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Shen X, Zeng T, Chen N, Li J, Wu R. NIMO: A Natural Product-Inspired Molecular Generative Model Based on Conditional Transformer. Molecules 2024; 29:1867. [PMID: 38675687 PMCID: PMC11053988 DOI: 10.3390/molecules29081867] [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: 03/05/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Natural products (NPs) have diverse biological activity and significant medicinal value. The structural diversity of NPs is the mainstay of drug discovery. Expanding the chemical space of NPs is an urgent need. Inspired by the concept of fragment-assembled pseudo-natural products, we developed a computational tool called NIMO, which is based on the transformer neural network model. NIMO employs two tailor-made motif extraction methods to map a molecular graph into a semantic motif sequence. All these generated motif sequences are used to train our molecular generative models. Various NIMO models were trained under different task scenarios by recognizing syntactic patterns and structure-property relationships. We further explored the performance of NIMO in structure-guided, activity-oriented, and pocket-based molecule generation tasks. Our results show that NIMO had excellent performance for molecule generation from scratch and structure optimization from a scaffold.
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Affiliation(s)
- Xiaojuan Shen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; (X.S.); (T.Z.); (N.C.)
| | - Tao Zeng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; (X.S.); (T.Z.); (N.C.)
| | - Nianhang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; (X.S.); (T.Z.); (N.C.)
| | - Jiabo Li
- ChemXAI Inc., 53 Barry Lane, Syosset, NY 11791, USA
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; (X.S.); (T.Z.); (N.C.)
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2
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Hui Z, Wen H, Zhu J, Deng H, Jiang X, Ye XY, Wang L, Xie T, Bai R. Discovery of plant-derived anti-tumor natural products: Potential leads for anti-tumor drug discovery. Bioorg Chem 2024; 142:106957. [PMID: 37939507 DOI: 10.1016/j.bioorg.2023.106957] [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: 08/29/2023] [Revised: 10/14/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Natural products represent a paramount source of novel drugs. Numerous plant-derived natural products have demonstrated potent anti-tumor properties, thereby garnering considerable interest in their potential as anti-tumor drugs. This review compiles an overview of 242 recently discovered natural products, spanning the period from 2018 to the present. These natural products, which include 69 terpenoids, 42 alkaloids, 39 flavonoids, 21 steroids, 14 phenylpropanoids, 5 quinolines and 52 other compounds, are characterized by their respective chemical structures, anti-tumor activities, and mechanisms of action. By providing an essential reference and fresh insights, this review aims to support and inspire researchers engaged in the fields of natural products and anti-tumor drug discovery.
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Affiliation(s)
- Zi Hui
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Hao Wen
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Junlong Zhu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Haowen Deng
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiaoying Jiang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiang-Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Liwei Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China.
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China.
| | - Renren Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China.
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3
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Filer CN. The remarkable reimagining of psilocybin. Nat Prod Res 2023:1-3. [PMID: 37919964 DOI: 10.1080/14786419.2023.2272285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 10/08/2023] [Indexed: 11/04/2023]
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4
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Paschoalino M, Marinho MDS, Santos IA, Grosche VR, Martins DOS, Rosa RB, Jardim ACG. An update on the development of antiviral against Mayaro virus: from molecules to potential viral targets. Arch Microbiol 2023; 205:106. [PMID: 36881172 PMCID: PMC9990066 DOI: 10.1007/s00203-023-03441-y] [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: 11/19/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Mayaro virus (MAYV), first isolated in 1954 in Trinidad and Tobago islands, is the causative agent of Mayaro fever, a disease characterized by fever, rashes, headaches, myalgia, and arthralgia. The infection can progress to a chronic condition in over 50% of cases, with persistent arthralgia, which can lead to the disability of the infected individuals. MAYV is mainly transmitted through the bite of the female Haemagogus spp. mosquito genus. However, studies demonstrate that Aedes aegypti is also a vector, contributing to the spread of MAYV beyond endemic areas, given the vast geographical distribution of the mosquito. Besides, the similarity of antigenic sites with other Alphavirus complicates the diagnoses of MAYV, contributing to underreporting of the disease. Nowadays, there are no antiviral drugs available to treat infected patients, being the clinical management based on analgesics and non-steroidal anti-inflammatory drugs. In this context, this review aims to summarize compounds that have demonstrated antiviral activity against MAYV in vitro, as well as discuss the potentiality of viral proteins as targets for the development of antiviral drugs against MAYV. Finally, through rationalization of the data presented herein, we wish to encourage further research encompassing these compounds as potential anti-MAYV drug candidates.
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Affiliation(s)
- Marina Paschoalino
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | | | - Igor Andrade Santos
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Victória Riquena Grosche
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.,Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Daniel Oliveira Silva Martins
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.,Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Rafael Borges Rosa
- Institute Aggeu Magalhães, Fiocruz Pernambuco, Recife, Pernambuco, Brazil.,Rodents Animal Facilities Complex, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil. .,Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil.
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5
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Asiamah I, Obiri SA, Tamekloe W, Armah FA, Borquaye LS. Applications of Molecular Docking in Natural Products-Based Drug Discovery. SCIENTIFIC AFRICAN 2023. [DOI: 10.1016/j.sciaf.2023.e01593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
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6
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Antidiabetic Potential of Commonly Available Fruit Plants in Bangladesh: Updates on Prospective Phytochemicals and Their Reported MoAs. Molecules 2022; 27:molecules27248709. [PMID: 36557843 PMCID: PMC9782115 DOI: 10.3390/molecules27248709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/03/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
Diabetes mellitus is a life-threatening disorder affecting people of all ages and adversely disrupts their daily functions. Despite the availability of numerous synthetic-antidiabetic medications and insulin, the demand for the development of novel antidiabetic medications is increasing due to the adverse effects and growth of resistance to commercial drugs in the long-term usage. Hence, antidiabetic phytochemicals isolated from fruit plants can be a very nifty option to develop life-saving novel antidiabetic therapeutics, employing several pathways and MoAs (mechanism of actions). This review focuses on the antidiabetic potential of commonly available Bangladeshi fruits and other plant parts, such as seeds, fruit peals, leaves, and roots, along with isolated phytochemicals from these phytosources based on lab findings and mechanism of actions. Several fruits, such as orange, lemon, amla, tamarind, and others, can produce remarkable antidiabetic actions and can be dietary alternatives to antidiabetic therapies. Besides, isolated phytochemicals from these plants, such as swertisin, quercetin, rutin, naringenin, and other prospective phytochemicals, also demonstrated their candidacy for further exploration to be established as antidiabetic leads. Thus, it can be considered that fruits are one of the most valuable gifts of plants packed with a wide spectrum of bioactive phytochemicals and are widely consumed as dietary items and medicinal therapies in different civilizations and cultures. This review will provide a better understanding of diabetes management by consuming fruits and other plant parts as well as deliver innovative hints for the researchers to develop novel drugs from these plant parts and/or their phytochemicals.
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7
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Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL, Plisson F. Natural product drug discovery in the artificial intelligence era. Chem Sci 2022; 13:1526-1546. [PMID: 35282622 PMCID: PMC8827052 DOI: 10.1039/d1sc04471k] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage, accessible software and affordable online education have democratized the use of artificial intelligence (AI) in many sectors and research areas. The last decades have introduced natural language processing and machine learning algorithms, two subfields of AI, to tackle NP drug discovery challenges and open up opportunities. In this article, we review and discuss the rational applications of AI approaches developed to assist in discovering bioactive NPs and capturing the molecular "patterns" of these privileged structures for combinatorial design or target selectivity.
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Affiliation(s)
- F I Saldívar-González
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - V D Aldas-Bulos
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
| | - J L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - F Plisson
- CONACYT - Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
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8
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Aro AO, Famuyide IM, Oyagbemi AA, Kabongo-Kayoka PN, McGaw LJ. In Vitro Potential of the Acetone Leaf Extract and Fractions of Psychotria capensis (Eckl.) Vatke (Rubiaceae) to Combat Co-Infection of Tuberculosis and Helminthiasis. Front Pharmacol 2022; 12:744137. [PMID: 35087402 PMCID: PMC8787188 DOI: 10.3389/fphar.2021.744137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/16/2021] [Indexed: 11/15/2022] Open
Abstract
Tuberculosis (TB) is a disease of global importance that affects millions of people. Approximately a quarter of the world’s population is currently infected with M. tuberculosis, and about 10% of those infected will develop into active disease, particularly immune compromised individuals. Helminthiasis is of global health importance, affecting over 2 billion people mostly in resource-poor countries. Co-infection with tuberculosis (TB) and helminths (worms) is an emerging global public health concern with both affecting about one-third of the global population. Chronic infection with helminths can result in impaired immune responses to TB as well as enhancing failure to TB therapy and BCG vaccination. Antimycobacterial and anthelmintic activities of the acetone extract and fractions of Psychotria capensis were evaluated, including their in vitro safety. In addition, the anti-inflammatory and immunomodulatory effect of the fractions and crude extract of P. capensis were assessed. Antimycobacterial activity of the extract and fractions was tested against four non-tuberculous mycobacteria (Mycobacterium smegmatis, M. fortuitum, M. aurum, M. bovis BCG) and pathogenic M. tuberculosis H37Rv while the Egg Hatch Assay (EHA) was used for the anthelmintic test on eggs of Haemonchus contortus. Cytotoxicity was determined against Vero kidney cells while in vitro immune modulation via cytokine production was determined on activated macrophages. The minimum inhibitory concentration (MIC) values of the Psychotria capensis acetone extract and fractions ranged from 39 to 1,250 μg/ml with the crude extract and hexane fraction having the best MIC values (both 39 μg/ml). In the EHA, the inhibitory concentration (IC50) ranged from 160 to 630 μg/ml with the hexane fraction having the best activity. The hexane and chloroform fractions were relatively non-toxic with LC50 values of 290 and 248 μg/ml respectively, while the acetone crude extract (64 μg/ml) and n-butanol fraction (71 μg/ml) were moderately toxic. The SI values (LC50/MIC) ranged from 0.1 to 7.4 with the hexane fraction having the highest value against M. smegmatis (7.4). The hexane fraction had the best dual anthelmintic and antimycobacterial activity. This fraction had the best NO inhibitory activity and was the least cytotoxic, indicating that its activity was not due to general metabolic toxicity, with 96.54% cell viability. Pro-inflammatory cytokines such as IL-12p70 were upregulated while IL-10 expression was inhibited by the extracts. Compounds were detected using GC-MS analysis, and in both the crude acetone extract and the hexane fraction was the diterpene neophytadiene, which has anti-inflammatory and antimicrobial activity. Finding alternative or complementary approaches to dealing with TB infections by, amongst other things, reducing the incidence of helminth infestations may lessen the burden of TB, contributing to slowing the spread of multi-drug resistance.
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Affiliation(s)
- Abimbola O Aro
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Science, University of South Africa, Florida, South Africa
| | - Ibukun M Famuyide
- Phytomedicine Programme, Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Ademola A Oyagbemi
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Prudence N Kabongo-Kayoka
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Science, University of South Africa, Florida, South Africa
| | - Lyndy J McGaw
- Phytomedicine Programme, Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
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Alam S, Sarker MMR, Sultana TN, Chowdhury MNR, Rashid MA, Chaity NI, Zhao C, Xiao J, Hafez EE, Khan SA, Mohamed IN. Antidiabetic Phytochemicals From Medicinal Plants: Prospective Candidates for New Drug Discovery and Development. Front Endocrinol (Lausanne) 2022; 13:800714. [PMID: 35282429 PMCID: PMC8907382 DOI: 10.3389/fendo.2022.800714] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/04/2022] [Indexed: 02/05/2023] Open
Abstract
Diabetes, a chronic physiological dysfunction affecting people of different age groups and severely impairs the harmony of peoples' normal life worldwide. Despite the availability of insulin preparations and several synthetic oral antidiabetic drugs, there is a crucial need for the discovery and development of novel antidiabetic drugs because of the development of resistance and side effects of those drugs in long-term use. On the contrary, plants or herbal sources are getting popular day by day to the scientists, researchers, and pharmaceutical companies all over the world to search for potential bioactive compound(s) for the discovery and development of targeted novel antidiabetic drugs that may control diabetes with the least unwanted effects of conventional antidiabetic drugs. In this review, we have presented the prospective candidates comprised of either isolated phytochemical(s) and/or extract(s) containing bioactive phytoconstituents which have been reported in several in vitro, in vivo, and clinical studies possessing noteworthy antidiabetic potential. The mode of actions, attributed to antidiabetic activities of the reported phytochemicals and/or plant extracts have also been described to focus on the prospective phytochemicals and phytosources for further studies in the discovery and development of novel antidiabetic therapeutics.
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Affiliation(s)
- Safaet Alam
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Md. Moklesur Rahman Sarker
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
- Pharmacology and Toxicology Research Division, Health Med Science Research Limited, Dhaka, Bangladesh
- *Correspondence: Md. Moklesur Rahman Sarker, ; ; orcid.org/0000-0001-9795-0608; Isa Naina Mohamed, ; orcid.org/0000-0001-8891-2423
| | | | | | - Mohammad A. Rashid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | | | - Chao Zhao
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo, Vigo, Spain
| | - Elsayed E. Hafez
- Plant Protection and Biomolecular Diagnosis Department, ALCRI (Arid Lands Cultivation Research Institute), City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Shah Alam Khan
- College of Pharmacy, National University of Science & Technology, Muscat, Oman
| | - Isa Naina Mohamed
- Pharmacology Department, Medicine Faculty, Universiti Kebangsaan Malaysia (The National University of Malaysia), Kuala Lumpur, Malaysia
- *Correspondence: Md. Moklesur Rahman Sarker, ; ; orcid.org/0000-0001-9795-0608; Isa Naina Mohamed, ; orcid.org/0000-0001-8891-2423
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10
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Zdouc MM, Iorio M, Maffioli SI, Crüsemann M, Donadio S, Sosio M. Planomonospora: A Metabolomics Perspective on an Underexplored Actinobacteria Genus. JOURNAL OF NATURAL PRODUCTS 2021; 84:204-219. [PMID: 33496580 PMCID: PMC7922807 DOI: 10.1021/acs.jnatprod.0c00807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 06/12/2023]
Abstract
Despite an excellent track record, microbial drug discovery suffers from high rates of rediscovery. Better workflows for the rapid investigation of complex extracts are needed to increase throughput and to allow early prioritization of samples. In addition, systematic characterization of poorly explored strains is seldomly performed. Here, we report a metabolomic study of 72 isolates belonging to the rare actinomycete genus Planomonospora, using a workflow of commonly used open access tools to investigate its secondary metabolites. The results reveal a correlation of chemical diversity and strain phylogeny, with classes of metabolites exclusive to certain phylogroups. We were able to identify previously reported Planomonospora metabolites, including the ureylene-containing oligopeptide antipain, the thiopeptide siomycin including new congeners, and the ribosomally synthesized peptides sphaericin and lantibiotic 97518. In addition, we found that Planomonospora strains can produce the siderophore desferrioxamine or a salinichelin-like peptide. Analysis of the genomes of three newly sequenced strains led to the detection of 59 gene cluster families, of which three were connected to products found by LC-MS/MS profiling. This study demonstrates the value of metabolomic studies to investigate poorly explored taxa and provides a first picture of the biosynthetic capabilities of the genus Planomonospora.
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Affiliation(s)
- Mitja M. Zdouc
- Naicons
Srl., Viale Ortles 22/4, 20139 Milano, Italy
- Swammerdam
Institute for Life Sciences, University
of Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| | | | | | - Max Crüsemann
- Institut
für Pharmazeutische Biologie, Rheinische
Friedrich-Wilhelms-Universität, Nußallee 6, 53115 Bonn, Germany
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11
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Protti ÍF, Rodrigues DR, Fonseca SK, Alves RJ, de Oliveira RB, Maltarollo VG. Do Drug-likeness Rules Apply to Oral Prodrugs? ChemMedChem 2021; 16:1446-1456. [PMID: 33471444 DOI: 10.1002/cmdc.202000805] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/12/2021] [Indexed: 12/21/2022]
Abstract
This paper describes a comparative analysis of the physicochemical and structural properties of prodrugs and their corresponding drugs with regard to drug-likeness rules. The dataset used in this work was obtained from the DrugBank. Sixty-five pairs of prodrugs/drugs were retrieved and divided into the following categories: carrier-linked to increase hydrophilic character, carrier-linked to increase absorption, and bioprecursors. We compared the physicochemical properties related to drug-likeness between prodrugs and drugs. Our results show that prodrugs do not always follow Lipinski's Rule of 5, especially as we observed 15 prodrugs with more than 10 hydrogen bond acceptors and 18 with a molecular weight greater than 500 Da. This fact highlights the importance of extending Lipinski's rules to encompass other parameters as both strategies (filtering of drug-like chemical libraries and prodrug design) aim to improve the bioavailability of compounds. Therefore, critical reasoning is fundamental to determine whether a structure has drug-like properties or could be considered a potential orally active compound in the drug-design pipeline.
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Affiliation(s)
- Ícaro F Protti
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Daniel R Rodrigues
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Sofia K Fonseca
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Ricardo J Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Renata B de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
| | - Vinícius G Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, BR 31270-901, Brazil
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12
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Topsentinol L Trisulfate, a Marine Natural Product That Targets Basal-like and Claudin-Low Breast Cancers. Mar Drugs 2021; 19:md19010041. [PMID: 33477536 PMCID: PMC7831112 DOI: 10.3390/md19010041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022] Open
Abstract
Patients diagnosed with basal-like breast cancer suffer from poor prognosis and limited treatment options. There is an urgent need to identify new targets that can benefit patients with basal-like and claudin-low (BL-CL) breast cancers. We screened fractions from our Marine Invertebrate Compound Library (MICL) to identify compounds that specifically target BL-CL breast cancers. We identified a previously unreported trisulfated sterol, i.e., topsentinol L trisulfate (TLT), which exhibited increased efficacy against BL-CL breast cancers relative to luminal/HER2+ breast cancer. Biochemical investigation of the effects of TLT on BL-CL cell lines revealed its ability to inhibit activation of AMP-activated protein kinase (AMPK) and checkpoint kinase 1 (CHK1) and to promote activation of p38. The importance of targeting AMPK and CHK1 in BL-CL cell lines was validated by treating a panel of breast cancer cell lines with known small molecule inhibitors of AMPK (dorsomorphin) and CHK1 (Ly2603618) and recording the increased effectiveness against BL-CL breast cancers as compared with luminal/HER2+ breast cancer. Finally, we generated a drug response gene-expression signature and projected it against a human tumor panel of 12 different cancer types to identify other cancer types sensitive to the compound. The TLT sensitivity gene-expression signature identified breast and bladder cancer as the most sensitive to TLT, while glioblastoma multiforme was the least sensitive.
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13
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Huang HZ, Qiu M, Lin JZ, Li MQ, Ma XT, Ran F, Luo CH, Wei XC, Xu RC, Tan P, Fan SH, Yang M, Han L, Zhang DK. Potential effect of tropical fruits Phyllanthus emblica L. for the prevention and management of type 2 diabetic complications: a systematic review of recent advances. Eur J Nutr 2021; 60:3525-3542. [PMID: 33439332 DOI: 10.1007/s00394-020-02471-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Phyllanthus emblica is a fruit widely consumed in subtropical areas, which is rich in polyphenols and other nutrients. There are increasing evidences that as a daily and nutritious fruit, it may have a positive role in controlling diabetic complications. According to the new study, its mechanisms include enhancing the functioning of insulin, reducing insulin resistance, activating the insulin-signaling pathway, protecting β-cells, scavenging free radicals, alleviating inflammatory reactions, and reducing the accumulation of advanced glycation end products. Owing to its few side effects, and low price, it should be easily accepted by patients and has potential for preventing diabetes. Taken together, Phyllanthus emblica may be an ideal fruit for controlling diabetic complications. This review highlights the latest findings of the role of Phyllanthus emblica in anti-diabetes and its complications, especially clarifies the molecular mechanism of the chemical components related to this effect, and prospects some existing problems and future research directions.
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Affiliation(s)
- Hao-Zhou Huang
- Pharmacy College, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of TCM, Chengdu, 611137, China
| | - Min Qiu
- Pharmacy College, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of TCM, Chengdu, 611137, China
| | - Jun-Zhi Lin
- Teaching Hospital of Chengdu University of TCM, Chengdu, 610072, China
| | - Meng-Qi Li
- Sichuan Nursing Vocational College, Chengdu, 610100, China
| | - Xi-Tao Ma
- Teaching Hospital of Chengdu University of TCM, Chengdu, 610072, China
| | - Fei Ran
- Pharmacy College, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of TCM, Chengdu, 611137, China
| | - Chuan-Hong Luo
- Pharmacy College, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of TCM, Chengdu, 611137, China
| | - Xi-Chuan Wei
- Pharmacy College, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of TCM, Chengdu, 611137, China
| | - Run-Chun Xu
- Pharmacy College, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of TCM, Chengdu, 611137, China
| | - Peng Tan
- State Key Laboratory of Biological Evaluation of Traditional Chinese Medicine Quality, National Administration of TCM, Sichuan Academy of Chinese Medicine Sciences, Chengdu, 610041, China
| | - San-Hu Fan
- Sanajon Pharmaceutical Group, Chengdu, 610000, China
| | - Ming Yang
- Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, People's Republic of China
| | - Li Han
- Pharmacy College, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of TCM, Chengdu, 611137, China.
| | - Ding-Kun Zhang
- Pharmacy College, State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of TCM, Chengdu, 611137, China.
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14
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Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. A Deep Learning Approach to Antibiotic Discovery. Cell 2020; 180:688-702.e13. [PMID: 32084340 DOI: 10.1016/j.cell.2020.01.021] [Citation(s) in RCA: 731] [Impact Index Per Article: 182.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 02/06/2023]
Abstract
Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to discover new antibiotics. To address this challenge, we trained a deep neural network capable of predicting molecules with antibacterial activity. We performed predictions on multiple chemical libraries and discovered a molecule from the Drug Repurposing Hub-halicin-that is structurally divergent from conventional antibiotics and displays bactericidal activity against a wide phylogenetic spectrum of pathogens including Mycobacterium tuberculosis and carbapenem-resistant Enterobacteriaceae. Halicin also effectively treated Clostridioides difficile and pan-resistant Acinetobacter baumannii infections in murine models. Additionally, from a discrete set of 23 empirically tested predictions from >107 million molecules curated from the ZINC15 database, our model identified eight antibacterial compounds that are structurally distant from known antibiotics. This work highlights the utility of deep learning approaches to expand our antibiotic arsenal through the discovery of structurally distinct antibacterial molecules.
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Affiliation(s)
- Jonathan M Stokes
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin Yang
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kyle Swanson
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wengong Jin
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andres Cubillos-Ruiz
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Nina M Donghia
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Craig R MacNair
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Lindsey A Carfrae
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Zohar Bloom-Ackermann
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Victoria M Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anush Chiappino-Pepe
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ian W Andrews
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Emma J Chory
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Tommi S Jaakkola
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Regina Barzilay
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - James J Collins
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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15
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McCallum JL, Vacon JND, Kirby CW. Ultra-Micro-Scale-Fractionation (UMSF) as a Powerful Tool for Bioactive Molecules Discovery. Molecules 2020; 25:E3677. [PMID: 32806767 PMCID: PMC7464926 DOI: 10.3390/molecules25163677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022] Open
Abstract
Herein is detailed the development and validation of an ultra-micro-scale-fractionation (UMSF) technique for the discovery of plant-based, bioactive molecules, coupling the advantages of ultra-performance liquid chromatography mass spectrometry (UPLC-MS) separations with microtiter plate-based bioassay screens. This novel one-step approach simultaneously uses UPLC to collect chemical profile information, while performing high-resolution fractionation, greatly improving workflow compared to methods relying on high-performance liquid chromatography (HPLC), solid phase extraction or flash systems for chromatographic separations. Using the UMSF technique, researchers are able to utilize smaller quantities of starting materials, reduce solvent consumption during fractionation, reduce laborious solvent dry down times, replace costly single-use solid-phase-extraction cartridges with reusable analytical-sale UPLC columns, reduce fractionation times to less than 10 min, while simultaneously generating chemical profile data of active fractions and enjoying superior chromatographic resolution. Using this technique, individual bioactive components can be readily purified, identified, and bioassayed in one step from crude extracts, thereby eliminating ambiguous synergistic effects often reported in plant-based natural products research. A successful case-study is presented illustrating the versatility of this technique in identifying lupulone as the principal cytotoxic component from hops (Humulus lupulus L.), using a brine shrimp (Artemia franciscana) model. These results confirm and expand upon previous cell-based bioassay studies using a more complex, multicellular organism, and add to our understanding of structure-function activity relationships for secondary metabolites in hops and the Cannabaceae plant family.
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Affiliation(s)
- Jason L. McCallum
- Agriculture and Agri-Food Canada, Charlottetown Research and Development Centre, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada; (J.N.D.V.); (C.W.K.)
| | - Jennifer N. D. Vacon
- Agriculture and Agri-Food Canada, Charlottetown Research and Development Centre, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada; (J.N.D.V.); (C.W.K.)
- University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Christopher W. Kirby
- Agriculture and Agri-Food Canada, Charlottetown Research and Development Centre, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada; (J.N.D.V.); (C.W.K.)
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16
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An enumeration of natural products from microbial, marine and terrestrial sources. PHYSICAL SCIENCES REVIEWS 2020. [DOI: 10.1515/psr-2018-0121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract
The discovery of a new drug is a multidisciplinary and very costly task. One of the major steps is the identification of a lead compound, i.e. a compound with a certain degree of potency and that can be chemically modified to improve its activity, metabolic properties, and pharmacokinetics profiles. Terrestrial sources (plants and fungi), microbes and marine organisms are abundant resources for the discovery of new structurally diverse and biologically active compounds. In this chapter, an attempt has been made to quantify the numbers of known published chemical structures (available in chemical databases) from natural sources. Emphasis has been laid on the number of unique compounds, the most abundant compound classes and the distribution of compounds in terrestrial and marine habitats. It was observed, from the recent investigations, that ~500,000 known natural products (NPs) exist in the literature. About 70 % of all NPs come from plants, terpenoids being the most represented compound class (except in bacteria, where amino acids, peptides, and polyketides are the most abundant compound classes). About 2,000 NPs have been co-crystallized in PDB structures.
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17
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Blagodatski A, Klimenko A, Jia L, Katanaev VL. Small Molecule Wnt Pathway Modulators from Natural Sources: History, State of the Art and Perspectives. Cells 2020; 9:cells9030589. [PMID: 32131438 PMCID: PMC7140537 DOI: 10.3390/cells9030589] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/25/2020] [Accepted: 02/28/2020] [Indexed: 02/07/2023] Open
Abstract
The Wnt signaling is one of the major pathways known to regulate embryonic development, tissue renewal and regeneration in multicellular organisms. Dysregulations of the pathway are a common cause of several types of cancer and other diseases, such as osteoporosis and rheumatoid arthritis. This makes Wnt signaling an important therapeutic target. Small molecule activators and inhibitors of signaling pathways are important biomedical tools which allow one to harness signaling processes in the organism for therapeutic purposes in affordable and specific ways. Natural products are a well known source of biologically active small molecules with therapeutic potential. In this article, we provide an up-to-date overview of existing small molecule modulators of the Wnt pathway derived from natural products. In the first part of the review, we focus on Wnt pathway activators, which can be used for regenerative therapy in various tissues such as skin, bone, cartilage and the nervous system. The second part describes inhibitors of the pathway, which are desired agents for targeted therapies against different cancers. In each part, we pay specific attention to the mechanisms of action of the natural products, to the models on which they were investigated, and to the potential of different taxa to yield bioactive molecules capable of regulating the Wnt signaling.
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Affiliation(s)
- Artem Blagodatski
- School of Biomedicine, Far Eastern Federal University, Vladivostok 690090, Russia;
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Correspondence: (A.B.); (V.L.K.)
| | - Antonina Klimenko
- School of Biomedicine, Far Eastern Federal University, Vladivostok 690090, Russia;
| | - Lee Jia
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China;
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou 350108, China
| | - Vladimir L. Katanaev
- School of Biomedicine, Far Eastern Federal University, Vladivostok 690090, Russia;
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China;
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- Correspondence: (A.B.); (V.L.K.)
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18
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Muhammad I, Rahman N, Nayab GE, Niaz S, Shah M, Afridi SG, Khan H, Daglia M, Capanoglu E. The Molecular Docking of Flavonoids Isolated from Daucus carota as a Dual Inhibitor of MDM2 and MDMX. Recent Pat Anticancer Drug Discov 2020; 15:154-164. [PMID: 32101134 DOI: 10.2174/1574892815666200226112506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/22/2020] [Accepted: 02/23/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Cancer is characterized by overexpression of p53 associated proteins, which down-regulate P53 signaling pathway. In cancer therapy, p53 activity can be restored by inhibiting the interaction of MDMX (2N0W) and MDM2 (4JGR) proteins with P53 protein. OBJECTIVE In the current, study in silico approaches were adapted to use a natural product as a source of cancer therapy. METHODS In the current study in silico approaches were adapted to use a natural product as a source of cancer therapy. For in silico studies, Chemdraw and Molecular Operating Environment were used for structure drawing and molecular docking, respectively. Flavonoids isolated from D. carota were docked with cancerous proteins. RESULT Based on the docking score analysis, we found that compound 7 was the potent inhibitor of both cancerous proteins and can be used as a potent molecule for inhibition of 2N0W and 4JGR interaction with p53. CONCLUSION Thus the compound 7 can be used for the revival of p53 signaling pathway function however, intensive in vitro and in vivo experiments are required to prove the in silico analysis.
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Affiliation(s)
- Ijaz Muhammad
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Noor Rahman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Gul E Nayab
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Sadaf Niaz
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Sahib G Afridi
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Maria Daglia
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Esra Capanoglu
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
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19
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Wen S, Wang F, Ji Z, Pan Y, Jian M, Bi Y, Zhou G, Luo L, Chen T, Li L, Ding Z, Abi ME, Liu A, Bao F. Salp15, a Multifunctional Protein From Tick Saliva With Potential Pharmaceutical Effects. Front Immunol 2020; 10:3067. [PMID: 31998324 PMCID: PMC6968165 DOI: 10.3389/fimmu.2019.03067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/16/2019] [Indexed: 12/30/2022] Open
Abstract
Ixodes ticks are the main vectors for a number of zoonotic diseases, including Lyme disease. Ticks secrete saliva directly into a mammalian host while feeding on the host's blood. This action serves to modulate host immunity and coagulation, thus allowing ticks to attach and feed upon their host. One of the most extensively studied components of tick saliva is Salp15. Research has shown that this protein binds specifically to CD4 molecules on the surface of T lymphocytes, interferes with TCR-mediated signaling transduction, inhibits CD4+ T cell activation and proliferation, and impedes the secretion of interleukin 2 (IL-2). Salp15 also binds specifically to dendritic cell dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) to up-regulate the expression of CD73 in regulatory T cells. Collectively, these findings render this salivary protein a potential candidate for a range of therapeutic applications. Here, we discuss our current understanding of Salp15 and the mechanisms that might be used to treat disease.
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Affiliation(s)
- Shiyuan Wen
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China.,The Center of Tropical Diseases, The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China.,The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Feng Wang
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China.,The Center of Tropical Diseases, The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China
| | - Zhenhua Ji
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - YingYi Pan
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Miaomiao Jian
- The Center of Tropical Diseases, The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - YunFeng Bi
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China.,The Center of Tropical Diseases, The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China
| | - Guozhong Zhou
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China.,The Center of Tropical Diseases, The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China
| | - Lisha Luo
- The Center of Tropical Diseases, The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Taigui Chen
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Lianbao Li
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Zhe Ding
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Manzama-Esso Abi
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Aihua Liu
- The Center of Tropical Diseases, The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Fukai Bao
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, China.,The Center of Tropical Diseases, The Institute for Tropical Medicine, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China
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20
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Agarwal G, Carcache PJB, Addo EM, Kinghorn AD. Current status and contemporary approaches to the discovery of antitumor agents from higher plants. Biotechnol Adv 2020; 38:107337. [PMID: 30633954 PMCID: PMC6614024 DOI: 10.1016/j.biotechadv.2019.01.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/13/2022]
Abstract
Higher plant constituents have afforded clinically available anticancer drugs. These include both chemically unmodified small molecules and their synthetic derivatives currently used or those in clinical trials as antineoplastic agents, and an updated summary is provided. In addition, botanical dietary supplements, exemplified by mangosteen and noni constituents, are also covered as potential cancer chemotherapeutic agents. Approaches to metabolite purification, rapid dereplication, and biological evaluation including analytical hyphenated techniques, molecular networking, and advanced cellular and animal models are discussed. Further, enhanced and targeted drug delivery systems for phytochemicals, including micelles, nanoparticles and antibody drug conjugates (ADCs) are described herein.
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Affiliation(s)
- Garima Agarwal
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Peter J Blanco Carcache
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Ermias Mekuria Addo
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - A Douglas Kinghorn
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
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21
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Aldholmi M, Marchand P, Ourliac-Garnier I, Le Pape P, Ganesan A. A Decade of Antifungal Leads from Natural Products: 2010-2019. Pharmaceuticals (Basel) 2019; 12:ph12040182. [PMID: 31842280 PMCID: PMC6958371 DOI: 10.3390/ph12040182] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/21/2022] Open
Abstract
In this review, we discuss novel natural products discovered within the last decade that are reported to have antifungal activity against pathogenic species. Nearly a hundred natural products were identified that originate from bacteria, algae, fungi, sponges, and plants. Fungi were the most prolific source of antifungal compounds discovered during the period of review. The structural diversity of these antifungal leads encompasses all the major classes of natural products including polyketides, shikimate metabolites, terpenoids, alkaloids, and peptides.
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Affiliation(s)
- Mohammed Aldholmi
- Department of Natural Products and Alternative Medicine, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Pascal Marchand
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000 Nantes, France; (P.M.); (I.O.-G.); (P.L.P.)
| | - Isabelle Ourliac-Garnier
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000 Nantes, France; (P.M.); (I.O.-G.); (P.L.P.)
| | - Patrice Le Pape
- Université de Nantes, Cibles et Médicaments des Infections et du Cancer, IICiMed, EA 1155, F-44000 Nantes, France; (P.M.); (I.O.-G.); (P.L.P.)
| | - A. Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Correspondence:
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22
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Bariotakis M, Georgescu L, Laina D, Oikonomou I, Ntagounakis G, Koufaki MI, Souma M, Choreftakis M, Zormpa OG, Smykal P, Sourvinos G, Lionis C, Castanas E, Karousou R, Pirintsos SA. From wild harvest towards precision agriculture: Use of Ecological Niche Modelling to direct potential cultivation of wild medicinal plants in Crete. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133681. [PMID: 31756796 DOI: 10.1016/j.scitotenv.2019.133681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Understanding the distribution of wild medicinal plants and areas that are suitable for cultivation of these plants is important for both conservation and agriculture. Here, we study ten taxa with known ethnopharmacological uses, which have been used extensively in traditional medicine and as culinary supplements. We aim to (1) predict and map the potential habitat suitability for these taxa across the study area, (2) investigate spatial patterns that could have management implications, such as niche similarities among the taxa and suitability "hotspots" with the use of novel indices, and (3) develop a platform where parts of this information can be accessed and utilized by all interested groups, from the policy-maker level to the individual practitioner level. Ecological Niche Models developed for each study taxon, based on topographic, bioclimatic, soil, and land use variables had high predictive power and were used as the basis for suitability visualization. A series of informative indices were also calculated and mapped, revealing spatial patterns not readily observable from the single-taxon predictions, and providing valuable information to managers. Finally, a web-based, easy-to-use application was also created, where the predicted suitability scores for the study area can be made accessible to anyone interested. The application can provide information both in a visual form (i.e. maps of predicted suitability) and in a numerical form (i.e. estimated suitability scores for all taxa in a given geographical location). This study provides the scientific tools to make a step towards cultivating a group of economically important wild medicinal plants in Crete, as well as the tools to disseminate this information to decision makers and practitioners, and eventually integrate the research findings in local agricultural practices.
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Affiliation(s)
- Michael Bariotakis
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR 741 00 Rethymnon, Greece
| | - Luciana Georgescu
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece
| | - Danae Laina
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece
| | - Ioanna Oikonomou
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece
| | - George Ntagounakis
- Botanical Garden, University of Crete, Gallos University Campus, GR 741 00 Rethymnon, Greece
| | | | - Maria Souma
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece
| | | | - Ourania Grigoriadou Zormpa
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR 741 00 Rethymnon, Greece
| | - Petr Smykal
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - George Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece
| | - Christos Lionis
- Clinic of Social and Family Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Elias Castanas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, Heraklion, Greece
| | - Regina Karousou
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stergios A Pirintsos
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR 741 00 Rethymnon, Greece.
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Cheminformatics Explorations of Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:1-35. [PMID: 31621009 DOI: 10.1007/978-3-030-14632-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The chemistry of natural products is fascinating and has continuously attracted the attention of the scientific community for many reasons including, but not limited to, biosynthesis pathways, chemical diversity, the source of bioactive compounds and their marked impact on drug discovery. There is a broad range of experimental and computational techniques (molecular modeling and cheminformatics) that have evolved over the years and have assisted the investigation of natural products. Herein, we discuss cheminformatics strategies to explore the chemistry and applications of natural products. Since the potential synergisms between cheminformatics and natural products are vast, we will focus on three major aspects: (1) exploration of the chemical space of natural products to identify bioactive compounds, with emphasis on drug discovery; (2) assessment of the toxicity profile of natural products; and (3) diversity analysis of natural product collections and the design of chemical collections inspired by natural sources.
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Grygorenko OO, Volochnyuk DM, Ryabukhin SV, Judd DB. The Symbiotic Relationship Between Drug Discovery and Organic Chemistry. Chemistry 2019; 26:1196-1237. [PMID: 31429510 DOI: 10.1002/chem.201903232] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/19/2019] [Indexed: 12/20/2022]
Abstract
All pharmaceutical products contain organic molecules; the source may be a natural product or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry underpins both existing and upcoming pharmaceutical products. The reverse relationship has also affected organic synthesis, changing its landscape towards increasingly complex targets. This Review article sets out to give a concise appraisal of this symbiotic relationship between organic chemistry and drug discovery, along with a discussion of the design concepts and highlighting key milestones along the journey. In particular, criteria for a high-quality compound library design enabling efficient virtual navigation of chemical space, as well as rise and fall of concepts for its synthetic exploration (such as combinatorial chemistry; diversity-, biology-, lead-, or fragment-oriented syntheses; and DNA-encoded libraries) are critically surveyed.
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Affiliation(s)
- Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Dmitriy M Volochnyuk
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine.,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kiev, 02660, Ukraine
| | - Sergey V Ryabukhin
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Duncan B Judd
- Awridian Ltd., Stevenage Bioscience Catalyst, Gunnelswood Road, Stevenage, Herts, SG1 2FX, UK
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25
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El-Naggar MH, Abdel Bar FM, Harsha C, Monisha J, Shimizu K, Kunnumakkara AB, Badria FA. Synthesis of new selective cytotoxic ricinine analogues against oral squamous cell carcinoma. Nat Prod Res 2019; 35:2145-2156. [PMID: 31526148 DOI: 10.1080/14786419.2019.1663513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sixteen new analogues were synthesized from ricinine and tested alongside with seven known analogues for their cytotoxic activity against oral cancer (SAS cells) and normal epithelial cells (L132 cells). In contrast to 5-FU, the synthesized ricinine analogues did not show toxicity to normal cells. However, some of them inhibited the proliferation of oral cancer cells at 25 µM as evident from the MTT assay results. Ricinine analogue (19) was shown to be the most active derivative (69.22% inhibition). Potential targets involved in the oral cancer inhibitory activity of compound 19 were investigated using in-silico studies and western blot analysis. PTP1B was predicted to be a target for ricinine using reverse docking approach. This prediction was confirmed by western blot analysis that revealed the downregulation of PTP1B protein by compound 19. Moreover, it showed downregulation of COX-2 which is also extensively expressed in oral cancer.
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Affiliation(s)
- Mai H El-Naggar
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516 Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Kafrelsheikh university, Kafrelsheikh, Egypt
| | - Fatma M Abdel Bar
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516 Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Choudhary Harsha
- Laboratory of Cancer Biology and DBT-AIST International Laboratory for Advanced Biomedicine, Biosciences and Bioengineering Department, Indian Institute of Technology Guwahati, Assam, India
| | - Javadi Monisha
- Laboratory of Cancer Biology and DBT-AIST International Laboratory for Advanced Biomedicine, Biosciences and Bioengineering Department, Indian Institute of Technology Guwahati, Assam, India
| | - Kuniyoshi Shimizu
- Systematic Forest and Forest Products Sciences Division, Agro-Environmental Sciences Department, Bioresource and Bioenvironmental Sciences Graduate School, Kyushu University, Fukuoka, Japan
| | - Ajaikumar B Kunnumakkara
- Laboratory of Cancer Biology and DBT-AIST International Laboratory for Advanced Biomedicine, Biosciences and Bioengineering Department, Indian Institute of Technology Guwahati, Assam, India
| | - Farid A Badria
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516 Egypt
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26
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Lorsbach BA, Sparks TC, Cicchillo RM, Garizi NV, Hahn DR, Meyer KG. Natural products: a strategic lead generation approach in crop protection discovery. PEST MANAGEMENT SCIENCE 2019; 75:2301-2309. [PMID: 30672097 DOI: 10.1002/ps.5350] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 05/14/2023]
Abstract
With the anticipated population growth in the coming decades, the changing regulatory environment, and the continued emergence of resistance to commercial pesticides, there is a constant need to discover new lead chemistries with novel modes of action. We have established a portfolio of approaches to accelerate lead generation. One of these approaches capitalizes on the rich bioactivity of natural products (NPs), highlighted by the numerous examples of NP-based crop protection compounds. Within Corteva Agriscience and the affiliated preceding companies, NPs have been a fruitful approach, for nearly three decades, to identifying and bringing to the market crop protection products inspired by or originating from NPs, . Included in these NP-based crop protection products are the spinosyns family of insecticides, and those from more recent areas of NP-based fungicidal chemistry, as highlighted in this perspective. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Beth A Lorsbach
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Thomas C Sparks
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Robert M Cicchillo
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Negar V Garizi
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Donald R Hahn
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
| | - Kevin G Meyer
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Crop Protection Discovery, Dow AgroSciences, Indianapolis, IN, USA
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27
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Affiliation(s)
- Nagy Morsy
- Department of Chemistry, Faculty of Sciences and Arts, Khulais, University of Jeddah, Jeddah, Saudi Arabia
- Department of Chemistry of Natural Compounds, National Research Centre, Dokki, Cairo, Egypt
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28
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Katanaev VL, Di Falco S, Khotimchenko Y. The Anticancer Drug Discovery Potential of Marine Invertebrates from Russian Pacific. Mar Drugs 2019; 17:E474. [PMID: 31426365 PMCID: PMC6723377 DOI: 10.3390/md17080474] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/13/2019] [Indexed: 12/19/2022] Open
Abstract
Despite huge efforts by academia and pharmaceutical industry, cancer remains the second cause of disease-related death in developed countries. Novel sources and principles of anticancer drug discovery are in urgent demand. Marine-derived natural products represent a largely untapped source of future drug candidates. This review focuses on the anticancer drug discovery potential of marine invertebrates from the North-West Pacific. The issues of biodiversity, chemodiversity, and the anticancer pharmacophore diversity this region hides are consecutively discussed. These three levels of diversity are analyzed from the point of view of the already discovered compounds, as well as from the assessment of the overall, still undiscovered and enormous potential. We further go into the predictions of the economic and societal benefits the full-scale exploration of this potential offers, and suggest strategic measures to be taken on the national level in order to unleash such full-scale exploration. The transversal and multi-discipline approach we attempt to build for the case of marine invertebrate-based anticancer drug discovery from a given region can be applied to other regions and disease conditions, as well as up-scaled to global dimensions.
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Affiliation(s)
- Vladimir L Katanaev
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, 1211 Geneva, Switzerland.
- School of Biomedicine, Far Eastern Federal University, 8 ul. Sukhanova, 690950 Vladivostok, Russia.
| | - Salvatore Di Falco
- The Institute of Economics and Econometrics, University of Geneva, UNIMAIL, Boulevard du Pont d'Arve 40, 1211 Geneva, Switzerland
| | - Yuri Khotimchenko
- School of Biomedicine, Far Eastern Federal University, 8 ul. Sukhanova, 690950 Vladivostok, Russia.
- National Scientific Center for Marine Biology, Far Eastern Branch of Russian Academy of Sciences, 690041 Vladivostok, Russia.
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29
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Silva DM, Costa PADA, Ribon AOB, Purgato GA, Gaspar DM, Diaz MAN. Plant Extracts Display Synergism with Different Classes of Antibiotics. AN ACAD BRAS CIENC 2019; 91:e20180117. [PMID: 31090789 DOI: 10.1590/0001-3765201920180117] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/25/2018] [Indexed: 11/22/2022] Open
Abstract
One manner in which plant-derived compounds exert their antibiotic potential is the synergism, a positive interaction between two compounds. Studies indicate that the use of plant extracts combined with antimicrobials may promote a significant reduction of the minimum inhibitory concentrations of antibiotics for bacterial strains. This study aimed to evaluate the activity of plant extracts and antibiotics as well as their combination on Staphylococcus aureus. The activity of 15 plant extracts was evaluated using diffusion assay. The minimum inhibitory concentrations (MICs) and the interactions between the extracts and antibiotics as well as compound emodin were evaluated with the checkerboard method. The active extracts were a hexane extract of the leaves of Baccharis dracunculifolia and the ethanol extracts of the leaves of Plectranthus ornatus, Inga edulis, Salvia officinalis and Senna macranthera. The Plectranthus ornatus extract displayed synergism with ampicillin (a β-lactam), kanamycin and gentamicin (aminoglycosides), with 8-fold reductions in the MIC. The same reduction was observed for the extracts of Salvia officinalis and Senna macranthera, which displayed the lowest MIC. Using these combinations resulted in a reduction in the minimum dose required for effective antimicrobial effects, which is interesting because it may decrease both the risk of side effects and the costs of treatment.
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Affiliation(s)
- Danielle M Silva
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, MG, Brazil
| | - Priscilla A DA Costa
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, MG, Brazil
| | - Andréa O B Ribon
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, MG, Brazil
| | - Gislaine A Purgato
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, MG, Brazil
| | - Diaz-Muñoz Gaspar
- Departamento de Química, Instituto de Ciências Exatas/ICEX, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Marisa A N Diaz
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, MG, Brazil
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30
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Braddock AA, Theodorakis EA. Marine Spirotetronates: Biosynthetic Edifices That Inspire Drug Discovery. Mar Drugs 2019; 17:md17040232. [PMID: 31010150 PMCID: PMC6521127 DOI: 10.3390/md17040232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/13/2019] [Accepted: 04/16/2019] [Indexed: 12/31/2022] Open
Abstract
Spirotetronates are actinomyces-derived polyketides that possess complex structures and exhibit potent and unexplored bioactivities. Due to their anticancer and antimicrobial properties, they have potential as drug hits and deserve further study. In particular, abyssomicin C and tetrocarcin A have shown significant promise against antibiotic-resistant S. aureus and tuberculosis, as well as for the treatment of various lymphomas and solid tumors. Improved synthetic routes to these compounds, particularly the class II spirotetronates, are needed to access sufficient quantities for structure optimization and clinical applications.
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Affiliation(s)
- Alexander A Braddock
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
| | - Emmanuel A Theodorakis
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA.
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31
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Ahmed S, Khan H, Fratantonio D, Hasan MM, Sharifi S, Fathi N, Ullah H, Rastrelli L. Apoptosis induced by luteolin in breast cancer: Mechanistic and therapeutic perspectives. PHYTOMEDICINE 2019; 59:152883. [PMID: 30986716 DOI: 10.1016/j.phymed.2019.152883] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/06/2019] [Accepted: 03/09/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Breast cancer is worldwide commonly found malignancy in women and effective treatment is regarded as a huge clinical challenge even in the presence of several options. Extensive literature is available that demonstrating polyphenols, the richly introduce phytopharmaceuticals as anticancer agents. Among these polyphenols, resveratrol, silibinin, quercetin, genistein, curcumin reported to have an awesome potential against breast cancer. However, till now no comprehensive survey found about the anticarcinogenic properties of luteolin against breast cancer. SCOPE AND APPROACH This review targeted the available literature on luteolin in the treatment of breast cancer, effects in combination with other anticancer drugs with possible mechanisms. KEY FINDINGS AND CONCLUSION An outstanding therapeutic potential of luteolin in the treatment of breast cancer has been recorded not just as a chemopreventive and chemotherapeutic agent yet complemented by its synergistic effects with other anticancer therapies such as cyclophosphamide, doxorubicin, and NSAID such as celecoxib, and possible underlying mechanisms. Ideally, this review will open new dimensions for luteolin as an effective and safe therapeutic agent in diminishing breast cancer.
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Affiliation(s)
- Salman Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali khan University Mardan 23200, Pakistan.
| | - Deborah Fratantonio
- "Bambino Gesù" Children's Hospital-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy.
| | - Muhammad Mohtasheemul Hasan
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Simin Sharifi
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazanin Fathi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hammad Ullah
- Department of Pharmacy, Abdul Wali khan University Mardan 23200, Pakistan
| | - Luca Rastrelli
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II, 84084, Fisciano, Italy
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33
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Stöter M, Janosch A, Barsacchi R, Bickle M. CellProfiler and KNIME: Open-Source Tools for High-Content Screening. Methods Mol Biol 2019; 1953:43-60. [PMID: 30912015 DOI: 10.1007/978-1-4939-9145-7_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-content screening (HCS) has established itself in the world of the pharmaceutical industry as an essential tool for drug discovery and drug development. HCS is currently starting to enter the academic world and might become a widely used technology. Given the diversity of problems tackled in academic research, HCS could experience some profound changes in the future, mainly with more imaging modalities and smart microscopes being developed. One of the limitations in the establishment of HCS in academia is flexibility and cost. Flexibility is important to be able to adapt the HCS setup to accommodate the multiple different assays typical of academia. Many cost factors cannot be avoided, but the costs of the software packages necessary to analyze large datasets can be reduced by using open-source software. We present and discuss the open-source software CellProfiler for image analysis and KNIME for data analysis and data mining that provide software solutions, which increase flexibility and keep costs low.
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Affiliation(s)
- Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Antje Janosch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Rico Barsacchi
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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Skubel SA, Dushenkov V, Graf BL, Niu Q, Poulev A, Kalariya HM, Foxcroft LC, Raskin I. Rapid, field-deployable method for collecting and preserving plant metabolome for biochemical and functional characterization. PLoS One 2018; 13:e0203569. [PMID: 30188945 PMCID: PMC6126852 DOI: 10.1371/journal.pone.0203569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/01/2018] [Indexed: 12/25/2022] Open
Abstract
Study of plant metabolome is a growing field of science that catalogs vast biochemical and functional diversity of phytochemicals. However, collecting and storing samples of plant metabolome, sharing these samples across the scientific community and making them compatible with bioactivity assays presents significant challenges to the advancement of metabolome research. We have developed a RApid Metabolome Extraction and Storage (RAMES) technology that allows efficient, highly compact, field-deployable collection and storage of libraries of plant metabolome. RAMES technology combines rapid extraction with immobilization of extracts on glass microfiber filter discs. Two grams of plant tissue extracted in ethanol, using a specially adapted Dremel® rotary tool, produces 25-35 replicas of 10 mm glass fiber discs impregnated with phytochemicals. These discs can be either eluted with solvents (such as 70% ethanol) to study the metabolomic profiles or used directly in a variety of functional assays. We have developed simple, non-sterile, anti-fungal, anti-bacterial, and anti-oxidant assays formatted for 24-multiwell plates directly compatible with RAMES discs placed inside the wells. Using these methods we confirmed activity in 30 out of 32 randomly selected anti-microbial medicinal plants and spices. Seven species scored the highest activity (total kill) in the anti-bacterial (bacteria from human saliva) and two anti-fungal screens (Fusarium spp. and Saccharomyces cerevisiae), providing functional validation of RAMES technology. RAMES libraries showed limited degradation of compounds after 12 months of storage at -20°C, while others remained stable. Fifty-eight percent of structures characterized in the extracts loaded onto RAMES discs could be eluted from the discs without significant losses. Miniaturized RAMES technology, as described and validated in this manuscript offers a labor, cost, and time-effective alternative to conventional collection of phytochemicals. RAMES technology enables creation of comprehensive metabolomic libraries from various ecosystems and geographical regions in a format compatible with further biochemical and functional studies.
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Affiliation(s)
- Sarah A. Skubel
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Vyacheslav Dushenkov
- Hostos Community College, City University of New York, Bronx, New York, United States of America
| | - Brittany L. Graf
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Qingwei Niu
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Alexander Poulev
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Hetalben M. Kalariya
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Llewellyn C. Foxcroft
- Centre for Invasion Biology (C•I•B), Department of Botany and Zoology, Stellenbosch University and Scientific Services, South African National Parks, Skukuza, South Africa
| | - Ilya Raskin
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
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Henson AB, Gromski PS, Cronin L. Designing Algorithms To Aid Discovery by Chemical Robots. ACS CENTRAL SCIENCE 2018; 4:793-804. [PMID: 30062108 PMCID: PMC6062836 DOI: 10.1021/acscentsci.8b00176] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Indexed: 05/25/2023]
Abstract
Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery.
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36
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Khan RA. Natural products chemistry: The emerging trends and prospective goals. Saudi Pharm J 2018; 26:739-753. [PMID: 29991919 PMCID: PMC6036106 DOI: 10.1016/j.jsps.2018.02.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023] Open
Abstract
The role and contributions of natural products chemistry in advancements of the physical and biological sciences, its interdisciplinary domains, and emerging of new avenues by providing novel applications, constructive inputs, thrust, comprehensive understanding, broad perspective, and a new vision for future is outlined. The developmental prospects in bio-medical, health, nutrition, and other interrelated sciences along with some of the emerging trends in the subject area are also discussed as part of the current review of the basic and core developments, innovation in techniques, advances in methodology, and possible applications with their effects on the sciences in general and natural products chemistry in particular. The overview of the progress and ongoing developments in broader areas of the natural products chemistry discipline, its role and concurrent economic and scientific implications, contemporary objectives, future prospects as well as impending goals are also outlined. A look at the natural products chemistry in providing scientific progress in various disciplines is deliberated upon.
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Affiliation(s)
- Riaz A. Khan
- Department of Medicinal Chemistry, Qassim University, Qassim 51452, Saudi Arabia
- Manav Rachna International University, National Capital Region, Faridabad, HR 121 004, India
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37
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Current strategies to induce secondary metabolites from microbial biosynthetic cryptic gene clusters. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1351-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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38
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Wang C, Zhang S, Wang Y, Huang SH, Hong R. Total synthesis of strictamine: a tutorial for novel and efficient synthesis. Org Chem Front 2018. [DOI: 10.1039/c7qo00837f] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The novelty and efficiency of the overall synthetic route are the key values being imparted to the younger generation of synthetic chemists. In this Highlights, synthesis of strictamine was tutored to students on the creativity of synthetic design.
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Affiliation(s)
- Chao Wang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances
- Shanghai Institute of Organic Chemistry (CAS)
- Shanghai 200032
- China
- University of Chinese Academy of Sciences
| | - Shiju Zhang
- College of Chemical and Environmental Engineering
- Shanghai Institute of Technology
- Shanghai
- China
| | - Yan Wang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances
- Shanghai Institute of Organic Chemistry (CAS)
- Shanghai 200032
- China
- University of Chinese Academy of Sciences
| | - Sha-Hua Huang
- College of Chemical and Environmental Engineering
- Shanghai Institute of Technology
- Shanghai
- China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances
- Shanghai Institute of Organic Chemistry (CAS)
- Shanghai 200032
- China
- University of Chinese Academy of Sciences
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39
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Brethon A, Chantalat L, Christin O, Clary L, Fournier JF, Gastreich M, Harris CS, Isabet T, Pascau J, Thoreau E, Roche D, Rodeschini V. New Caspase-1 inhibitor by scaffold hopping into bio-inspired 3D-fragment space. Bioorg Med Chem Lett 2017; 27:5373-5377. [PMID: 29157864 DOI: 10.1016/j.bmcl.2017.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/25/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Abstract
Virtual fragmentation of a library of 12,000 compounds inspired by natural products led to a dataset of 153,000 fragments that was used as a source to identify effective P2-P3 scaffold replacement solutions for peptidic Caspase-1 inhibitors. Our strategy led to the identification of an original 2-azabicyclo-octane scaffold (2-ABO) that was further elaborated into the potent Caspase-1 inhibitor CD10847 (IC50 = 17 nM). The crystal structure of Caspase-1 in complex with CD10847 was obtained, and its binding mode was shown to be similar to the one predicted by docking and in good agreement with other known inhibitors.
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Affiliation(s)
- Anne Brethon
- Edelris, 115 Avenue Lacassagne, 69003 Lyon, France
| | | | | | | | | | - Marcus Gastreich
- BioSolveIT GmbH, An der Ziegelei 79, 53757 Sankt Augustin, Germany
| | | | - Tatiana Isabet
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin - BP 48, 91192 Gif-sur-Yvette Cedex, France
| | | | | | - Didier Roche
- Edelris, 115 Avenue Lacassagne, 69003 Lyon, France.
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40
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Bernardini S, Tiezzi A, Laghezza Masci V, Ovidi E. Natural products for human health: an historical overview of the drug discovery approaches. Nat Prod Res 2017; 32:1926-1950. [DOI: 10.1080/14786419.2017.1356838] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- S. Bernardini
- Laboratory of Plant Cytology and Biotechnology, Department for the Innovation in Biological, Agrofood and Forestal Systems (DIBAF), Tuscia University, Viterbo, Italy
| | - A. Tiezzi
- Laboratory of Plant Cytology and Biotechnology, Department for the Innovation in Biological, Agrofood and Forestal Systems (DIBAF), Tuscia University, Viterbo, Italy
| | - V. Laghezza Masci
- Laboratory of Plant Cytology and Biotechnology, Department for the Innovation in Biological, Agrofood and Forestal Systems (DIBAF), Tuscia University, Viterbo, Italy
| | - E. Ovidi
- Laboratory of Plant Cytology and Biotechnology, Department for the Innovation in Biological, Agrofood and Forestal Systems (DIBAF), Tuscia University, Viterbo, Italy
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41
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Galloylation of polyphenols alters their biological activity. Food Chem Toxicol 2017; 105:223-240. [DOI: 10.1016/j.fct.2017.04.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/23/2017] [Accepted: 04/15/2017] [Indexed: 01/08/2023]
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42
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Schneider P, Schneider G. Privileged Structures Revisited. Angew Chem Int Ed Engl 2017; 56:7971-7974. [PMID: 28558125 PMCID: PMC5502582 DOI: 10.1002/anie.201702816] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/16/2017] [Indexed: 12/13/2022]
Abstract
Privileged structures inspire compound library design in medicinal chemistry. We performed a comprehensive analysis of 1.4 million bioactive compounds, with the aim of assessing the prevalence of certain molecular frameworks. We used the Shannon entropy formalism to quantify the promiscuity of the most frequently observed atom scaffolds across the annotated target families. This analysis revealed an apparent inverse relationship between hydrogen-bond-acceptor count of a scaffold and its potential promiscuity. The results further suggest that chemically easily accessible scaffolds can serve as templates for the generation of bespoke compound libraries with differing degrees of multiple target engagement, and heterocyclic, sp3 -rich frameworks are particularly suited for target-focused library design. The outcome of our study enables us to place some of the many narratives surrounding the concept of privileged structures into a critical context.
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Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 48093ZurichSwitzerland
- inSili.com LLCSegantinisteig 38049ZurichSwitzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 48093ZurichSwitzerland
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43
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Affiliation(s)
- Petra Schneider
- Departement Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule (ETH); Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
- inSili.com GmbH; Segantinisteig 3 8049 Zürich Schweiz
| | - Gisbert Schneider
- Departement Chemie und Angewandte Biowissenschaften; Eidgenössische Technische Hochschule (ETH); Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
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44
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Naman CB, Rattan R, Nikoulina SE, Lee J, Miller BW, Moss NA, Armstrong L, Boudreau PD, Debonsi HM, Valeriote FA, Dorrestein PC, Gerwick WH. Integrating Molecular Networking and Biological Assays To Target the Isolation of a Cytotoxic Cyclic Octapeptide, Samoamide A, from an American Samoan Marine Cyanobacterium. JOURNAL OF NATURAL PRODUCTS 2017; 80:625-633. [PMID: 28055219 PMCID: PMC5758054 DOI: 10.1021/acs.jnatprod.6b00907] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Integrating LC-MS/MS molecular networking and bioassay-guided fractionation enabled the targeted isolation of a new and bioactive cyclic octapeptide, samoamide A (1), from a sample of cf. Symploca sp. collected in American Samoa. The structure of 1 was established by detailed 1D and 2D NMR experiments, HRESIMS data, and chemical degradation/chromatographic (e.g., Marfey's analysis) studies. Pure compound 1 was shown to have in vitro cytotoxic activity against several human cancer cell lines in both traditional cell culture and zone inhibition bioassays. Although there was no particular selectivity between the cell lines tested for samoamide A, the most potent activity was observed against H460 human non-small-cell lung cancer cells (IC50 = 1.1 μM). Molecular modeling studies suggested that one possible mechanism of action for 1 is the inhibition of the enzyme dipeptidyl peptidase (CD26, DPP4) at a reported allosteric binding site, which could lead to many downstream pharmacological effects. However, this interaction was moderate when tested in vitro at up to 10 μM and only resulted in about 16% peptidase inhibition. Combining bioassay screening with the cheminformatics strategy of LC-MS/MS molecular networking as a discovery tool expedited the targeted isolation of a natural product possessing both a novel chemical structure and a desired biological activity.
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Affiliation(s)
- C. Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Ramandeep Rattan
- Division of Gynecology Oncology, Department of Women’s Health Services, Henry Ford Hospital, Detroit, Michigan 48202, United States
| | - Svetlana E. Nikoulina
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - John Lee
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Bailey W. Miller
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Nathan A. Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Lorene Armstrong
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Paul D. Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Hosana M. Debonsi
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Frederick A. Valeriote
- Division of Hematology and Oncology, Department of Internal Medicine, Henry Ford Hospital, Detroit, Michigan 48202, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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45
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A Review of Black Salve: Cancer Specificity, Cure, and Cosmesis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:9184034. [PMID: 28246541 PMCID: PMC5299188 DOI: 10.1155/2017/9184034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/28/2016] [Indexed: 11/28/2022]
Abstract
Black salve is a topical escharotic used for the treatment of skin cancer. Although promoted as a safe and effective alternative to conventional management by its proponents, limited clinical research has been undertaken to assess its efficacy and potential toxicities. Patients are increasingly utilizing the Internet as a source of health information. As a minimally regulated space, the quality and accuracy of this information vary considerably. This review explores four health claims made by black salve vendors, investigating its natural therapy credentials, tumour specificity, and equivalence to orthodox medicine in relation to skin cancer cure rates and cosmesis. Based upon an analysis of in vitro constituent cytotoxicity, in vivo post black salve histology, and experience with Mohs paste, black salve is likely to possess normal tissue toxicity with some cancer cell lines being relatively resistant to its effects. This may explain the incongruous case study reports of excessive scarring, deformity, and treatment failure.
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46
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Song H, Wang H, Liang J, Qian C, Wu S, Xu W, Wu B, Liu X, Li P, Yang H. Integration of Multiple Analytical and Computational Tools for the Discovery of High‐Potency Enzyme Inhibitors from Herbal Medicines. ChemMedChem 2016; 11:2588-2597. [DOI: 10.1002/cmdc.201600489] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Hui‐Peng Song
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Hong Wang
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Jin‐Xiu Liang
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Cheng Qian
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Si‐Qi Wu
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Wen‐Jun Xu
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Bin Wu
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Xin‐Guang Liu
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Ping Li
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
| | - Hua Yang
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 210009 China
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47
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Lopes G, Pinto E, Salgueiro L. Natural Products: An Alternative to Conventional Therapy for Dermatophytosis? Mycopathologia 2016; 182:143-167. [PMID: 27771883 DOI: 10.1007/s11046-016-0081-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/09/2016] [Indexed: 12/13/2022]
Abstract
The increased incidence of fungal infections, associated with the widespread use of antifungal drugs, has resulted in the development of resistance, making it necessary to discover new therapeutic alternatives. Among fungal infections, dermatophytoses constitute a serious public health problem, affecting 20-25 % of the world population. Medicinal plants represent an endless source of bioactive molecules, and their volatile and non-volatile extracts are clearly recognized for being the historical basis of therapeutic health care. Because of this, the research on natural products with antifungal activity against dermatophytes has considerably increased in recent years. However, despite the recognized anti-dermatophytic potential of natural products, often advantageous face to commercial drugs, there is still a long way to go until their use in therapeutics. This review attempts to summarize the current status of anti-dermatophytic natural products, focusing on their mechanism of action, the developed pharmaceutical formulations and their effectiveness in human and animal models of infection.
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Affiliation(s)
- Graciliana Lopes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123, Porto, Portugal
| | - Eugénia Pinto
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123, Porto, Portugal. .,Microbiology Service, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal.
| | - Lígia Salgueiro
- CNC.IBILI/Faculty of Pharmacy, University of Coimbra, Azinhaga de S. Comba, 3000-354, Coimbra, Portugal
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48
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Abstract
Many food-derived phytochemical compounds and their derivatives represent a cornucopia of new anticancer compounds. Despite extensive study of luteolin, the literature has no information on the exact mechanisms or molecular targets through which it deters cancer progression. This review discusses existing data on luteolin's anticancer activities and then offers possible explanations for and molecular targets of its cancer-preventive action. Luteolin prevents tumor development largely by inactivating several signals and transcription pathways essential for cancer cells. This review also offers insights into the molecular mechanisms and targets through which luteolin either prevents cancer or mediates cancer cell death.
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49
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El Sayed OH, Asker MMS, Swelim MA, Abbas IH, Attwa AI, El Awady ME. Production of hydroxy marilone C as a bioactive compound from Streptomyces badius. J Genet Eng Biotechnol 2016; 14:161-168. [PMID: 30647610 PMCID: PMC6299901 DOI: 10.1016/j.jgeb.2016.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 04/09/2016] [Accepted: 04/21/2016] [Indexed: 12/03/2022]
Abstract
Hydroxy marilone C is a bioactive metabolite produced from the culture broth of Streptomyces badius isolated from Egyptian soil. Hydroxy marilone C was purified and fractionated by a silica gel column with a gradient mobile phase dichloromethane (DCM):methanol then Sephadex LH-20 column using methanol as a mobile phase. It was subjected to many procedures such as infrared (IR), nuclear magnetic resonance (NMR), Mass spectroscopy (MS) and UV spectroscopy for elucidation of its structure. It was evaluated for antioxidant, cytotoxicity against human alveolar basal epithelial cell line (A-549) and human breast adenocarcinoma cell line (MCF-7) and antiviral activities; showed that the maximum antioxidant activity was 78.8% at 3 mg/ml after 90 min. and the IC50 value against DPPH radical found about 1.5 mg/ml after 60 min. Using MTT assay the effect of the pure compound on the proliferation of A-549 cells and MCF-7 cells was 443 μg/ml and 147.9 μg/ml, respectively, while for detection of antiviral activity using Madin-Darby canine kidney (MDCK) cells the maximum cytotoxicity was at 27.9% and IC50 was 128.1 μg/ml. The maximum concentration required for protecting 50% of the virus-infected cells against H1N1 viral cytopathogenicity (EC50) was 33.25% for 80 μg/ml. These results indicated that the hydroxy marilone C has potential antitumor and antiviral activities.
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Affiliation(s)
- Osama H El Sayed
- Department of Microbial Biotechnology, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Mohsen M S Asker
- Department of Microbial Biotechnology, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Mahmoud A Swelim
- Botany Department, Faculty of Science, Benha University, Benha, Egypt
| | - Ibrahim H Abbas
- Botany Department, Faculty of Science, Benha University, Benha, Egypt
| | - Aziza I Attwa
- Department of Microbial Biotechnology, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Mohamed E El Awady
- Department of Microbial Biotechnology, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
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50
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Coulerie P, Poullain C. New Caledonia: A Hot Spot for Valuable Chemodiversity Part 3: Santalales, Caryophyllales, and Asterids. Chem Biodivers 2016; 13:366-79. [PMID: 26937845 DOI: 10.1002/cbdv.201500101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 04/15/2015] [Indexed: 11/09/2022]
Abstract
The flora of New Caledonia encompasses more than 3000 plant species and an endemism of almost 80%. New Caledonia is even considered as one of the 34 'hot spots' for biodiversity. Considering the current global loss of biodiversity and the fact that several drugs and pesticides become obsolete, there is an urgent need to increase sampling and research on new natural products. In this context, here, we reviewed the chemical knowledge available on New Caledonian native flora from economical perspectives. We expect that a better knowledge of the economic potential of plant chemistry will encourage the plantation of native plants for the development of a sustainable economy which will participate in the conservation of biodiversity. This review is divided into three parts, and the third part which is presented here summarizes the scientific literature related to the chemistry of endemic santalales, caryophyllales, and asterids. We show that the high rate of endemism is correlated with the originality of phytochemicals encountered in New Caledonian plants. A total of 176 original natural compounds have been identified from these plants, whereas many species have not been investigated so far. We also discuss the economic potential of plants and molecules with consideration of their medicinal and industrial perspectives. This review finally highlights several groups, such as Sapotaceae, that are unexplored in New Caledonia despite the high chemical interest in them. These plants are considered to have priority in future chemical investigations.
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Affiliation(s)
- Paul Coulerie
- Institut Agronomique Néo-Calédonien, Connaissance et Amélioration des Agrosystèmes, BP A5, 98848, Noumea Cedex, New Caledonia.,School of Pharmaceutical Sciences, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211, Geneva 4
| | - Cyril Poullain
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, Labex LERMIT, 1 Avenue de la Terrasse, FR-91198, Gif-sur-Yvette Cedex.,Stratoz, 5, Rue de la Baume, FR-75008, Paris
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