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Ali MA, Sheikh H, Yaseen M, Faruqe MO, Ullah I, Kumar N, Bhat MA, Mollah MNH. Exploring the Therapeutic Potential of Petiveria alliacea L. Phytochemicals: A Computational Study on Inhibiting SARS-CoV-2's Main Protease (Mpro). Molecules 2024; 29:2524. [PMID: 38893400 PMCID: PMC11173994 DOI: 10.3390/molecules29112524] [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: 04/12/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/21/2024] Open
Abstract
The outbreak of SARS-CoV-2, also known as the COVID-19 pandemic, is still a critical risk factor for both human life and the global economy. Although, several promising therapies have been introduced in the literature to inhibit SARS-CoV-2, most of them are synthetic drugs that may have some adverse effects on the human body. Therefore, the main objective of this study was to carry out an in-silico investigation into the medicinal properties of Petiveria alliacea L. (P. alliacea L.)-mediated phytocompounds for the treatment of SARS-CoV-2 infections since phytochemicals have fewer adverse effects compared to synthetic drugs. To explore potential phytocompounds from P. alliacea L. as candidate drug molecules, we selected the infection-causing main protease (Mpro) of SARS-CoV-2 as the receptor protein. The molecular docking analysis of these receptor proteins with the different phytocompounds of P. alliacea L. was performed using AutoDock Vina. Then, we selected the three top-ranked phytocompounds (myricitrin, engeletin, and astilbin) as the candidate drug molecules based on their highest binding affinity scores of -8.9, -8.7 and -8.3 (Kcal/mol), respectively. Then, a 100 ns molecular dynamics (MD) simulation study was performed for their complexes with Mpro using YASARA software, computed RMSD, RMSF, PCA, DCCM, MM/PBSA, and free energy landscape (FEL), and found their almost stable binding performance. In addition, biological activity, ADME/T, DFT, and drug-likeness analyses exhibited the suitable pharmacokinetics properties of the selected phytocompounds. Therefore, the results of this study might be a useful resource for formulating a safe treatment plan for SARS-CoV-2 infections after experimental validation in wet-lab and clinical trials.
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Affiliation(s)
- Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
- Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Humaira Sheikh
- Department of Chemistry, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj 8100, Bangladesh;
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, Faculty of Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ihsan Ullah
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur 313001, Rajasthan, India;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
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Dai Z, Wu Y, Xiong Y, Wu J, Wang M, Sun X, Ding X, Yang L, Sun X, Ge G. CYP1A inhibitors: Recent progress, current challenges, and future perspectives. Med Res Rev 2024; 44:169-234. [PMID: 37337403 DOI: 10.1002/med.21982] [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: 12/09/2022] [Revised: 03/28/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Mammalian cytochrome P450 1A (CYP1A) are key phase I xenobiotic-metabolizing enzymes that play a distinctive role in metabolic activation or metabolic clearance of a variety of procarcinogens, drugs, and endogenous substances. Human CYP1A subfamily contains two members (hCYP1A1 and hCYP1A2), which are known to catalyze the oxidative activation of some environmental procarcinogens into carcinogenic species. Increasing evidence has demonstrated that CYP1A inhibitor therapies are promising strategies for cancer chemoprevention or overcoming CYP1A-associated drug toxicity and resistance. Herein, we reviewed recent advances in the discovery and characterization of hCYP1A inhibitors, from the discovery approaches to structural features and biomedical applications of hCYP1A inhibitors. The inhibition potentials, inhibition modes, and inhibition constants of all reported hCYP1A inhibitors are comprehensively summarized. Meanwhile, the structural features and structure-activity relationships of different classes of hCYP1A1 and hCYP1A2 inhibitors are analyzed and discussed in depth. Furthermore, the major challenges and future directions for this field are presented and highlighted. Collectively, the information and knowledge presented here will strongly facilitate the researchers to discover and develop more efficacious CYP1A inhibitors for specific purposes, such as chemo-preventive agents or as tool molecules in hCYP1A-related fundamental studies.
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Affiliation(s)
- Ziru Dai
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Wu
- Shanghai Frontiers Science Center for TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuan Xiong
- Shanghai Frontiers Science Center for TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jingjing Wu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Min Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiao Sun
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinxin Ding
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, America
| | - Ling Yang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Xiaobo Sun
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center for TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Wright EB, Lannigan DA. Therapeutic targeting of p90 ribosomal S6 kinase. Front Cell Dev Biol 2023; 11:1297292. [PMID: 38169775 PMCID: PMC10758423 DOI: 10.3389/fcell.2023.1297292] [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: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
The Serine/Threonine protein kinase family, p90 ribosomal S6 kinases (RSK) are downstream effectors of extracellular signal regulated kinase 1/2 (ERK1/2) and are activated in response to tyrosine kinase receptor or G-protein coupled receptor signaling. RSK contains two distinct kinase domains, an N-terminal kinase (NTKD) and a C-terminal kinase (CTKD). The sole function of the CTKD is to aid in the activation of the NTKD, which is responsible for substrate phosphorylation. RSK regulates various homeostatic processes including those involved in transcription, translation and ribosome biogenesis, proliferation and survival, cytoskeleton, nutrient sensing, excitation and inflammation. RSK also acts as a major negative regulator of ERK1/2 signaling. RSK is associated with numerous cancers and has been primarily studied in the context of transformation and metastasis. The development of specific RSK inhibitors as cancer therapeutics has lagged behind that of other members of the mitogen-activated protein kinase signaling pathway. Importantly, a pan-RSK inhibitor, PMD-026, is currently in phase I/1b clinical trials for metastatic breast cancer. However, there are four members of the RSK family, which have overlapping and distinct functions that can vary in a tissue specific manner. Thus, a problem for transitioning a RSK inhibitor to the clinic may be the necessity to develop isoform specific inhibitors, which will be challenging as the NTKDs are very similar to each other. CTKD inhibitors have limited use as therapeutics as they are not able to inhibit the activity of the NTKD but could be used in the development of proteolysis-targeting chimeras.
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Affiliation(s)
- Eric B. Wright
- Department Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Deborah A. Lannigan
- Department Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
- Department Pathology, Vanderbilt University Medical Center, Nashville, TN, United States
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Corzo Parada L, Urueña C, Leal-García E, Barreto A, Ballesteros-Ramírez R, Rodríguez-Pardo V, Fiorentino S. Doxorubicin Activity Is Modulated by Traditional Herbal Extracts in a 2D and 3D Multicellular Sphere Model of Leukemia. Pharmaceutics 2023; 15:1690. [PMID: 37376139 DOI: 10.3390/pharmaceutics15061690] [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: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The modulation of the tumor microenvironment by natural products may play a significant role in the response of tumor cells to chemotherapy. In this study, we evaluated the effect of extracts derived from P2Et (Caesalpinia spinosa) and Anamú-SC (Petiveria alliacea) plants, previously studied by our group, on the viability and ROS levels in the K562 cell line (Pgp- and Pgp+), endothelial cells (ECs, Eahy.926 cell line) and mesenchymal stem cells (MSC) cultured in 2D and 3D. The results show that: (a) the two botanical extracts are selective on tumor cells compared to doxorubicin (DX), (b) cytotoxicity is independent of the modulation of intracellular ROS for plant extracts, unlike DX, (c) the interaction with DX can be influenced by chemical complexity and the expression of Pgp, (d) the 3D culture shows a greater sensitivity of the tumor cells to chemotherapy, in co-treatment with the extracts. In conclusion, the effect of the extracts on the viability of leukemia cells was modified in multicellular spheroids with MSC and EC, suggesting that the in vitro evaluation of these interactions can contribute to the comprehension of the pharmacodynamics of the botanical drugs.
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Affiliation(s)
- Laura Corzo Parada
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Claudia Urueña
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Efraín Leal-García
- Departamento de Ortopedia y Traumatología, Facultad de Medicina, Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá 110231, Colombia
| | - Alfonso Barreto
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Ricardo Ballesteros-Ramírez
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Viviana Rodríguez-Pardo
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Susana Fiorentino
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
- Departamento de Ortopedia y Traumatología, Facultad de Medicina, Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá 110231, Colombia
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Wooten J, Mavingire N, Araújo CA, Aja J, Wauchope S, Delgoda R, Brantley E. Dibenzyl trisulfide induces caspase-independent death and lysosomal membrane permeabilization of triple-negative breast cancer cells. Fitoterapia 2022; 160:105203. [PMID: 35489582 PMCID: PMC9979099 DOI: 10.1016/j.fitote.2022.105203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 01/25/2023]
Abstract
The Petiveria alliacea L. (P. alliacea) plant is traditionally used in folklore medicine throughout tropical regions of the world to treat arthritis, asthma, and cancer. Dibenzyl trisulfide (DTS) is one of the active ingredients within the P. alliacea plant. Triple-negative breast cancer (TNBC) is associated with a poor prognosis, particularly among women of West African ancestry, due in part to limited effective therapy. Though potent anticancer actions of DTS have been reported in a TNBC cell line, the mechanism of DTS-mediated cytotoxicity and cell death remains ill-defined. In the current study, we show that DTS exhibits cytotoxicity in a panel of triple-negative breast cancer (TNBC) cells derived from patients of European and West African ancestry. We found that DTS inhibits proliferation and migration of CRL-2335 cells derived from a patient of West African ancestry. DTS induces the expression of pro-apoptotic genes BAK1, GADD45a, and LTA in CRL2335 cells though it primarily promotes caspase-independent CRL-2335 cell death. DTS also promotes destabilization of the lysosomal membrane resulting in cathepsin B release in CRL-2335 cells. Finally, Kaplan-Meier survival curves reveal that higher expression of BAK1 and LTA in tumors from patients with TNBC is associated with longer relapse-free survival. Collectively, our data suggest that DTS confers promising antitumor efficacy in TNBC, in part, via lysosomal-mediated, caspase-independent cell death to warrant furthering its development as an anticancer agent.
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Affiliation(s)
- Jonathan Wooten
- Department of Basic Sciences, Loma Linda University Health School of Medicine, Loma Linda, CA, United States of America; Center for Health Disparities and Molecular Medicine, Loma Linda University Health School of Medicine, Loma Linda, CA, United States of America.
| | - Nicole Mavingire
- Department of Basic Sciences, Loma Linda University Health School of Medicine, Loma Linda, CA, United States of America.
| | - Cristina A. Araújo
- Department of Basic Sciences, Loma Linda University Health School of Medicine, Loma Linda, CA, US,Center for Health Disparities and Molecular Medicine, Loma Linda University Health School of Medicine, Loma Linda, CA, US
| | - Joyce Aja
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City, Philippines.
| | - Shaniece Wauchope
- Natural Products Institute, University of the West Indies, Mona, Kingston 7, Jamaica.
| | - Rupika Delgoda
- Natural Products Institute, University of the West Indies, Mona, Kingston 7, Jamaica.
| | - Eileen Brantley
- Department of Basic Sciences, Loma Linda University Health School of Medicine, Loma Linda, CA, United States of America; Center for Health Disparities and Molecular Medicine, Loma Linda University Health School of Medicine, Loma Linda, CA, United States of America.
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Clarke N, Irvine W. In Silico Design and SAR Study of Dibenzyl Trisulfide Analogues for Improved CYP1A1 Inhibition. Chemistry 2022; 11:e202200016. [PMID: 35610057 PMCID: PMC9130049 DOI: 10.1002/open.202200016] [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: 01/21/2022] [Revised: 04/17/2022] [Indexed: 11/23/2022]
Abstract
Dibenzyl trisulfide (DTS) is a natural compound with potential cancer‐preventive properties occurring in Petiveria alliacea L., an ethnomedicinal plant native to the Americas. Previous studies revealed its inhibitory activity toward cytochrome P450 (CYP)1 enzymes, key in the activation of environmental pollutants. Accordingly, the aim of this study was to design novel DTS analogues, aimed at improving not only inhibitory activity, but also specificity toward CYP1A1. This was achieved by targeting interactions with CYP1A1 residues of identified importance. Three‐dimensional structures for the novel analogues were subjected to molecular docking with several CYP isoforms, before being ranked in terms of binding affinity to CYP1A1. With three hydrogen bond donors, two hydrogen bond acceptors, a molecular mass of 361 Da, and a log P of 3.72, the most promising DTS analogue obeys Lipinski's rule of five. Following synthesis and in vitro validation of its CYP1A1‐inhibitory properties, this compound may be useful in future cancer‐preventive approaches.
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Affiliation(s)
- Nishani Clarke
- Phillips Academy, 180 Main Street, Andover, MA-01810, USA
| | - William Irvine
- Natural Products Institute, University of the West Indies Mona, Kingston 7, Jamaica
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