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Tang S, He B, Liu Y, Wang L, Liang Y, Wang J, Jin H, Wei M, Ren W, Suo Z, Xu Y. A dual-signal mode electrochemical aptasensor based on tetrahedral DNA nanostructures for sensitive detection of citrinin in food using PtPdCo mesoporous nanozymes. Food Chem 2024; 460:140739. [PMID: 39116770 DOI: 10.1016/j.foodchem.2024.140739] [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: 05/20/2024] [Revised: 07/17/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
Citrinin (CIT) is a mycotoxin with nephrotoxicity and hepatotoxicity, presenting a significant threat to human health that is often overlooked. Therefore, a dual-signal mode (DPV and SWV) aptasensor for citrinin (CIT) detection was constructed based on tetrahedral DNA nanostructures (TDN) in this study. Furthermore, PtPdCo mesoporous nanozymes exhibit catalase-like catalytic functions, generating significant electrochemical signals through a Fenton-like reaction. Meanwhile their excellent Methylene Blue (MB) loading capability ensures independent dual signal outputs. The RecJf exonuclease-assisted (RecJf Exo-assisted) process can expand the linear detection range, enabling further amplification of the signal. Under optimized conditions, the constructed aptaensor exhibited excellent detection performance with limits of detection (LODs) of 7.67 × 10-3 ng·mL-1 (DPV mode) and 1.57 × 10-3 ng·mL-1 (SWV mode). Due to its multiple signal amplification and highly accurate dual-signal mode detection capability, this aptasensor shows promising potential for the in situ detection.
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Affiliation(s)
- Shi Tang
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China
| | - Baoshan He
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China.
| | - Yao Liu
- Henan Scientific Research Platform Service Center, Zhengzhou, Henan 450003, PR China
| | - Longdi Wang
- COFCO Lijin (Tianjin) Grain and Oil Co., Ltd., Tianjin, 300112, PR China
| | - Ying Liang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, PR China
| | - Jinshui Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, PR China.
| | - Huali Jin
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China
| | - Min Wei
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China
| | - Wenjie Ren
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China
| | - Zhiguang Suo
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China
| | - Yiwei Xu
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China
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2
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Xu T, Yang J, Li D, Challa M, Zou C, Deng P, Zhang SL, Xu B. Discovery of novel natural-product-derived mutant isocitrate dehydrogenases 1 inhibitors: Structure-based virtual screening, biological evaluation and structure-activity relationship study. Eur J Med Chem 2024; 275:116610. [PMID: 38896992 DOI: 10.1016/j.ejmech.2024.116610] [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: 05/15/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
Abstract
Mutations in IDH1 are commonly observed across various cancers, causing the conversion of α-KG to 2-HG. Elevated levels of 2-HG disrupt histone and DNA demethylation processes, promoting tumor development. Consequently, there is substantial interest in developing small molecule inhibitors targeting the mutant enzymes. Herein, we report a structure-based high-throughput virtual screening strategy using a natural products library, followed by hit-to-lead optimization. Through this process, we discover a potent compound, named 11s, which exhibited significant inhibition to IDH1 R132H and IDH1 R132C with IC50 values of 124.4 and 95.7 nM, respectively. Furthermore, 11s effectively reduced 2-HG formation, with EC50 values of 182 nM in U87 R132H cell, and 84 nM in HT-1080 cell. In addition, 11s significantly reduced U87 R132H and HT-1080 cell proliferation with GC50 values of 3.48 and 1.38 μM, respectively. PK-PD experiments further confirmed that compound 11s significantly decreased 2-HG formation in an HT-1080 xenograft mouse model, resulting in notable suppression of tumor growth without apparent loss in body weight.
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Affiliation(s)
- Tieling Xu
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China
| | - Junya Yang
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China
| | - Dongsheng Li
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China
| | - Mahesh Challa
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, PR China
| | - Cheng Zou
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, PR China
| | - Ping Deng
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Shao-Lin Zhang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, PR China.
| | - Biao Xu
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China.
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3
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Cai PC, Liang XJ, Feng QX, Bao XF, Chen GL. Synthesis and evaluation of L-quebrachitol derivatives against platelet aggregation. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:824-832. [PMID: 38509703 DOI: 10.1080/10286020.2024.2326582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Thrombosis plays an important role in the occurrence and development of cardiovascular and cerebrovascular diseases that contribute to high mortality and morbidity in patients. L-(-)-Quebrachitol (QCT), a natural product, was first isolated from quebracho bark. It can inhibit PAF receptor and decrease gastric damage induced by indomethacin, as a drug against platelet aggregation. Here, five QCT derivatives were synthesized and investigated for their inhibitory effects on platelet aggregation. Among them, compound 3a showed anticoagulant effects comparable to aspirin, while compound 4b showed dose-independent inhibitory activities in rats that were stronger than aspirin.
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Affiliation(s)
- Peng-Cheng Cai
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin-Jie Liang
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Qi-Xun Feng
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xue-Fei Bao
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Guo-Liang Chen
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
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4
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Adessi TG, Wagner PM, Bisogno FR, Nicotra VE, Guido ME, García ME. Enhancing structural diversity through chemical engineering of Ambrosia tenuifolia extract for novel anti-glioblastoma compounds. Sci Rep 2024; 14:14229. [PMID: 38902325 PMCID: PMC11190268 DOI: 10.1038/s41598-024-63639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/30/2024] [Indexed: 06/22/2024] Open
Abstract
Natural products are an unsurpassed source of leading structures in drug discovery. The biosynthetic machinery of the producing organism offers an important source for modifying complex natural products, leading to analogs that are unattainable by chemical semisynthesis or total synthesis. In this report, through the combination of natural products chemistry and diversity-oriented synthesis, a diversity-enhanced extracts approach is proposed using chemical reactions that remodel molecular scaffolds directly on extracts of natural resources. This method was applied to subextract enriched in sesquiterpene lactones from Ambrosia tenuifolia (Fam. Asteraceae) using acid media conditions (p-toluenesulfonic acid) to change molecular skeletons. The chemically modified extract was then fractionated by a bioguided approach to obtain the pure compounds responsible for the anti-glioblastoma (GBM) activity in T98G cell cultures. Indeed, with the best candidate, chronobiological experiments were performed to evaluate temporal susceptibility to the treatment on GBM cell cultures to define the best time to apply the therapy. Finally, bioinformatics tools were used to supply qualitative and quantitative information on the physicochemical properties, chemical space, and structural similarity of the compound library obtained. As a result, natural products derivatives containing new molecular skeletons were obtained, with possible applications as chemotherapeutic agents against human GBM T98G cell cultures.
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Affiliation(s)
- Tonino G Adessi
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Paula M Wagner
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Córdoba, Argentina
| | - Fabricio R Bisogno
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC-CONICET), Córdoba, Argentina
| | - Viviana E Nicotra
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Mario E Guido
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Córdoba, Argentina
| | - Manuela E García
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina.
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina.
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5
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Mohan S, Krishnan L, Madhusoodanan N, Sobha A, Jalaja R, Kumaran A, Vankadari N, Purushothaman J, Somappa SB. Linker-Based Pharmacophoric Design and Semisynthesis of Labdane Conjugates Active against Multi-Faceted Inflammatory Targets. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6389-6401. [PMID: 38494644 DOI: 10.1021/acs.jafc.3c09536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Prolonged inflammation leads to the genesis of various inflammatory diseases such as atherosclerosis, cancer, inflammatory bowel disease, Alzheimer's, etc. The uncontrolled inflammatory response is characterized by the excessive release of pro-inflammatory mediators such as nitric oxide (NO), tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), interleukin-1alpha (IL-1α), and inflammatory enzymes such as cyclooxygenase-2 (COX-2). Hence, the downregulation of these inflammatory mediators is an active therapy to control aberrant inflammation and tissue damage. To address this, herein, we present the rational design and synthesis of novel phytochemical entities (NPCEs) through strategic linker-based molecular hybridization of aromatic/heteroaromatic fragments with the labdane dialdehyde, isolated from the medicinally and nutritionally significant rhizomes of the plant Curcuma amada. To validate the anti-inflammatory potential, we employed a comprehensive in vitro study assessing its inhibitory effect on the COX-2 enzyme and other inflammatory mediators, viz., NO, TNF-α, IL-6, and IL-1α, in bacterial lipopolysaccharide-stimulated macrophages, as well as in-silico molecular modeling studies targeting the inflammation regulator COX-2 enzyme. Among the synthesized novel compounds, 5f exhibited the highest anti-inflammatory potential by inhibiting the COX-2 enzyme (IC50 = 17.67 ± 0.89 μM), with a 4-fold increased activity relative to the standard drug indomethacin (IC50 = 67.16 ± 0.17 μM). 5f also significantly reduced the levels of LPS-induced NO, TNF-α, IL-6, and IL-1α, much better than the positive control. Molecular mechanistic studies revealed that 5f suppressed the expression of COX-2 and pro-inflammatory cytokine release dose-dependently, which was associated with the inhibition of the NF-κB signaling pathway. This infers that the labdane derivative 5f is a promising lead candidate as an anti-inflammatory agent to further explore its therapeutic landscape.
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Affiliation(s)
- Sangeetha Mohan
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Lekshmy Krishnan
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
| | - Nithya Madhusoodanan
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Anjali Sobha
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Renjitha Jalaja
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
| | - Alaganandam Kumaran
- Agro Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Naveen Vankadari
- Department of Biochemistry and Pharmacology, Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Jayamurthy Purushothaman
- Agro Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Sasidhar B Somappa
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
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6
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Chen Y, Zhang S, Li T, Ma Q, Yuan Y, Jia X. Oxidants Controlled C-H Bond Functionalization of N-Aryltetrahydroisoquinolines: The Construction of the Quaternary Carbon Center and Cleavage of the C-N Bond. Chemistry 2024; 30:e202303151. [PMID: 37875461 DOI: 10.1002/chem.202303151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
Initiated by triarylamine radical cation salt (TBPA), the direct C-H bond functionalization of α-N-aryltetrahydroisoquinoline esters was smoothly realized, giving a series of α-hydroxylated derivatives with a quaternary carbon center in good yields. Differently, in the presence of tert-butyl nitrite (TBN), the C-N single bond was cleaved to keto esters. The mechanistic study revealed that these reactions were mediated by a similar mechanism, in which the N-nitrosation might provide a driving force to the C-N bond cleavage.
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Affiliation(s)
- Yuqin Chen
- School of Chemistry and Chemical Engineering, Yangzhou University, Siwangting Road 180, Yangzhou, Jiangsu, 225002, China
| | - Shuwei Zhang
- School of Chemistry and Chemical Engineering, Yangzhou University, Siwangting Road 180, Yangzhou, Jiangsu, 225002, China
| | - Tong Li
- School of Chemistry and Chemical Engineering, Yangzhou University, Siwangting Road 180, Yangzhou, Jiangsu, 225002, China
| | - Qiyuan Ma
- School of Chemistry and Chemical Engineering, Yangzhou University, Siwangting Road 180, Yangzhou, Jiangsu, 225002, China
| | - Yu Yuan
- School of Chemistry and Chemical Engineering, Yangzhou University, Siwangting Road 180, Yangzhou, Jiangsu, 225002, China
| | - Xiaodong Jia
- School of Chemistry and Chemical Engineering, Yangzhou University, Siwangting Road 180, Yangzhou, Jiangsu, 225002, China
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7
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Jachak GR, Kashinath K, Vasudevan N, Athawale PR, Choudhury R, Dange SS, Agarwal H, Barthwal MK, Reddy DS. Comprehensive Study on Solomonamides: Total Synthesis, Stereochemical Revision, and SAR Studies toward Identification of Simplified Lead. J Org Chem 2023; 88:17088-17133. [PMID: 38051995 DOI: 10.1021/acs.joc.3c01987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Solomonamides, a pair of macrocyclic peptide natural products originating from marine sources, have garnered significant attention within the synthetic community owing to their marked anti-inflammatory efficacy and intricate molecular architectures. In this paper, we present a very detailed investigation into solomonamides, including the challenges associated with the total synthesis, the evolution of our synthetic strategies, structural reassignment, synthesis of all possible stereoisomeric macrocycles, biological assessment, structure-activity relationship (SAR) studies, etc. Within the ambit of this total synthesis, diverse strategies for macrocyclization were rigorously explored, encompassing the Friedel-Crafts acylation, cyclization involving the aniline NH2 moiety, macrolactamization utilizing Gly-NH2, and Heck macrocyclization methodologies. In addition, an array of intriguing chemical transformations were devised, including but not limited to photo-Fries rearrangement, Wacker oxidation, ligand-free Heck macrocyclization, oxidative cleavage of indole, synthesis of contiguous stereocenters via substrate/reagent-controlled protocols, and simultaneous making and breaking of olefinic moieties. The findings of this investigation revealed a structurally simplified lead compound. Remarkably, the lead compound, while possessing structural simplification in comparison to the intricate solomonamide counterparts, demonstrates equipotent in vivo anti-inflammatory efficacy.
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Affiliation(s)
- Gorakhnath R Jachak
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - K Kashinath
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - N Vasudevan
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Paresh R Athawale
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rahul Choudhury
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santoshkumar S Dange
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Heena Agarwal
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Pharmacology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India
| | - Manoj Kumar Barthwal
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Pharmacology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India
| | - D Srinivasa Reddy
- Division of Organic Chemistry, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
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8
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Andrade MA, Mottin M, Sousa BKDP, Barbosa JARG, Dos Santos Azevedo C, Lasse Silva C, Gonçalves de Andrade M, Motta FN, Maulay-Bailly C, Amand S, Santana JMD, Horta Andrade C, Grellier P, Bastos IMD. Identification of novel Zika virus NS3 protease inhibitors with different inhibition modes by integrative experimental and computational approaches. Biochimie 2023; 212:143-152. [PMID: 37088408 DOI: 10.1016/j.biochi.2023.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/14/2023] [Accepted: 04/07/2023] [Indexed: 04/25/2023]
Abstract
Zika virus (ZIKV) infection is associated with severe neurological disorders and congenital malformation. Despite efforts to eradicate the disease, there is still neither vaccine nor approved drugs to treat ZIKV infection. The NS2B-NS3 protease is a validated drug target since it is essential to polyprotein virus maturation. In the present study, we describe an experimental screening of 2,320 compounds from the chemical library of the Muséum National d'Histoire Naturelle of Paris on ZIKV NS2B-NS3 protease. A total of 96 hits were identified with 90% or more of inhibitory activity at 10 μM. Amongst the most active compounds, five were analyzed for their inhibitory mechanisms by kinetics assays and computational approaches such as molecular docking. 2-(3-methoxyphenoxy) benzoic acid (compound 945) show characteristics of a competitive inhibition (Ki = 0.49 μM) that was corroborated by its molecular docking at the active site of the NS2B-NS3 protease. Taxifolin (compound 2292) behaves as an allosteric inhibitor whereas 3,8,9-trihydroxy-2-methyl-1H-phenalen-1-one (compound 128), harmol (compound 368) and anthrapurpurin (compound 1499) show uncompetitive inhibitions. These new NS2B-NS3 protease inhibitors are valuable hits to further hit-to-lead optimization.
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Affiliation(s)
- Milene Aparecida Andrade
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | - Melina Mottin
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, Brazil; Laboratory for Molecular Modeling and Drug Design - LabMol, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Bruna K de P Sousa
- Laboratory for Molecular Modeling and Drug Design - LabMol, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | | | - Clênia Dos Santos Azevedo
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | - Camila Lasse Silva
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | | | - Flávia Nader Motta
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, Brazil; Faculdade de Ceilândia, Universidade de Brasília, Brasília, Brazil
| | - Christine Maulay-Bailly
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Séverine Amand
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Jaime Martins de Santana
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | - Carolina Horta Andrade
- Laboratory for Molecular Modeling and Drug Design - LabMol, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Philippe Grellier
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France.
| | - Izabela M D Bastos
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, Brazil.
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9
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Stojković P, Kostić A, Lupšić E, Jovanović NT, Novaković M, Nedialkov P, Trendafilova A, Pešić M, Opsenica IM. Novel hybrids of sclareol and 1,2,4-triazolo[1,5-a]pyrimidine show collateral sensitivity in multidrug-resistant glioblastoma cells. Bioorg Chem 2023; 138:106605. [PMID: 37201322 DOI: 10.1016/j.bioorg.2023.106605] [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: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
The synthesis of 24 hybrid molecules, consisting of naturally occurring sclareol (SCL) and synthetic 1,2,4-triazolo[1,5-a]pyrimidines (TPs), is described. New compounds were designed with the aim of improving the cytotoxic properties, activity, and selectivity of the parent compounds. Six analogs (12a-f) contained 4-benzylpiperazine linkage, while 4-benzyldiamine linkage was present in eighteen derivatives (12g-r and 13a-f). Hybrids 13a-f consist of two TP units. After purification, all hybrids (12a-r and 13a-f), as well as their precursors (9a-e and 11a-c), were tested on human glioblastoma U87 cells. More than half of the tested synthesized molecules, 16 out of 31, caused a significant reduction of U87 cell viability (more than 75% reduction) at 30 µM. The concentration-dependent cytotoxicity of these 16 compounds was also examined on U87 cells, corresponding multidrug-resistant (MDR) U87-TxR cells with increased P-glycoprotein (P-gp) expression and activity, and normal lung fibroblasts MRC-5. Importantly, 12l and 12r were active in the nanomolar range, while seven compounds (11b, 11c, 12i, 12l, 12n, 12q, and 12r) were more selective towards glioblastoma cells than SCL. All compounds except 12r evaded MDR, showing even better cytotoxicity in U87-TxR cells. In particular, 11c, 12a, 12g, 12j, 12k, 12m, 12n, and SCL showed collateral sensitivity. Hybrid compounds 12l, 12q, and 12r decreased P-gp activity to the same extent as a well-known P-gp inhibitor - tariquidar (TQ). Hybrid compound 12l and its precursor 11c affected different cellular processes including the cell cycle, cell death, and mitochondrial membrane potential, and changed the levels of reactive oxygen and nitrogen species (ROS/RNS) in glioblastoma cells. Collateral sensitivity towards MDR glioblastoma cells was caused by the modulation of oxidative stress accompanied by inhibition of mitochondria.
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Affiliation(s)
- Pavle Stojković
- University of Belgrade - Faculty of Chemistry, PO Box 51, Studentski Trg 16, 11158 Belgrade, Serbia
| | - Ana Kostić
- Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Ema Lupšić
- Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Nataša Terzić Jovanović
- University of Belgrade - Institute of Chemistry, Technology, and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11000 Belgrade, Serbia
| | - Miroslav Novaković
- University of Belgrade - Institute of Chemistry, Technology, and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11000 Belgrade, Serbia.
| | - Paraskev Nedialkov
- Department of Pharmacognosy, Faculty of Pharmacy, Medical University of Sofia, 2, Dunav St., 1000, Sofia, Bulgaria
| | - Antoaneta Trendafilova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev St, Bl. 9, 1113, Sofia, Bulgaria
| | - Milica Pešić
- Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Igor M Opsenica
- University of Belgrade - Faculty of Chemistry, PO Box 51, Studentski Trg 16, 11158 Belgrade, Serbia.
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10
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Adessi TG, Cantero J, Ballesteros-Casallas A, García ME, Nicotra VE, Paulino M. Identification of potential biological target for trypanocidal sesquiterpene lactones derivatives. J Biomol Struct Dyn 2023; 41:14510-14523. [PMID: 36856082 DOI: 10.1080/07391102.2023.2183031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
Sesquiterpene lactones are natural products of the Asteraceae family that have shown trypanocidal activity against Trypanosoma cruzi, even exceeding the effectiveness of drugs used in the treatment of American trypanosomiasis. However, there is no agreement on their mechanism of action and their specificity to interact with parasite proteins. For this reason, we aimed to find biological targets that can interact with these compounds by reverse virtual screening with ligand pharmacophores and putative binding sites and the use of bioinformatic databases. Therefore, 41 possible biological targets were found, and four of them (with crystallized proteins), interfering directly or indirectly in the trypanosomatid redox system, were studied in detail. As a first approach, we focused on the study of trypanothione reductase, and protein-ligand interaction fingerprint analyses were performed to find binding site determinants that promote a possible inhibition of the enzyme. This study contributes to the understanding of one of the putative mechanisms of action of sesquiterpene lactones on one of the numerous suggested targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tonino G Adessi
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Jorge Cantero
- Centro de Investigaciones Médicas, Facultad de Ciencias de la Salud, Universidad Nacional del Este, Minga Guazu, Paraguay
- Área Bioinformática, Departamento DETEMA, Facultad de Química, Universidad de la República, Uruguay
| | | | - Manuela E García
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Viviana E Nicotra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Margot Paulino
- Área Bioinformática, Departamento DETEMA, Facultad de Química, Universidad de la República, Uruguay
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Li J, Sheng H, Wang Y, Lai Z, Wang Y, Cui S. Scaffold Hybrid of the Natural Product Tanshinone I with Piperidine for the Discovery of a Potent NLRP3 Inflammasome Inhibitor. J Med Chem 2023; 66:2946-2963. [PMID: 36786612 DOI: 10.1021/acs.jmedchem.2c01967] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Natural products provide inspiration and have proven to be the most valuable source for drug discovery. Herein, we report a scaffold hybrid strategy of Tanshinone I for the discovery of NLRP3 inflammasome inhibitors. 36 compounds were designed and synthesized, and the cheminformatic analyses showed that these compounds occupy a unique chemical space. The biological evaluation identified compounds 5j, 12a, and 12d as NLRP3 inflammasome inhibitors with significant potency, selectivity, and drug-likeness. Mechanistic studies revealed that these Tanshinone I derivatives could inhibit the degradation of the protein NLRP3 and block the oligomerization of NLRP3-induced apoptosis-associated speck-like proteins, thus inhibiting NLRP3 inflammasome activation. In addition, the water solubility, in vitro metabolic stability, and oral bioavailability of these compounds were also greatly improved compared to Tanshinone I. Therefore, this protocol provides a new structural evolution of Tanshinone I and a new class of potent NLRP3 inflammasome inhibitors.
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Affiliation(s)
- Jiaming Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongda Sheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingchao Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhencheng Lai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sunliang Cui
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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12
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Wang Z, Xiong Y, Peng Y, Zhang X, Li S, Peng Y, Peng X, Zhuo L, Jiang W. Natural product evodiamine-inspired medicinal chemistry: Anticancer activity, structural optimization and structure-activity relationship. Eur J Med Chem 2023; 247:115031. [PMID: 36549115 DOI: 10.1016/j.ejmech.2022.115031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
It is a well-known phenomenon that natural products can serve as powerful drug leads to generate new molecular entities with novel therapeutic utility. Evodiamine (Evo), a major alkaloid component in traditional Chinese medicine Evodiae Fructus, is considered a desirable lead scaffold as its multifunctional pharmacological properties. Although natural Evo has suboptimal biological activity, poor pharmacokinetics, low water solubility, and chemical instability, medicinal chemists have succeeded in producing synthetic analogs that overshadow the deficiency of Evo in terms of further clinical application. Recently, several reviews on the synthesis, structural modification, mechanism pharmacological actions, structure-activity relationship (SAR) of Evo have been published, while few reviews that incorporates intensive structural basis and extensive SAR are reported. The purpose of this article is to review the structural basis, anti-cancer activities, and mechanisms of Evo and its derivatives. Emphasis will be placed on the optimizing strategies to improve the anticancer activities, such as structural modifications, pharmacophore combination and drug delivery systems. The current review would benefit further structural modifications of Evo to discover novel anticancer drugs.
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Affiliation(s)
- Zhen Wang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; School of Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Yongxia Xiong
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Ying Peng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; School of Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xi Zhang
- School of Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Shuang Li
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yan Peng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xue Peng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Linsheng Zhuo
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; Postdoctoral Station for Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Weifan Jiang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; Postdoctoral Station for Basic Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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13
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Valipour M. Recruitment of chalcone's potential in drug discovery of anti-SARS-CoV-2 agents. Phytother Res 2022; 36:4477-4490. [PMID: 36208000 PMCID: PMC9874432 DOI: 10.1002/ptr.7651] [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: 06/23/2022] [Revised: 09/09/2022] [Accepted: 09/22/2022] [Indexed: 01/27/2023]
Abstract
Chalcone is an interesting scaffold found in the structure of many naturally occurring molecules. Medicinal chemists are commonly interested in designing new chalcone-based structures because of having the α, β-unsaturated ketone functional group, which allows these compounds to participate in Michael's reaction and create strong covalent bonds at the active sites of the targets. Some studies have identified several natural chalcone-based compounds with the ability to inhibit the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus proteases. A few years after the advent of the coronavirus disease 2019 pandemic and the publication of many findings in this regard, there is some evidence that suggests chalcone scaffolding has great potential for use in the design and development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibitors. Artificial placement of this scaffold in the structure of optimized anti-SARS-CoV-2 compounds can potentially provide irreversible inhibition of the viral cysteine proteases 3-chymotrypsin-like protease and papain-like protease by creating Michael interaction. Despite having remarkable capabilities, the use of chalcone scaffold in drug design and discovery of SARS-CoV-2 inhibitors seems to have been largely neglected. This review addresses issues that could lead to further consideration of chalcone scaffolding in the structure of SARS-CoV-2 protease inhibitors in the future.
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Affiliation(s)
- Mehdi Valipour
- Razi Drug Research Center, Iran University of Medical SciencesTehranIran
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14
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Detoxification of the Mycotoxin Citrinin by a Manganese Peroxidase from Moniliophthora roreri. Toxins (Basel) 2022; 14:toxins14110801. [PMID: 36422974 PMCID: PMC9693499 DOI: 10.3390/toxins14110801] [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: 10/05/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Citrinin (CIT) is a mycotoxin found in foods and feeds and most commonly discovered in red yeast rice, a food additive made from ordinary rice by fermentation with Monascus. Currently, no enzyme is known to be able to degrade CIT effectively. In this study, it was discovered that manganese peroxidase (MrMnP) from Moniliophthora roreri could degrade CIT. The degradation appeared to be fulfilled by a combination of direct and indirect actions of the MrMnP with the CIT. Pure CIT, at a final concentration of 10 mg/L, was completely degraded by MrMnP within 72 h. One degradation product was identified to be dihydrocitrinone. The toxicity of the CIT-degradation product decreased, as monitored by the increased survival rate of the Caco-2 cells incubated with MrMnP-treated CIT. In addition, MrMnP could degrade CIT (with a starting concentration of up to 4.6 mg/L) completely contaminated in red yeast rice. MrMnP serves as an excellent candidate enzyme for CIT detoxification.
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15
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Ali NM, Tahir HM, Khan MK, Khan KU, Mazhar B, Chaudhry M, Dar M, Faiqa S. Synthesis of Cinnamum zeylanicum and Acacia nilotica Extracts and Their Antibacterial Activity against Staphylococcus aureus and Streptococcus pyogenes. J Oleo Sci 2022; 71:845-852. [PMID: 35661066 DOI: 10.5650/jos.ess22030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Different plants are used medically and thofese therapeutic plants have great importance for healing contagious wounds. This herbal treatment is actually also a substitute of different antibiotics and having less side effects on intestinal systems of animals. The foremost concern of this study was to observe the antibacterial activity of Cinnamum zeylanicum and Acacia nilotica. Pathogenic bacteria obtained from wound samples and later identified by biochemical and molecular characterization. Methanol (an organic solvent) was used to extract Cinnamum zeylanicum and Acacia nilotica to check their antimicrobial exertion by using agar diffusion method. Different antibiotics such as, ampicillin, oflaxocin, ticarcillin and cefexime, showed their susceptibility toward antibiotics. The zone of inhibitions for antibiotic and plant extracts' antibacterial activity were measured. Pathogenic bacteria were identified as Staphylococcus aureus and Streptococcus pyogenesby molecular characterization. These bacteria showed susceptibility to antibiotics and also the plant extracts. Antibiotic oflaxocin showed maximum activity against these two pathogens (12.25 ± 0.44 and 12.375 ± 0.47) while antibiotic cefixime showed minimum effect (1.25 ± 0.28 and 0.625 ± 0.25). Plant extracts showed significant antibacterial activity with maximum activity (14 ± 0.9 by Acacia nilotica and 12 ± 0.5 by Cinnamum zeylanicum) in 100% solution. It can be concluded thatmethanolic extract of traditional therapeutic plants proved to be a promising source of antimicrobial agents against antibiotic resistant bacteria. Cinnamum zeylanicum and Acacia nilotica were observed to be competent as antibacterial tool against pathogenic bacterial strains.
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Affiliation(s)
| | | | | | | | - Bushra Mazhar
- Department of Zoology, Government College University Lahore
| | - Maham Chaudhry
- Department of Zoology, Government College University Lahore
| | - Mariam Dar
- Department of Zoology, Government College University Lahore
| | - Syeda Faiqa
- Department of Zoology, Government College University Lahore
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Pan- and isoform-specific inhibition of Hsp90: Design strategy and recent advances. Eur J Med Chem 2022; 238:114516. [DOI: 10.1016/j.ejmech.2022.114516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/11/2022]
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17
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Guilhon-Simplicio F, Serrão CKR, Pinto ACDS, Pacheco PAF, Faria RX, da Rocha DR, Ferreira VF, Pereira-Junior RC, Matheeussen A, Baán A, Kiekens F, de Meneses Pereira M, Lima ES, Winter HD, Cos P. Semisynthetic triterpenes led to the generation of selective antitrypanosomal lead compounds. Chem Biol Drug Des 2022; 99:868-883. [PMID: 35313075 DOI: 10.1111/cbdd.14040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 12/25/2020] [Accepted: 03/05/2022] [Indexed: 11/26/2022]
Abstract
Triterpenes α,β-amyrin are naturally occurring molecules that can serve as building blocks for synthesizing new chemical entities. This study synthesized acyl, carboxyesther, NSAID, and nitrogenous derivatives and evaluated their antimicrobial activity. A cyclodextrin complexation method was developed to improve the solubility of the derivatives. Of the 17 derivatives tested, five exhibited activity against Trypanosoma cruzi, T. brucei, Leishmania infantum, Candida albicans, Staphylococcus aureus, and Escherichia coli. The 9a/9b mixture showed weak activity against the parasites (IC50 24.45-40.32 μM). However, it showed no activity for the other microorganisms. Derivatives 14a/14b exhibited potent activity against T. cruzi (IC50 2.0 nM) in this tested concentration did not show activity to the other microorganisms and were not cytotoxic. Derivatives 15a/15b and 16a/16b demonstrated relevant activity against the parasites (IC50 2.24-5.44 μM), but were also cytotoxic. Derivatives 17a/17b showed low activity against the tested parasites (IC50 21.70-22.79 μM), but they were selective since they did not show activity against other microorganisms. In docking studies, in general, all derivatives showed complementarity with the CYP51 binding site of the trypanosomatid mainly by hydrophobic interactions; thus, it is not conclusive that the molecules act by inhibiting this enzyme. Our results showed that triterpenes derivatives with antitrypanosomal activity could be synthesized by an inexpensive and rapid method.
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Affiliation(s)
| | | | | | | | | | | | | | | | - An Matheeussen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Adrienn Baán
- Laboratory of Pharmaceutical Technology and Biopharmacy, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Filip Kiekens
- Laboratory of Pharmaceutical Technology and Biopharmacy, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | | | - Emerson Silva Lima
- Faculty of Pharmaceutical Sciences, Federal University of Amazonas, Manaus, Brazil
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
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de Castro Barbosa E, Alves TMA, Kohlhoff M, Jangola STG, Pires DEV, Figueiredo ACC, Alves ÉAR, Calzavara-Silva CE, Sobral M, Kroon EG, Rosa LH, Zani CL, de Oliveira JG. Searching for plant-derived antivirals against dengue virus and Zika virus. Virol J 2022; 19:31. [PMID: 35193667 PMCID: PMC8861615 DOI: 10.1186/s12985-022-01751-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 01/23/2022] [Indexed: 12/21/2022] Open
Abstract
Background The worldwide epidemics of diseases as dengue and Zika have triggered an intense effort to repurpose drugs and search for novel antivirals to treat patients as no approved drugs for these diseases are currently available. Our aim was to screen plant-derived extracts to identify and isolate compounds with antiviral properties against dengue virus (DENV) and Zika virus (ZIKV).
Methods Seven thousand plant extracts were screened in vitro for their antiviral properties against DENV-2 and ZIKV by their viral cytopathic effect reduction followed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method, previously validated for this purpose. Selected extracts were submitted to bioactivity-guided fractionation using high- and ultrahigh-pressure liquid chromatography. In parallel, high-resolution mass spectrometric data (MSn) were collected from each fraction, allowing compounds into the active fractions to be tracked in subsequent fractionation procedures. The virucidal activity of extracts and compounds was assessed by using the plaque reduction assay. EC50 and CC50 were determined by dose response experiments, and the ratio (EC50/CC50) was used as a selectivity index (SI) to measure the antiviral vs. cytotoxic activity. Purified compounds were used in nuclear magnetic resonance spectroscopy to identify their chemical structures. Two compounds were associated in different proportions and submitted to bioassays against both viruses to investigate possible synergy. In silico prediction of the pharmacokinetic and toxicity (ADMET) properties of the antiviral compounds were calculated using the pkCSM platform. Results We detected antiviral activity against DENV-2 and ZIKV in 21 extracts obtained from 15 plant species. Hippeastrum (Amaryllidaceae) was the most represented genus, affording seven active extracts. Bioactivity-guided fractionation of several extracts led to the purification of lycorine, pretazettine, narciclasine, and narciclasine-4-O-β-D-xylopyranoside (NXP). Another 16 compounds were identified in active fractions. Association of lycorine and pretazettine did not improve their antiviral activity against DENV-2 and neither to ZIKV. ADMET prediction suggested that these four compounds may have a good metabolism and no mutagenic toxicity. Predicted oral absorption, distribution, and excretion parameters of lycorine and pretazettine indicate them as candidates to be tested in animal models. Conclusions Our results showed that plant extracts, especially those from the Hippeastrum genus, can be a valuable source of antiviral compounds against ZIKV and DENV-2. The majority of compounds identified have never been previously described for their activity against ZIKV and other viruses. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01751-z.
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Affiliation(s)
- Emerson de Castro Barbosa
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil
| | - Tânia Maria Almeida Alves
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil
| | - Markus Kohlhoff
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil
| | - Soraya Torres Gaze Jangola
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil
| | - Douglas Eduardo Valente Pires
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Anna Carolina Cançado Figueiredo
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil
| | - Érica Alessandra Rocha Alves
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil
| | - Carlos Eduardo Calzavara-Silva
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil
| | - Marcos Sobral
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, Campus Dom Bosco - Praça Dom Helvécio, 74, São João del-Rei, Minas Gerais, 36301-160, Brasil
| | - Erna Geessien Kroon
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brasil
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brasil
| | - Carlos Leomar Zani
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil.
| | - Jaquelline Germano de Oliveira
- Instituto René Rachou - Fiocruz Minas, Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brasil.
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Adessi TG, Ana Y, Stempin CC, García MC, Bisogno FR, Nicotra VE, García ME. Psilostachyins as trypanocidal compounds: Bioguided fractionation of Ambrosia tenuifolia chemically modified extract. PHYTOCHEMISTRY 2022; 194:113014. [PMID: 34798411 DOI: 10.1016/j.phytochem.2021.113014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
This work focusses on the chemical diversification of an Ambrosia tenuifolia extract and its bioguided fractionation, aiming to unveil the chemical entity responsible for the trypanocidal activity. Besides, a revision of the phytochemical study of this species, based on previous reports of the antiparasitic psilostachyins A and C as main compounds, was conducted. To improve the biological properties of a plant extract through a simple chemical reaction, the oxidative diversification of the dichloromethane extract of this plant species was carried out. A bioguided fractionation of a chemically modified extract was performed by evaluating the inhibitory activity against Trypanosoma cruzi trypomastigotes. This experiment led to the isolation of one of the most active compounds. In general terms, epoxidized metabolites were obtained as a result of the oxidation of the major metabolite of the species. The trypanocidal activity of some tested metabolites overperformed the reference drug, benznidazole, displaying no cytotoxicity at trypanocidal concentrations. Key structure-activity relationships were obtained for designing previously undescribed antiparasitic sesquiterpene lactones.
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Affiliation(s)
- Tonino G Adessi
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Ciudad Universitaria, X5000HUA, Córdoba, Argentina; Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Yamile Ana
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Ciudad Universitaria, X5000HUA, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Córdoba, Argentina
| | - Cinthia C Stempin
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Ciudad Universitaria, X5000HUA, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Córdoba, Argentina
| | - Mónica C García
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Ciudad Universitaria, X5000HUA, Córdoba, Argentina; Unidad de Investigación y Desarrollo en Tecnología Farmacéutica, (UNITEFA-CONICET), Córdoba, Argentina
| | - Fabricio R Bisogno
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Ciudad Universitaria, X5000HUA, Córdoba, Argentina; Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC-CONICET), Córdoba, Argentina
| | - Viviana E Nicotra
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Ciudad Universitaria, X5000HUA, Córdoba, Argentina; Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Manuela E García
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Ciudad Universitaria, X5000HUA, Córdoba, Argentina; Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina.
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dos Santos Varjão MT, Duarte AWF, Rosa LH, Alexandre-Moreira MS, de Queiroz AC. Leishmanicidal activity of fungal bioproducts: A systematic review. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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21
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Wu XD, Huang S, Shi Y, Shen Y, Tu WC, Leng Y, Zhao QS. Design, synthesis and structural-activity relationship studies of phanginin A derivatives for regulating SIK1-cAMP/CREB signaling to suppress hepatic gluconeogenesis. Eur J Med Chem 2022; 232:114171. [DOI: 10.1016/j.ejmech.2022.114171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/24/2022] [Accepted: 01/30/2022] [Indexed: 11/30/2022]
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22
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Munipalle K, Kommalapati VK, Patel HK, Olanipekun BE, Tangutur AD, Ponnapalli MG. Targeting Neuroblastoma by Limonoids from the Underutilized Fruits of
Xylocarpus granatum. ChemistrySelect 2022. [DOI: 10.1002/slct.202103479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kiran Munipalle
- Centre for Natural Products and Traditional Knowledge CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad Telangana State India 500 007
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Vamsi Krishna Kommalapati
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Applied Biology CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad Telangana State India 500 007
| | - Hemendra Kumar Patel
- Centre for Natural Products and Traditional Knowledge CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad Telangana State India 500 007
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Bolatito Eunice Olanipekun
- Centre for Natural Products and Traditional Knowledge CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad Telangana State India 500 007
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Chemistry Kwara State University Malete, PMB 1530 Kwara State Nigeria
| | - Anjana Devi Tangutur
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Applied Biology CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad Telangana State India 500 007
| | - Mangala Gowri Ponnapalli
- Centre for Natural Products and Traditional Knowledge CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad Telangana State India 500 007
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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23
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Li Z, Rong D, Cao Y, Hu R, Huang G. Efficient Synthesis of Novel Spiro[indoline-3,5'-pyrano[2,3-d]pyrimidin]-2-one Derivatives and Antitumor Activity Evaluation. HETEROCYCLES 2022. [DOI: 10.3987/com-22-14658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Li G, Lou M, Qi X. A brief overview of classical natural product drug synthesis and bioactivity. Org Chem Front 2022. [DOI: 10.1039/d1qo01341f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This manuscript briefly overviewed the total synthesis and structure–activity relationship studies of eight classical natural products, which emphasizes the important role of total synthesis in natural product-based drug development.
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Affiliation(s)
- Gen Li
- National Institute of Biological Sciences (NIBS), 7 Science Park Road ZGC Life Science Park, Beijing 102206, China
| | - Mingliang Lou
- National Institute of Biological Sciences (NIBS), 7 Science Park Road ZGC Life Science Park, Beijing 102206, China
| | - Xiangbing Qi
- National Institute of Biological Sciences (NIBS), 7 Science Park Road ZGC Life Science Park, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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25
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Feng Y, Wang W, Zhang Y, Fu X, Ping K, Zhao J, Lei Y, Mou Y, Wang S. Synthesis and biological evaluation of celastrol derivatives as potential anti-glioma agents by activating RIP1/RIP3/MLKL pathway to induce necroptosis. Eur J Med Chem 2021; 229:114070. [PMID: 34968902 DOI: 10.1016/j.ejmech.2021.114070] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 11/15/2022]
Abstract
Celastrol, a quinone methide triterpenoid, possesses potential anti-glioma activity. However, its relatively low activity limit its application as an effective agent for glioma treatment. In search for effective anti-glioma agents, this work designed and synthesized two series of celastrol C-3 OH and C-20 COOH derivatives 4a-4o and 6a-6o containing 1, 2, 3-triazole moiety. Their anti-glioma activities against four human glioma cell lines (A172, LN229, U87, and U251) were then evaluated using MTT assay in vitro. Results showed that compound 6i (IC50 = 0.94 μM) exhibited substantial antiproliferative activity against U251 cell line, that was 4.7-fold more potent than that of celastrol (IC50 = 4.43 μM). In addition, compound 6i remarkably inhibited the colony formation and migration of U251 cells. Further transmission electron microscopy and mitochondrial depolarization assays in U251 cells indicated that the potent anti-glioma activity of 6i was attributed to necroptosis. Mechanism investigation revealed that compound 6i induced necroptosis mainly by activating the RIP1/RIP3/MLKL pathway. Additionally, compound 6i exerted acceptable BBB permeability in mice and inhibited U251 cell proliferation in an in vivo zebrafish xenograft model, obviously. In summary, compound 6i might be a promising lead compound for potent celastrol derivatives as anti-glioma agents.
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Affiliation(s)
- Yao Feng
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang, 110016, China
| | - Wenbao Wang
- College of Pharmacy, Qiqihar Medical University, Qiqihar, 161006, Heilongjiang, China
| | - Yan Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang, 110016, China
| | - Xuefeng Fu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang, 110016, China
| | - Kunqi Ping
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang, 110016, China
| | - Jiaxing Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang, 110016, China
| | - Yu Lei
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang, 110016, China
| | - Yanhua Mou
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang, 110016, China.
| | - Shaojie Wang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang, 110016, China.
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Louka XP, Sklirou AD, Le Goff G, Lopes P, Papanagnou ED, Manola MS, Benayahu Y, Ouazzani J, Trougakos IP. Isolation of an Extract from the Soft Coral Symbiotic Microorganism Salinispora arenicola Exerting Cytoprotective and Anti-Aging Effects. Curr Issues Mol Biol 2021; 44:14-30. [PMID: 35723381 PMCID: PMC8928968 DOI: 10.3390/cimb44010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 01/10/2023] Open
Abstract
Cells have developed a highly integrated system responsible for proteome stability, namely the proteostasis network (PN). As loss of proteostasis is a hallmark of aging and age-related diseases, the activation of PN modules can likely extend healthspan. Here, we present data on the bioactivity of an extract (SA223-S2BM) purified from the strain Salinispora arenicola TM223-S2 that was isolated from the soft coral Scleronephthya lewinsohni; this coral was collected at a depth of 65 m from the mesophotic Red Sea ecosystem EAPC (south Eilat, Israel). Treatment of human cells with SA223-S2BM activated proteostatic modules, decreased oxidative load, and conferred protection against oxidative and genotoxic stress. Furthermore, SA223-S2BM enhanced proteasome and lysosomal-cathepsins activities in Drosophila flies and exhibited skin protective effects as evidenced by effective inhibition of the skin aging-related enzymes, elastase and tyrosinase. We suggest that the SA223-S2BM extract constitutes a likely promising source for prioritizing molecules with anti-aging properties.
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Affiliation(s)
- Xanthippi P. Louka
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (X.P.L.); (A.D.S.); (E.-D.P.); (M.S.M.)
| | - Aimilia D. Sklirou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (X.P.L.); (A.D.S.); (E.-D.P.); (M.S.M.)
| | - Géraldine Le Goff
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91190 Gif-sur-Yvette, France; (G.L.G.); (P.L.); (J.O.)
| | - Philippe Lopes
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91190 Gif-sur-Yvette, France; (G.L.G.); (P.L.); (J.O.)
| | - Eleni-Dimitra Papanagnou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (X.P.L.); (A.D.S.); (E.-D.P.); (M.S.M.)
| | - Maria S. Manola
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (X.P.L.); (A.D.S.); (E.-D.P.); (M.S.M.)
| | - Yehuda Benayahu
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel;
| | - Jamal Ouazzani
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91190 Gif-sur-Yvette, France; (G.L.G.); (P.L.); (J.O.)
| | - Ioannis P. Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (X.P.L.); (A.D.S.); (E.-D.P.); (M.S.M.)
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27
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Jaisi A, Prema, Madla S, Lee YE, Septama A, Morita H. Investigation of HIV-1 Viral Protein R Inhibitory Activities of Twelve Thai Medicinal Plants and Their Commercially Available Major Constituents. Chem Biodivers 2021; 18:e2100540. [PMID: 34599555 DOI: 10.1002/cbdv.202100540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/01/2021] [Indexed: 01/11/2023]
Abstract
Viral protein R (Vpr) is an accessory protein in Human immunodeficiency virus-1 (HIV-1) and has been suggested as an attractive target for HIV disease treatment. Investigations of the ethanolic extracts of twelve Thai herbs revealed that the extracts of the Punica granatum fruits, the Centella asiatica aerials, the Citrus hystrix fruit peels, the Caesalpinia sappan heartwoods, the Piper betel leaves, the Alpinia galangal rhizomes, the Senna tora seeds, the Zingiber cassumunar rhizomes, the Rhinacanthus nasutus leaves, and the Plumbago indica roots exhibited the anti-Vpr activity in HeLa cells harboring the TREx plasmid encoding full-length Vpr (TREx-HeLa-Vpr cells). Moreover, the investigation of the selected main constituents in Punica granatum, Centella asiatica, A. galangal, and Caesalpinia sappan indicated that punicalagin, asiaticoside, ellagic acid, madecassic acid, madecassoside, zingerone, brazilin, and asiatic acid possessed anti-Vpr activities at the 10 μM concentration. Among the tested extracts and compounds, the extracts from Centella asiatica and Citrus hystrix and the compounds, punicalagin and asiaticoside, showed the most potent anti-Vpr activities without any cytotoxicity, respectively.
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Affiliation(s)
- Amit Jaisi
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand.,Drug and Cosmetics Excellence Center, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Prema
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama, 930-0194, Japan
| | - Siribhorn Madla
- School of Pharmacy, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Yuan-E Lee
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama, 930-0194, Japan
| | - Abdi Septama
- Research Center for Chemistry, National Research and Innovation Agency (BRIN), Serpong, Tangereng Selatan, 15314, Indonesia
| | - Hiroyuki Morita
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama, 930-0194, Japan
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28
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Zhou X, Feng X, Wang D, Chen D, Wu G, Yan Z, Lyu X, Wang H, Yang JM, Zhao Y. Synthesis and bioactivity studies of covalent inhibitors derived from (-)-Chaetominine. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Phanumartwiwath A, Kesornpun C, Sureram S, Hongmanee P, Pungpo P, Kamsri P, Punkvang A, Eurtivong C, Kittakoop P, Ruchirawat S. Antitubercular and antibacterial activities of isoxazolines derived from natural products: Isoxazolines as inhibitors of Mycobacterium tuberculosis InhA. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/17475198211047801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Isoxazoline derivatives of the natural products eugenol, 1’- S-acetoxychavicol acetate and sclareol are prepared through 1,3-dipolar cycloaddition reactions in an aqueous buffered system. The compounds are evaluated for their antitubercular and antibacterial activities. Compounds 2, 2a and 3f display strong antitubercular activity with minimum inhibitory concentration values of 26.68, 17.89 and 14.58 µM, respectively. Furthermore, derivative 3f exhibits antibacterial activity against Bacillus cereus (minimum inhibitory concentration value of 29.16 µM). Isoxazoline derivatives of 1’- S-acetoxychavicol acetate demonstrate improvements in cytotoxicity, and derivative 3f of sclareol demonstrates improved antitubercular and antibacterial activities. Isoxazolines derived from natural products exhibit Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) inhibitory activity, and molecular modelling predicts that they form hydrogen bonding and hydrophobic interactions with NADH and with the key residues of the InhA binding site.
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Affiliation(s)
- Anuchit Phanumartwiwath
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
- College of Public Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Poonpilas Hongmanee
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Chatchakorn Eurtivong
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
| | - Prasat Kittakoop
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
| | - Somsak Ruchirawat
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
- Chulabhorn Research Institute, Bangkok, Thailand
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30
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Karageorgis G, Foley DJ, Laraia L, Brakmann S, Waldmann H. Pseudo Natural Products-Chemical Evolution of Natural Product Structure. Angew Chem Int Ed Engl 2021; 60:15705-15723. [PMID: 33644925 PMCID: PMC8360037 DOI: 10.1002/anie.202016575] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/27/2021] [Indexed: 01/05/2023]
Abstract
Pseudo-natural products (PNPs) combine natural product (NP) fragments in novel arrangements not accessible by current biosynthesis pathways. As such they can be regarded as non-biogenic fusions of NP-derived fragments. They inherit key biological characteristics of the guiding natural product, such as chemical and physiological properties, yet define small molecule chemotypes with unprecedented or unexpected bioactivity. We iterate the design principles underpinning PNP scaffolds and highlight their syntheses and biological investigations. We provide a cheminformatic analysis of PNP collections assessing their molecular properties and shape diversity. We propose and discuss how the iterative analysis of NP structure, design, synthesis, and biological evaluation of PNPs can be regarded as a human-driven branch of the evolution of natural products, that is, a chemical evolution of natural product structure.
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Affiliation(s)
- George Karageorgis
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
| | - Daniel J. Foley
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: School of Physical and Chemical SciencesUniversity of CanterburyPrivate Bag 4800Christchurch8140New Zealand
| | - Luca Laraia
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: Department of ChemistryTechnical University of Denmark, kemitorvet 2072800 Kgs.LyngbyDenmark
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
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31
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Zhang Q, Yang Z, Wang Q, Liu S, Zhou T, Zhao Y, Zhang M. Asymmetric Total Synthesis of Hetidine-Type C 20-Diterpenoid Alkaloids: (+)-Talassimidine and (+)-Talassamine. J Am Chem Soc 2021; 143:7088-7095. [PMID: 33938219 DOI: 10.1021/jacs.1c01865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, we report the first asymmetric total synthesis of (+)-talassimidine and (+)-talassamine, two hetidine-type C20-diterpenoid alkaloids. A highly regio- and diastereoselective 1,3-dipolar cycloaddition of an azomethine ylide yielded a chiral tetracyclic intermediate in high enantiopurity, thus providing the structural basis for asymmetric assembly of the hexacyclic hetidine skeleton. In this key step, the introduction of a single chiral center induces four new continuous chiral centers. Another key transformation is the dearomative cyclopropanation of the benzene ring and subsequent SN2-like ring opening of the resultant cyclopropane ring with water as a nucleophile, which not only establishes the B ring but also precisely installs the difficult-to-achieve equatorial C7-OH group.
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Affiliation(s)
- Quanzheng Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zhao Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Qi Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Shuangwei Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Tao Zhou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yankun Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Min Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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32
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Wang Z, Hui C. Contemporary advancements in the semi-synthesis of bioactive terpenoids and steroids. Org Biomol Chem 2021; 19:3791-3812. [PMID: 33949606 DOI: 10.1039/d1ob00448d] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many natural products have intriguing biological properties that arise from their fascinating chemical structures. However, the intrinsic complexity of the structural skeleton and the reactive functional groups on natural products pose tremendous challenges to chemical syntheses. Semi-synthesis uses chemical compounds isolated from natural sources as the starting materials to produce other novel compounds with distinct chemical and medicinal properties. In particular, advancements in various types of sp3 C-H bond functionalization reactions and skeletal rearrangement methods have contributed to the re-emergence of semi-synthesis as an efficient approach for the synthesis of structurally complex bioactive natural products. Here, we begin with a brief discussion of several bioactive natural products that were obtained via a semi-synthetic approach between 2008 and 2015 and we then discuss in-depth contemporary advancements in the semi-synthesis of bioactive terpenoids and steroids reported during 2016-2020.
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Affiliation(s)
- Zhuo Wang
- Southern University of Science and Technology, School of Medicine, Shenzhen, 518055, People's Republic of China.
| | - Chunngai Hui
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
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Hossain S, Urbi Z, Karuniawati H, Mohiuddin RB, Moh Qrimida A, Allzrag AMM, Ming LC, Pagano E, Capasso R. Andrographis paniculata (Burm. f.) Wall. ex Nees: An Updated Review of Phytochemistry, Antimicrobial Pharmacology, and Clinical Safety and Efficacy. Life (Basel) 2021; 11:348. [PMID: 33923529 PMCID: PMC8072717 DOI: 10.3390/life11040348] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023] Open
Abstract
Infectious disease (ID) is one of the top-most serious threats to human health globally, further aggravated by antimicrobial resistance and lack of novel immunization options. Andrographis paniculata (Burm. f.) Wall. ex Nees and its metabolites have been long used to treat IDs. Andrographolide, derived from A. paniculata, can inhibit invasive microbes virulence factors and regulate the host immunity. Controlled clinical trials revealed that A. paniculata treatment is safe and efficacious for acute respiratory tract infections like common cold and sinusitis. Hence, A. paniculata, mainly andrographolide, could be considered as an excellent candidate for antimicrobial drug development. Considering the importance, medicinal values, and significant role as antimicrobial agents, this study critically evaluated the antimicrobial therapeutic potency of A. paniculata and its metabolites, focusing on the mechanism of action in inhibiting invasive microbes and biofilm formation. A critical evaluation of the secondary metabolites with the aim of identifying pure compounds that possess antimicrobial functions has further added significant values to this study. Notwithstanding that A. paniculata is a promising source of antimicrobial agents and safe treatment for IDs, further empirical research is warranted.
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Affiliation(s)
- Sanower Hossain
- Department of Biomedical Science, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia
| | - Zannat Urbi
- Department of Industrial Biotechnology, Faculty of Industrial Sciences & Technology, Universiti Malaysia Pahang, Kuantan 26300, Pahang, Malaysia;
| | - Hidayah Karuniawati
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Muhammadiyah Surakarta, Surakarta 57102, Indonesia;
| | - Ramisa Binti Mohiuddin
- Department of Pharmacy, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh 1902, Tangail, Bangladesh;
| | - Ahmed Moh Qrimida
- Department of Agriculture, Higher Institute of Overall Occupations-Sooq Al Khamees Imsahil, Tripoli 1300, Libya; (A.M.Q.); (A.M.M.A.)
| | - Akrm Mohamed Masaud Allzrag
- Department of Agriculture, Higher Institute of Overall Occupations-Sooq Al Khamees Imsahil, Tripoli 1300, Libya; (A.M.Q.); (A.M.M.A.)
| | - Long Chiau Ming
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei;
| | - Ester Pagano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy;
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
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Karageorgis G, Foley DJ, Laraia L, Brakmann S, Waldmann H. Pseudo Natural Products—Chemical Evolution of Natural Product Structure. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016575] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- George Karageorgis
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
| | - Daniel J. Foley
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Current address: School of Physical and Chemical Sciences University of Canterbury Private Bag 4800 Christchurch 8140 New Zealand
| | - Luca Laraia
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Current address: Department of Chemistry Technical University of Denmark, kemitorvet 207 2800 Kgs. Lyngby Denmark
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Strasse 4a 44227 Dortmund Germany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Strasse 4a 44227 Dortmund Germany
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Zhang H, Ahima J, Yang Q, Zhao L, Zhang X, Zheng X. A review on citrinin: Its occurrence, risk implications, analytical techniques, biosynthesis, physiochemical properties and control. Food Res Int 2021; 141:110075. [DOI: 10.1016/j.foodres.2020.110075] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022]
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Sodium ion channels as potential therapeutic targets for cancer metastasis. Drug Discov Today 2021; 26:1136-1147. [PMID: 33545383 DOI: 10.1016/j.drudis.2021.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/31/2020] [Accepted: 01/27/2021] [Indexed: 12/28/2022]
Abstract
Is it possible to develop drugs for the treatment of a specific type of metastatic cancer by targeting sodium ion channels?
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Solovyev I, Eremeyeva M, Zhukovsky D, Dar'in D, Krasavin M. Cyclic diazo compounds in the construction of spirocyclic scaffolds. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152671] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Cheng WC, Liu WJ, Hu KH, Tan YL, Lin YT, Chen WA, Lo LC. Rapid Synthesis of a Natural Product-Inspired Uridine Containing Library. ACS COMBINATORIAL SCIENCE 2020; 22:600-607. [PMID: 32833425 DOI: 10.1021/acscombsci.0c00011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The preparation of natural product-inspired nucleoside analogs using solution-phase parallel synthesis is described. The key intermediates containing alkyne and N-protected amino moieties were developed to allow for further skeleton and substituent diversity using click chemistry and urea or amide bond formation. Rapid purification was accomplished using solid-phase extraction. The obtained library comprised 80 molecules incorporating two diversity positions and one chiral center, each of which was efficiently prepared in good purity and acceptable overall yield. A bacterial morphology study was also performed.
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Affiliation(s)
- Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Cheng-Kung University, Tainan 701, Taiwan
- Department of Applied Chemistry, National Chiayi University, Chiayi 600, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Wan-Ju Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Kung-Hsiang Hu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yee-Ling Tan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yan-Ting Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Wei-An Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Lee-Chiang Lo
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
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Wu ZC, Boger DL. The quest for supernatural products: the impact of total synthesis in complex natural products medicinal chemistry. Nat Prod Rep 2020; 37:1511-1531. [PMID: 33169762 PMCID: PMC7678878 DOI: 10.1039/d0np00060d] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: 2000 up to 2020This review presents select recent advances in the medicinal chemistry of complex natural products that are prepared by total synthesis. The underlying studies highlight enabling divergent synthetic strategies and methods that permit the systematic medicinal chemistry studies of key analogues bearing deep-seated structural changes not readily accessible by semisynthetic or biosynthetic means. Select and recent examples are detailed where the key structural changes are designed to improve defined properties or to overcome an intrinsic limitation of the natural product itself. In the examples presented, the synthetic efforts provided supernatural products, a term first introduced by our colleague Ryan Shenvi (Synlett, 2016, 27, 1145-1164), with properties superseding the parent natural product. The design principles and approaches for creating the supernatural products are highlighted with an emphasis on the properties addressed that include those that improve activity or potency, increase selectivity, enhance durability, broaden the spectrum of activity, improve chemical or metabolic stability, overcome limiting physical properties, add mechanisms of action, enhance PK properties, overcome drug resistance, and/or improve in vivo efficacy. Some such improvements may be regarded by some as iterative enhancements whereas others, we believe, truly live up to their characterization as supernatural products. Most such efforts are also accompanied by advances in synthetic organic chemistry, inspiring the development of new synthetic methodology and providing supernatural products with improved synthetic accessibility.
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Affiliation(s)
- Zhi-Chen Wu
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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Liu Z, Huang D, Zheng S, Song Y, Liu B, Sun J, Niu Z, Gu Q, Xu J, Xie L. Deep learning enables discovery of highly potent anti-osteoporosis natural products. Eur J Med Chem 2020; 210:112982. [PMID: 33158578 DOI: 10.1016/j.ejmech.2020.112982] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/16/2020] [Accepted: 09/24/2020] [Indexed: 01/13/2023]
Abstract
A pre-trained self-attentive message passing neural network (P-SAMPNN) model was developed based on our anti-osteoclastogenesis dataset for virtual screening purpose. Validation processes proved that P-SAMPNN model was significantly superior to the other base line models. A commercially available natural product library was virtually screened by the P-SAMPNN model and resulted in confirmed 5 hits from 10 selected virtual hits. Among the confirmed hits, compounds AP-123/40765213 and AE-562/43462182 are the nanomolar inhibitors against osteoclastogenesis with a new scaffold. Further studies indicate that AP-123/40765213 and AE-562/43462182 significantly suppress the mRNA expression of RANK and downregulate the expressions of osteoclasts-related genes Ctsk, Nfatc1, and Tracp. Our work demonstrated that P-SAMPNN method can guide phenotype-based drug discovery.
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Affiliation(s)
- Zhihong Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Dane Huang
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Province Engineering Technology Research Institute of T.C.M., Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, 510095, China
| | - Shuangjia Zheng
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; School of Data and Computer Science, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ying Song
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, 510006, China
| | - Bingdong Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Jingyuan Sun
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhangming Niu
- Aladdin Healthcare Technologies Ltd., 24-26, Baltic Street West, London EC1Y OUR, UK
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; School of Biotechnology and Health Sciences, Wuyi University, 99 Yingbin Road, Jiangmen, 529020, China.
| | - Liwei Xie
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
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Kumar R, Bidgood CL, Levrier C, Gunter JH, Nelson CC, Sadowski MC, Davis RA. Synthesis of a Unique Psammaplysin F Library and Functional Evaluation in Prostate Cancer Cells by Multiparametric Quantitative Single Cell Imaging. JOURNAL OF NATURAL PRODUCTS 2020; 83:2357-2366. [PMID: 32691595 DOI: 10.1021/acs.jnatprod.0c00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The spirooxepinisoxazoline alkaloid psammaplysin F (1) was selected as a scaffold for the generation of a unique screening library for both drug discovery and chemical biology research. Large-scale extraction and isolation chemistry was performed on a marine sponge (Hyattella sp.) collected from the Great Barrier Reef in order to acquire >200 mg of the desired bromotyrosine-derived alkaloidal scaffold. Parallel solution-phase semisynthesis was employed to generate a series of psammaplysin-based urea (2-9) and amide analogues (10-11) in low to moderate yields. The chemical structures of all analogues were characterized using NMR and MS data. The absolute configuration of psammaplysin F and all semisynthetic analogues was determined as 6R, 7R by comparison of ECD data with literature values. All compounds (1-11) were evaluated for their effect on cell cycle distribution and changes to cancer metabolism in LNCaP prostate cancer cells using a multiparametric quantitative single-cell imaging approach. These investigations identified that in LNCaP cells psammaplysin F and some urea analogues caused loss of mitochondrial membrane potential, fragmentation of the mitochondrial tubular network, chromosome misalignment, and cell cycle arrest in mitosis.
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Affiliation(s)
- Rohitesh Kumar
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia
| | - Charles L Bidgood
- Queensland University of Technology, Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Claire Levrier
- Queensland University of Technology, Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Jennifer H Gunter
- Queensland University of Technology, Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Colleen C Nelson
- Queensland University of Technology, Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Martin C Sadowski
- Queensland University of Technology, Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia
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Deans BJ, Just J, Smith JA, Bissember AC. Development and Applications of Water‐based Extraction Methods in Natural Products Isolation Chemistry. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Bianca J. Deans
- School of Natural Sciences ChemistryUniversity of Tasmania Hobart Australia
| | - Jeremy Just
- School of Natural Sciences ChemistryUniversity of Tasmania Hobart Australia
| | - Jason A. Smith
- School of Natural Sciences ChemistryUniversity of Tasmania Hobart Australia
| | - Alex C. Bissember
- School of Natural Sciences ChemistryUniversity of Tasmania Hobart Australia
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Fang Y, Yang C, Yu Z, Li X, Mu Q, Liao G, Yu B. Natural products as LSD1 inhibitors for cancer therapy. Acta Pharm Sin B 2020; 11:S2211-3835(20)30616-X. [PMID: 32837872 PMCID: PMC7305746 DOI: 10.1016/j.apsb.2020.06.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Natural products generally fall into the biologically relevant chemical space and always possess novel biological activities, thus making them a rich source of lead compounds for new drug discovery. With the recent technological advances, natural product-based drug discovery is now reaching a new era. Natural products have also shown promise in epigenetic drug discovery, some of them have advanced into clinical trials or are presently being used in clinic. The histone lysine specific demethylase 1 (LSD1), an important class of histone demethylases, has fundamental roles in the development of various pathological conditions. Targeting LSD1 has been recognized as a promising therapeutic option for cancer treatment. Notably, some natural products with different chemotypes including protoberberine alkaloids, flavones, polyphenols, and cyclic peptides have shown effectiveness against LSD1. These natural products provide novel scaffolds for developing new LSD1 inhibitors. In this review, we mainly discuss the identification of natural LSD1 inhibitors, analysis of the co-crystal structures of LSD1/natural product complex, antitumor activity and their modes of action. We also briefly discuss the challenges faced in this field. We believe this review will provide a landscape of natural LSD1 inhibitors.
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Key Words
- AML, acute myeloid leukemia
- CCC, cut countercurrent chromatography
- CD11b, integrin alpha M
- CD14, cluster of differentiation 14
- CD86, cluster of differentiation 86
- COVID-19, coronavirus disease
- Cancer therapy
- CoREST, RE1-silencing transcription factor co-repressor
- Drug discovery
- EMT, epithelial–mesenchymal transition
- EVOO, extra virgin olive oil
- EdU, 5-ethynyl-20-deoxyuridine
- Epigenetic regulation
- FAD, flavin adenine dinucleotide
- FDA, U.S. Food and Drug Administration
- GGA, geranylgeranoic acid
- H3K4, histone H3 lysine 4
- H3K9, histone H3 lysine 9
- HDAC, histone deacetylase
- HRP, horseradish peroxidase
- Histone demethylase
- Kt, competitive inhibition constant
- LSD1 inhibitors
- LSD1, lysine-specific histone demethylase 1A
- MAO-A, monoamine oxidase A
- MHC, myosin heavy chain
- MMA, methylmalonic acid
- NAD, nicotinamide adenine dinucleotide
- NTRK2, neurotrophic receptor tyrosine kinase 2
- Natural products
- PDX, patient-derived xenograft
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SARs, structure–activity relationship studies
- SIRT1, sirtuin 1
- SOX2, sex determining region Y-box 2
- SPR, surface plasmon resonance
- TCP, tranylcypromine
- THF, tetrahydrofolate
- Tm, melting temperature
- iPS, induced pluripotent stem
- mRNA, messenger RNA
- siRNA, small interfering RNA
- ΔΨm, mitochondrial transmembrane potential
- α-MG, α-mangostin
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Affiliation(s)
- Yuan Fang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Chao Yang
- Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhiqiang Yu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaochuan Li
- The People's Hospital of Gaozhou, Gaozhou 525200, China
| | - Qingchun Mu
- The People's Hospital of Gaozhou, Gaozhou 525200, China
| | - Guochao Liao
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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Zhao XB, Ha W, Gao K, Shi YP. Precisely Traceable Drug Delivery of Azoreductase-Responsive Prodrug for Colon Targeting via Multimodal Imaging. Anal Chem 2020; 92:9039-9047. [PMID: 32501673 DOI: 10.1021/acs.analchem.0c01220] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report the development of an azoreductase-responsive prodrug AP-N═N-Cy in which the precursor compound AP, a readily available podophyllotoxin derivative, is linked with a NIR fluorophore (Cy) via a multifunctional azobenzene group. This type of azo-based prodrug can serve as not only an azoreductase-responsive NIR probe to real-time tracking of the drug delivery process but also a delivery platform for an anticancer compound (AdP). We have shown that cleavage of the multifunctional azobenzene group in AP-N═N-Cy only occurred in the presence of azoreductase, which specifically secretes in the colon, resulting in direct release of AdP through an in situ modification of a phenylamino group on the precursor AP. Moreover, introduction of the azobenzene group endows the prodrug with an unique fluorescence "off-on" property and served as a switch to "turn on" the fluorescence of Cy as consequence of a self-elimination reaction with breakage of an azo bond. Such a prodrug can be administered orally and exhibit high stability and low toxicity before arriving at the colon. In view of the synchronism of drug release and the fluorescence turn-on process, the fluorescence imaging method was utilized to precisely trace drug delivery in vitro, ex vivo, and in vivo. Distinguishingly, the biodistribution of AdP and Cy in various tissues was further precisely mapped at the molecular level using imaging mass spectrometry. To the best of our knowledge, this is the first time that the in vivo real-time precise tracking of the colon-specific drug release and biodistribution was reported via a multimodal imaging method.
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Affiliation(s)
- Xiao-Bo Zhao
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wei Ha
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, People's Republic of China
| | - Kun Gao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yan-Ping Shi
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, People's Republic of China
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Inhibitory Effects of AF-343, a Mixture of Cassia tora L., Ulmus pumila L., and Taraxacum officinale, on Compound 48/80-Mediated Allergic Responses in RBL-2H3 Cells. Molecules 2020; 25:molecules25102434. [PMID: 32456051 PMCID: PMC7288106 DOI: 10.3390/molecules25102434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/14/2020] [Accepted: 05/17/2020] [Indexed: 12/13/2022] Open
Abstract
The purpose of this study was to determine the antiallergic effects of AF-343, a mixture of natural plant extracts from Cassia tora L., Ulmus pumila L., and Taraxacum officinale, on rat basophilic leukemia (RBL-2H3) cells. The inhibitory effects on cell degranulation, proinflammatory cytokine secretion, and reactive oxygen species (ROS) production were studied in compound 48/80-treated RBL-2H3 cells. The bioactive compounds in AF-343 were also identified by HPLC–UV. AF-343 was found to effectively suppress compound 48/80-induced β-hexosaminidase release, and interleukin (IL)-4 and tumor necrosis factor-α (TNF-α) production in RBL-2H3 cells. In addition, AF-343 exhibited DPPH free radical scavenging effects in vitro (half-maximal inhibitory concentration (IC50) = 105 μg/mL) and potently inhibited compound 48/80-induced cellular ROS generation in a 2′,7′-dichlorofluorescein diacetate (DCFH-DA) assay. Specifically, treatment with AF-343 exerted stronger antioxidant effects in vitro and antiallergic effects in cells than treatment with three single natural plant extracts. Furthermore, AF-343 was observed to contain bioactive compounds, including catechin, aurantio-obtusin, and chicoric acid, which have been reported to elicit antiallergic responses. This study reveals that AF-343 attenuates allergic responses via suppression of β-hexosaminidase release, IL-4 and TNF-α secretion, and ROS generation, perhaps through mechanisms related to catechin, aurantio-obtusin, and chicoric acid. The results indicate that AF-343 can be considered a treatment for various allergic diseases.
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Gong G, Qi J, Lv Y, Dong S, Cao C, Li D, Zhao R, Li Z, Chen X. Discovery of 1,3-Disubstituted 2,5-Diketopiperazine Derivatives as Potent Class I HDACs Inhibitors. Chem Pharm Bull (Tokyo) 2020; 68:466-472. [PMID: 32378544 DOI: 10.1248/cpb.c20-00056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Histone deacetylases (HDACs) as attractive targets in many diseases therapies has been studied extensively, and its application in cancer research is the most important. Here, we developed a series of derivatives containing natural 2,5-diketopiperazine (DKP) skeleton. Several compounds exhibited distinct HDAC1 inhibitory activities, in particular 2a (IC50 = 405 nM). The selectivity profile for representative 2a indicated that this series of compounds had a preference for HDAC1-3. Additionally, 2a showed the best growth inhibitory activities against K562 and HL-60 tumor cell line with IC50 values of 4.23 and 4.16 µM, respectively. This work may lay the foundation for developing DKP-based HDAC inhibitors as a potential anticancer agent.
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Affiliation(s)
- Guoliang Gong
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University
| | - Ye Lv
- The Second Affiliated Hospital of Xi'an Jiaotong University
| | - Shuai Dong
- Key Laboratory of Tropical Biological Resources, Ministry of Education
| | - Chenyu Cao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University
| | - Ding Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University
| | - Ru Zhao
- The Second Affiliated Hospital of Xi'an Jiaotong University
| | - Zhen Li
- The Second Affiliated Hospital of Xi'an Jiaotong University
| | - Xin Chen
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University
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Machado VR, Jacques AV, Marceli NS, Biavatti MW, Santos-Silva MC. Anti-leukemic activity of semisynthetic derivatives of lupeol. Nat Prod Res 2020; 35:4494-4501. [PMID: 32178533 DOI: 10.1080/14786419.2020.1737051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In our previous work, lupeol was isolated from aerial parts of V. scorpioides and modified by semisynthetic approach. The purpose of this study was to investigate the cytotoxicity of lupeol and its derivatives previously prepared on the human K562 acute myeloid leukemia cell and human Jurkat acute lymphoid leukemia cell in vitro. Compounds 3β-hydroxylup-20(29)-en-30-al (2), lup-20(30)-en-3β,29-diol (3), 3β-acetoxylup-20(29)-en-30-al (5) and 3β-acetoxy-30-hydroxylup-20(29)-ene (6) presented cytotoxicity with IC50 ranging from 11.72 to 56.15 µM at 24 h of incubation for both cell lines. Most of the active compounds (3, 5 and 6) were selective to leukemia cells, in compare with healthy cells. The hemolysis assay showed high blood compatibility of the cytotoxic lupeol derivatives which makes possible an intravenous administration of these compounds aiming to the potential to development of anti-leukemic drugs.
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Affiliation(s)
- Vanessa Rocha Machado
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil
| | - Amanda Virtuoso Jacques
- Department of Clinical Analysis, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil
| | - Natália Stefanes Marceli
- Department of Clinical Analysis, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil
| | - Maique Weber Biavatti
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil
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48
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Rastelli G, Pellati F, Pinzi L, Gamberini MC. Repositioning Natural Products in Drug Discovery. Molecules 2020; 25:molecules25051154. [PMID: 32143476 PMCID: PMC7179106 DOI: 10.3390/molecules25051154] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 01/10/2023] Open
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49
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Cavaca LA, López-Coca IM, Silvero G, Afonso CA. The olive-tree leaves as a source of high-added value molecules: Oleuropein. BIOACTIVE NATURAL PRODUCTS 2020. [DOI: 10.1016/b978-0-12-817903-1.00005-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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50
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Hannigan GD, Prihoda D, Palicka A, Soukup J, Klempir O, Rampula L, Durcak J, Wurst M, Kotowski J, Chang D, Wang R, Piizzi G, Temesi G, Hazuda DJ, Woelk CH, Bitton DA. A deep learning genome-mining strategy for biosynthetic gene cluster prediction. Nucleic Acids Res 2019; 47:e110. [PMID: 31400112 PMCID: PMC6765103 DOI: 10.1093/nar/gkz654] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 07/09/2019] [Accepted: 08/08/2019] [Indexed: 11/17/2022] Open
Abstract
Natural products represent a rich reservoir of small molecule drug candidates utilized as antimicrobial drugs, anticancer therapies, and immunomodulatory agents. These molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The increase in full microbial genomes and similar resources has led to development of BGC prediction algorithms, although their precision and ability to identify novel BGC classes could be improved. Here we present a deep learning strategy (DeepBGC) that offers reduced false positive rates in BGC identification and an improved ability to extrapolate and identify novel BGC classes compared to existing machine-learning tools. We supplemented this with random forest classifiers that accurately predicted BGC product classes and potential chemical activity. Application of DeepBGC to bacterial genomes uncovered previously undetectable putative BGCs that may code for natural products with novel biologic activities. The improved accuracy and classification ability of DeepBGC represents a major addition to in-silico BGC identification.
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Affiliation(s)
- Geoffrey D Hannigan
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - David Prihoda
- Big Data Solutions, MSD Czech Republic s.r.o., Prague, Czech Republic.,Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Andrej Palicka
- AI & Big Data Analytics, MSD Czech Republic s.r.o., Prague, Czech Republic
| | - Jindrich Soukup
- Data Science, MSD Czech Republic s.r.o., Prague, Czech Republic
| | - Ondrej Klempir
- Bioinformatics & Cheminformatics Solutions, MSD Czech Republic s.r.o., Prague, Czech Republic
| | - Lena Rampula
- NLP, MSD Czech Republic s.r.o., Prague, Czech Republic
| | - Jindrich Durcak
- Bioinformatics & Cheminformatics Solutions, MSD Czech Republic s.r.o., Prague, Czech Republic
| | - Michael Wurst
- AI & Big Data Analytics, MSD Czech Republic s.r.o., Prague, Czech Republic
| | - Jakub Kotowski
- AI & Big Data Analytics, MSD Czech Republic s.r.o., Prague, Czech Republic
| | - Dan Chang
- Genetics & Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | - Rurun Wang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - Grazia Piizzi
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - Gergely Temesi
- Bioinformatics & Cheminformatics Solutions, MSD Czech Republic s.r.o., Prague, Czech Republic
| | - Daria J Hazuda
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA.,Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, PA, USA
| | - Christopher H Woelk
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - Danny A Bitton
- Bioinformatics & Cheminformatics Solutions, MSD Czech Republic s.r.o., Prague, Czech Republic
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