] [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: 05/24/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023]
Abstract
Alzheimer's disease (AD) is a deteriorating neural disorder, and currently, available drugs are ineffective in its treatment. Emblica officinalis (Amla) is widely recognised in the Indian medicinal system for ameliorative effects in managing diabetes, hyperlipidaemia and neurological diseases. Thus, we aimed to identify the active phytoconstituents of E. officinalis and their role in inhibiting the potential targets for the possible treatment of AD. The network pharmacology approach, gene ontology, molecular docking and molecular dynamics simulation (MDS) studies were performed. A total of 36 bioactive components in E. officinalis, 95 predicted anti-AD targets, and 3398 AD-related targets were identified from different databases. The network analysis showed that BACE1, ABCB1 and AChE, CA2 are the most potential AD targets. Based on gene ontology and topology analysis results, BACE1 was a significant target related to AD pathways, and quercetin, kaempferol and myricetin showed the highest interaction with target genes. The molecular docking results found that rutin and quercetin displayed better binding affinities -7.5, -5.67 kcal/mol than the BACE1 bound internal ligand. Furthermore, MDS results suggested that quercetin and rutin could be potential inhibitors against BACE-1 protein and may have therapeutic effects in treating AD. Such promising results could be further helpful in new drug discovery against AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhairiya Agarwal
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh, India
| | - Jatin Malik
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh, India
| | - Neeru Bhanwala
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh, India
| | - Ramesh Ambatwar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh, India
| | - Sumit Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh, India
| | - Lokesh Chandrakar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh, India
| | - Ashok Kumar Datusalia
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh, India
| | - Gopal L Khatik
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh, India
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Brust CA, Swanson MA, Bohn LM. Structural and functional insights into the G protein-coupled receptors: CB1 and CB2. Biochem Soc Trans 2023; 51:1533-1543. [PMID: 37646476 PMCID: PMC10586759 DOI: 10.1042/bst20221316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/01/2023]
Abstract
The cannabinoid receptors CB1 and CB2 mediate a variety of physiological processes and continue to be explored as desirable drug targets. Both receptors are activated by the endogenous endocannabinoids and the psychoactive components of marijuana. Over the years, many efforts have been made to make selective ligands; however, the high degree of homology between cannabinoid receptor subtypes introduces challenges in studying either receptor in isolation. Recent advancements in structure biology have resulted in a surge of high-resolution structures, enriching our knowledge and understanding of receptor structure and function. In this review, of recent cannabinoid receptor structures, key features of the inactive and active state CB1 and CB2 are presented. These structures will provide additional insight into the modulation and signaling mechanism of cannabinoid receptors CB1 and CB2 and aid in the development of future therapeutics.
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Affiliation(s)
- Christina A. Brust
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, U.S.A
- The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, La Jolla, CA 92037, U.S.A
| | - Matthew A. Swanson
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, U.S.A
- The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, La Jolla, CA 92037, U.S.A
| | - Laura M. Bohn
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, U.S.A
- The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, La Jolla, CA 92037, U.S.A
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10
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Eskandrani R, Al-Rasheed LS, Ansari SA, Bakheit AH, Almehizia AA, Almutairi M, Alkahtani HM. Targeting Transcriptional CDKs 7, 8, and 9 with Anilinopyrimidine Derivatives as Anticancer Agents: Design, Synthesis, Biological Evaluation and In Silico Studies. Molecules 2023; 28:molecules28114271. [PMID: 37298748 DOI: 10.3390/molecules28114271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are promising targets in chemotherapy. In this study, we report a series of 2-anilinopyrimidine derivatives with CDK inhibitory activity. Twenty-one compounds were synthesized and their CDK inhibitory and cytotoxic activities were evaluated. The representative compounds demonstrate potent antiproliferative activities toward different solid cancer cell lines and provide a promising strategy for the treatment of malignant tumors. Compound 5f was the most potent CDK7 inhibitor (IC50 = 0.479 µM), compound 5d was the most potent CDK8 inhibitor (IC50 = 0.716 µM), and compound 5b was the most potent CDK9 inhibitor (IC50 = 0.059 µM). All the compounds satisfied the Lipinski's rule of five (molecular weight < 500 Da, number of hydrogen bond acceptors <10, and octanol-water partition coefficient and hydrogen bond donor values below 5). Compound 5j is a good candidate for lead optimization because it has a non-hydrogen atom (N) of 23, an acceptable ligand efficiency value of 0.38673, and an acceptable ligand lipophilic efficiency value of 5.5526. The synthesized anilinopyrimidine derivatives have potential as anticancer agents.
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Affiliation(s)
- Razan Eskandrani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Lamees S Al-Rasheed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdulrahman A Almehizia
- Drug Exploration and Development (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Maha Almutairi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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11
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Abuelizz HA, Bakheit AH, Marzouk M, El-Senousy WM, Abdellatif MM, Mostafa GAE, Saquib Q, Hassan SB, Al-Salahi R. Antiviral activity of some benzo[g]quinazolines against coxsackievirus B4: biological screening and docking study. Pharmacol Rep 2023:10.1007/s43440-023-00495-z. [PMID: 37210695 PMCID: PMC10200032 DOI: 10.1007/s43440-023-00495-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Serotype coxsackievirus B (CVB) infection has been linked to viral myocarditis, dilated cardiomyopathy, meningitis, and pancreatitis in children and young adults. As of yet, no antiviral drug has been authorized for the treatment of coxsackievirus infection. Therefore, there is perpetual demand for new therapeutic agents and the improvement of existing ones. Benzo[g]quinazolines, the subject of several well-known heterocyclic systems, have risen to prominence and played a significant role in the development of antiviral agents, particularly those for anti-coxsackievirus B4 infection. METHODS This study investigated the cytotoxicity of the target benzo[g]quinazolines (1-16) in the BGM cells line as well as their anti-coxsackievirus B4 activity. Determination of CVB4 titers using a plaque assay. RESULTS Most of the target benzoquinazolines exhibited antiviral activity, however, compounds 1-3 appeared to be the most effective (reduction percentages of 66.7, 70, and 83.3%, respectively). The binding mechanisms and interactions of the three most active 1-3 with the constitutive amino acids in the active site of the multi-target of coxsackievirus B4 (3Clpro and RdRp) targets were also investigated using molecular docking. CONCLUSION The anti coxsackievirus B4 activity has resulted, and the top three active benzoquinazolines (1-3) have bonded to and interacted with the constitutive amino acids in the active region of the multi-target coxsackievirus B4 (RdRp and 3Clpro). Further research is required in the lab. to determine the exact benzoquinazolines mechanism of action.
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Affiliation(s)
- Hatem A Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohamed Marzouk
- Organic Chemicals Industries Division, Chemistry of Tanning Materials and Leather Technology Department, National Research Centre, Dokki, 12622, Cairo, Egypt
| | - Waled M El-Senousy
- Environmental Virology Laboratory, Water Pollution Research Department, Environment and Climate Change Research Institute and Food-Borne Viruses Group, Centre of Excellence for Advanced Sciences, National Research Centre (NRC), 33 El-Buhouth Street, Dokki, 12622, Giza, Egypt
| | - Mohamed M Abdellatif
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Osawa, Tokyo, 192-0397, Japan
| | - Gamal A E Mostafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Quaiser Saquib
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Sawsan B Hassan
- Department of Chemistry, Faculty of Science and Technology, Al-Neelain University, Khartoum, Sudan
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.
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12
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Zan R, Wu Q, Chen Y, Wu G, Zhang H, Zhu L. Identification of Novel Dipeptidyl Peptidase-IV Inhibitory Peptides in Chickpea Protein Hydrolysates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:8211-8219. [PMID: 37191584 DOI: 10.1021/acs.jafc.3c00603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Dipeptidyl peptidase-IV (DPP-IV) is one of the main targets for blood sugar control. Some food protein-derived peptides are thought to have DPP-IV inhibitory (DPP-IVi) activity. In this study, chickpea protein hydrolysates (CPHs) obtained through Neutrase hydrolysis for 60 min (CPHs-Pro-60) exhibited the highest DPP-IVi activity. DPP-IVi activity after simulated in vitro gastrointestinal digestion was maintained at >60%. Peptide libraries are established after the identification of peptide sequences. Molecular docking verified that the four screened peptides (AAWPGHPEF, LAFP, IAIPPGIPYW, and PPGIPYW) could bind to the active center of DPP-IV. Notably, IAIPPGIPYW exhibited the most potent DPP-IVi activity (half maximal inhibitory concentration (IC50): 12.43 μM). Both IAIPPGIPYW and PPGIPYW exhibited excellent DPP-IVi activity in Caco-2 cells. These results indicated that chickpea could be used as a source of natural hypoglycemic peptides for food and nutritional applications.
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Affiliation(s)
- Rong Zan
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| | - Qiming Wu
- Nutrilite Health Institute, Shanghai 201203, China
| | - Yiling Chen
- Amway (China) Botanical R&D Center, Wuxi 214115, China
| | - Gangcheng Wu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| | - Hui Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| | - Ling Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
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13
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Stasiulewicz A, Lesniak A, Bujalska-Zadrożny M, Pawiński T, Sulkowska JI. Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation. J Chem Inf Model 2023; 63:1012-1027. [PMID: 36693026 PMCID: PMC9930120 DOI: 10.1021/acs.jcim.2c01503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cannabinoid receptor type 2 (CB2) is a very promising therapeutic target for a variety of potential indications. However, despite the existence of multiple high affinity CB2 ligands, none have yet been approved as a drug. Therefore, it would be beneficial to explore new chemotypes of CB2 ligands. The recent elucidation of CB2 tertiary structure allows for rational hit identification with structure-based (SB) methods. In this study, we established a virtual screening workflow based on SB techniques augmented with ligand-based ones, including molecular docking, MM-GBSA binding energy calculations, pharmacophore screening, and QSAR. We screened nearly 7 million drug-like, commercially available compounds. We selected 16 molecules for in vitro evaluation and identified two novel, selective CB2 antagonists with Ki values of 65 and 210 nM. Both compounds are structurally diverse from CB2 ligands known to date. The established virtual screening protocol may prove useful for hit identification for CB2 and similar molecular targets. The two novel CB2 ligands provide a desired starting point for future optimization and development of potential drugs.
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Affiliation(s)
- Adam Stasiulewicz
- Department
of Drug Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland,Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Anna Lesniak
- Department
of Pharmacodynamics, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Magdalena Bujalska-Zadrożny
- Department
of Pharmacodynamics, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Tomasz Pawiński
- Department
of Drug Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Joanna I. Sulkowska
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland,E-mail:
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14
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Li LP, Li HX, Zhou H, Li WY, Wang RL, Zhang YC, Ma Y. Exploring the mechanism of C473D mutation on CDC25B causing weak binding affinity with CDK2/CyclinA by molecular dynamics study. J Biomol Struct Dyn 2023; 41:12552-12564. [PMID: 36655391 DOI: 10.1080/07391102.2023.2166995] [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: 09/03/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023]
Abstract
CDC25B belongs to the CDC25 family, and it plays an important part in regulating the activity of CDK/CyclinA. Studies have shown that CDC25B is closely related to cancer development. When CYS473 on CDC25B is mutated into ASP, the affinity between CDC25B and CDK2/CyclinA weakens, and their dissociation speed is greatly improved. However, the mechanism by which the CDC25BC473D mutant weakens its binding to CDK2/CyclinA is unclear. In order to study the effect of CDC25BC473D mutants on CDK2/CyclinA substrates, we constructed and verified the rationality of the CDC25BWT:CDK2/CyclinA system and CDC25BC473D:CDK2/CyclinA system and conducted molecular dynamics (MD) simulation analysis. In the post-analysis, the fluctuations of residues ARG488-SER499, LYS541-TRP550 on CDC25B and residues ASP206-ASP210 on CDK2 were massive in the mutant CDC25BC473D:CDK2/CyclinA system. And the interactions between residue ARG492 and residue GLU208, residue ARG544 and residue GLU42, residue ARG544 and TRP550 were weakened in the mutant CDC25BC473D:CDK2/CyclinA system. The results showed that when CYS473 on CDC25B was mutated into ASP473, the mutant CDC25BC473D:CDK2/CyclinA system was less stable than the wild-type CDC25BWT:CDK2/CyclinA system. Finally, active site CYS473 of CDC25B was speculated to be the key residue, which had great effects on the binding between CDC25BCYS473 and CDK2 in the CDC25BC473D:CDK2/CyclinA system. Consequently, overall analyses appeared in this study ultimately provided a useful understanding of the weak interactions between CDC25BCYS473D and CDK2/CyclinA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Li-Peng Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Hao-Xin Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Hui Zhou
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Wei-Ya Li
- China Department of Pharmacy, Tianjin Medical University, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Run-Ling Wang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Ying-Chi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
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15
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Xu Q, Li J, Cao S, Ma G, Zhao X, Wang Q, Wei X, Yu H, Wang Z. Thyroid hormone activities of neutral and anionic hydroxylated polybrominated diphenyl ethers to thyroid receptor β: A molecular dynamics study. CHEMOSPHERE 2023; 311:136920. [PMID: 36273606 DOI: 10.1016/j.chemosphere.2022.136920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) have been identified as the strong endocrine disrupting chemicals to humans, which show structural similarity with endogenous thyroid hormones (THs) and thus disrupt the functioning of THs through competitive binding with TH receptors (TRs). Although previous studies have reported the hormone activities of some OH-PBDEs on TH receptor β (TRβ), the interaction mechanism remains unclear. Furthermore, hydroxyl dissociation of OH-PBDEs may alter their TR disrupting activities, which has not yet been investigated in depth. In this work, we selected 18 OH-PBDEs with neutral and anionic forms and performed molecular dynamics (MD) simulations to estimate their binding interactions with the ligand binding domain (LBD) of TRβ. The results demonstrate that most of OH-PBDEs have stronger binding affinities to TRβ-LBD than their anionic counterparts, and the hydroxyl dissociation of ligands differentiate the major driving force for their binding. More Br atoms in OH-PBDEs can result in stronger binding potential with TRβ-LBD. Moreover, 5 hydrophobic residues, including Met313, Leu330, Ile276, Leu346, and Phe272, are identified to have important contributions to bind OH-PBDEs. These results clarify the binding mechanism of OH(O-)-PBDEs to TRβ-LBD at the molecular level, which can provide a solid theoretical basis for accurate assessment of TH disrupting effects of these chemicals.
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Affiliation(s)
- Qi Xu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Jian Li
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China; Institute of Physical Oceanography and Remote Sensing, Ocean College, Zhejiang University, Zheda Road 1, 316021, Zhoushan, China
| | - Shang Cao
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Guangcai Ma
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China.
| | - Xianglong Zhao
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Qiuyi Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Xiaoxuan Wei
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Yingbin Avenue 688, 321004, Jinhua, China.
| | - Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, China
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16
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Cai H, Xu Y, Guo S, He X, Sun J, Li X, Li C, Yin W, Cheng X, Jiang H, Xu HE, Xie X, Jiang Y. Structures of adenosine receptor A 2BR bound to endogenous and synthetic agonists. Cell Discov 2022; 8:140. [PMID: 36575181 PMCID: PMC9794776 DOI: 10.1038/s41421-022-00503-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/29/2022] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hongmin Cai
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Youwei Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shimeng Guo
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xinheng He
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Sun
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Li
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changyao Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wanchao Yin
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China
| | - Xi Cheng
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - H Eric Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Xin Xie
- CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Yi Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Lingang Laboratory, Shanghai, China.
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17
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FANANİ A, KURNİATİN PA, WAHYUDİ ST, NURCHOLİS W, AMBARSARİ L. Molecular Dynamics Simulation of E412 Catalytic Residue Mutation of GOx-IPBCC. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2022. [DOI: 10.18596/jotcsa.1088587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The enzyme glucose oxidase from Aspergillus niger has a homodimeric structure, consisting of two identical subunits with a molecular weight of 150,000 Daltons. In this study, we used the structure of the enzyme glucose oxidase from Aspergillus niger IPBCC.08.610 (GOx-IPBCC), this enzyme had a total activity of 92.87 U (μmol/min) and a Michaelis-Menten constant (Km) of 2.9 mM (millimolar). This study was conducted to predict the molecular dynamics of E412 (Glu412) residue catalytic mutation belonging to the GOx-IPBCC enzyme was determine the effect of changes in the catalytic residue on substrate binding (β-D-glucose). The results of molecular docking of 19 mutant structures, six E412 mutant homologous structures were selected (E412C, E412K, E412Q, E412T, E412, E412V, and E412W), which were evaluated using molecular dynamics simulation for 50 ns. The results showed a decrease in ∆G values in two mutant structures is E412C and E412T, and there is one mutant structure that increased ∆G values, namely E412W, these three mutant structures showed the best stability, bond interaction, and salt bridge profile according to molecular dynamics simulation.
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18
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Whiting ZM, Yin J, de la Harpe SM, Vernall AJ, Grimsey NL. Developing the Cannabinoid Receptor 2 (CB2) pharmacopoeia: past, present, and future. Trends Pharmacol Sci 2022; 43:754-771. [PMID: 35906103 DOI: 10.1016/j.tips.2022.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/28/2022]
Abstract
Cannabinoid Receptor 2 (CB2) is a G protein-coupled receptor (GPCR) with considerable, though as yet unrealised, therapeutic potential. Promising preclinical data supports the applicability of CB2 activation in autoimmune and inflammatory diseases, pain, neurodegeneration, and osteoporosis. A diverse pharmacopoeia of cannabinoid ligands is available, which has led to considerable advancements in the understanding of CB2 function and extensive preclinical evaluation. However, until recently, most CB2 ligands were highly lipophilic and as such not optimal for clinical application due to unfavourable physicochemical properties. A number of strategies have been applied to develop CB2 ligands to achieve closer to 'drug-like' properties and a few such compounds have now undergone clinical trial. We review the current state of CB2 ligand development and progress in optimising physicochemical properties, understanding advanced molecular pharmacology such as functional selectivity, and clinical evaluation of CB2-targeting compounds.
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Affiliation(s)
- Zak M Whiting
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Jiazhen Yin
- Department of Chemistry, Division of Sciences, University of Otago, Dunedin, New Zealand
| | - Sara M de la Harpe
- Department of Chemistry, Division of Sciences, University of Otago, Dunedin, New Zealand
| | - Andrea J Vernall
- Department of Chemistry, Division of Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Natasha L Grimsey
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand.
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19
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Liddle I, Glass M, Tyndall JDA, Vernall AJ. Covalent cannabinoid receptor ligands - structural insight and selectivity challenges. RSC Med Chem 2022; 13:497-510. [PMID: 35694688 PMCID: PMC9132230 DOI: 10.1039/d2md00006g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
X-ray crystallography and cryogenic electronic microscopy have provided significant advancement in the knowledge of GPCR structure and have allowed the rational design of GPCR ligands. The class A GPCRs cannabinoid receptor type 1 and type 2 are implicated in many pathophysiological processes and thus rational design of drug and tool compounds is of great interest. Recent structural insight into cannabinoid receptors has already led to a greater understanding of ligand binding sites and receptor residues that likely contribute to ligand selectivity. Herein, classes of heterocyclic covalent cannabinoid receptor ligands are reviewed in light of the recent advances in structural knowledge of cannabinoid receptors, with particular discussion regarding covalent ligand selectivity and rationale design.
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Affiliation(s)
- Ian Liddle
- Department of Chemistry, University of Otago Dunedin New Zealand +64 3 479 5214
| | - Michelle Glass
- Department of Pharmacology and Toxicology, University of Otago Dunedin New Zealand
| | | | - Andrea J Vernall
- Department of Chemistry, University of Otago Dunedin New Zealand +64 3 479 5214
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20
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Computational Insight into Biotransformation Profiles of Organophosphorus Flame Retardants to Their Diester Metabolites by Cytochrome P450. Molecules 2022; 27:molecules27092799. [PMID: 35566150 PMCID: PMC9102461 DOI: 10.3390/molecules27092799] [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: 04/13/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/05/2023] Open
Abstract
Biotransformation of organophosphorus flame retardants (OPFRs) mediated by cytochrome P450 enzymes (CYPs) has a potential correlation with their toxicological effects on humans. In this work, we employed five typical OPFRs including tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), tris(1-chloro-2-propyl) phosphate (TCIPP), tri(2-chloroethyl) phosphate (TCEP), triethyl phosphate (TEP), and 2-ethylhexyl diphenyl phosphate (EHDPHP), and performed density functional theory (DFT) calculations to clarify the CYP-catalyzed biotransformation of five OPFRs to their diester metabolites. The DFT results show that the reaction mechanism consists of Cα-hydroxylation and O-dealkylation steps, and the biotransformation activities of five OPFRs may follow the order of TCEP ≈ TEP ≈ EHDPHP > TCIPP > TDCIPP. We further performed molecular dynamics (MD) simulations to unravel the binding interactions of five OPFRs in the CYP3A4 isoform. Binding mode analyses demonstrate that CYP3A4-mediated metabolism of TDCIPP, TCIPP, TCEP, and TEP can produce the diester metabolites, while EHDPHP metabolism may generate para-hydroxyEHDPHP as the primary metabolite. Moreover, the EHDPHP and TDCIPP have higher binding potential to CYP3A4 than TCIPP, TCEP, and TEP. This work reports the biotransformation profiles and binding features of five OPFRs in CYP, which can provide meaningful clues for the further studies of the metabolic fates of OPFRs and toxicological effects associated with the relevant metabolites.
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Muddagoni N, Dasari M, Bathula R, Potlapally SR. Tin (
IV
) Chloride catalyzed one‐pot synthesis, characterization and docking studies of 4‐aminoquinoline derivatives as Myt1 inhibitors. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Narasimha Muddagoni
- Nizam College, Department of Chemistry Osmania University, Basheerbagh Hyderabad‐500001 Telangana India
| | - Mahendar Dasari
- Nizam College, Department of Chemistry Osmania University, Basheerbagh Hyderabad‐500001 Telangana India
| | - Revanth Bathula
- Nizam College, Department of Chemistry Osmania University, Basheerbagh Hyderabad‐500001 Telangana India
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22
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Ji S, Yang W, Yu W. Understanding the role of the CB1 toggle switch in interaction networks using molecular dynamics simulation. Sci Rep 2021; 11:22369. [PMID: 34785728 PMCID: PMC8595625 DOI: 10.1038/s41598-021-01767-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
The cannabinoid receptor 1 (CB1) is a class A G-protein coupled receptor (GPCR) that can exert various effects on the human body through the endocannabinoid system. Understanding CB1 activation has many benefits for the medical use of cannabinoids. A previous study reported that CB1 has two notable residues referred to as the toggle switch, F3.36 and W6.48, which are important for its activation mechanism. We performed a molecular dynamics simulation with a mutation in the toggle switch to examine its role in active and inactive states. We also examined structural changes, the residue-residue interaction network, and the interaction network among helices and loops of wildtype and mutant CB1 for both activation states. As a result, we found that the energetic changes in the hydrogen-bond network of the Na+ pocket, extracellular N-terminus-TM2-ECL1-TM3 interface including D2.63-K3.28 salt-bridge, and extracellular ECL2-TM5-ECL3-TM6 interface directly linked to the toggle switch contribute to the stability of CB1 by the broken aromatic interaction of the toggle switch. It makes the conformation of inactive CB1 receptor to be unstable. Our study explained the role of the toggle switch regarding the energetic interactions related to the Na+ pocket and extracellular loop interfaces, which could contribute to a better understanding of the activation mechanism of CB1.
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Affiliation(s)
- Sangho Ji
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu, 42988, Republic of Korea
| | - Wonjin Yang
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu, 42988, Republic of Korea
| | - Wookyung Yu
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu, 42988, Republic of Korea. .,Core Protein Resources Center, DGIST, 333 Techno jungang-daero, 42988, Daegu, Republic of Korea.
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Aviz-Amador A, Contreras-Puentes N, Mercado-Camargo J. Virtual screening using docking and molecular dynamics of cannabinoid analogs against CB 1 and CB 2 receptors. Comput Biol Chem 2021; 95:107590. [PMID: 34700256 DOI: 10.1016/j.compbiolchem.2021.107590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 09/09/2021] [Accepted: 10/07/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND Cannabis sativa has been attributed to different pharmacological properties. A number of secondary metabolites such as tetrahydrocannabinol (THC), cannabinol (CBD), and different analogs, with highly promising biological activity on CB1 and CB2 receptors, have been identified. METHODS Thus, this study aimed was to evaluate the activity of THC, CBD, and their analogs using molecular docking and molecular dynamics simulations (MD) methods. Initially, the molecules (ligands) were selected by bioinformatics searches in databases. Subsequently, CB1 and CB2 receptors were retrieved from the protein data bank database. Afterward, each receptor and its ligands were optimized to perform molecular docking. Then, MD Simulation was performed with the most stable ligand-receptor complexes. Finally, the Molecular Mechanics-Generalized Born Surface Area (MM-PBSA) method was applied to analyze the binding free energy between ligands and cannabinoid receptors. RESULTS The results obtained showed that ligand LS-61176 presented the best affinity in the molecular docking analysis. Also, this analog could be a CB1 negative allosteric modulator like CBD and probably an agonist in CB2 like THC and CBD according to their dynamic behavior in silico. The possibility of having a THC and a CBD analog (LS-61176) as a promising molecule for experimental evaluation since it could have no central side-effects on CB1 and have effects of CB2 useful in pain, inflammation, and some immunological disorders. Docking results were validate using ROC curve for both cannabinoids receptor where AUC for CB1 receptor was 0.894±0.024, and for CB2 receptor AUC was 0.832±0032, indicating good affinity prediction.
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Affiliation(s)
- Antistio Aviz-Amador
- Pharmacology and Therapeutic Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Neyder Contreras-Puentes
- Pharmacology and Therapeutic Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia; GINUMED, Faculty of Medicine, Rafael Nuñez University Corporation, Cartagena, Colombia.
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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Mei LC, Wang YL, Wu FX, Wang F, Hao GF, Yang GF. HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study. Brief Bioinform 2021; 22:bbaa373. [PMID: 33406224 PMCID: PMC7929440 DOI: 10.1093/bib/bbaa373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 01/18/2023] Open
Abstract
Protein-nucleic acid interactions play essential roles in many biological processes, such as transcription, replication and translation. In protein-nucleic acid interfaces, hotspot residues contribute the majority of binding affinity toward molecular recognition. Hotspot residues are commonly regarded as potential binding sites for compound molecules in drug design projects. The dynamic property is a considerable factor that affects the binding of ligands. Computational approaches have been developed to expedite the prediction of hotspot residues on protein-nucleic acid interfaces. However, existing approaches overlook hotspot dynamics, despite their essential role in protein function. Here, we report a web server named Hotspots In silico Scanning on Nucleic Acid and Protein Interface (HISNAPI) to analyze hotspot residue dynamics by integrating molecular dynamics simulation and one-step free energy perturbation. HISNAPI is capable of not only predicting the hotspot residues in protein-nucleic acid interfaces but also providing insights into their intensity and correlation of dynamic motion. Protein dynamics have been recognized as a vital factor that has an effect on the interaction specificity and affinity of the binding partners. We applied HISNAPI to the case of SARS-CoV-2 RNA-dependent RNA polymerase, a vital target of the antiviral drug for the treatment of coronavirus disease 2019. We identified the hotspot residues and characterized their dynamic behaviors, which might provide insight into the target site for antiviral drug design. The web server is freely available via a user-friendly web interface at http://chemyang.ccnu.edu.cn/ccb/server/HISNAPI/ and http://agroda.gzu.edu.cn:9999/ccb/server/HISNAPI/.
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Affiliation(s)
- Long-Can Mei
- College of Chemistry, Central China Normal University
| | | | | | | | | | - Guang-Fu Yang
- Pesticide Science from Nankai University, Tianjin, China
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King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery. Front Mol Biosci 2021; 8:712085. [PMID: 34458321 PMCID: PMC8387144 DOI: 10.3389/fmolb.2021.712085] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 01/11/2023] Open
Abstract
The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
- Department of Materials Science and Engineering, University of California, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
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27
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Chitranshi N, Kumar A, Sheriff S, Gupta V, Godinez A, Saks D, Sarkar S, Shen T, Mirzaei M, Basavarajappa D, Abyadeh M, Singh SK, Dua K, Zhang KYJ, Graham SL, Gupta V. Identification of Novel Cathepsin B Inhibitors with Implications in Alzheimer's Disease: Computational Refining and Biochemical Evaluation. Cells 2021; 10:cells10081946. [PMID: 34440715 PMCID: PMC8391575 DOI: 10.3390/cells10081946] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Amyloid precursor protein (APP), upon proteolytic degradation, forms aggregates of amyloid β (Aβ) and plaques in the brain, which are pathological hallmarks of Alzheimer’s disease (AD). Cathepsin B is a cysteine protease enzyme that catalyzes the proteolytic degradation of APP in the brain. Thus, cathepsin B inhibition is a crucial therapeutic aspect for the discovery of new anti-Alzheimer’s drugs. In this study, we have employed mixed-feature ligand-based virtual screening (LBVS) by integrating pharmacophore mapping, docking, and molecular dynamics to detect small, potent molecules that act as cathepsin B inhibitors. The LBVS model was generated by using hydrophobic (HY), hydrogen bond acceptor (HBA), and hydrogen bond donor (HBD) features, using a dataset of 24 known cathepsin B inhibitors of both natural and synthetic origins. A validated eight-feature pharmacophore hypothesis (Hypo III) was utilized to screen the Maybridge chemical database. The docking score, MM-PBSA, and MM-GBSA methodology was applied to prioritize the lead compounds as virtual screening hits. These compounds share a common amide scaffold, and showed important interactions with Gln23, Cys29, His110, His111, Glu122, His199, and Trp221. The identified inhibitors were further evaluated for cathepsin-B-inhibitory activity. Our study suggests that pyridine, acetamide, and benzohydrazide compounds could be used as a starting point for the development of novel therapeutics.
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Affiliation(s)
- Nitin Chitranshi
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
- Correspondence: (N.C.); (V.G.); Tel.: +61-(02)-9850-2804 (N.C.)
| | - Ashutosh Kumar
- Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Kanagawa, Japan; (A.K.); (K.Y.J.Z.)
| | - Samran Sheriff
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Veer Gupta
- School of Medicine, Faculty of Health, Deakin University, Geelong, VIC 3220, Australia;
| | - Angela Godinez
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Danit Saks
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Soumalya Sarkar
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Ting Shen
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Mehdi Mirzaei
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Devaraj Basavarajappa
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Morteza Abyadeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran;
| | - Sachin K. Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kam Y. J. Zhang
- Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Kanagawa, Japan; (A.K.); (K.Y.J.Z.)
| | - Stuart L. Graham
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Vivek Gupta
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
- Correspondence: (N.C.); (V.G.); Tel.: +61-(02)-9850-2804 (N.C.)
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Zhao D, Zhong S. Binding mechanisms of varic acid inhibitors on protein tyrosine phosphatase 1B and in silico design of the novel derivatives. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1929970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dan Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, People’s Republic of China
| | - Shijun Zhong
- School of Bioengineering, Dalian University of Technology, Dalian, People’s Republic of China
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29
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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Cetin A. In silico studies on stilbenolignan analogues as SARS-CoV-2 Mpro inhibitors. Chem Phys Lett 2021; 771:138563. [PMID: 33776065 PMCID: PMC7983322 DOI: 10.1016/j.cplett.2021.138563] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
COVID-19, a new strain of coronavirus family, was identified at the end of 2019 in China. The COVID-19 virus spread rapidly all over the world. Scientists strive to find virus-specific antivirals for the treatment of COVID-19. The present study reports a molecular docking study of the stilbenolignans and SARS-CoV-2 main protease (SARS-CoV-2 Mpro) inhibitors. The detailed interactions between the stilbenolignan analogues and SARS-CoV-2 Mpro inhibitors were determined as hydrophobic bonds, hydrogen bonds and electronic bonds, inhibition activity, ligand efficiency, bonding type and distance and etc. The binding energies of the stilbenolignan analogues were obtained from the molecular docking of SARS-CoV-2 Mpro. Lehmbachol D, Maackolin, Gnetucleistol, Gnetifolin F, Gnetofuran A and Aiphanol were found to be -7.7, -8.2, -7.3, -8.5, -8.0 and -7.3 kcal/mol, respectively. Osirus, Molinspiration and SwissADME chemoinformatic tools were used to examine ADMET properties, pharmacokinetic parameters and toxicological characteristics of the stilbenolignan analogues. All analogues obey the Lipinski's rule of five. Furthermore, stilbenolignan analogues were studied to predict their binding affinities against SARS-CoV-2 Mpro using molecular modeling and simulation techniques, and the binding free energy calculations of all complexes were calculated using the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) method. With the data presented here it has been observed that these analogues may be a good candidate for SARS-CoV-2 Mpro in vivo studies, so more research can be done on stilbenolignan analogues.
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Dipeptidyl peptidase-IV inhibitory activity of millet protein peptides and the related mechanisms revealed by molecular docking. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110587] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Arooj M, Shehadi I, Nassab CN, Mohamed AA. Physicochemical stability study of protein–benzoic acid complexes using molecular dynamics simulations. Amino Acids 2020; 52:1353-1362. [DOI: 10.1007/s00726-020-02897-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 09/23/2020] [Indexed: 12/16/2022]
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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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