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Priyanka K, Sahoo RN, Nanda A, Kanhar S, Das C, Sahu A, Naik PK, Nayak AK. Wound Healing Activity of Topical Herbal Gels Containing Barringtonia acutangula Fruit Extract: In silico and In vivo Studies. Chem Biodivers 2024; 21:e202400147. [PMID: 38687689 DOI: 10.1002/cbdv.202400147] [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: 01/18/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
The current study describes the efficacy of B. acutangula fruit extract in wound healing via incorporation within topical gels. B. acutangula fruit extract was produced by solvent extraction method. The bioactive extract was incorporated within Carbopol 940-based topical gels, which were applied topically over the excision and incision wounds. The change in healing process was observed till 20 days. The percentages of closure of excision wound area were 92.89 % and 93.43 %, when treated with topical herbal gels containing B. acutangula fruit extract of 5 % and 10 %, respectively. The tensile strengths of incision area in rats treated with topical herbal gels containing 5 % and 10 % methanol extract of B. acutangula fruits were found to be 25±5.12 g and 30±4.10 g, respectively. The wound healing activity of topical herbal gels containing B. acutangula fruit extract in rats was found to be significant when compared with that of the reference standard and untreated groups. In addition, in silico studies suggested about good skin permeability and binding to the proteins responsible for delaying wound healing. It can be concluded that this topical herbal gels containing B. acutangula fruit extract could be used clinically for the treatment of wounds.
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Affiliation(s)
- Kumari Priyanka
- Department of Pharmacy, Usha Martin University, Ranchi, 835103, Jharkhand, India
| | - Rudra Narayan Sahoo
- School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751003, Odisha, India
| | - Ashirbad Nanda
- School of Pharmacy and Life Sciences, Centurion University of Technology and Management, Bhubaneswar, 752050, Odisha, India
| | - Satish Kanhar
- School of Pharmacy and Life Sciences, Centurion University of Technology and Management, Bhubaneswar, 752050, Odisha, India
| | - Chandan Das
- School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751003, Odisha, India
| | - Abhijit Sahu
- Center of Excellence, Natural Products & Therapeutics, Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, 768019, Odisha, India
| | - Pradeep Kumar Naik
- Center of Excellence, Natural Products & Therapeutics, Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, 768019, Odisha, India
| | - Amit Kumar Nayak
- School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751003, Odisha, India
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Shafiq N, Mehroze A, Sarwar W, Arshad U, Parveen S, Rashid M, Farooq A, Rafiq N, Wondmie GF, Bin Jardan YA, Brogi S, Bourhia M. Exploration of phenolic acid derivatives as inhibitors of SARS-CoV-2 main protease and receptor binding domain: potential candidates for anti-SARS-CoV-2 therapy. Front Chem 2023; 11:1251529. [PMID: 37822772 PMCID: PMC10562575 DOI: 10.3389/fchem.2023.1251529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
Severe acute respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the etiological virus of Coronavirus Disease 2019 (COVID-19) which has been a public health concern due to its high morbidity and high mortality. Hence, the search for drugs that incapacitate the virus via inhibition of vital proteins in its life cycle is ongoing due to the paucity of drugs in clinical use against the virus. Consequently, this study was aimed at evaluating the potentials of natural phenolics against the Main protease (Mpro) and the receptor binding domain (RBD) using molecular modeling techniques including molecular docking, molecular dynamics (MD) simulation, and density functional theory (DFT) calculations. To this end, thirty-five naturally occurring phenolics were identified and subjected to molecular docking simulation against the proteins. The results showed the compounds including rosmarinic acid, cynarine, and chlorogenic acid among many others possessed high binding affinities for both proteins as evident from their docking scores, with some possessing lower docking scores compared to the standard compound (Remdesivir). Further subjection of the hit compounds to drug-likeness, pharmacokinetics, and toxicity profiling revealed chlorogenic acid, rosmarinic acid, and chicoric acid as the compounds with desirable profiles and toxicity properties, while the study of their electronic properties via density functional theory calculations revealed rosmarinic acid as the most reactive and least stable among the sets of lead compounds that were identified in the study. Molecular dynamics simulation of the complexes formed after docking revealed the stability of the complexes. Ultimately, further experimental procedures are needed to validate the findings of this study.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Aiman Mehroze
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Warda Sarwar
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Uzma Arshad
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Ariba Farooq
- Department of Chemistry, University of Lahore, Lahore, Pakistan
| | - Naila Rafiq
- Department of Biochemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | | | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Simone Brogi
- Department of Pharmacy, Pisa University, Pisa, Italy
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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Ullah S, Rahman W, Ullah F, Ullah A, Ahmad G, Ijaz M, Ullah H, Zheng Z, Gao T. AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV. Database (Oxford) 2023; 2023:baad056. [PMID: 37594855 PMCID: PMC10437090 DOI: 10.1093/database/baad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Serious illnesses caused by viruses are becoming the world's most critical public health issues and lead millions of deaths each year in the world. Thousands of studies confirmed that the plant-derived medicines could play positive therapeutic effects on the patients with viral diseases. Since thousands of antiviral phytochemicals have been identified as lifesaving drugs in medical research, a comprehensive database is highly desirable to integrate the medicinal plants with their different medicinal properties. Therefore, we provided a friendly antiviral phytochemical database AVPCD covering 2537 antiviral phytochemicals from 383 medicinal compounds and 319 different families with annotation of their scientific, family and common names, along with the parts used, disease information, active compounds, links of relevant articles for COVID-19, cancer, HIV and malaria. Furthermore, each compound in AVPCD was annotated with its 2D and 3D structure, molecular formula, molecular weight, isomeric SMILES, InChI, InChI Key and IUPAC name and 21 other properties. Each compound was annotated with more than 20 properties. Specifically, a scoring method was designed to measure the confidence of each phytochemical for the viral diseases. In addition, we constructed a user-friendly platform with several powerful modules for searching and browsing the details of all phytochemicals. We believe this database will facilitate global researchers, drug developers and health practitioners in obtaining useful information against viral diseases.
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Affiliation(s)
- Shahid Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Wajeeha Rahman
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Farhan Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Anees Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Gulzar Ahmad
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Muhammad Ijaz
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Hameed Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Zilong Zheng
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Tianshun Gao
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P. R. China
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Shin SH, Hur G, Kim NR, Park JHY, Lee KW, Yang H. A machine learning-integrated stepwise method to discover novel anti-obesity phytochemicals that antagonize the glucocorticoid receptor. Food Funct 2023; 14:1869-1883. [PMID: 36723137 DOI: 10.1039/d2fo03466b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
As a type of stress hormone, glucocorticoids (GCs) affect numerous physiological pathways by binding to the glucocorticoid receptor (GR) and regulating the transcription of various genes. However, when GCs are dysregulated, the resulting hypercortisolism may contribute to various metabolic disorders, including obesity. Thus, attempts have been made to discover potent GR antagonists that can reverse excess-GC-related metabolic diseases. Phytochemicals are a collection of valuable bioactive compounds that are known for their wide variety of chemotypes. Recently, various computational methods have been developed to obtain active phytochemicals that can modulate desired target proteins. In this study, we developed a workflow comprising two consecutive quantitative structure-activity relationship-based machine learning models to discover novel GR-antagonizing phytochemicals. These two models collectively identified 65 phytochemicals that bind to and antagonize GR. Of these, nine commercially available phytochemicals were validated for GR-antagonist and anti-obesity activities. In particular, we confirmed that demethylzeylasteral, a phytochemical of the Tripterygium wilfordii Radix, exhibits potent anti-obesity activity in vitro through GR antagonism.
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Affiliation(s)
- Seo Hyun Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Gihyun Hur
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Na Ra Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Jung Han Yoon Park
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. .,Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.,Advanced Institutes of Convergence Technology, Seoul National University, Suwon, 16229, Republic of Korea
| | - Hee Yang
- Department of Food and Nutrition, Kookmin University, Seoul 02707, Republic of Korea.
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Ritz M, Ahmad N, Brueck T, Mehlmer N. Comparative Genome-Wide Analysis of Two Caryopteris x Clandonensis Cultivars: Insights on the Biosynthesis of Volatile Terpenoids. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12030632. [PMID: 36771729 PMCID: PMC9921992 DOI: 10.3390/plants12030632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 05/31/2023]
Abstract
Caryopteris x Clandonensis, also known as bluebeard, is an ornamental plant containing a large variety of terpenes and terpene-like compounds. Four different cultivars were subjected to a principal component analysis to elucidate variations in terpenoid-biosynthesis and consequently, two representative cultivars were sequenced on a genomic level. Functional annotation of genes as well as comparative genome analysis on long read datasets enabled the identification of cultivar-specific terpene synthase and cytochrome p450 enzyme sequences. This enables new insights, especially since terpenoids in research and industry are gaining increasing interest due to their importance in areas such as food preservation, fragrances, or as active ingredients in pharmaceutical formulations. According to BUSCO assessments, the presented genomes have an average size of 355 Mb and about 96.8% completeness. An average of 52,090 genes could be annotated as putative proteins, whereas about 42 were associated with terpene synthases and about 1340 with cytochrome p450 enzymes.
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Nutraceuticals as Supportive Therapeutic Agents in Diabetes and Pancreatic Ductal Adenocarcinoma: A Systematic Review. BIOLOGY 2023; 12:biology12020158. [PMID: 36829437 PMCID: PMC9953002 DOI: 10.3390/biology12020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
The correlation between pancreatic ductal adenocarcinoma (PDAC) and diabetes-related mechanisms support the hypothesis that early therapeutic strategies targeting diabetes can contribute to PDAC risk reduction and treatment improvement. A systematic review was conducted, using PubMed, Embase and Cochrane Library databases, to evaluate the current evidence from clinical studies qualitatively examining the efficacy of four natural products: Curcumin-Curcuma longa L.; Thymoquinone-Nigella sativa L.; Genistein-Glycine max L.; Ginkgo biloba L.; and a low-carbohydrate ketogenic diet in type 2 diabetes (T2D) and PDAC treatment. A total of 28 clinical studies were included, showing strong evidence of inter-study heterogeneity. Used as a monotherapy or in combination with chemo-radiotherapy, the studied substances did not significantly improve the treatment response of PDAC patients. However, pronounced therapeutic efficacy was confirmed in T2D. The natural products and low-carbohydrate ketogenic diet, combined with the standard drugs, have the potential to improve T2D treatment and thus potentially reduce the risk of cancer development and improve multiple biological parameters in PDAC patients.
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Amiri F, Moghadam A, Tahmasebi A, Niazi A. Identification of key genes involved in secondary metabolite biosynthesis in Digitalis purpurea. PLoS One 2023; 18:e0277293. [PMID: 36893121 PMCID: PMC9997893 DOI: 10.1371/journal.pone.0277293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 10/25/2022] [Indexed: 03/10/2023] Open
Abstract
The medicinal plant Digitalis purpurea produces cardiac glycosides that are useful in the pharmaceutical industry. These bioactive compounds are in high demand due to ethnobotany's application to therapeutic procedures. Recent studies have investigated the role of integrative analysis of multi-omics data in understanding cellular metabolic status through systems metabolic engineering approach, as well as its application to genetically engineering metabolic pathways. In spite of numerous omics experiments, most molecular mechanisms involved in metabolic pathways biosynthesis in D. purpurea remain unclear. Using R Package Weighted Gene Co-expression Network Analysis, co-expression analysis was performed on the transcriptome and metabolome data. As a result of our study, we identified transcription factors, transcriptional regulators, protein kinases, transporters, non-coding RNAs, and hub genes that are involved in the production of secondary metabolites. Since jasmonates are involved in the biosynthesis of cardiac glycosides, the candidate genes for Scarecrow-Like Protein 14 (SCL14), Delta24-sterol reductase (DWF1), HYDRA1 (HYD1), and Jasmonate-ZIM domain3 (JAZ3) were validated under methyl jasmonate treatment (MeJA, 100 μM). Despite early induction of JAZ3, which affected downstream genes, it was dramatically suppressed after 48 hours. SCL14, which targets DWF1, and HYD1, which induces cholesterol and cardiac glycoside biosynthesis, were both promoted. The correlation between key genes and main metabolites and validation of expression patterns provide a unique insight into the biosynthesis mechanisms of cardiac glycosides in D. purpurea.
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Affiliation(s)
- Fatemeh Amiri
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
- * E-mail:
| | | | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
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GC–MS and Network Pharmacology Analysis of the Ayurvedic Fermented Medicine, Chandanasava, Against Chronic Kidney and Cardiovascular Diseases. Appl Biochem Biotechnol 2022; 195:2803-2828. [PMID: 36418713 PMCID: PMC9684947 DOI: 10.1007/s12010-022-04242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 11/25/2022]
Abstract
Chandanasava is an Ayurvedic polyherbal fermented traditional medicine (FTM) used by traditional practitioners for millennia. Nevertheless, the mode of action and functional targets are still unknown. The current study includes a pharmacological network analysis to identify the Chandanasava compounds interacting with target proteins involved in chronic kidney disease (CKD) and cardiovascular disease (CVD). Sixty-one Chandanasava phytochemicals were obtained by GC-MS and screened using the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP). The disease target genes were obtained from DisGeNET and GeneCards databases. Forty-five phytocompounds and 135 potential targets were screened for CKD and CVD target proteins and protein interaction networks were constructed. The pharmacological network was deciphered employing target proteins involved in the mechanical action of Chandanasava. The results indicated that 10 bioactive compounds exhibited higher binding affinity patterns with the screened 42 CKD and CVD target proteins. Gene Ontology and KEGG analysis revealed target pathways involved in CKD and CVD, which were further explored by detailed analysis and network-coupled drug profile screening. The molecular docking results showed piperine and melatonin as effective inhibitors/regulators of the hub genes of CKD and CVD. The current study establishing authentic bioactive compounds in FTM is based on deeper insights into recognized Ayurvedic medicines. Representing the workflow of the network pharmacological analysis.
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Zhang X, Chen H, Lin H, Wen R, Yang F. High-Throughput Screening and Molecular Dynamics Simulation of Natural Products for the Identification of Anticancer Agents against MCM7 Protein. Appl Bionics Biomech 2022; 2022:8308192. [PMID: 36157125 PMCID: PMC9499818 DOI: 10.1155/2022/8308192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 11/18/2022] Open
Abstract
Minichromosome maintenance complex component 7 (MCM7) belongs to the minichromosome maintenance family that is necessary for the initiation of eukaryotic DNA replication. Overexpression of the MCM7 protein is linked to cellular proliferation and is accountable for critical malignancy in many cancers. Mechanistically, the suppression of MCM7 greatly lowers the cellular proliferation associated with cancer. Advances in immunotherapy have revolutionized treatments for many types of cancer. To date, no effective small molecular candidate has been found that can stop the advancement of cancer produced by the MCM7 protein. Here, we present the findings of methods that used a combination of structure-assisted drug design, high-throughput virtual screening, and simulations studies to swiftly generate lead compounds against MCM7 protein. In the current study, we designed efficient compounds that may combat all emerging cancer targeting the common MCM7 protein. For this objective, a molecular docking and molecular dynamics (MD) simulation-based virtual screening of 29,000 NPASS library was carried out. As a consequence of using specific pharmacological, physiological, and ADMET criteria, four new prevailing compounds, NPA000018, NPA000111, NPA00305, and NPA014826, were successfully selected. The MD simulations were also used for a time period of 50 ns to evaluate for stability and dynamics behavior of the compounds. Eventually, compounds NPA000111 and NPA014826 were found to be highly potent against MCM7 protein. According to our results, the selected compounds may be effective in treating certain cancer subtypes, for which additional follow-up experimental validation is recommended.
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Affiliation(s)
- Xin Zhang
- Breast Surgery Department, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou 350009, China
| | - Hui Chen
- Breast Surgery Department, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou 350009, China
| | - Hui Lin
- Breast Surgery Department, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou 350009, China
| | - Ronglan Wen
- Breast Surgery Department, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou 350009, China
| | - Fan Yang
- Breast Surgery Department, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou 350009, China
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In vitro antioxidant and cytotoxicity activities and in silico anticancer property of methanolic leaf extract of Leucas indica. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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11
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Balarastaghi S, Delirrad M, Jafari A, Majidi M, Sadeghi M, Zare-Zardini H, Karimi G, Ghorani-Azam A. Potential benefits versus hazards of herbal therapy during pregnancy; a systematic review of available literature. Phytother Res 2022; 36:824-841. [PMID: 35023227 DOI: 10.1002/ptr.7363] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/03/2021] [Accepted: 12/10/2021] [Indexed: 11/07/2022]
Abstract
The use of herbal medicine has considerably grown worldwide in the past two decades. Studies have shown that the prevalence of herbal diet therapy in pregnancy ranged from 1% to 60% in different societies. Many clinical reports have shown that some herbal medicines may have toxic effects on pregnant women and their fetuses because active ingredients of some medicinal plants can readily pass through the biological barriers (e.g., placental barrier). In the present study, we aimed to systematically review the literature to discover potential benefits versus the hazards of herbal therapy during pregnancy. For this purpose, a comprehensive literature review was performed, and after the literature search and selection of the appropriate documents, the desired data were extracted and reported. From 35 articles with a total of 39,950 study population, the results showed that some medicinal plants could cause severe toxicity on mothers and fetuses, in addition to abortion during pregnancy. It was also shown that some plants may lead to developmental abnormalities or fetal death. Findings of this survey showed that some herbal medicines have toxic, teratogenic, and abortive potential, particularly in the first trimester of pregnancy because active ingredients of some medicinal plants are able to pass through the placental barrier and reach the fetus.
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Affiliation(s)
- Soudabeh Balarastaghi
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Delirrad
- Department of Forensic Medicine and Toxicology, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Abbas Jafari
- Department of Clinical Toxicology, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
- Cellular and Molecular Research Center, Research Institute on Cellular and Molecular Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mohammad Majidi
- Department of Forensic Medicine and Toxicology, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mahmood Sadeghi
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
| | - Hadi Zare-Zardini
- Hematology and Oncology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Sciences, Farhangian University, Isfahan, Iran
| | - Gholamreza Karimi
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Adel Ghorani-Azam
- Department of Forensic Medicine and Toxicology, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
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Wainwright CL, Teixeira MM, Adelson DL, Buenz EJ, David B, Glaser KB, Harata-Lee Y, Howes MJR, Izzo AA, Maffia P, Mayer AM, Mazars C, Newman DJ, Nic Lughadha E, Pimenta AM, Parra JA, Qu Z, Shen H, Spedding M, Wolfender JL. Future Directions for the Discovery of Natural Product-Derived Immunomodulating Drugs. Pharmacol Res 2022; 177:106076. [PMID: 35074524 DOI: 10.1016/j.phrs.2022.106076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 02/06/2023]
Abstract
Drug discovery from natural sources is going through a renaissance, having spent many decades in the shadow of synthetic molecule drug discovery, despite the fact that natural product-derived compounds occupy a much greater chemical space than those created through synthetic chemistry methods. With this new era comes new possibilities, not least the novel targets that have emerged in recent times and the development of state-of-the-art technologies that can be applied to drug discovery from natural sources. Although progress has been made with some immunomodulating drugs, there remains a pressing need for new agents that can be used to treat the wide variety of conditions that arise from disruption, or over-activation, of the immune system; natural products may therefore be key in filling this gap. Recognising that, at present, there is no authoritative article that details the current state-of-the-art of the immunomodulatory activity of natural products, this in-depth review has arisen from a joint effort between the International Union of Basic and Clinical Pharmacology (IUPHAR) Natural Products and Immunopharmacology, with contributions from a Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation number of world-leading researchers in the field of natural product drug discovery, to provide a "position statement" on what natural products has to offer in the search for new immunomodulatory argents. To this end, we provide a historical look at previous discoveries of naturally occurring immunomodulators, present a picture of the current status of the field and provide insight into the future opportunities and challenges for the discovery of new drugs to treat immune-related diseases.
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Affiliation(s)
- Cherry L Wainwright
- Centre for Natural Products in Health, Robert Gordon University, Aberdeen, UK.
| | - Mauro M Teixeira
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Brazil.
| | - David L Adelson
- Molecular & Biomedical Science, University of Adelaide, Australia.
| | - Eric J Buenz
- Nelson Marlborough Institute of Technology, New Zealand.
| | - Bruno David
- Green Mission Pierre Fabre, Pierre Fabre Laboratories, Toulouse, France.
| | - Keith B Glaser
- AbbVie Inc., Integrated Discovery Operations, North Chicago, USA.
| | - Yuka Harata-Lee
- Molecular & Biomedical Science, University of Adelaide, Australia
| | - Melanie-Jayne R Howes
- Royal Botanic Gardens Kew, Richmond, Surrey, UK; Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, UK.
| | - Angelo A Izzo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Italy.
| | - Pasquale Maffia
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Italy; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.
| | - Alejandro Ms Mayer
- Department of Pharmacology, College of Graduate Studies, Midwestern University, IL, USA.
| | - Claire Mazars
- Green Mission Pierre Fabre, Pierre Fabre Laboratories, Toulouse, France.
| | | | | | - Adriano Mc Pimenta
- Laboratory of Animal Venoms and Toxins, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - John Aa Parra
- Laboratory of Animal Venoms and Toxins, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Zhipeng Qu
- Molecular & Biomedical Science, University of Adelaide, Australia
| | - Hanyuan Shen
- Molecular & Biomedical Science, University of Adelaide, Australia
| | | | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.
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Li P, Zhang H, Zhang W, Zhang Y, Zhan L, Wang N, Chen C, Fu B, Zhao J, Zhou X, Guo S, Chen J. TMNP: a transcriptome-based multi-scale network pharmacology platform for herbal medicine. Brief Bioinform 2021; 23:6470973. [PMID: 34933331 DOI: 10.1093/bib/bbab542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/08/2021] [Accepted: 11/24/2021] [Indexed: 11/12/2022] Open
Abstract
One of the most difficult problems that hinder the development and application of herbal medicine is how to illuminate the global effects of herbs on the human body. Currently, the chemo-centric network pharmacology methodology regards herbs as a mixture of chemical ingredients and constructs the 'herb-compound-target-disease' connections based on bioinformatics methods, to explore the pharmacological effects of herbal medicine. However, this approach is severely affected by the complexity of the herbal composition. Alternatively, gene-expression profiles induced by herbal treatment reflect the overall biological effects of herbs and are suitable for studying the global effects of herbal medicine. Here, we develop an online transcriptome-based multi-scale network pharmacology platform (TMNP) for exploring the global effects of herbal medicine. Firstly, we build specific functional gene signatures for different biological scales from molecular to higher tissue levels. Then, specific algorithms are designed to measure the correlations of transcriptional profiles and types of gene signatures. Finally, TMNP uses pharmacotranscriptomics of herbal medicine as input and builds associations between herbs and different biological scales to explore the multi-scale effects of herb medicine. We applied TMNP to a single herb Astragalus membranaceus and Xuesaitong injection to demonstrate the power to reveal the multi-scale effects of herbal medicine. TMNP integrating herbal medicine and multiple biological scales into the same framework, will greatly extend the conventional network pharmacology model centering on the chemical components, and provide a window for systematically observing the complex interactions between herbal medicine and the human body. TMNP is available at http://www.bcxnfz.top/TMNP.
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Affiliation(s)
- Peng Li
- College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Haoran Zhang
- College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Wuxia Zhang
- College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Yuanyuan Zhang
- College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Lingmin Zhan
- College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Ning Wang
- School of Computer and Information Technology and Beijing Key Lab of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing 100044, China
| | - Caiping Chen
- College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Bangze Fu
- School of Biomedicine, Beijing City University, Beijing 100094, China
| | - Jinzhong Zhao
- College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Xuezhong Zhou
- School of Computer and Information Technology and Beijing Key Lab of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing 100044, China
| | - Shuzhen Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jianxin Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
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Potential Anti- Mycobacterium tuberculosis Activity of Plant Secondary Metabolites: Insight with Molecular Docking Interactions. Antioxidants (Basel) 2021; 10:antiox10121990. [PMID: 34943093 PMCID: PMC8750514 DOI: 10.3390/antiox10121990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) is a recurrent and progressive disease, with high mortality rates worldwide. The drug-resistance phenomenon of Mycobacterium tuberculosis is a major obstruction of allelopathy treatment. An adverse side effect of allelopathic treatment is that it causes serious health complications. The search for suitable alternatives of conventional regimens is needed, i.e., by considering medicinal plant secondary metabolites to explore anti-TB drugs, targeting the action site of M. tuberculosis. Nowadays, plant-derived secondary metabolites are widely known for their beneficial uses, i.e., as antioxidants, antimicrobial agents, and in the treatment of a wide range of chronic human diseases (e.g., tuberculosis), and are known to “thwart” disease virulence. In this regard, in silico studies can reveal the inhibitory potential of plant-derived secondary metabolites against Mycobacterium at the very early stage of infection. Computational approaches based on different algorithms could play a significant role in screening plant metabolites against disease virulence of tuberculosis for drug designing.
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15
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Shrihastini V, Muthuramalingam P, Adarshan S, Sujitha M, Chen JT, Shin H, Ramesh M. Plant Derived Bioactive Compounds, Their Anti-Cancer Effects and In Silico Approaches as an Alternative Target Treatment Strategy for Breast Cancer: An Updated Overview. Cancers (Basel) 2021; 13:cancers13246222. [PMID: 34944840 PMCID: PMC8699774 DOI: 10.3390/cancers13246222] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer is one of the most common malignant diseases that occur worldwide, among which breast cancer is the second leading cause of death in women. The subtypes are associated with differences in the outcome and were selected for treatments according to the estrogen receptor, progesterone receptor, and human epidermal growth factor receptor. Triple-negative breast cancer, one of the subtypes of breast cancer, is difficult to treat and can even lead to death. If breast cancer is not treated during the initial stages, it may spread to nearby organs, a process called metastasis, through the blood or lymph system. For in vitro studies, MCF-7, MDA-MB-231, MDA-MB-468, and T47B are the most commonly used breast cancer cell lines. Clinically, chemotherapy and radiotherapy are usually expensive and can also cause side effects. To overcome these issues, medicinal plants could be the best alternative for chemotherapeutic drugs with fewer side effects and cost-effectiveness. Furthermore, the genes involved in breast cancer can be regulated and synergized with signaling molecules to suppress the proliferation of breast cancer cells. In addition, nanoparticles encapsulating (nano-encapsulation) medicinal plant extracts showed a significant reduction in the apoptotic and cytotoxic activities of breast cancer cells. This present review mainly speculates an overview of the native medicinal plant derived anti-cancerous compounds with its efficiency, types and pathways involved in breast cancer along with its genes, the mechanism of breast cancer brain metastasis, chemoresistivity and its mechanism, bioinformatics approaches which could be an effective alternative for drug discovery.
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Affiliation(s)
- Vijayakumar Shrihastini
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641062, Tamil Nadu, India; (V.S.); (M.S.)
| | - Pandiyan Muthuramalingam
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641062, Tamil Nadu, India; (V.S.); (M.S.)
- Correspondence: (P.M.); (J.-T.C.)
| | - Sivakumar Adarshan
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; (S.A.); (M.R.)
| | - Mariappan Sujitha
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641062, Tamil Nadu, India; (V.S.); (M.S.)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
- Correspondence: (P.M.); (J.-T.C.)
| | - Hyunsuk Shin
- Department of Horticultural Sciences, Gyeongsang National University, Jinju 52725, Korea;
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; (S.A.); (M.R.)
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16
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Turning Waste into Beneficial Resource: Implication of Ageratum conyzoides L. in Sustainable Agriculture, Environment and Biopharma Sectors. Mol Biotechnol 2021; 64:221-244. [PMID: 34628588 PMCID: PMC8502239 DOI: 10.1007/s12033-021-00409-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/21/2021] [Indexed: 12/14/2022]
Abstract
The annual herb, Ageratum conyzoides L. (Asteraceae), is distributed throughout the world. Although invasive, it can be very useful as a source of essential oils, pharmaceuticals, biopesticides, and bioenergy. However, very limited information exists on the molecular basis of its different utility as previous investigations were mainly focused on phytochemical/biological activity profiling. Here we have explored various properties of A. conyzoides that may offer environmental, ecological, agricultural, and health benefits. As this aromatic plant harbors many important secondary metabolites that may have various implications, biotechnological interventions such as genomics, metabolomics and tissue-culture can be indispensable tools for their mass-production. Further, A. conyzoides acts as a natural reservoir of begomoviruses affecting a wide range of plant species. As the mechanisms of disease spreading and crop infection are not fully clear, whole-genome sequencing and various advanced molecular technologies including RNAi, CRISPER/Cas9, multi-omics approaches, etc., may aid to decipher the molecular mechanism of such disease development and thus, can be useful in crop protection. Overall, improved knowledge of A. conyzoides is not only essential for developing sustainable weed control strategy but can also offer potential ways for biomedicinal, environment, safe and clean agriculture applications.
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Dutta T, Anand U, Saha SC, Mane AB, Prasanth DA, Kandimalla R, Proćków J, Dey A. Advancing urban ethnopharmacology: a modern concept of sustainability, conservation and cross-cultural adaptations of medicinal plant lore in the urban environment. CONSERVATION PHYSIOLOGY 2021; 9:coab073. [PMID: 34548925 PMCID: PMC8448427 DOI: 10.1093/conphys/coab073] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/26/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
The discipline 'urban ethnopharmacology' emerged as a collection of traditional knowledge, ancient civilizations, history and folklore being circulated since generations, usage of botanical products, palaeobotany and agronomy. Non-traditional botanical knowledge increases the availability of healthcare and other essential products to the underprivileged masses. Intercultural medicine essentially involves 'practices in healthcare that bridge indigenous medicine and western medicine, where both are considered as complementary'. A unique aspect of urban ethnopharmacology is its pluricultural character. Plant medicine blossomed due to intercultural interactions and has its roots in major anthropological events of the past. Unani medicine was developed by Khalif Harun Al Rashid and Khalif Al Mansur by translating Greek and Sanskrit works. Similarly, Indo-Aryan migration led to the development of Vedic culture, which product is Ayurveda. Greek medicine reached its summit when it travelled to Egypt. In the past few decades, ethnobotanical field studies proliferated, especially in the developed countries to cope with the increasing demands of population expansion. At the same time, sacred groves continued to be an important method of conservation across several cultures even in the urban aspect. Lack of scientific research, validating the efficiency, messy applications, biopiracy and slower results are the main constrains to limit its acceptability. Access to resources and benefit sharing may be considered as a potential solution. Indigenous communities can copyright their traditional formulations and then can collaborate with companies, who have to provide the original inventors with a fair share of the profits since a significant portion of the health economy is generated by herbal medicine. Search string included the terms 'Urban' + 'Ethnopharmacology', which was searched in Google Scholar to retrieve the relevant literature. The present review aims to critically analyse the global concept of urban ethnopharmacology with the inherent plurality of the cross-cultural adaptations of medicinal plant use by urban people across the world.
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Affiliation(s)
- Tusheema Dutta
- Ethnopharmacology and Natural Product Research Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Suchismita Chatterjee Saha
- Department of Zoology, Nabadwip Vidyasagar College (Affiliated to the University of Kalyani), Nabadwip, West Bengal, 741302, India
| | - Abhijit Bhagwan Mane
- Department of Zoology, Dr. Patangrao Kadam Mahavidyalaya, Sangli, (Affiliated to Shivaji University of Kolhapur), Maharashtra, 416308, India
| | - Dorairaj Arvind Prasanth
- Department of Microbiology, School of Biosciences, Periyar University, Salem, 636011, Tamilnadu, India
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad, 500007, Telangana, India
- Department of Biochemistry, Kakatiya Medical College, Warangal, 506007, Telangana, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland
| | - Abhijit Dey
- Ethnopharmacology and Natural Product Research Laboratory, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
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18
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Liana D, Rungsihirunrat K. Phytochemical screening, antimalarial activities, and genetic relationship of 16 indigenous Thai Asteraceae medicinal plants: A combinatorial approach using phylogeny and ethnobotanical bioprospecting in antimalarial drug discovery. J Adv Pharm Technol Res 2021; 12:254-260. [PMID: 34345604 PMCID: PMC8300331 DOI: 10.4103/japtr.japtr_238_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/22/2021] [Accepted: 04/26/2021] [Indexed: 11/08/2022] Open
Abstract
Emergence of artemisinin resistance leads the people to discover the new candidate for antimalarial drug. Combinatorial phylogeny and ethnobotanical approach may be useful to minimize the expenditure and time in laboratory testing. Seven hundred and thirty-three ethnomedicinal plants were listed from literature search. Obtained 340 internal transcribed spacer (ITS) sequences of plant list which met criteria were retrieved from GenBank NCBI and analyzed by MUSCLE and maximum likelihood phylogenetic test to generate the phylogenetic tree. Interactive phylogenetic tree was generated by Interactive Tree of Life (ITOL, https://itol.embl.de) and showed strong clustered pattern on Asteraceae. Afterward, 16 species of Asteraceae were selected to investigate the antimalarial activity, phytochemical, and genetic diversity. The presence of phytochemical was determined by standard method. DNA fluorescence-based assay was performed to determine the antimalarial activity against 3D7 Plasmodium falciparum. IC50μg/mL was used to categorize antimalarial activity. On the other hand, ITS universal primer was used to amplify and sequence the obtained extracted DNA of tested plant by cetyltrimethylammonium bromide method. Phylogenetic analyses were performed by MAFFT and RAxML with automatic bootstrapping. ITOL and Adobe Illustrator were used to generate interactive phylogenetic tree. All species tested showed the presence of phenolics and flavonoids, whereas alkaloids and terpenoids were shown vary among tested extracts. Among 16 species tested, 1 species exhibited good-moderate (Sphaeranthus indicus, IC506.59 μg/mL), 4 weak (Artemisia chinensis, Artemisia vulgaris, Tridax procumbens, and Blumea balsamifera), and 3 very weak (Eupatorium capillifolium, Wedelia trilobata, and Vernonia cinerea). Generated phylogenetic tree by ITS data was able to separate the tested species into their tribal classification. In addition, new medicinal properties of A. chinensis were discovered. Combining phylogeny approach with ethnobotanical data is useful to narrow down the selection of antimalarial plants candidate.
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Affiliation(s)
- Desy Liana
- Department of Public Health Sciences, College of Public Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanchana Rungsihirunrat
- Department of Public Health Sciences, College of Public Health Sciences, Chulalongkorn University, Bangkok, Thailand
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19
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Ahmad MH, Jatau AI, Alshargi OY, Julde SM, Mohammed M, Muhammad S, Mustapha S, Bala AA, Wada AS, Aminu M, Usman AM. Ethnopharmacological uses, phytochemistry, pharmacology, and toxicology of Olax subscorpioidea Oliv (Olacaceae): a review. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00264-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
The plant Olax subscorpioidea Oliv (Olacaceae) is a shrub that is widely available in Africa. It has been used in traditional medicine to treat various diseases including asthma, pain, inflammation, gastrointestinal and central nervous system (CNS) disorders, cough, diabetes mellitus, cancer, infectious diseases, hepatic diseases, and many other diseases. Several phytochemical and pharmacological investigations were conducted on this plant. However, comprehensive information on this medicinally important plant is not available in the literature. Therefore, in this review, we aimed to provide comprehensive and critical information on all the reported ethnomedicinal uses, phytochemistry, pharmacological activities, and potential toxicity of Olax subscorpioidea to highlight its therapeutic potentials based on traditional usage and identify research gaps as a basis for further investigations to develop novel therapeutic compounds.
Main body
The available information about the plant was retrieved from the online bibliographic databases (PubMed and Google Scholar) and published PhD dissertation using the search terms Olax subscorpioidea, traditional uses, ethnomedicinal uses, phytochemistry, pharmacology, toxicology, and safety. Phytochemical studies have shown that the plant contains several bioactive compounds such as rutin, morin, quercetin, caffeic acid, santalbic acid, n-hexadecanoic acid, squalene, nonacosane, hentriacontane, and many more compounds. Also, pharmacological investigations revealed that Olax subscorpioidea has antidepressant, antiepileptic, anti-Alzheimer’s, cytotoxic, antioxidant, antihyperlipidemic, analgesic, antiinflammatory, antiarthritic, antidiabetic, anticancer, antiulcer, antimicrobial, hepatoprotective, apoptotic, antiprotease, and other CNS effects.
Conclusion
Several pharmacological studies on Olax subscorpioidea have established its ethnopharmacological uses. However, there are limited phytochemical and pharmacological studies to validate other folkloric claims of the plant. Therefore, extensive phytochemical and further pre-clinical efficacy and safety evaluations to fully establish its therapeutic potentials and elucidate its mechanisms of pharmacological actions could be necessary.
Graphical abstract
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20
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Ahammad F, Alam R, Mahmud R, Akhter S, Talukder EK, Tonmoy AM, Fahim S, Al-Ghamdi K, Samad A, Qadri I. Pharmacoinformatics and molecular dynamics simulation-based phytochemical screening of neem plant (Azadiractha indica) against human cancer by targeting MCM7 protein. Brief Bioinform 2021; 22:6217720. [PMID: 33834183 DOI: 10.1093/bib/bbab098] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022] Open
Abstract
Minichromosome maintenance complex component 7 (MCM7) belongs to the minichromosome maintenance family that is important for the initiation of eukaryotic DNA replication. Overexpression of the MCM7 protein is relative to cellular proliferation and responsible for aggressive malignancy in various cancers. Mechanistically, inhibition of MCM7 significantly reduces the cellular proliferation associated with cancer. To date, no effective small molecular candidate has been identified that can block the progression of cancer induced by the MCM7 protein. Therefore, the study has been designed to identify small molecular-like natural drug candidates against aggressive malignancy associated with various cancers by targeting MCM7 protein. To identify potential compounds against the targeted protein a comprehensive in silico drug design including molecular docking, ADME (Absorption, Distribution, Metabolism and Excretion), toxicity, and molecular dynamics (MD) simulation approaches has been applied. Seventy phytochemicals isolated from the neem tree (Azadiractha indica) were retrieved and screened against MCM7 protein by using the molecular docking simulation method, where the top four compounds have been chosen for further evaluation based on their binding affinities. Analysis of ADME and toxicity properties reveals the efficacy and safety of the selected four compounds. To validate the stability of the protein-ligand complex structure MD simulations approach has also been performed to the protein-ligand complex structure, which confirmed the stability of the selected three compounds including CAS ID:105377-74-0, CID:12308716 and CID:10505484 to the binding site of the protein. In the study, a comprehensive data screening process has performed based on the docking, ADMET properties, and MD simulation approaches, which found a good value of the selected four compounds against the targeted MCM7 protein and indicates as a promising and effective human anticancer agent.
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Affiliation(s)
- Foysal Ahammad
- Department of Biological Science, Faculty of science, King Abdul-Aziz University, Jeddah-21589, Saudi Arabia.,Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University and Science and Technology University, Jashore-7408, Bangladesh
| | - Rahat Alam
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University and Science and Technology University, Jashore-7408, Bangladesh
| | - Rasel Mahmud
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail-1902, Bangladesh
| | - Shahina Akhter
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC) Block # D, Floor # 11, Foy's Lake, Khulshi, Chittagong 4202, Bangladesh
| | - Enamul Kabir Talukder
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University and Science and Technology University, Jashore-7408, Bangladesh
| | - Al Mahmud Tonmoy
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Zoology, Institute of Dhaka College, University of Dhaka, Dhaka-1000, Bangladesh
| | - Salman Fahim
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Bachelor of medicine and Bachelor of Surgery (MBBS), CARe Medical College, 2, 1-A Iqbal Road, Dhaka-1207, Bangladesh
| | - Khalid Al-Ghamdi
- Department of Biological Science, Faculty of science, King Abdul-Aziz University, Jeddah-21589, Saudi Arabia
| | - Abdus Samad
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore-7408, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University and Science and Technology University, Jashore-7408, Bangladesh
| | - Ishtiaq Qadri
- Department of Biological Science, Faculty of science, King Abdul-Aziz University, Jeddah-21589, Saudi Arabia
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21
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Khan DA, Hamdani SDA, Iftikhar S, Malik SZ, Zaidi NUSS, Gul A, Babar MM, Ozturk M, Turkyilmaz Unal B, Gonenc T. Pharmacoinformatics approaches in the discovery of drug-like antimicrobials of plant origin. J Biomol Struct Dyn 2021; 40:7612-7628. [PMID: 33663347 DOI: 10.1080/07391102.2021.1894982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Medicinal plants have served as an important source for addressing the ailments of humans and animals alike. The emergence of advanced technologies in the field of drug discovery and development has helped in isolating various bioactive phytochemicals and developing them as drugs. Owing to their significant pharmacological benefits and minimum adverse effects, they not only serve as good candidates for therapeutics themselves but also help in the identification and development of related drug like molecules against various metabolic and infectious diseases. The ever-increasing diversity, severity and incidence of infectious diseases has resulted in an exaggerated mortality and morbidity levels. Geno-proteomic mutations in microbes, irrational prescribing of antibiotics, antimicrobial resistance and human population explosion, all call for continuous efforts to discover and develop alternated therapeutic options against the microbes. This review article describes the pharmacoinformatics tools and methods which are currently used in the discovery of bioactive phytochemicals, thus making the process more efficient and effective. The pharmacological aspects of the drug discovery and development process have also been reviewed with reference to the in silico activities. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Duaa Ahmad Khan
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Syed Damin Abbas Hamdani
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan.,Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Sahar Iftikhar
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Sohaib Zafar Malik
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Najam-Us-Sahar Sadaf Zaidi
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Mustafeez Mujtaba Babar
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Munir Ozturk
- Botany Department and Centre for Environmental Studies, Ege University, Izmir, Turkey
| | - Bengu Turkyilmaz Unal
- Biotechnology Department, Arts & Sciences Faculty, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Tuba Gonenc
- Department of Pharmacognosy, Faculty of Pharmacy, Izmir Katip Çelebi University, Izmir, Turkey
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22
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Rosero A, Granda L, Berdugo-Cely JA, Šamajová O, Šamaj J, Cerkal R. A Dual Strategy of Breeding for Drought Tolerance and Introducing Drought-Tolerant, Underutilized Crops into Production Systems to Enhance Their Resilience to Water Deficiency. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1263. [PMID: 32987964 PMCID: PMC7600178 DOI: 10.3390/plants9101263] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
Water scarcity is the primary constraint on crop productivity in arid and semiarid tropical areas suffering from climate alterations; in accordance, agricultural systems have to be optimized. Several concepts and strategies should be considered to improve crop yield and quality, particularly in vulnerable regions where such environmental changes cause a risk of food insecurity. In this work, we review two strategies aiming to increase drought stress tolerance: (i) the use of natural genes that have evolved over time and are preserved in crop wild relatives and landraces for drought tolerance breeding using conventional and molecular methods and (ii) exploiting the reservoir of neglected and underutilized species to identify those that are known to be more drought-tolerant than conventional staple crops while possessing other desired agronomic and nutritive characteristics, as well as introducing them into existing cropping systems to make them more resilient to water deficiency conditions. In the past, the existence of drought tolerance genes in crop wild relatives and landraces was either unknown or difficult to exploit using traditional breeding techniques to secure potential long-term solutions. Today, with the advances in genomics and phenomics, there are a number of new tools available that facilitate the discovery of drought resistance genes in crop wild relatives and landraces and their relatively easy transfer into advanced breeding lines, thus accelerating breeding progress and creating resilient varieties that can withstand prolonged drought periods. Among those tools are marker-assisted selection (MAS), genomic selection (GS), and targeted gene editing (clustered regularly interspaced short palindromic repeat (CRISPR) technology). The integration of these two major strategies, the advances in conventional and molecular breeding for the drought tolerance of conventional staple crops, and the introduction of drought-tolerant neglected and underutilized species into existing production systems has the potential to enhance the resilience of agricultural production under conditions of water scarcity.
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Affiliation(s)
- Amparo Rosero
- Corporación Colombiana de Investigación Agropecuaria–AGROSAVIA, Centro de Investigación Turipaná, Km 13 vía Montería, 250047 Cereté, Colombia;
| | - Leiter Granda
- Department of Crop Science, Breeding and Plant Medicine, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (L.G.); (R.C.)
| | - Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria–AGROSAVIA, Centro de Investigación Turipaná, Km 13 vía Montería, 250047 Cereté, Colombia;
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (O.Š.); (J.Š.)
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (O.Š.); (J.Š.)
| | - Radim Cerkal
- Department of Crop Science, Breeding and Plant Medicine, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; (L.G.); (R.C.)
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Singh PA, Bajwa N, Naman S, Baldi A. A Review on Robust Computational Approaches Based Identification and Authentication of Herbal Raw Drugs. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817666200304125520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Over the last decade, there has been a sudden rise in the demand for herbal
as well as Information and Technology (IT) industry around the world. Identification of plant
species has become useful and relevant to all the members of the society including farmers, traders,
hikers, etc. Conventional authentication techniques such as morphological characterization,
histological methods, and optical microscopy require multiple skills which are tedious, timeconsuming
and difficult to learn for non-experts. This creates a hurdle for individuals interested in
acquiring knowledge of species. Relying on rapid, economical and computerized approaches to
identify and authenticate medicinal plants has become a recent development.
Objective:
The purpose of this review is to summarize artificial intelligence-based technologies for
wider dissemination of common plant-based knowledge such as identification and authentication
to common people earlier limited to only experts.
Methods:
A robust plant identification design enabling automated plant-organ and feature-based
identification utilizing pattern recognition and image processing techniques resulting in image retrieval
and recognition has been highlighted in this review for all the concerned stakeholders. Attempts
have been made to compare conventional authentication methods with advanced computerized
techniques to emphasize the advantages and future applications of an automated identification
system in countering adulteration and providing fair trade opportunities to farmers.
Results:
Major findings suggested that microscopical features such as shape and size of calcium
oxalate crystals, trichomes, scleriods, stone cells, fibers, etc. are the essential descriptors for identification
and authentication of herbal raw drugs using computational approaches.
Conclusion:
This computational design can be successfully employed to address quality issues of
medicinal plants. Therefore, computational techniques proved as a milestone in the growth of agriculture
and medicinal plant industries.
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Affiliation(s)
- Preet Amol Singh
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda- 151001, Punjab, India
| | - Neha Bajwa
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda- 151001, Punjab, India
| | - Subh Naman
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda- 151001, Punjab, India
| | - Ashish Baldi
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda- 151001, Punjab, India
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Thangavel N, Al Bratty M, Javed SA, Ahsan W, Alhazmi HA. Critical Insight into the Design of PPAR-γ Agonists by Virtual Screening Techniques. Curr Drug Discov Technol 2020; 16:82-90. [PMID: 29493458 DOI: 10.2174/1570163815666180227164028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/20/2018] [Accepted: 02/20/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND Design of novel PPAR-γ modulators with better binding efficiency and fewer side effects to treat type 2 diabetes is still a challenge for medicinal chemists. Cost and time efficient computational methods have presently become an integral part of research in nuclear receptors and their ligands, enabling hit to lead identification and lead optimization. This review will focus on cutting-edge technologies used in most recent studies on the design of PPAR- γ agonists and will discuss the chemistry of few molecules which emerged successful. METHODS Literature review was carried out in google scholar using customized search from 2011- 2017. Computer-aided design methods presented in this article were used as search terms to retrieve corresponding literature. RESULTS Virtual screening of natural product libraries is an effective strategy to harness nature as the source of ligands for PPARs. Rigid and induced fit docking and core hopping approach in docking are rapid screening methods to predict the PPAR- γ and PPAR-α/ γ dual agonistic activity. Onedimensional drug profile matching is one of the recent virtual screening methods by which an antiprotozoal drug, Nitazoxanide was identified as a PPAR- γ agonist. CONCLUSION It is concluded that to achieve a convincing and reliable design of PPAR-γ agonist by virtual screening techniques, customized workflow comprising of appropriate models is essential in which methods may be applied either sequentially or simultaneously.
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Affiliation(s)
- Neelaveni Thangavel
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box. 114, Jazan 45 142, Saudi Arabia
| | - Mohammed Al Bratty
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box. 114, Jazan 45 142, Saudi Arabia
| | - Sadique Akhtar Javed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box. 114, Jazan 45 142, Saudi Arabia
| | - Waquar Ahsan
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box. 114, Jazan 45 142, Saudi Arabia
| | - Hassan A Alhazmi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box. 114, Jazan 45 142, Saudi Arabia
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25
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Sharma V, Gelin LFF, Sarkar IN. Identifying Herbal Adverse Events From Spontaneous Reporting Systems Using Taxonomic Name Resolution Approach. Bioinform Biol Insights 2020; 14:1177932220921350. [PMID: 32595273 PMCID: PMC7297479 DOI: 10.1177/1177932220921350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/01/2020] [Indexed: 12/15/2022] Open
Abstract
The efficacy and safety of herbal supplements suffer from challenges due to non-uniform representation of ingredient terms within biomedical and observational health data sources. The nature of how supplement data are reported within Spontaneous Reporting Systems (SRS) can limit analyses of supplement-associated adverse events due to the use of incorrect nomenclature or failing to identify herbs. This study aimed to extract, standardize, and summarize supplement-relevant reports from two SRSs: (1) Food and Drug Administration Adverse Event Reporting System (FAERS) and (2) Canada Vigilance Adverse Reaction (CVAR) database. A thesaurus of plant names was developed and integrated with a mapping and normalization approach that accommodated misspellings and variants. The reports gathered from FAERS between the years 2004 and 2016 show 185,915 herbal and 7,235,330 non-herbal accounting for 2.51%. The data from CVAR found 36,940 reports of herbal and 503,580 non-herbal reports between the years 1965 and 2017 for a total of 6.83%. Although not all cases were actual adverse events due to numerous variables and incomplete reporting, it is interesting to note that the herbs most frequently reported and significantly associated with adverse events were as follows: Avena sativa (Oats), Cannabis sativa (marijuana), Digitalis purpurea (foxglove), Humulus lupulus (hops), Hypericum perforatum (St John’s Wort), Paullinia cupana (guarana), Phleum pretense (timothy-grass), Silybum marianum (milk thistle), Taraxacum officinale (Dandelion), and Valeriana officinalis (valerian). Using a scalable approach for mapping and resolution of herb names allowed data-driven exploration of potential adverse events from sources that have remained isolated in this specific area of research. The results from this study highlight several herb-associated safety issues providing motivation for subsequent in-depth analyses, including those that focus on the scope and severity of potential safety issues with supplement use.
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Affiliation(s)
- Vivekanand Sharma
- Center for Biomedical Informatics, Brown University, Providence, RI, USA
| | | | - Indra Neil Sarkar
- Center for Biomedical Informatics, Brown University, Providence, RI, USA.,Rhode Island Quality Institute, Providence, RI, USA
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26
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Yuan F, Li K, Zhou C, Zhou H, Liu H, Chai H, Lu F, Zhang H. Identification of two novel highly inducible promoters from Bacillus licheniformis by screening transcriptomic data. Genomics 2020; 112:1866-1871. [DOI: 10.1016/j.ygeno.2019.10.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 07/31/2019] [Accepted: 10/29/2019] [Indexed: 11/26/2022]
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27
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Ma X, Meng Y, Wang P, Tang Z, Wang H, Xie T. Bioinformatics-assisted, integrated omics studies on medicinal plants. Brief Bioinform 2019; 21:1857-1874. [PMID: 32706024 DOI: 10.1093/bib/bbz132] [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] [Received: 07/05/2019] [Revised: 09/03/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein-protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.
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Affiliation(s)
- Xiaoxia Ma
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou 311121, P.R. China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Yijun Meng
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Pu Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Zhonghai Tang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, P.R. China
| | - Huizhong Wang
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, P.R. China
| | - Tian Xie
- Hangzhou Normal University, Hangzhou 311121, P.R. China.,Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou 311121, P.R. China.,Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, P.R. China
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28
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Neelawala D, Rajapakse S, Kumbukgolla WW. Potential of medicinal plants to treat dengue. INTERNATIONAL JOURNAL OF ONE HEALTH 2019. [DOI: 10.14202/ijoh.2019.86-91] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Dengue is a major public health challenge worldwide, particularly in tropical areas. Nearly 390 million infections and 22,000 deaths occur every year. At present, there are no specific therapeutics available to treat dengue; however, possible treatment procedures are explained in the traditional medical systems (TMSs), such as Sri Lankan TMS, Indian Ayurvedic, Unani, and Siddha TMS. In these TMSs, medicinal plants have been used in several ways against dengue, such as virocides, larvicides, and mosquito repellents. Therefore, medicinal plants inherit biologically active compounds/lead compounds that are yet to be identified chemically and physiologically. Herein, we discuss the possible applications of crude plant extracts and isolated phytochemicals from medicinal plants such as quercetin, sulfated galactomannans, flavonoids, and glabranine in controlling dengue. Moreover, medicinal plant-based therapeutics can be safer, cost-effective, and non-toxic. Therefore, this paper reviews the medicinal plants that are used in TMSs to manage dengue, the phytochemicals they contain, and mode of action of these phytochemicals such as virocides, larvicides, and mosquito repellents.
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Affiliation(s)
- Dulanjalee Neelawala
- Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Anuradhapura 50000, Sri Lanka
| | - Sanjaya Rajapakse
- Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Anuradhapura 50000, Sri Lanka
| | - Wikum Widuranga Kumbukgolla
- Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Anuradhapura 50000, Sri Lanka
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29
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Liu L, Wang H. The Recent Applications and Developments of Bioinformatics and Omics Technologies in Traditional Chinese Medicine. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190102125403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background:Traditional Chinese Medicine (TCM) is widely utilized as complementary health care in China whose acceptance is still hindered by conventional scientific research methodology, although it has been exercised and implemented for nearly 2000 years. Identifying the molecular mechanisms, targets and bioactive components in TCM is a critical step in the modernization of TCM because of the complexity and uniqueness of the TCM system. With recent advances in computational approaches and high throughput technologies, it has become possible to understand the potential TCM mechanisms at the molecular and systematic level, to evaluate the effectiveness and toxicity of TCM treatments. Bioinformatics is gaining considerable attention to unearth the in-depth molecular mechanisms of TCM, which emerges as an interdisciplinary approach owing to the explosive omics data and development of computer science. Systems biology, based on the omics techniques, opens up a new perspective which enables us to investigate the holistic modulation effect on the body.Objective:This review aims to sum up the recent efforts of bioinformatics and omics techniques in the research of TCM including Systems biology, Metabolomics, Proteomics, Genomics and Transcriptomics.Conclusion:Overall, bioinformatics tools combined with omics techniques have been extensively used to scientifically support the ancient practice of TCM to be scientific and international through the acquisition, storage and analysis of biomedical data.
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Affiliation(s)
- Lin Liu
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| | - Hao Wang
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
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30
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Malik A, Arooj M, Butt TT, Zahid S, Zahid F, Jafar TH, Waquar S, Gan SH, Ahmad S, Mirza MU. In silico and in vivo characterization of cabralealactone, solasodin and salvadorin in a rat model: potential anti-inflammatory agents. DRUG DESIGN DEVELOPMENT AND THERAPY 2018; 12:1431-1443. [PMID: 29872266 PMCID: PMC5973396 DOI: 10.2147/dddt.s154169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background The present study investigates the hepato- and DNA-protective effects of standardized extracts of Cleome brachycarpa (cabralealactone), Solanum incanum (solasodin), and Salvadora oleioides (salvadorin) in rats. Materials and methods Hepatotoxicity was induced with intraperitoneal injection of carbon tetrachloride (CCl4) (1 mL/kg b.wt.) once a week for 12 weeks. The hepato- and DNA protective effects of the extracts in different combinations were compared with that of a standard drug Clavazin (200 mg/kg b.wt.). Tissue alanine aminotransferase, alpha-fetoprotein, tumor necrosis factor alpha (TNF-α), isoprostanes-2α, malondialdehyde, and 8-hydroxydeoxyguanosine, the significant hallmarks of oxidative stress, were studied. Results Histopathological findings of the liver sections from the rat group which received CCl4+cabralealactone, solasodin, and salvadorin demonstrated improved centrilobular hepatocyte regeneration with moderate areas of congestion and infiltration comparable with Clavazin. For in silico study, the identified compounds were subjected to molecular docking with cyclooxygenase-2 and TNF-α followed by a molecular dynamics study, which indicated their potential as anti-inflammatory agents. Conclusion Cabralealactone, solasodin, and salvadorin confer some hepatoprotective and DNA-damage protective effects against CCl4-induced toxicity. They successfully restored the normal architecture of hepatocytes and have the potential to be used as inhibitor to main culprits, that is, cyclooxygenase-2 and TNF-α. They can combat oxidative stress and liver injuries both as mono and combinational therapies. However, combination therapy has more ameliorating effects.
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Affiliation(s)
- Arif Malik
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore, Pakistan
| | - Mahwish Arooj
- University College of Medicine and Dentistry (UCMD), University of Lahore, Lahore, Pakistan
| | | | - Sara Zahid
- Faculty of Pharmacy, University of Lahore, Lahore, Pakistan
| | - Fatima Zahid
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore, Pakistan
| | - Tassadaq Hussain Jafar
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore, Pakistan
| | - Sulayman Waquar
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore, Pakistan
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Subang Jaya, Malaysia
| | - Sarfraz Ahmad
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore, Pakistan
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
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31
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Buenz EJ, Verpoorte R, Bauer BA. The Ethnopharmacologic Contribution to Bioprospecting Natural Products. Annu Rev Pharmacol Toxicol 2018; 58:509-530. [DOI: 10.1146/annurev-pharmtox-010617-052703] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eric J. Buenz
- Nelson Marlborough Institute of Technology, Nelson 7010, New Zealand
| | - Rob Verpoorte
- Natural Products Laboratory, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
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32
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Yea SJ, Kim BY, Kim C, Yi MY. A framework for the targeted selection of herbs with similar efficacy by exploiting drug repositioning technique and curated biomedical knowledge. JOURNAL OF ETHNOPHARMACOLOGY 2017; 208:117-128. [PMID: 28687508 DOI: 10.1016/j.jep.2017.06.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
ETHNO PHARMACOLOGICAL RELEVANCE Plants have been the most important natural resources for traditional medicine and for the modern pharmaceutical industry. They have been in demand in regards to finding alternative medicinal herbs with similar efficacy. Due to the very low probability of discovering useful compounds by random screening, researchers have advocated for using targeted selection approaches. Furthermore, because drug repositioning can speed up the process of drug development, an integrated technique that exploits chemical, genetic, and disease information has been recently developed. Building upon these findings, in this paper, we propose a novel framework for the targeted selection of herbs with similar efficacy by exploiting drug repositioning technique and curated modern scientific biomedical knowledge, with the goal of improving the possibility of inferring the traditional empirical ethno-pharmacological knowledge. MATERIALS AND METHODS To rank candidate herbs on the basis of similarities against target herb, we proposed and evaluated a framework that is comprised of the following four layers: links, extract, similarity, and model. In the framework, multiple databases are linked to build an herb-compound-protein-disease network which was composed of one tripartite network and two bipartite networks allowing comprehensive and detailed information to be extracted. Further, various similarity scores between herbs are calculated, and then prediction models are trained and tested on the basis of theses similarity features. RESULTS The proposed framework has been found to be feasible in terms of link loss. Out of the 50 similarities, the best one enhanced the performance of ranking herbs with similar efficacy by about 120-320% compared with our previous study. Also, the prediction model showed improved performance by about 180-480%. While building the prediction model, we identified the compound information as being the most important knowledge source and structural similarity as the most useful measure. CONCLUSIONS In the proposed framework, we took the knowledge of herbal medicine, chemistry, biology, and medicine into consideration to rank herbs with similar efficacy in candidates. The experimental results demonstrated that the performances of framework outperformed the baselines and identified the important knowledge source and useful similarity measure.
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Affiliation(s)
- Sang-Jun Yea
- Graduate School of Knowledge Service Engineering, Korea Advanced Institute of Science and Technology, Republic of Korea; K-herb Research Center, Korea Institute of Oriental Medicine, Republic of Korea
| | - Bu-Yeo Kim
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Republic of Korea
| | - Chul Kim
- K-herb Research Center, Korea Institute of Oriental Medicine, Republic of Korea.
| | - Mun Yong Yi
- Graduate School of Knowledge Service Engineering, Korea Advanced Institute of Science and Technology, Republic of Korea.
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Silva RHM, Lima NDFM, Lopes AJO, Vasconcelos CC, de Mesquita JWC, de Mesquita LSS, Lima FCVM, Ribeiro MNDS, Ramos RM, Cartágenes MDSDS, Garcia JBS. Antinociceptive Activity of Borreria verticillata: In vivo and In silico Studies. Front Pharmacol 2017; 8:283. [PMID: 28588488 PMCID: PMC5439013 DOI: 10.3389/fphar.2017.00283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/04/2017] [Indexed: 01/08/2023] Open
Abstract
Borreria verticillata (L.) G. Mey. known vassourinha has antibacterial, antimalarial, hepatoprotective, antioxidative, analgesic, and anti-inflammatory, however, its antinociceptive action requires further studies. Aim of the study evaluated the antinociceptive activity of B. verticillata hydroalcoholic extract (EHBv) and ethyl acetate fraction (FAc) by in vivo and in silico studies. In vivo assessment included the paw edema test, writhing test, formalin test and tail flick test. Wistar rats and Swiss mice were divided into 6 groups and given the following treatments oral: 0.9% NaCl control group (CTRL), 10 mg/kg memantine (MEM), 10 mg/kg indomethacin (INDO), 500 mg/kg EHBv (EHBv 500), 25 mg/kg FAc (FAc 25) and 50 mg/kg FAc (FAc 50). EHBv, FAc 25 and 50 treatments exhibited anti-edematous and peripheral antinociceptive effects. For in silico assessment, compounds identified in FAc were subjected to molecular docking with COX-2, GluN1a and GluN2B. Ursolic acid (UA) was the compound with best affinity parameters (binding energy and inhibition constant) for COX-2, GluN1a, GluN2B, and was selected for further analysis with molecular dynamics (MD) simulations. In MD simulations, UA exhibited highly frequent interactions with residues Arg120 and Glu524 in the COX-2 active site and NMDA, whereby it might prevent COX-2 and NMDA receptor activation. Treatment with UA 10 mg/Kg showed peripheral and central antinociceptive effect. The antinociceptive effect of B. verticillata might be predominantly attributed to peripheral actions, including the participation of anti-inflammatory components. Ursolic acid is the main active component and seems to be a promising source of COX-2 inhibitors and NMDA receptor antagonists.
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Affiliation(s)
- Rosa H M Silva
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - Nathália de Fátima M Lima
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - Alberto J O Lopes
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - Cleydlenne C Vasconcelos
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - José W C de Mesquita
- Laboratory of Pharmacognosy, Department of Pharmacy, Federal University of MaranhãoSão Luís, Brazil
| | - Ludmilla S S de Mesquita
- Laboratory of Pharmacognosy, Department of Pharmacy, Federal University of MaranhãoSão Luís, Brazil
| | - Fernando C V M Lima
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - Maria N de S Ribeiro
- Laboratory of Pharmacognosy, Department of Pharmacy, Federal University of MaranhãoSão Luís, Brazil
| | - Ricardo M Ramos
- Research Laboratory Information Systems, Department of Information, Environment, Health and Food Production, Federal Institute of PiauíTeresina, Brazil
| | | | - João B S Garcia
- Experimental Study of Pain Laboratory, Department of Pain and Palliative Care, Federal University of MaranhãoSão Luís, Brazil
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Guo Q, Zheng K, Fan D, Zhao Y, Li L, Bian Y, Qiu X, Liu X, Zhang G, Ma C, He X, Lu A. Wu-Tou Decoction in Rheumatoid Arthritis: Integrating Network Pharmacology and In Vivo Pharmacological Evaluation. Front Pharmacol 2017; 8:230. [PMID: 28515692 PMCID: PMC5414545 DOI: 10.3389/fphar.2017.00230] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 04/12/2017] [Indexed: 12/22/2022] Open
Abstract
Purpose: This study aimed to explore underlying action mechanism of Wu-Tou decoction (WTD) in rheumatoid arthritis (RA) through network pharmacology prediction and experimental verification. Methods: Chemical compounds and human target proteins of WTD as well as RA-related human genes were obtained from TCM Database @ Taiwan, PubChem and GenBank, respectively. Subsequently, molecular networks and canonical pathways presumably involved in the treatment of WTD on RA were generated by ingenuity pathway analysis (IPA) software. Furthermore, experimental validation was carried out with MIP-1β-induced U937 cell model and collagen induced arthritis (CIA) rat model. Results: CCR5 signaling pathway in macrophages was shown to be the top one shared signaling pathway associated with both cell immune response and cytokine signaling. In addition, protein kinase C (PKC) δ and p38 in this pathway were treated as target proteins of WTD in RA. In vitro experiments indicated that WTD inhibited MIP-1β-induced production of TNF-α, MIP-1α, and RANTES as well as phosphorylation of CCR5, PKC δ, and p38 in U937 cells. WTD treatment maintained the inhibitory effects on production of TNF-α and RANTES in MIP-1β-induced U937 cells after CCR5 knockdown. In vivo experiments demonstrated that WTD ameliorated symptoms in CIA rats, decreased the levels of IL-1β, IL-2, IL-6, TNF-α, MIP-1α, MIP-2, RANTES, and IP-10 in serum of CIA rats, as well as mRNA levels of MIP-1α, MIP-2, RANTES, and IP-10 in ankle joints of CIA rats. Furthermore, WTD also lowered the phosphorylation levels of CCR5, PKC δ and p38 in both ankle joints and macrophages in ankle joints from CIA rats. Conclusion: It was demonstrated in this research that WTD played a role in inhibiting inflammatory response in RA which was closely connected with the modulation effect of WTD on CCR5 signaling pathway in macrophages.
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Affiliation(s)
- Qingqing Guo
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical SciencesBeijing, China
| | - Kang Zheng
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist UniversityKowloon Tong, Hong Kong
| | - Danping Fan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical SciencesBeijing, China
| | - Yukun Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical SciencesBeijing, China.,School of Basic Medical Sciences, Shanghai University of Traditional Chinese MedicineShanghai, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical SciencesBeijing, China
| | - Yanqin Bian
- School of Basic Medical Sciences, Shanghai University of Traditional Chinese MedicineShanghai, China
| | - Xuemei Qiu
- School of Life Science and Engineering, Southwest Jiaotong UniversityChengdu, China
| | - Xue Liu
- School of Life Science and Engineering, Southwest Jiaotong UniversityChengdu, China
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist UniversityKowloon Tong, Hong Kong
| | - Chaoying Ma
- School of Life Science and Engineering, Southwest Jiaotong UniversityChengdu, China
| | - Xiaojuan He
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical SciencesBeijing, China.,Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist UniversityKowloon Tong, Hong Kong
| | - Aiping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist UniversityKowloon Tong, Hong Kong.,School of Basic Medical Sciences, Shanghai University of Traditional Chinese MedicineShanghai, China
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Zhang H, Ma S, Feng Z, Wang D, Li C, Cao Y, Chen X, Liu A, Zhu Z, Zhang J, Zhang G, Chai Y, Wang L, Xie XQ. Cardiovascular Disease Chemogenomics Knowledgebase-guided Target Identification and Drug Synergy Mechanism Study of an Herbal Formula. Sci Rep 2016; 6:33963. [PMID: 27678063 PMCID: PMC5039409 DOI: 10.1038/srep33963] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/25/2016] [Indexed: 12/14/2022] Open
Abstract
Combination therapy is a popular treatment for various diseases in the clinic. Among the successful cases, Traditional Chinese Medicinal (TCM) formulae can achieve synergistic effects in therapeutics and antagonistic effects in toxicity. However, characterizing the underlying molecular synergisms for the combination of drugs remains a challenging task due to high experimental expenses and complication of multicomponent herbal medicines. To understand the rationale of combination therapy, we investigated Sini Decoction, a well-known TCM consisting of three herbs, as a model. We applied our established diseases-specific chemogenomics databases and our systems pharmacology approach TargetHunter to explore synergistic mechanisms of Sini Decoction in the treatment of cardiovascular diseases. (1) We constructed a cardiovascular diseases-specific chemogenomics database, including drugs, target proteins, chemicals, and associated pathways. (2) Using our implemented chemoinformatics tools, we mapped out the interaction networks between active ingredients of Sini Decoction and their targets. (3) We also in silico predicted and experimentally confirmed that the side effects can be alleviated by the combination of the components. Overall, our results demonstrated that our cardiovascular disease-specific database was successfully applied for systems pharmacology analysis of a complicated herbal formula in predicting molecular synergetic mechanisms, and led to better understanding of a combinational therapy.
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Affiliation(s)
- Hai Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Dongyao Wang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Chengjian Li
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Yan Cao
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Xiaofei Chen
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Aijun Liu
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Zhenyu Zhu
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Junping Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Guoqing Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Yifeng Chai
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Sharma V, Law W, Balick MJ, Sarkar IN. Identifying Plant-Human Disease Associations in Biomedical Literature: A Case Study. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2016; 2016:84-93. [PMID: 27595045 PMCID: PMC5009952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The impact of ethnobotanical data from surveys of traditional medicinal uses ofplants can be enhanced through the validation of biomedical knowledge that may be embedded in literature. This study aimed to explore the use of informatics approaches, including natural language processing and terminology resources, for extracting and comparing ethnobotanical leads from biomedical literature indexed in MEDLINE. Using ethnobotanical data for plant species described in Primary Health Care Manuals of the Micronesian islands of Palau and Pohnpei, the results of this study were done relative to disease concepts from the "Mental, Behavioral And Neurodevelopmental Disorders " ICD-9-CM category. The results from this feasibility study suggest that informatics methods can be used to extract and prioritize relevant ethnobotanical information from biomedical knowledge literature.
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Affiliation(s)
- Vivekanand Sharma
- Center for Biomedical Informatics, Brown University, Providence, RI USA
| | - Wayne Law
- Institute of Economic Botany, The New York Botanical Garden, Bronx, NY USA
| | - Michael J. Balick
- Institute of Economic Botany, The New York Botanical Garden, Bronx, NY USA
| | - Indra Neil Sarkar
- Center for Biomedical Informatics, Brown University, Providence, RI USA
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Sneha P, Doss CGP. Molecular Dynamics: New Frontier in Personalized Medicine. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 102:181-224. [PMID: 26827606 DOI: 10.1016/bs.apcsb.2015.09.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine.
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Affiliation(s)
- P Sneha
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - C George Priya Doss
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India.
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Sheth BP, Thaker VS. Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses. Pharmacogn Mag 2015; 11:S570-4. [PMID: 27013796 PMCID: PMC4787090 DOI: 10.4103/0973-1296.172963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. OBJECTIVE To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. MATERIALS AND METHODS The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. RESULTS The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. CONCLUSION A strategy as used here, incorporating the integrated use of DNA barcoding and protein structural analyses could be adopted, as a novel rapid and economic procedure, especially in cases when protein coding loci are considered. SUMMARY Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. A herbal powder was obtained from a herbalist in the local vicinity of Rajkot, Gujarat. An integrated approach using DNA barcoding and structural analyses was carried out to identify the herbal powder. The herbal powder was identified as Cassia javanica L.
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Affiliation(s)
- Bhavisha P. Sheth
- Department of Biosciences, Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Saurashtra University, Rajkot, Gujarat, India
| | - Vrinda S. Thaker
- Department of Biosciences, Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Saurashtra University, Rajkot, Gujarat, India
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de Carvalho Nilo Bitu V, de Carvalho Nilo Bitu V, Matias EFF, de Lima WP, da Costa Portelo A, Coutinho HDM, de Menezes IRA. Ethnopharmacological study of plants sold for therapeutic purposes in public markets in Northeast Brazil. JOURNAL OF ETHNOPHARMACOLOGY 2015; 172:265-72. [PMID: 26099635 DOI: 10.1016/j.jep.2015.06.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/13/2015] [Accepted: 06/14/2015] [Indexed: 05/27/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Studies of ethnobiological nature favor the rescue of popular culture, preventing important cultural and biological information from being lost over time. Another interesting point is that it can support bioprospecting studies focusing on the discovery of new drugs. OBJECTIVE OF THE STUDY Our aim was to conduct a survey of plants sold for therapeutic purposes in public markets in the Crajubar Triangle in Northeast Brazil. MATERIALS AND METHODS Using a questionnaire, data were collected regarding the part of the plant used, method of preparation, quantity needed, instructions for use and known adverse effects. From the data obtained, we calculated the relative importance of species and informant consensus factor. RESULTS Vendors indicated 91 useful species from a therapeutic point of view, distributed in 49 plant families. The preparation methods most frequently mentioned by informants were decoction, infusion, sauce with part of the plant in water and lozenge. The informants of this study mentioned bark, leaves, seeds and roots as parts of the plant most sold for therapeutic use. Disorders of the digestive system was the disease/disorder category with the highest consensus among the vendors, and the species Ximenia americana, Lippia gracillis, Stryphnodendron rotundifolium, Anacardium occidentale, Hymenaea courbail, Myracrodruon urundeuva, Amburana cearensis and Himatanthus drasticus were the most versatile among the plants sold in markets. CONCLUSIONS Vendors indicated 91 species belonging to 49 botanical families and 89 genera. The most frequent forms of preparation were decoction, infusion and sauce made with part of the plant in water. The most common form of administration was oral. Bark and leaves were the plant parts most used. Thirteen species showed great versatility regarding their use. We noted 291 indications for use in 13 disease/disorder categories.
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Affiliation(s)
- Vanessa de Carvalho Nilo Bitu
- Faculdade de Ciências Aplicadas Doutor Leão Sampaio, Lab. Bioquímica/Fisiologia, Avenida Leão Sampaio, Km 03 - Lagoa Seca, Juazeiro CEP 63180-000, Ceará, Brasil
| | - Valdeneide de Carvalho Nilo Bitu
- Faculdade de Ciências Aplicadas Doutor Leão Sampaio, Lab. Bioquímica/Fisiologia, Avenida Leão Sampaio, Km 03 - Lagoa Seca, Juazeiro CEP 63180-000, Ceará, Brasil
| | - Edinardo Fagner Ferreira Matias
- Faculdade de Ciências Aplicadas Doutor Leão Sampaio, Lab. Bioquímica/Fisiologia, Avenida Leão Sampaio, Km 03 - Lagoa Seca, Juazeiro CEP 63180-000, Ceará, Brasil
| | - Wenderson Pinheiro de Lima
- Faculdade de Ciências Aplicadas Doutor Leão Sampaio, Lab. Bioquímica/Fisiologia, Avenida Leão Sampaio, Km 03 - Lagoa Seca, Juazeiro CEP 63180-000, Ceará, Brasil
| | - Aline da Costa Portelo
- Faculdade de Ciências Aplicadas Doutor Leão Sampaio, Lab. Bioquímica/Fisiologia, Avenida Leão Sampaio, Km 03 - Lagoa Seca, Juazeiro CEP 63180-000, Ceará, Brasil
| | - Henrique Douglas Melo Coutinho
- Faculdade de Ciências Aplicadas Doutor Leão Sampaio, Lab. Bioquímica/Fisiologia, Avenida Leão Sampaio, Km 03 - Lagoa Seca, Juazeiro CEP 63180-000, Ceará, Brasil
| | - Irwin Rose Alencar de Menezes
- Universidade Regional do Cariri, Departamento de Química Biológica, Laboratório de Farmacologia e Química Molecular (LFQM), Rua Coronel Antonio Luiz s/n, Pimenta, Crato CEP 63106-100, Ceará, Brasil
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Herb Network Analysis for a Famous TCM Doctor's Prescriptions on Treatment of Rheumatoid Arthritis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 2015:451319. [PMID: 25983850 PMCID: PMC4423032 DOI: 10.1155/2015/451319] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 12/29/2022]
Abstract
Traditional Chinese Medicine (TCM) doctors always prescribe various herbal formulae tailored to individual patients. However, there is still a lack of appropriate methods to study the rule and potential biological basis underlying the numerous prescriptions. Here we developed an Herb-Compound-Target-Disease coherent network approach to analyze 871 herbal prescriptions from a TCM master, Mr. Ji-Ren Li, in his clinical practice on treatment of rheumatoid arthritis (RA). The core herb networks were extracted from Mr. Li's prescriptions. Then, we predicted target profiles of compounds in core herb networks and calculated potential synergistic activities among them. We further found that the target sets of core herbs overlapped significantly with the RA related biological processes and pathways. Moreover, we detected a possible connection between the prescribed herbs with different properties such as Cold and Hot and the Western drugs with different actions such as immunomodulatory and hormone regulation on treatment of RA. In summary, we explored a new application of TCM network pharmacology on the analysis of TCM prescriptions and detected the networked core herbs, their potential synergistic and biological activities, and possible connections with drugs. This work offers a novel way to understand TCM prescriptions in clinical practice.
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Zhang C, Jiang M, Zhang G, Bian ZX, Lu AP. Progress and perspectives of biomarker discovery in Chinese medicine research. Chin J Integr Med 2014. [PMID: 25182156 DOI: 10.1007/s11655-014-1848-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Indexed: 10/24/2022]
Abstract
Biomarker discovery in Chinese medicine (CM) has recently attracted a great deal of attention, owing to the promise of high-throughput technologies development and the potential of Chinese herbal medicine. Furthermore, it seems that pattern classification in CM might be serving as inspirational analogy and a practical guide, which might contribute to biomarkers discovery rather than just being used as diagnostic method. Although much work is still needed to identify markers, efforts are now being directed towards discovering biomarkers or biomarkers based network that could target herbal formulae. In this article, we review progress in biomarker discovery development, discuss current biomarker discovery in CM highlighting challenges and opportunities of pattern classification and presenting a perspective of the future integrative modeling approaches as an emerging trend in biomarker discovery.
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Affiliation(s)
- Chi Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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The first set of expressed sequence tags (EST) from the medicinal mushroom Agaricus subrufescens delivers resource for gene discovery and marker development. Appl Microbiol Biotechnol 2014; 98:7879-92. [PMID: 24917377 DOI: 10.1007/s00253-014-5844-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
Agaricus subrufescens is one of the most important culinary-medicinal cultivable mushrooms with potentially high-added-value products and extended agronomical valorization. The development of A. subrufescens-related technologies is hampered by, among others, the lack of suitable molecular tools. Thus, this mushroom is considered as a genomic orphan species with a very limited number of available molecular markers or sequences. To fill this gap, this study reports the generation and analysis of the first set of expressed sequence tags (EST) for A. subrufescens. cDNA fragments obtained from young sporophores (SP) and vegetative mycelium in liquid culture (CL) were sequenced using 454 pyrosequencing technology. After assembly process, 4,989 and 5,125 sequences were obtained in SP and CL libraries, respectively. About 87% of the EST had significant similarity with Agaricus bisporus-predicted proteins, and 79% correspond to known proteins. Functional categorization according to Gene Ontology could be assigned to 49% of the sequences. Some gene families potentially involved in bioactive compound biosynthesis could be identified. A total of 232 simple sequence repeats (SSRs) were identified, and a set of 40 EST-SSR polymorphic markers were successfully developed. This EST dataset provides a new resource for gene discovery and molecular marker development. It constitutes a solid basis for further genetic and genomic studies in A. subrufescens.
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Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level. PLoS Comput Biol 2014; 10:e1003432. [PMID: 24453957 PMCID: PMC3894162 DOI: 10.1371/journal.pcbi.1003432] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/20/2013] [Indexed: 02/02/2023] Open
Abstract
Awareness that disease susceptibility is not only dependent on genetic make up, but can be affected by lifestyle decisions, has brought more attention to the role of diet. However, food is often treated as a black box, or the focus is limited to few, well-studied compounds, such as polyphenols, lipids and nutrients. In this work, we applied text mining and Naïve Bayes classification to assemble the knowledge space of food-phytochemical and food-disease associations, where we distinguish between disease prevention/amelioration and disease progression. We subsequently searched for frequently occurring phytochemical-disease pairs and we identified 20,654 phytochemicals from 16,102 plants associated to 1,592 human disease phenotypes. We selected colon cancer as a case study and analyzed our results in three directions; i) one stop legacy knowledge-shop for the effect of food on disease, ii) discovery of novel bioactive compounds with drug-like properties, and iii) discovery of novel health benefits from foods. This works represents a systematized approach to the association of food with health effect, and provides the phytochemical layer of information for nutritional systems biology research. Until recently diet was considered a supplier of energy and building blocks for growth and development. However, current research in the field suggests that the complex mixture of natural compounds present in our food has a variety of biological activities and plays an important role for health maintenance and disease prevention. The mixture of bioactive components of our diet interacts with the human body through complex processes that modify network function and stability. In order to increase our limited understanding on how components of food affect human health, we borrow methods that are well established in medical and pharmacological research. By using text mining in PubMed abstracts we collected more than 20,000 diverse chemical structures present in our diet, while by applying chemoinformatics methods we could systematically explore their numerous targets. Integrating the above datasets with food-disease associations allowed us to use a statistical framework for identifying specific phytochemicals as perturbators of drug targets and disease related pathways.
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Gu P, Chen H. Modern bioinformatics meets traditional Chinese medicine. Brief Bioinform 2013; 15:984-1003. [DOI: 10.1093/bib/bbt063] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Sharma V, Sarkar IN. Leveraging biodiversity knowledge for potential phyto-therapeutic applications. J Am Med Inform Assoc 2013; 20:668-79. [PMID: 23518859 PMCID: PMC3721164 DOI: 10.1136/amiajnl-2012-001445] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/02/2013] [Accepted: 03/02/2013] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE To identify and highlight the feasibility, challenges, and advantages of providing a cross-domain pipeline that can link relevant biodiversity information for phyto-therapeutic assessment. MATERIALS AND METHODS A public repository of clinical trials information (ClinicalTrials.gov) was explored to determine the state of plant-based interventions under investigation. RESULTS The results showed that ≈ 15% of drug interventions in ClinicalTrials.gov were potentially plant related, with about 60% of them clustered within 10 taxonomic families. Further analysis of these plant-based interventions identified ≈ 3.7% of associated plant species as endangered as determined from the International Union for the Conservation of Nature Red List. DISCUSSION The diversity of the plant kingdom has provided human civilization with life-sustaining food and medicine for centuries. There has been renewed interest in the investigation of botanicals as sources of new drugs, building on traditional knowledge about plant-based medicines. However, data about the plant-based biodiversity potential for therapeutics (eg, based on genetic or chemical information) are generally scattered across a range of sources and isolated from contemporary pharmacological resources. This study explored the potential to bridge biodiversity and biomedical knowledge sources. CONCLUSIONS The findings from this feasibility study suggest that there is an opportunity for developing plant-based drugs and further highlight taxonomic relationships between plants that may be rich sources for bioprospecting.
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Affiliation(s)
- Vivekanand Sharma
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Indra Neil Sarkar
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
- Biomedical Informatics Unit, Center for Clinical and Translational Science, University of Vermont, Burlington, Vermont, USA
- Department of Computer Science, University of Vermont, Burlington, Vermont, USA
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Leveraging concept-based approaches to identify potential phyto-therapies. J Biomed Inform 2013; 46:602-14. [PMID: 23665360 DOI: 10.1016/j.jbi.2013.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 04/24/2013] [Accepted: 04/25/2013] [Indexed: 02/04/2023]
Abstract
The potential of plant-based remedies has been documented in both traditional and contemporary biomedical literature. Such types of text sources may thus be sources from which one might identify potential plant-based therapies ("phyto-therapies"). Concept-based analytic approaches have been shown to uncover knowledge embedded within biomedical literature. However, to date there has been limited attention towards leveraging such techniques for the identification of potential phyto-therapies. This study presents concept-based analytic approaches for the retrieval and ranking of associations between plants and human diseases. Focusing on identification of phyto-therapies described in MEDLINE, both MeSH descriptors used for indexing and MetaMap inferred UMLS concepts are considered. Furthermore, the identification and ranking consider both direct (i.e., plant concepts directly correlated with disease concepts) and inferred (i.e., plant concepts associated with disease concepts based on shared signs and symptoms) relationships. Based on the two scoring methodologies used in this study, it was found that a Vector Space Model approach outperformed probabilistic reliability based inferences. An evaluation of the approach is provided based on therapeutic interventions catalogued in both ClinicalTrials.gov and NDF-RT. The promising findings from this feasibility study highlight the challenges and applicability of concept-based analytic strategies for distilling phyto-therapeutic knowledge from text based knowledge sources like MEDLINE.
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