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Ali T, Jan I, Ramachandran R, Bashir R, Andrabi KI, Bader GN. Molecular docking and dynamics simulation of farnesol as a potential anticancer agent targeting mTOR pathway. In Silico Pharmacol 2024; 12:89. [PMID: 39351011 PMCID: PMC11438742 DOI: 10.1007/s40203-024-00259-4] [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: 08/09/2024] [Accepted: 09/08/2024] [Indexed: 10/04/2024] Open
Abstract
Farnesol is a natural acyclic sesquiterpene alcohol, found in various essential oils such as, lemon grass, citronella, tuberose, neroli, and musk. It has a molecular mass of 222.372 g/mol and chemical formula of C₁₅H₂₆O. The main objective of this study was to assess the effect of farnesol on mTOR and its two downstream effectors, p70S6K and eIF4E, which are implicated in the development of cancer, via molecular dynamic simulation, and docking analysis in an in silico study. A multilayer, primarily computer-based analysis was conducted to assess farnesol's anticancer potential, with a focus on primary cancer targets. From the calculations performed, farnesol showed a binding affinity of - 9.66 kcal/mol, followed by binding affinity of - 7.4 kcal/mol and - 7.8 kcal/mol for mTOR, p70S6K and eIF4E respectively. Rapamycin showed the binding affinity of - 10.45 kcal/mol for mTOR, for p70S6K and eIF4E the calculated binding affinity was - 10.65 kcal/mol and 8.16 kcal/mol respectively. The binding affinity of farnesol was comparable to the standard drug rapamycin indicating its potential as an mTOR inhibitor. Molecular dynamics simulations suggest that the ligands (farnesol and rapamycin) were well trapped within the active site of the protein over a time gap of 50 ns. It is clear that farnesol showed relatively stable MD simulation results, with minor fluctuations and maintains a consistent binding orientation, suggesting a strong and stable interaction with the target proteins when compared to simulation data of standard drug. This study explores the potential of farnesol as an anticancer agent through an in-silico approach, focusing on its interaction with mTOR and its downstream effectors. Inhibition of mTOR signaling pathway may be responsible for the anticancer effect of farnesol. As this pathway plays a crucial role in cell proliferation and survival, making it a significant target in cancer research.
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Affiliation(s)
- Tabasum Ali
- Department of Pharmaceutical Sciences, School of Applied Science and Technology, University of Kashmir, Srinagar, Jammu, Kashmir 190006 India
- GrowthFactorSignalingLaboratory, Department of Biotechnology, University of Kashmir, Kashmir, J&K190006 India
| | - Ifat Jan
- Department of Pharmaceutical Sciences, School of Applied Science and Technology, University of Kashmir, Srinagar, Jammu, Kashmir 190006 India
- GrowthFactorSignalingLaboratory, Department of Biotechnology, University of Kashmir, Kashmir, J&K190006 India
| | - Rajath Ramachandran
- Molecular Science and Technology Department, Ajou University, Ajou, 16499 Republic of Korea
| | - Rabiah Bashir
- Department of Pharmaceutical Sciences, School of Applied Science and Technology, University of Kashmir, Srinagar, Jammu, Kashmir 190006 India
| | - Khurshid Iqbal Andrabi
- GrowthFactorSignalingLaboratory, Department of Biotechnology, University of Kashmir, Kashmir, J&K190006 India
| | - Ghulam Nabi Bader
- Department of Pharmaceutical Sciences, School of Applied Science and Technology, University of Kashmir, Srinagar, Jammu, Kashmir 190006 India
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Cheng S, Zou Y, Zhang M, Bai S, Tao K, Wu J, Shi Y, Wu Y, Lu Y, He K, Sun P, Su X, Hou S, Han B. Single-cell RNA sequencing reveals the heterogeneity and intercellular communication of hepatic stellate cells and macrophages during liver fibrosis. MedComm (Beijing) 2023; 4:e378. [PMID: 37724132 PMCID: PMC10505372 DOI: 10.1002/mco2.378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/11/2023] [Accepted: 08/24/2023] [Indexed: 09/20/2023] Open
Abstract
Uncontrolled and excessive progression of liver fibrosis is thought to be the prevalent pathophysiological cause of liver cirrhosis and hepatocellular cancer, and there are currently no effective antifibrotic therapeutic options available. Intercellular communication and cellular heterogeneity in the liver are involved in the progression of liver fibrosis, but the exact nature of the cellular phenotypic changes and patterns of interregulatory remain unclear. Here, we performed single-cell RNA sequencing on nonparenchymal cells (NPCs) isolated from normal and fibrotic mouse livers. We identified eight main types of cells, including endothelial cells, hepatocytes, dendritic cells, B cells, natural killer/T (NK/T) cells, hepatic stellate cells (HSCs), cholangiocytes and macrophages, and revealed that macrophages and HSCs exhibit the most variance in transcriptional profile. Further analyses of HSCs and macrophage subpopulations and ligand-receptor interaction revealed a high heterogeneity characterization and tightly interregulated network of these two groups of cells in liver fibrosis. Finally, we uncovered a profibrotic Thbs1+ macrophage subcluster, which expands in mouse and human fibrotic livers, activating HSCs via PI3K/AKT/mTOR signaling pathway. Our findings decode unanticipated insights into the heterogeneity of HSCs and macrophages and their intercellular crosstalk at a single-cell level, and may provide potential therapeutic strategies in liver fibrosis.
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Affiliation(s)
- Sheng Cheng
- Department of General SurgeryTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal OncologyHongqiao International Institute of MedicineTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yunhan Zou
- Department of Biochemistry and Molecular Cell BiologyShanghai Key Laboratory for Tumor Microenvironment and InflammationShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Man Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Shihao Bai
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Kun Tao
- Department of PathologyTongren HospitalShanghai Jiaotong University School of MedicineShanghaiChina
| | - Jiaoxiang Wu
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal OncologyHongqiao International Institute of MedicineTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yi Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersBio‐X InstitutesShanghai Jiao Tong UniversityShanghaiChina
- eHealth Program of Shanghai Anti‐Doping LaboratoryShanghai University of SportShanghaiChina
| | - Yuelan Wu
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal OncologyHongqiao International Institute of MedicineTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yinzhong Lu
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal OncologyHongqiao International Institute of MedicineTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Department of AnesthesiologyTongren Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Kunyan He
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Peng Sun
- Department of General SurgeryTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xianbin Su
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- eHealth Program of Shanghai Anti‐Doping LaboratoryShanghai University of SportShanghaiChina
| | - Shangwei Hou
- Department of AnesthesiologyTongren Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Bo Han
- Department of General SurgeryTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Key Laboratory for Translational Research and Innovative Therapeutics of Gastrointestinal OncologyHongqiao International Institute of MedicineTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
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Parate S, Kumar V, Hong JC, Lee KW. Investigation of Macrocyclic mTOR Modulators of Rapamycin Binding Site via Pharmacoinformatics Approaches. Comput Biol Chem 2023; 104:107875. [PMID: 37148678 DOI: 10.1016/j.compbiolchem.2023.107875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/08/2023]
Abstract
The PI3K/Akt/mTOR is an essential intracellular signaling pathway in which the serine/threonine mTOR kinase portrays a major role in cell growth, proliferation and survival. The mTOR kinase is frequently dysregulated in a broad spectrum of cancers, thus making it a potential target. Rapamycin and its analogs (rapalogs) allosterically inhibit mTOR, thereby dodging the deleterious effects prompted by ATP-competitive mTOR inhibitors. However, the available mTOR allosteric site inhibitors exhibit low oral bioavailability and suboptimal solubility. Bearing in mind this narrow therapeutic window of the current allosteric mTOR inhibitors, an in silico study was designed in search of new macrocyclic inhibitors. The macrocycles from the ChemBridge database (12,677 molecules) were filtered for their drug-likeness properties and the procured compounds were subjected for molecular docking within the binding cleft between FKBP25 and FRB domains of mTOR. The docking analysis resulted with 15 macrocycles displaying higher scores than the selective mTOR allosteric site inhibitor, DL001. The docked complexes were refined by subsequent molecular dynamics simulations for a period of 100 ns. Successive binding free energy computation revealed a total of 7 macrocyclic compounds (HITS) demonstrating better binding affinity than DL001, towards mTOR. The consequent assessment of pharmacokinetic properties resulted in HITS with similar or better properties than the selective inhibitor, DL001. The HITS from this investigation could act as effective mTOR allosteric site inhibitors and serve as macrocyclic scaffolds for developing compounds targeting the dysregulated mTOR.
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Affiliation(s)
- Shraddha Parate
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Applied Life Science, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, South Korea; Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden.
| | - Vikas Kumar
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, South Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Applied Life Science, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, South Korea.
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, South Korea.
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Fu YS, Ho WY, Kang N, Tsai MJ, Wu J, Huang L, Weng CF. Pharmaceutical Prospects of Curcuminoids for the Remedy of COVID-19: Truth or Myth. Front Pharmacol 2022; 13:863082. [PMID: 35496320 PMCID: PMC9047796 DOI: 10.3389/fphar.2022.863082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/01/2022] [Indexed: 01/09/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus, and has rapidly spread worldwide as a pandemic. The vaccines, repurposed drugs, and specific treatments have led to a surge of novel therapies and guidelines nowadays; however, the epidemic of COVID-19 is not yet fully combated and is still in a vital crisis. In repositioning drugs, natural products are gaining attention because of the large therapeutic window and potent antiviral, immunomodulatory, anti-inflammatory, and antioxidant properties. Of note, the predominant curcumoid extracted from turmeric (Curcuma longa L.) including phenolic curcumin influences multiple signaling pathways and has demonstrated to possess anti-inflammatory, antioxidant, antimicrobial, hypoglycemic, wound healing, chemopreventive, chemosensitizing, and radiosensitizing spectrums. In this review, all pieces of current information related to curcumin-used for the treatment and prevention of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through in vitro, in vivo, and in silico studies, clinical trials, and new formulation designs are retrieved to re-evaluate the applications based on the pharmaceutical efficacy of clinical therapy and to provide deep insights into knowledge and strategy about the curcumin's role as an immune booster, inflammatory modulator, and therapeutic agent against COVID-19. Moreover, this study will also afford a favorable application or approach with evidence based on the drug discovery and development, pharmacology, functional foods, and nutraceuticals for effectively fighting the COVID-19 pandemic.
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Affiliation(s)
- Yaw-Syan Fu
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China,Department of Basic Medical Science, Institute of Respiratory Disease, Xiamen Medical College, Xiamen, China
| | - Wan-Yi Ho
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ning Kang
- Department of Otorhinolaryngology, the Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - May-Jywan Tsai
- Department of Neurosurgery, Neurological Institute, Neurological Institute, Taipei, Taiwan
| | - Jingyi Wu
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China
| | - Liyue Huang
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China
| | - Ching-Feng Weng
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China,Department of Basic Medical Science, Institute of Respiratory Disease, Xiamen Medical College, Xiamen, China,*Correspondence: Ching-Feng Weng, ,
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5
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Shams R, Ito Y, Miyatake H. Mapping of mTOR drug targets: Featured platforms for anti-cancer drug discovery. Pharmacol Ther 2021; 232:108012. [PMID: 34624427 DOI: 10.1016/j.pharmthera.2021.108012] [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: 08/17/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022]
Abstract
The mammalian/mechanistic target of rapamycin (mTOR) is a regulatory protein kinase involved in cell growth and proliferation. mTOR is usually assembled in two different complexes with different regulatory mechanisms, mTOR complex 1 (mTORC1) and mTORC2, which are involved in different functions such as cell proliferation and cytoskeleton assembly, respectively. In cancer cells, mTOR is hyperactivated in response to metabolic alterations and/or oncogenic signals to overcome the stressful microenvironments. Therefore, recent research progress for mTOR inhibition involves a variety of compounds that have been developed to disturb the metabolic processes of cancer cells through mTOR inhibition. In addition to competitive or allosteric inhibition, a new inhibition strategy that emerged mTOR complexes destabilization has recently been a concern. Here, we review the history of mTOR and its inhibition, along with the timeline of the mTOR inhibitors. We also introduce prospective drug targets to inhibit mTOR by disrupting the complexation of the components with peptides and small molecules.
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Affiliation(s)
- Raef Shams
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, RIKEN, Wako, Saitama 351-0198, Japan; Department of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, RIKEN, Wako, Saitama 351-0198, Japan; Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
| | - Hideyuki Miyatake
- Department of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan; Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan.
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Sharma V, Panwar A, Sharma A, Punj V, Saini RV, Saini AK, Sharma AK. A comparative molecular dynamic simulation study on potent ligands targeting mTOR/FRB domain for breast cancer therapy. Biotechnol Appl Biochem 2021; 69:1339-1347. [PMID: 34056758 DOI: 10.1002/bab.2206] [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: 02/08/2021] [Accepted: 05/19/2021] [Indexed: 11/10/2022]
Abstract
Our study aimed to develop and find out the best drug candidate against the mechanistic target of rapamycin (mTOR/FRB) domain having a critical role in the aetiology of breast cancer. The FKBP12-rapamycin-binding (FRB) domain in the essential phosphoinositide 3 kinase/mammalian target of rapamycin (PI3K/AKT/mTOR) pathway has been a vital player in the disease progression in breast cancer. By using structure-based drug designing , the best possible targets have been identified and developed. The three-dimensional structure of the target protein was generated using I-TASSER. The ligands were generated against the most suitable target active site using standard tools for active site identification. Furthermore, the seed molecule was drawn using Chemsketch, which was then grown into the pocket using Ligbuilder. The obtained ligands were further validated using online programs for bioavailability and toxicity, followed by molecular dynamic simulations. The study concludes that the equilibrated NVT-NPT complexes indicate LIG2 stability over LIG3. RMSD and RMSF have shown that the complex of LIG2 is more stable than LIG3. LIG2 has the potential antagonistic properties to target the mTOR/FRB domain and has therapeutic implications for breast cancer.
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Affiliation(s)
- Varruchi Sharma
- Depatment of Biotechnology, Sri Guru Gobind Singh College, Chandigarh, India
| | - Anil Panwar
- Department of Molecular Biology, Biotechnology & Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, India
| | - Anupam Sharma
- MMIS, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vasu Punj
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Reena V Saini
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Adesh K Saini
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Anil K Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
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Carvacrol: An In Silico Approach of a Candidate Drug on HER2, PI3K α, mTOR, hER- α, PR, and EGFR Receptors in the Breast Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:8830665. [PMID: 33163084 PMCID: PMC7607278 DOI: 10.1155/2020/8830665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
Carvacrol is a phenol monoterpene found in aromatic plants specially in Lamiaceae family, which has been evaluated in an experimental model of breast cancer. However, any proposed mechanism based on its antitumor effect has not been reported. In our previous study, carvacrol showed a protective effect on 7,12-dimethylbenz[α]anthracene- (DMBA-) induced breast cancer in female rats. The main objective in this research was to evaluate by using in silico study the carvacrol on HER2, PI3Kα, mTOR, hER-α, PR, and EGFR receptors involved in breast cancer progression by docking analysis, molecular dynamic, and drug-likeness evaluation. A multilevel computational study to evaluate the antitumor potential of carvacrol focusing on the main targets involved in the breast cancer was carried out. The in silico study starts with protein-ligand docking of carvacrol followed by ligand pathway calculations, molecular dynamic simulations, and molecular mechanics energies combined with the Poisson-Boltzmann (MM/PBSA) calculation of the free energy of binding for carvacrol. As result, the in silico study led to the identification of carvacrol with strong binding affinity on mTOR receptor. Additionally, in silico drug-likeness index for carvacrol showed a good predicted therapeutic profile of druggability. Our findings suggest that mTOR signaling pathway could be responsible for its preventive effect in the breast cancer.
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Siniprasad P, Nair B, Balasubramaniam V, Sadanandan P, Namboori PK, Nath LR. Evaluation of Kaempferol as AKT Dependent mTOR Regulator via Targeting FKBP-12 in Hepatocellular Carcinoma: An In silico Approach. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200623115703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background:
Hepatocellular carcinomas (HCCs) are inherently chemotherapy-resistant
tumors with about 30-50% activation of PI3K/Akt/mTOR pathway, and this pathway is not aberrant
in normal cells. Therefore, targeting the PI3K/Akt/mTOR pathway has become a promising strategy
in drug designing to combat liver cancer. Recently, many studies with phytochemicals suggest few classes
of compounds, especially flavonoids, to be useful in down-regulating the PI3K/Akt/mTOR pathway corresponding
to HCC. In the present study, an attempt is made to explore flavonoids, from which the best
mTORC1 inhibitor against hepatocellular carcinoma is selected using computational molecular modeling.
Methods:
In the present study, we performed a virtual screening method with phytochemicals of
flavonoid category. To ensure proper bioavailability and druggability, pharmacokinetic and interaction
parameters have been used to screen the molecules. The target protein molecules have been selected
from the RCSB. The interaction studies have been conducted using Biovia Discovery Studio
client version 17.2.0.1.16347 and the pharmacokinetic predictions have been made through ADMET
SAR. The responsiveness towards the regulation of the mTOR pathway varies from person to person,
demanding a pharmacogenomic approach in the analysis. The genetic variants (Single Nucleotide
Variants-SNVs) corresponding to the mutations have been identified.
Results and Discussion:
The study identified phytoconstituents with better interaction with receptor
FKBP12, a Rapamycin binding domain which is the target of Rapamycin and its analogues for
mTORC1 inhibition in HCC. Another protein, ‘AKT serine/threonine-protein kinase’ has been identified,
which is associated with activation of mTORC1. The molecular interaction studies (docking
studies) and ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis were
used to identify the affinity between selected phytoconstituents as mTORC1 inhibitor against Hepatocellular
carcinoma. The docking studies support Kaempferol to be a potential ligand with docking
score values of 33.4 (3CQU-3D structure of AKT1)] and 27.3 (2FAP-3D structure of FRB domain
of mTOR) respectively as compared to that of standard drug Everolimus with 24.4 (3CQU-3D structure
of AKT1) and 20.1 (2FAP-3D structure of FRB domain of mTOR) respectively. Docking studies
along with ADMET results show that Kaempferol has favorable drug likeliness properties and
binds to the same active site (site1) of the targeted proteins (3CQU-3D structure of AKT1) and
(2FAP-3D structure of FRB domain of mTOR) where the standard drug Everolimus is known to
bind.
Conclusion:
The study exhibited that Kaempferol had a better binding affinity towards the receptor
FKBP12, a Rapamycin Binding Domain and AKT serine/threonine-protein kinase resulting in its
better efficacy in the mTORC1 inhibition as when compared with standard drug Everolimus against
HCC. To the best of our knowledge, no studies have been reported on Kaempferol as mTORC1 inhibitor
against Hepatocellular carcinoma.
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Affiliation(s)
- Pooja Siniprasad
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Bhagyalakshmi Nair
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Vaisali Balasubramaniam
- Computational Chemistry Group (CCG), Computational Engineering and Networking, Amrita Vishwa Vidyapeetham, Amritanagar, Coimbatore-641112, India
| | - Prashanth Sadanandan
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Puliyapally Krishnan Namboori
- Computational Chemistry Group (CCG), Computational Engineering and Networking, Amrita Vishwa Vidyapeetham, Amritanagar, Coimbatore-641112, India
| | - Lekshmi Reghu Nath
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
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Zhang N, Ma S. Research Progress of 70 kDa Ribosomal Protein S6 Kinase (P70S6K) Inhibitors as Effective Therapeutic Tools for Obesity, Type II Diabetes and Cancer. Curr Med Chem 2020; 27:4699-4719. [PMID: 31942845 DOI: 10.2174/0929867327666200114113139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/06/2019] [Accepted: 01/05/2020] [Indexed: 01/07/2023]
Abstract
At present, diseases such as obesity, type Ⅱ diabetes and cancer have brought serious health problems, which are closely related to mTOR pathway. 70 kDa ribosomal protein S6 kinase (p70S6K), as a significant downstream effector of mTOR, mediates protein synthesis, RNA processing, glucose homeostasis, cell growth and apoptosis. Inhibiting the function of p70S6K can reduce the risk of obesity which helps to treat dyslipidemia, enhance insulin sensitivity, and extend the life span of mammals. Therefore, p70S6K has become a potential target for the treatment of these diseases. So far, except for the first p70S6K specific inhibitor PF-4708671 developed by Pfizer and LY2584702 developed by Lilai, all of them are in preclinical research. This paper briefly introduces the general situation of p70S6K and reviews their inhibitors in recent years, which are mainly classified into two categories: natural compounds and synthetic compounds. In particular, their inhibitory activities, structure-activity relationships (SARs) and mechanisms are highlighted.
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Affiliation(s)
- Na Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education) School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education) School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
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Chaudhary M, Kumar N, Baldi A, Chandra R, Babu MA, Madan J. 4-Bromo-4’-chloro pyrazoline analog of curcumin augmented anticancer activity against human cervical cancer, HeLa cells: in silico-guided analysis, synthesis, and in vitro cytotoxicity. J Biomol Struct Dyn 2019; 38:1335-1353. [DOI: 10.1080/07391102.2019.1604266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Monika Chaudhary
- IKG Punjab Technical University, Jalandhar, Punjab, India
- Department of Medicinal Chemistry, Hindu College of Pharmacy, Sonepat, Haryana, India
| | - Neeraj Kumar
- Department of Chemistry, University of Delhi, Delhi, India
| | - Ashish Baldi
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, Punjab, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi, India
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
| | - M. Arockia Babu
- Department of Pharmaceutics, Chandigarh College of Pharmacy, Mohali, Punjab, India
| | - Jitender Madan
- Department of Pharmaceutics, Chandigarh College of Pharmacy, Mohali, Punjab, India
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Jeyaraman P, Alagarraj A, Natarajan R. In silico and in vitro studies of transition metal complexes derived from curcumin-isoniazid Schiff base. J Biomol Struct Dyn 2019; 38:488-499. [PMID: 30767624 DOI: 10.1080/07391102.2019.1581090] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A series of transition metal complexes have been synthesized from biologically active curcumin and isoniazid Schiff base. They are characterized by various spectral techniques like UV-Vis, Fourier transform infrared (FT-IR), nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR) and mass spectroscopies. Moreover, elemental analysis, magnetic susceptibility and molar conductivity measurements are also carried out. All these data evidence that the metal complexes acquire square planar except zinc(II) which adopts a tetrahedral geometry, and they are non-electrolytic in nature. Groove mode of binding between the calf thymus DNA (CT DNA) and metal complexes is confirmed by electronic absorption titration, viscosity and cyclic voltammetry studies. In addition to that, all the metal complexes are able to cleave pUC 19 DNA. Optimized geometry and ground-state electronic structure calculations of all the synthesized compounds are established out by density functional theory (DFT) using B3LYP method which theoretically reveals that copper(II) complex explores higher stability and higher biological accessibility. This is experimentally corroborated by antimicrobial studies. In silico Absorption, Distribution, Metabolism, Excretion (ADME) studies reveal the biological potential of all synthesized complexes, and also biological activity of the ligand is predicted by PASS online biological activity prediction software. Molecular docking studies are also carried out to confirm the groove mode of binding and receptor-complex interactions.
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Affiliation(s)
- Porkodi Jeyaraman
- Research Department of Chemistry, VHNSN College, Virudhunagar, Tamil Nadu, India
| | - Arunadevi Alagarraj
- Research Department of Chemistry, VHNSN College, Virudhunagar, Tamil Nadu, India
| | - Raman Natarajan
- Research Department of Chemistry, VHNSN College, Virudhunagar, Tamil Nadu, India
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Kamshad M, Jahanshah Talab M, Beigoli S, Sharifirad A, Chamani J. Use of spectroscopic and zeta potential techniques to study the interaction between lysozyme and curcumin in the presence of silver nanoparticles at different sizes. J Biomol Struct Dyn 2018; 37:2030-2040. [PMID: 29757090 DOI: 10.1080/07391102.2018.1475258] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This article describes, for the first time, the effect of three different sizes of silver nanoparticles on the binding of curcumin to lysozyme as examined by spectroscopic and zeta potential techniques at physiological conditions. The binding constants of curcumin to lysozyme in the presence of silver nanoparticles were measured. Based on the results of synchronous fluorescence and three-dimensional fluorescence spectroscopy, the presence of the different sizes of silver nanoparticles caused conformational changes in lysozyme during the binding of curcumin. Such changes were also observed when increasing the curcumin concentration. The results of fluorescence resonance energy transfer theory indicated that different sizes of silver nanoparticles could change the binding distance between curcumin and lysozyme. Based on the red edge excitation shift approach, we concluded that the limited mobility around the Trp residues decreased in the presence of silver nanoparticles with bigger size. Under resonance light scattering, the aggregation of curcumin on lysozyme in the presence of silver nanoparticles can play a major role in functional proteins. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maryam Kamshad
- a Department of Biology, Faculty of Sciences , Mashhad Branch, Islamic Azad University , Mashhad , Iran
| | - Mahtab Jahanshah Talab
- a Department of Biology, Faculty of Sciences , Mashhad Branch, Islamic Azad University , Mashhad , Iran
| | - Sima Beigoli
- b Endoscopic and Minimally Invasive Surgery Research Center, Mashhad University of Medical Sciences , Mashhad , Iran
| | - Atena Sharifirad
- c Department of Biology, Faculty of Sciences , Neyshabur Branch, Islamic Azad University , Neyshabur , Iran
| | - Jamshidkhan Chamani
- a Department of Biology, Faculty of Sciences , Mashhad Branch, Islamic Azad University , Mashhad , Iran
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Liu J, Liu L, Tian Z, Li Y, Shi C, Shi J, Wei S, Zhao Y, Zhang C, Bai B, Chen Z, Zhang H. In Silico Discovery of a Small Molecule Suppressing Lung Carcinoma A549 Cells Proliferation and Inducing Autophagy via mTOR Pathway Inhibition. Mol Pharm 2018; 15:5427-5436. [PMID: 30346178 DOI: 10.1021/acs.molpharmaceut.8b00996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Li Liu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi’an, Shaanxi Province 710072, China
- Laboratory Animal Center, Air Force Medical University, No. 169 Changle West Road, Xi’an, Shaanxi Province 710032, China
| | - Zhen Tian
- College of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road, NO. 48, Yangzhou, Jiangsu Province 225009, China
| | - Yifan Li
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Changhong Shi
- Laboratory Animal Center, Air Force Medical University, No. 169 Changle West Road, Xi’an, Shaanxi Province 710032, China
| | - Junling Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi’an, Shaanxi Province 710072, China
| | - Sanhua Wei
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Air Force Medical University, No. 569 Xinsi Road, Xi’an, Shaanxi 710038, China
| | - Yong Zhao
- Laboratory Animal Center, Air Force Medical University, No. 169 Changle West Road, Xi’an, Shaanxi Province 710032, China
| | - Caiqing Zhang
- Laboratory Animal Center, Air Force Medical University, No. 169 Changle West Road, Xi’an, Shaanxi Province 710032, China
| | - Bing Bai
- Laboratory Animal Center, Air Force Medical University, No. 169 Changle West Road, Xi’an, Shaanxi Province 710032, China
| | - Zhinan Chen
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, School of Basic Medicine, Air Force Medical University, Xi’an, Shaanxi Province 710032, China
| | - Hai Zhang
- Laboratory Animal Center, Air Force Medical University, No. 169 Changle West Road, Xi’an, Shaanxi Province 710032, China
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, School of Basic Medicine, Air Force Medical University, Xi’an, Shaanxi Province 710032, China
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Niu X, Gao Y, Yu Y, Yang Y, Wang G, Sun L, Wang H. Molecular Modelling reveals the inhibition mechanism and structure-activity relationship of curcumin and its analogues to Staphylococcal aureus Sortase A. J Biomol Struct Dyn 2018; 37:1220-1230. [PMID: 29546799 DOI: 10.1080/07391102.2018.1453380] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Previous studies found that the activity of Sortase A, a bacterial surface protein from Staphylococcus aureus, was inhibited by curcumin and its analogues. To explore this inhibitory mechanism, Sortase A and its inhibitors in complex systems were studied by molecular docking, molecular modelling, binding energy decomposition calculation and steered molecular dynamics simulations. Energy decomposition analysis indicated that PRO-163, LEU-169, GLN-172, ILE-182 and ILE-199 are key residues in Sortase A-inhibitor complexes. Furthermore, interactions between the methoxyl group on the benzene ring in the conjugated molecule (curcumin, demethoxycurcumin, bisdemethoxycurcumin) and VAL-168, LEU-169 and GLN-172 induce the inhibitory activity based on the energy decomposition and distance analyses between the whole residues and inhibitors. However, because of its coiled structure, the non-conjugated molecule, tetrahydrocurcumin, with key residues in the binding sites of Sortase A, interacted weakly with SrtA, leading to the loss of inhibitory activity. Based on these results, the methoxyl group on the benzene ring in the conjugated molecule largely influenced the inhibitory activity of the Sortase A inhibitors.
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Affiliation(s)
- Xiaodi Niu
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Yawen Gao
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Yiding Yu
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Yanan Yang
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Guizhen Wang
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Lin Sun
- a College of Food Science and Engineering , Jilin University , Changchun , China
| | - Hongsu Wang
- a College of Food Science and Engineering , Jilin University , Changchun , China
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