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Jia XN, Wang WJ, Yin B, Zhou LJ, Zhen YQ, Zhang L, Zhou XL, Song HN, Tang Y, Gao F. Deep Learning Promotes the Screening of Natural Products with Potential Microtubule Inhibition Activity. ACS OMEGA 2022; 7:28334-28341. [PMID: 35990425 PMCID: PMC9386835 DOI: 10.1021/acsomega.2c02854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Natural microtubule inhibitors, such as paclitaxel and ixabepilone, are key sources of novel medications, which have a considerable influence on anti-tumor chemotherapy. Natural product chemists have been encouraged to create novel methodologies for screening the new generation of microtubule inhibitors from the enormous natural product library. There have been major advancements in the use of artificial intelligence in medication discovery recently. Deep learning algorithms, in particular, have shown promise in terms of swiftly screening effective leads from huge compound libraries and producing novel compounds with desirable features. We used a deep neural network to search for potent β-microtubule inhibitors in natural goods. Eleutherobin, bruceine D (BD), and phorbol 12-myristate 13-acetate (PMA) are three highly effective natural compounds that have been found as β-microtubule inhibitors. In conclusion, this paper describes the use of deep learning to screen for effective β-microtubule inhibitors. This research also demonstrates the promising possibility of employing deep learning to develop drugs from natural products for a wider range of disorders.
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Affiliation(s)
- Xiao-Nan Jia
- School
of Life Science and Engineering, Southwest
Jiaotong University, Chengdu 610031, PR China
| | - Wei-Jia Wang
- School
of Computer Science and Engineering, University
of Electronic Science and Technology of China, Chengdu 610054, PR China
| | - Bo Yin
- School
of Life Science and Engineering, Southwest
Jiaotong University, Chengdu 610031, PR China
| | - Lin-Jing Zhou
- School
of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu 610054, PR China
| | - Yong-Qi Zhen
- School
of Life Science and Engineering, Southwest
Jiaotong University, Chengdu 610031, PR China
| | - Lan Zhang
- School
of Life Science and Engineering, Southwest
Jiaotong University, Chengdu 610031, PR China
| | - Xian-Li Zhou
- School
of Life Science and Engineering, Southwest
Jiaotong University, Chengdu 610031, PR China
| | - Hai-Ning Song
- Department
of Pharmacy, The Third People’s Hospital of Chengdu and College
of Medicine, Southwest Jiaotong University, Chengdu 610031, PR China
| | - Yong Tang
- School
of Computer Science and Engineering, University
of Electronic Science and Technology of China, Chengdu 610054, PR China
| | - Feng Gao
- School
of Life Science and Engineering, Southwest
Jiaotong University, Chengdu 610031, PR China
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2
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Wu YJ, Meanwell NA. Geminal Diheteroatomic Motifs: Some Applications of Acetals, Ketals, and Their Sulfur and Nitrogen Homologues in Medicinal Chemistry and Drug Design. J Med Chem 2021; 64:9786-9874. [PMID: 34213340 DOI: 10.1021/acs.jmedchem.1c00790] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acetals and ketals and their nitrogen and sulfur homologues are often considered to be unconventional and potentially problematic scaffolding elements or pharmacophores for the design of orally bioavailable drugs. This opinion is largely a function of the perception that such motifs might be chemically unstable under the acidic conditions of the stomach and upper gastrointestinal tract. However, even simple acetals and ketals, including acyclic molecules, can be sufficiently robust under acidic conditions to be fashioned into orally bioavailable drugs, and these structural elements are embedded in many effective therapeutic agents. The chemical stability of molecules incorporating geminal diheteroatomic motifs can be modulated by physicochemical design principles that include the judicious deployment of proximal electron-withdrawing substituents and conformational restriction. In this Perspective, we exemplify geminal diheteroatomic motifs that have been utilized in the discovery of orally bioavailable drugs or drug candidates against the backdrop of understanding their potential for chemical lability.
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Affiliation(s)
- Yong-Jin Wu
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Nicholas A Meanwell
- Department of Discovery and Chemistry and Molecular Technologies, Bristol-Myers Squibb PRI, PO Box 4000, Princeton, New Jersey 08543-4000, United States
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3
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Kachalaki S, Ebrahimi M, Mohamed Khosroshahi L, Mohammadinejad S, Baradaran B. Cancer chemoresistance; biochemical and molecular aspects: a brief overview. Eur J Pharm Sci 2016; 89:20-30. [PMID: 27094906 DOI: 10.1016/j.ejps.2016.03.025] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 02/02/2016] [Accepted: 03/31/2016] [Indexed: 01/27/2023]
Abstract
The effectiveness of chemotherapy is one of the main challenges in cancer treatment and resistance to classic drugs and traditional treatment processes is an obstacle to this goal. Drug resistance that may be inherent or adventitious can cause poor treatment outcome and tumor relapse. In most cases, resistance to a drug can lead to resistance to many other drugs structure and function of which is not necessarily similar to the first drug. This phenomenon is the main mechanism behind failure of many of metastatic cancers. There are various molecular mechanisms involved in multidrug resistance, including change in the activity of membrane transporters (such as ABC transporters), increase of drug metabolism, change of the target enzyme (such as mutations that change thymidylate synthase and topoisomerases), promotion of DNA damage repair, and escape from drug induced apoptosis. Clinical and laboratory investigations on biomarkers involved in the response to chemotherapy have characterized the key factors behind the failure of treatments. Knowing the molecular factors involved in drug resistance may help us to develop new strategies for more promising chemotherapy and reduce the rate of relapse. In this brief review, molecular mechanisms and tumor microenvironment leading to decreased drug sensitivity, and strategies of reversing drug resistance are described.
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Affiliation(s)
- Saeed Kachalaki
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mina Ebrahimi
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | | | - Sina Mohammadinejad
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Meanwell NA. Improving Drug Design: An Update on Recent Applications of Efficiency Metrics, Strategies for Replacing Problematic Elements, and Compounds in Nontraditional Drug Space. Chem Res Toxicol 2016; 29:564-616. [DOI: 10.1021/acs.chemrestox.6b00043] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research & Development, Wallingford, Connecticut 06492, United States
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Abdel-Gawad H, Mahdy F, Hashad A, Elgemeie GH. Fate of 14C-ethion insecticide in the presence of deltamethrin and dimilin pesticides in cotton seeds and oils, removal of ethion residues in oils, and bioavailability of its bound residues to experimental animals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:12287-12293. [PMID: 25420216 DOI: 10.1021/jf504010h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ethyl-1-(14)C-ethion and some of its degradation products have been prepared for comparison purposes. Cotton plants were treated with (14)C-ethion alone and in the presence of deltamethrin and dimilin pesticides under conditions simulating local agricultural practice. (14)C-Residues in seeds were determined at harvest time; about 47.5% of (14)C-activity was associated with oil. After further extraction of seeds with ethanol, the ethanol-soluble (14)C-residues accounted for 10.6% of the total seed residues, whereas the cake contained about 37.3% of the total residues as bound residues in the case of ethion only. The bound residues decreased in the presence of deltamethrin and dimilin pesticides and amounted to 8.1 and 10.4% of the total residues, respectively. About 95% of the (14)C-activity in the crude oil could be eliminated by simulated commercial processes locally used for oil refining. Chromatographic analysis of crude cotton oil revealed the presence of ethion monooxon, O,O-diethyl phosphorothioate, and O,O-diethyl phosphoric acid in addition to one unknown compound in the case of ethion alone or ethion and dimilin. The same degradation products are found in the case of ethion and deltamethrin in addition to ethion dioxon, whereas ethanol extract revealed the presence of ethion dioxon and O,O-diethyl phosphoric acid as free metabolites. Acid hydrolysis of the conjugated metabolites in the ethanol extract yielded O,O-diethyl S-hydroxymethyl phosphorodithioate. The bound residues were quite readily bioavailable to the rats. After feeding rats with the cake containing ethion-bound residues, a substantial amount (60%) of (14)C-residues was eliminated in the urine, whereas the (14)C-residues excreted in expired air and feces were 10 and 9%, respectively. About 11% of the radioactive residues were distributed among various organs.
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Affiliation(s)
- Hassan Abdel-Gawad
- Applied Organic Chemistry Department, National Research Centre , Dokki, Cairo, Egypt
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Jin J, Cai D, Bi H, Zhong G, Zeng H, Gu L, Huang Z, Huang M. Comparative pharmacokinetics of paclitaxel after oral administration of Taxus yunnanensis extract and pure paclitaxel to rats. Fitoterapia 2013; 90:1-9. [DOI: 10.1016/j.fitote.2013.06.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 11/25/2022]
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7
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Xue X, Liang XJ. Overcoming drug efflux-based multidrug resistance in cancer with nanotechnology. CHINESE JOURNAL OF CANCER 2012; 31:100-9. [PMID: 22237039 PMCID: PMC3777470 DOI: 10.5732/cjc.011.10326] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Multidrug resistance (MDR), which significantly decreases the efficacy of anticancer drugs and causes tumor recurrence, has been a major challenge in clinical cancer treatment with chemotherapeutic drugs for decades. Several mechanisms of overcoming drug resistance have been postulated. Well known P-glycoprotein (P-gp) and other drug efflux transporters are considered to be critical in pumping anticancer drugs out of cells and causing chemotherapy failure. Innovative theranostic (therapeutic and diagnostic) strategies with nanoparticles are rapidly evolving and are anticipated to offer opportunities to overcome these limits. In this review, we discuss the mechanisms of drug efflux-mediated resistance and the application of multiple nanoparticle-based platforms to overcome chemoresistance and improve therapeutic outcome.
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Affiliation(s)
- Xue Xue
- National Center for Nanoscience and Technology of China, Beijing 100190, People's Republic of China
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8
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Mishra BB, Tiwari VK. Natural products: An evolving role in future drug discovery. Eur J Med Chem 2011; 46:4769-807. [DOI: 10.1016/j.ejmech.2011.07.057] [Citation(s) in RCA: 565] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 07/29/2011] [Accepted: 07/30/2011] [Indexed: 11/16/2022]
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9
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Dong X, Mumper RJ. Nanomedicinal strategies to treat multidrug-resistant tumors: current progress. Nanomedicine (Lond) 2010; 5:597-615. [PMID: 20528455 DOI: 10.2217/nnm.10.35] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Multidrug resistance (MDR) is a major impediment to the success of cancer chemotherapy. P-glycoprotein is an important and the best-known membrane transporter involved in MDR. Several strategies have been used to address MDR, especially P-glycoprotein-mediated drug resistance in tumors. However, clinical success has been limited, largely due to issues regarding lack of efficacy and/or safety. Nanoparticles have shown the ability to target tumors based on their unique physical and biological properties. To date, nanoparticles have been investigated primarily to address P-glycoprotein and the observed improved anticancer efficacy suggests that nanomedicinal strategies provide a new opportunity to overcome MDR. This article focuses on nanotechnology-based formulations and current nanomedicine approaches to address MDR in tumors and discusses the proposed mechanisms of action.
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Affiliation(s)
- Xiaowei Dong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0082, USA
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10
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Abdel-Gawad H, Hegazi B. Fate of 14C-ethyl prothiofos insecticide in canola seeds and oils. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2010; 45:116-122. [PMID: 20390940 DOI: 10.1080/03601230903471878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Canola plants were treated with (14)C- prohiofos under conditions simulating local agricultural practices. (14)C-residues in seeds were determined at different time intervals. At harvest time about 32 % of (14)C-activity was associated with oil. The methanol soluble (14)C-residues accounted for 12 % of the total seed residues after further seeds extraction, while the cake contained about 49 % of the total residues. About 69 % of the (14)C-activity in the crude oil could be eliminated by simulated commercial processes locally used for oil refining. Chromatographic analysis of crude and refined oil revealed the presence of the parent compound together with three metabolites which were identified as prothiofos oxon, O-ethyl phosphorothioate and O-ethyl S-propyl phosphorothioate, besides one unknown compound. While methanol extract revealed the presence of despropylthio prothiofos and O-ethyl phosphoric acid as free metabolites acid hydrolysis of the conjugated metabolites in the methanol extract yielded 2, 4-dichlorophenole which was detected by color. When rats were fed the extracted cake for 72 hours, the bound residues were found to be bioavailable. The main excretion route was via the expired air (42 %), while the (14)C-residues excreted in urine and feces were 30 % and 11 %, respectively. The radioactivity detected among various organs accounted to 7.5 %.Chromatographic analysis of urine indicated the presence of prothiofos oxon, O-ethyl phosphoric acid and 2, 4-dichlorophenole as main degradation products of prothiofos in free and conjugated form.
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11
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Butler MS. Natural products to drugs: natural product-derived compounds in clinical trials. Nat Prod Rep 2008; 25:475-516. [PMID: 18497896 DOI: 10.1039/b514294f] [Citation(s) in RCA: 509] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Natural product and natural product-derived compounds that are being evaluated in clinical trials or are in registration (as at 31st December 2007) have been reviewed, as well as natural product-derived compounds for which clinical trials have been halted or discontinued since 2005. Also discussed are natural product-derived drugs launched since 2005, new natural product templates and late-stage development candidates.
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Affiliation(s)
- Mark S Butler
- MerLion Pharmaceuticals, 1 Science Park Road, The Capricorn 05-01, Singapore Science Park II, Singapore 117528.
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12
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Ismael GFV, Rosa DD, Mano MS, Awada A. Novel cytotoxic drugs: old challenges, new solutions. Cancer Treat Rev 2007; 34:81-91. [PMID: 17905518 DOI: 10.1016/j.ctrv.2007.08.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 07/26/2007] [Accepted: 08/07/2007] [Indexed: 11/29/2022]
Abstract
The discovery of cytotoxic agents was revolutionary for anticancer therapy in the last century, improving survival rates and the quality of life of patients with different types of tumours. However, the development of agents that combine efficacy, safety and convenience remains a great challenge, due to the narrow therapeutic index of some drugs, the fact that they may damage not only cancer cells, but also normal and healthy tissue and the occurrence of resistance, limiting anticancer efficacy. Novel cytotoxic agents have brought certain advantages over the conventional ones, such as shorter administration time, mechanisms to overcome drug resistance and lower incidence of adverse events. In this review we highlight the development of promising novel cytotoxic drugs that will hopefully offer not only gains in efficacy, but also in safety, tolerability and convenience in the treatment of patients with cancer.
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Affiliation(s)
- Gustavo F V Ismael
- Department of Medical Oncology, Jules Bordet Institute, Université Libre de Bruxelles, Belgium
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Anand N, Kapoor M, Ahmad K, Koul S, Parshad R, Manhas KS, Sharma RL, Qazi GN, Taneja SC. Arthrobacter sp.: a lipase of choice for the kinetic resolution of racemic arylazetidinone precursors of taxanoid side chains. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.04.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Over the past two decades, the taxanes have played a significant role in the treatment of various malignancies. However, the poor solubility of these compounds necessitates the inclusion of surfactant vehicles in their commercial formulations. Cremophor EL and polysorbate 80 have long comprised the standard solvent system for paclitaxel and docetaxel, respectively. A number of pharmacologic and biologic effects related to both of these drug formulations have been described, including clinically relevant acute hypersensitivity reactions and peripheral neuropathy. In addition, these solvents affect the disposition of intravenously administered solubilized drugs and leach plasticizers from polyvinylchloride infusion sets. A number of strategies to develop formulations of surfactant-free taxanes have been developed. They include albumin nanoparticles, polyglutamates, taxane analogs and prodrugs, emulsions, and lipsomes. An overview of these novel formulations of taxanes, their mechanisms of action, pharmacokinetics, dose and administration, adverse effects, and clinical efficacy will be discussed.
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Affiliation(s)
- K L Hennenfent
- St Louis College of Pharmacy, Ortho Biotech Clinical Affairs, LLC, St Louis, MO, USA
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Hotta K, Ueoka H. New cytotoxic agents: a review of the literature. Crit Rev Oncol Hematol 2005; 55:45-65. [PMID: 15927843 DOI: 10.1016/j.critrevonc.2005.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Revised: 01/01/2005] [Accepted: 01/28/2005] [Indexed: 10/25/2022] Open
Abstract
The goal of treatment for patients with advanced cancer is to prolong survival, control symptoms, and reduce disease-related complications. Despite the introduction of many cytotoxic agents during the past decade, only modest improvement in survival has been achieved. In order to urgently improve these situations, new cytotoxic agents as well as molecular-targeted agents are now under investigation. In this article, we reviewed the latest information regarding antitumor activity, toxicity, pharmacokinetics, and clinical application of the new cytotoxic agents.
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Affiliation(s)
- Katsuyuki Hotta
- Health and Environmental Center, Okayama University, 2-1-1, Tsushimanaka, Okayama 700-8530, Japan.
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16
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Butler MS. Natural products to drugs: natural product derived compounds in clinical trials. Nat Prod Rep 2005; 22:162-95. [PMID: 15806196 DOI: 10.1039/b402985m] [Citation(s) in RCA: 337] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Natural product and natural product-derived compounds that are being evaluated in clinical trials or in registration (current 31 December 2004) have been reviewed. Natural product derived drugs launched in the United States of America, Europe and Japan since 1998 and new natural product templates discovered since 1990 are discussed.
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Affiliation(s)
- Mark S Butler
- MerLion Pharmaceuticals, 1 Science Park Road, The Capricorn #05-01, Singapore Science Park II, Singapore 117528.
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