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Nahar J, Boopathi V, Murugesan M, Rupa EJ, Yang DC, Kang SC, Mathiyalagan R. Investigating the Anticancer Activity of G-Rh1 Using In Silico and In Vitro Studies (A549 Lung Cancer Cells). Molecules 2022; 27. [PMID: 36500403 DOI: 10.3390/molecules27238311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022]
Abstract
Ginsenoside Rh1 (G-Rh1), a possible bioactive substance isolated from the Korean Panax ginseng Meyer, has a wide range of pharmacological effects. In this study, we have investigated the anticancer efficacy of G-Rh1 via in silico and in vitro methodologies. This study mainly focuses on the two metastatic regulators, Rho-associated protein kinase 1 (ROCK1) and RhoA, along with other standard apoptosis regulators. The ROCK1 protein is a member of the active serine/threonine kinase family that is crucial for many biological processes, including cell division, differentiation, and death, as well as many cellular processes and muscle contraction. The abnormal activation of ROCK1 kinase causes several disorders, whereas numerous studies have also shown that RhoA is expressed highly in various cancers, including colon, lung, ovarian, gastric, and liver malignancies. Hence, inhibiting both ROCK1 and RhoA will be promising in preventing metastasis. Therefore, the molecular level interaction of G-Rh1 with the ROCK1 and RhoA active site residues from the preliminary screening clearly shows its inhibitory potential. Molecular dynamics simulation and principal component analysis give essential insights for comprehending the conformational changes that result from G-Rh1 binding to ROCK1 and RhoA. Further, MTT assay was employed to examine the potential cytotoxicity in vitro against human lung cancer cells (A549) and Raw 264.7 Murine macrophage cells. Thus, G-Rh1 showed significant cytotoxicity against human lung adenocarcinoma (A549) at 100 µg/mL. In addition, we observed an elevated level of reactive oxygen species (ROS) generation, perhaps promoting cancer cell toxicity. Additionally, G-Rh1 suppressed the mRNA expression of RhoA, ROCK1, MMP1, and MMP9 in cancer cell. Accordingly, G-Rh1 upregulated the p53, Bax, Caspase 3, caspase 9 while Bcl2 is downregulated intrinsic pathway. The findings from our study propose that the anticancer activity of G-Rh1 may be related to the induction of apoptosis by the RhoA/ROCK1 signaling pathway. As a result, this study evaluated the functional drug-like compound G-Rh1 from Panax ginseng in preventing and treating lung cancer adenocarcinoma via regulating metastasis and apoptosis.
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Mateen RM, Tariq A, Afzal MS, Ali M, Tipu I, Hussain M, Saleem M, Naveed M. TULP3 NLS inhibition: an in silico study to hamper cargo transport to nucleus. J Biomol Struct Dyn 2022:1-9. [PMID: 35510584 DOI: 10.1080/07391102.2022.2070283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
TULP3 is involved in cell regulation pathways including transcription and signal transduction. In some pathological states like in cancers, increased level of TULP3 has been observed so it can serve as a potential target to hamper the activation of those pathways. We propose a novel idea of inhibiting nuclear localization signal (NLS) to interrupt nuclear translocation of TULP3 so that the downstream activations of pathways are blocked. In current in silico study, 3D structure of TULP3 was modeled using 8 different tools including I-TASSER, CABS-FOLD, Phyre2, PSIPRED, RaptorX, Robetta, Rosetta and Prime by Schrödinger. Best structure was selected after quality evaluation by SAVES and implied for the investigation of NLS sequence. Mapped NLS sequence was further used to dock with natural ligand importin-α as control docking to validate the NLS sequence as binding site. After docking and molecular dynamics (MD) simulation validation, these residues were used as binding side for subsequent docking studies. 70 alkaloids were selected after intensive literature survey and were virtually docked with NLS sequence where natural ligand importin-α is supposed to be bound. This study demonstrates the virtual inhibition of NLS sequence so that it paves a way for future in-vivo studies to use NLS as a new drug target for cancer therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rana Muhammad Mateen
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Asma Tariq
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sohail Afzal
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Muhammad Ali
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Imran Tipu
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Mureed Hussain
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Mahjabeen Saleem
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Naveed
- Department of Life Sciences, University of Central Punjab, Lahore, Pakistan
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Tahir RA, Sehgal SA. Pharmacoinformatics and Molecular Docking Studies Reveal Potential Novel Compounds Against Schizophrenia by Target SYN II. Comb Chem High Throughput Screen 2019; 21:175-181. [PMID: 29436999 DOI: 10.2174/1386207321666180213092018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/01/2018] [Accepted: 02/03/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Synapsin II regulates neurotransmitter release from mature nerve terminals and plays important role in the formation of new nerve terminals. The associations of SYN II are identified in various studies that are linked to the onset of Schizophrenia. Schizophrenia is characterized by abnormal behavior like obsession, dampening of emotions and auditory hallucination. METHODS The bioinformatics approaches were utilized for structural modeling and docking analyses of SYN II followed by pharmacophore generation to identify potent inhibitors. RESULTS The comparative modeling approach was employed to generate the 3D model having 82.404% quality factor calculated by Errat. Pharmacophore was constructed by utilizing merge molecular and chemical features of selected five FDA approved Schizophrenia drugs by LigandScout 4.1.5. Comparative docking analyses were performed by utilizing the selected drugs and top screened hits by GOLD and AutoDock Vina. CONCLUSION It was proposed that Aripiprazole drug and scrutinized compounds have strong binding affinities among the other selected drugs. The reported compounds may be used for further analyses in the drug discovery processes, as they have shown good human intestinal absorption and are noncarcinogenic. The present study provides the structural insights which may be used for further understating of the Schizophrenia therapeutic purposes by targeting SYN II and other inhibitors haunting.
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Affiliation(s)
- Rana Adnan Tahir
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan.,Beijing Key Laboratory of Separation and Analysis in Biomedical and Pharmaceuticals, Department of Biomedical Engineering, School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Sheikh Arslan Sehgal
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan.,State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences; Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Khan H, Jaiswal V, Kulshreshtha S, Khan A. Potential Angiotensin Converting Enzyme Inhibitors from Moringa oleifera. Recent Pat Biotechnol 2019; 13:239-248. [PMID: 30747089 DOI: 10.2174/1872208313666190211114229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/03/2019] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Hypertension is the chronic medical condition and it affected billions of people worldwide. Natural medicines are the main alternatives to treatment for a majority of people suffering from hypertension. Niazicin-A, Niazimin-A, and Niaziminin-B compounds from Moringa oleifera ethanolic leave extract were reported to have potent antihypertensive activity. OBJECTIVE These compounds were targeted with Angiotensin-converting enzyme [ACE] which is one of the main regulatory enzymes of the renin-angiotensin system. METHODS Protein-ligand docking of these compounds with [ACE] [both domain N and C] was conceded out through Autodock vina and visualization was done by chimera. Pharmacokinetics study of these compounds was predicted by ADME-Toxicity Prediction. RESULTS Niazicin-A, Niazimin-A, and Niaziminin-B showed high binding affinity with ACE and partially blocked the active sites of the enzyme. Niazicin-A, Niazimin-A and Niaziminin-B showed the estimated free binding energy of -7.6kcal/mol kcal/mol, -8.8kcal/mol and -8.0kcal/mol respectively with C-domain of ACE and -7.9kcal/mol, -8.5kcal/mol and -7.7kcal/mol respectively with N-domain of ACE. The compounds showed better binding energy with angiotensinconverting enzyme in comparison to Captopril -5.5kcal/mol and -5.6kcal/mol and Enalapril [standard] -8.4kcal/mol and -7.5kcal/mol with C and N domain, respectively. CONCLUSION Computationally, the selected bioactive molecules have shown better binding energy to known standard drugs which have been already known for inhibition of ACE and can further act as a pharmacophore for in vitro and in vivo studies in the development of alternative medicine.
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Affiliation(s)
- Huma Khan
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan-173229, Himachal Pradesh, India
| | - Varun Jaiswal
- School of Electrical and Computer Science Engineering, Shoolini University, Solan-173229, Himachal Pradesh, India
| | - Saurabh Kulshreshtha
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan-173229, Himachal Pradesh, India
| | - Azhar Khan
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan-173229, Himachal Pradesh, India
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Karkute SG, Koley TK, Yengkhom BK, Tripathi A, Srivastava S, Maurya A, Singh B. Anti-diabetic Phenolic Compounds of Black Carrot (Daucus carota Subspecies sativus var. atrorubens Alef.) Inhibit Enzymes of Glucose Metabolism: An in silico and in vitro Validation. Med Chem 2018; 14:641-649. [PMID: 29493459 DOI: 10.2174/1573406414666180301092819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 02/06/2018] [Accepted: 02/20/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Black carrot is known to be effective against Type 2 diabetes. The phenolic compounds present in black carrot are responsible for this property, but limited information was available about the mechanism of action and target enzymes. OBJECTIVE The present study aims at understanding molecular interactions of phenolic compounds of black carrot with enzymes involved in glucose metabolism in human to identify the potential inhibitor that can be used as candidate drug molecule to control diabetes. METHOD In vitro assay for inhibition of α-amylase, α-glucosidase and DPP-IV was carried out using black carrot purified extract and the standard inhibitor acarbose and vildagliptin, recpectively. The inhibition activity of selected phenolic compounds was also studied by in silico docking with all these three enzymes for the proper understanding of interactions. Encapsulation of purified black carrot extract was also carried out. RESULTS In vitro IC50 value of purified extract was found to be better than the standard inhibitor acarbose for α-amylase and α-glucosidase, and vildagliptin for DPP-IV. Similarly, docking scores of few anthocyanin molecules were found to be higher than their respective inhibitors, suggesting more effective inhibition. Among anthocyanin molecules of black carrot, cyanidin 3-xylosyl galactoside was found to be the potential drug to inhibit these enzymes, whereas dipeptidyl peptidase IV was identified as the best target to control diabetes with anthocyanins of black carrot. CONCLUSION Anthocyanins from black carrot were found to be effective to control diabetes and very first time we propose that cyanidin 3-xylosyl galactoside is the best potential molecule for inhibiting enzymes involved in glucose metabolism. The study also shows the encapsulation of anthocyanin compounds using β-cyclodextrin.
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Affiliation(s)
- Suhas G Karkute
- ICAR-Indian Institute of Vegetable Research, Varanasi- 221305, India
| | - Tanmay K Koley
- ICAR-Indian Institute of Vegetable Research, Varanasi- 221305, India
| | - Bijen K Yengkhom
- ICAR-Indian Institute of Vegetable Research, Varanasi- 221305, India
| | - Ajay Tripathi
- ICAR-Indian Institute of Vegetable Research, Varanasi- 221305, India
| | | | - Arti Maurya
- ICAR-Indian Institute of Vegetable Research, Varanasi- 221305, India
| | - Bijendra Singh
- ICAR-Indian Institute of Vegetable Research, Varanasi- 221305, India
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Nivedha AK, Makeneni S, Foley BL, Tessier MB, Woods RJ. Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff. J Comput Chem 2014; 35:526-39. [PMID: 24375430 PMCID: PMC3936473 DOI: 10.1002/jcc.23517] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 10/14/2013] [Accepted: 11/24/2013] [Indexed: 11/10/2022]
Abstract
Docking algorithms that aim to be applicable to a broad range of ligands suffer reduced accuracy because they are unable to incorporate ligand-specific conformational energies. Here, we develop a set of Carbohydrate Intrinsic (CHI) energy functions that quantify the conformational properties of oligosaccharides, based on the values of their glycosidic torsion angles. The relative energies predicted by the CHI energy functions mirror the conformational distributions of glycosidic linkages determined from a survey of oligosaccharide-protein complexes in the protein data bank. Addition of CHI energies to the standard docking scores in Autodock 3, 4.2, and Vina consistently improves pose ranking of oligosaccharides docked to a set of anticarbohydrate antibodies. The CHI energy functions are also independent of docking algorithm, and with minor modifications, may be incorporated into both theoretical modeling methods, and experimental NMR or X-ray structure refinement programs.
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Affiliation(s)
- Anita K. Nivedha
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30606
| | - Spandana Makeneni
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30606
| | - B. Lachele Foley
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30606
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30606
| | - Robert J. Woods
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30606
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
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