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Tang J, Jin J, Huang Z, An F, Huang C, Jiang W. The discovery of subunit-selective GluN1/GluN2B NMDAR antagonist via pharmacophere-based virtual screening. Exp Biol Med (Maywood) 2023; 248:2560-2577. [PMID: 38282535 PMCID: PMC10854469 DOI: 10.1177/15353702231220666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/05/2024] [Indexed: 01/30/2024] Open
Abstract
The incidence and mortality rates of neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, are gradually increasing worldwide. Numerous studies have demonstrated that N-methyl-D-aspartic acid receptor (NMDAR)-mediated excitotoxicity contributes to neurodegenerative diseases. Ifenprodil, a subtype-selective NMDAR antagonist, showed strong therapeutic potential. However, it suffers from low oral bioavailability and off-target side effects. In this study, natural compounds were identified for selective inhibition of GluN1/GluN2B NMDAR of human. We obtained a set of natural compounds (n = 81,366) from COCONUT, TIPdb, PAMDB, CMNPD, YMDB, and NPAtlas databases, and then virtually screened by an ifenprodil-structure-based pharmacophore model and molecular docking. The top 100 compounds were selected for binding affinity prediction via batch drug-target affinity (BatchDTA). Then, the top 50 compounds were analyzed by absorption, distribution, metabolism, excretion, toxicity (ADMET). Molecular dynamics involving molecular mechanics/position-Boltzmann surface area (MM-PBSA) calculation were performed to further screening. The top 15 compounds with strong binding affinity and ifenprodil, a proven GluN2B-selective NMDAR antagonist, were subjected to molecular dynamic simulations (100 ns), root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), H-bonds, solvent accessible surface area (SASA), principal component analysis (PCA), and binding free energy calculations. Based on these analyses, one possible lead compound carrying positive charges (CNP0099440) was identified, with great binding affinity and less off-target activity by contrast to ifenprodil. CNP0099440 has great potential to be a GluN1/GluN2B NMDAR antagonist candidate and can be further detected via in vitro and in vivo experiments.
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Affiliation(s)
- Jialing Tang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
| | - Ju Jin
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
| | - Zhihong Huang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Faliang An
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Caiguo Huang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
| | - Wenli Jiang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
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2
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Ullah S, Rahman W, Ullah F, Ullah A, Ahmad G, Ijaz M, Ullah H, Zheng Z, Gao T. AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV. Database (Oxford) 2023; 2023:baad056. [PMID: 37594855 PMCID: PMC10437090 DOI: 10.1093/database/baad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Serious illnesses caused by viruses are becoming the world's most critical public health issues and lead millions of deaths each year in the world. Thousands of studies confirmed that the plant-derived medicines could play positive therapeutic effects on the patients with viral diseases. Since thousands of antiviral phytochemicals have been identified as lifesaving drugs in medical research, a comprehensive database is highly desirable to integrate the medicinal plants with their different medicinal properties. Therefore, we provided a friendly antiviral phytochemical database AVPCD covering 2537 antiviral phytochemicals from 383 medicinal compounds and 319 different families with annotation of their scientific, family and common names, along with the parts used, disease information, active compounds, links of relevant articles for COVID-19, cancer, HIV and malaria. Furthermore, each compound in AVPCD was annotated with its 2D and 3D structure, molecular formula, molecular weight, isomeric SMILES, InChI, InChI Key and IUPAC name and 21 other properties. Each compound was annotated with more than 20 properties. Specifically, a scoring method was designed to measure the confidence of each phytochemical for the viral diseases. In addition, we constructed a user-friendly platform with several powerful modules for searching and browsing the details of all phytochemicals. We believe this database will facilitate global researchers, drug developers and health practitioners in obtaining useful information against viral diseases.
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Affiliation(s)
- Shahid Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Wajeeha Rahman
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Farhan Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Anees Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Gulzar Ahmad
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Muhammad Ijaz
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Hameed Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200, Pakistan
| | - Zilong Zheng
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P. R. China
| | - Tianshun Gao
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P. R. China
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3
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Shinde S, Satpute DP, Behera SK, Kumar D. Computational Biology of BRCA2 in Male Breast Cancer, through Prediction of Probable nsSNPs, and Hit Identification. ACS OMEGA 2022; 7:30447-30461. [PMID: 36061650 PMCID: PMC9434626 DOI: 10.1021/acsomega.2c03851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Male breast cancer (MBC) is a relatively rare disease, but emerging data recommend the development of novel therapeutics considering its alarming threats. Compared to female breast cancer (FBC), MBC is reportedly associated with inferior outcomes (poor survival) owing to their late diagnosis and lack of adequate treatment. Treatment typically correlates with FBC, involving surgical removal of the breast tissue along with chemo/hormonal/radiation therapy, the tamoxifen being a standard adjuvant. Considering the distinct immunophenotypic (implying different pathogenesis and progression) differences from FBC, the identification of diagnostics, prognostics, and therapeutics for MBC is highly desirable. In this context, we have analyzed the most deleterious nsSNPs of BRCA2, a human tumor suppressor gene constituting the potential biomarker for tumors including MBC, to predict the structural changes associated with the mutants hampering the normal protein-protein and protein-ligand interactions, resulting in MBC progression. Among 27 nsSNPs confined to 21 rsIDs pertaining to MBC, the 19 nsSNPs constituting 14 rsIDs have been predicted as highly deleterious. We believe that these nsSNPs could serve as potential biomarkers for diagnostic and prognostic purposes and could be the pivotal target for MBC drug discovery. Subsequently, the study highlights the exploration of the key nsSNPs (of BRCA2 associated with the MBC) and its applications toward the identification of therapeutic hit TIP006136 following the homology modeling, virtual screening of 5284 phytochemicals retrieved from the TIPdb (a database of phytochemicals from indigenous plants in Taiwan) database, molecular docking (against native and mutant BRCA2), dynamic simulations (against native and mutant BRCA2), density functional theory (DFT), and molecular electrostatic potential. To the best of our knowledge, this is the first report to use diverse computational modules to investigate the important nsSNPs of BRCA2 related to MBC, implying that TIP006136 could be a potential hit and must be studied further (in vitro and in vivo) to establish its anticancer property and efficacy against MBC.
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Affiliation(s)
- Sangita
Dattatray Shinde
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Dinesh Parshuram Satpute
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Santosh Kumar Behera
- Department
of Biotechnology, National Institute of
Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Dinesh Kumar
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
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4
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Kant V, Kumar P, Ranjan R, Kumar P, Mandal D, Vijayakumar S. In silico screening, molecular dynamic simulations, and in vitro activity of selected natural compounds as an inhibitor of Leishmania donovani 3-mercaptopyruvate sulfurtransferase. Parasitol Res 2022; 121:2093-2109. [PMID: 35536513 PMCID: PMC9085559 DOI: 10.1007/s00436-022-07532-5] [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: 11/15/2021] [Accepted: 04/20/2022] [Indexed: 11/26/2022]
Abstract
In Leishmania sp., the enzymes of de novo cysteine biosynthesis pathway require sulfide. Other organisms utilize sulfide through the sulfide reduction pathway, but Leishmania lacks the gene that encodes these enzymes. Hence, the major source of sulfide for Leishmania is believed to be from the action of 3-mercaptopyruvate sulfurtransferase (3MST) on 3-mercapto-pyruvate (3MP). There has been no effort reported in the past to screen inhibitors against L. donovani 3MST (Ld3MST). As a result, this study examines natural compounds that are potent against Ld3MST and validates it by in vitro activity and cytotoxicity tests. Initially, a library of ~ 5000 natural compounds was subjected to molecular docking approach for screening, and the best hit was validated using a long-term molecular dynamic simulation (MD). Among the docking results, quercetine-3-rutinoside (Rutin) was deemed the best hit. The results of the MD indicated that Rutin was highly capable of interacting with the varied active site segments, possibly blocking substrate access. Additionally, promastigotes and amastigotes were tested for Rutin activity and the IC50 was found to be 40.95 and 90.09 μM, respectively. Similarly, the cytotoxicity assay revealed that Rutin was not toxic even at a concentration of 819.00 μM to THP-1 cell lines. Additionally, the Ld3MST was cloned, purified, and evaluated for enzyme activity in the presence of Rutin. Reduction in the enzyme activity (~ 85%) was observed in the presence of ~ 40 μM Rutin. Thus, this study suggests that Rutin may act as a potent inhibitor of Ld3MST. With further in vivo investigations, Rutin could be a small molecule of choice for combating leishmaniasis.
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Affiliation(s)
- Vishnu Kant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India
| | - Pawan Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India
| | - Ravi Ranjan
- Division of Bioinformatics, ICMR-Rajendra Memorial Institute of Medical Sciences, Patna, Bihar, India
| | - Prakash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India
| | - Debabrata Mandal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India.
| | - Saravanan Vijayakumar
- Division of Bioinformatics, ICMR-Rajendra Memorial Institute of Medical Sciences, Patna, Bihar, India.
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5
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An insilico study of KLK-14 protein and its inhibition with curcumin and its derivatives. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02209-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Pinto GP, Hendrikse NM, Stourac J, Damborsky J, Bednar D. Virtual screening of potential anticancer drugs based on microbial products. Semin Cancer Biol 2021; 86:1207-1217. [PMID: 34298109 DOI: 10.1016/j.semcancer.2021.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 01/20/2023]
Abstract
The development of microbial products for cancer treatment has been in the spotlight in recent years. In order to accelerate the lengthy and expensive drug development process, in silico screening tools are systematically employed, especially during the initial discovery phase. Moreover, considering the steadily increasing number of molecules approved by authorities for commercial use, there is a demand for faster methods to repurpose such drugs. Here we present a review on virtual screening web tools, such as publicly available databases of molecular targets and libraries of ligands, with the aim to facilitate the discovery of potential anticancer drugs based on microbial products. We provide an entry-level step-by-step description of the workflow for virtual screening of microbial metabolites with known protein targets, as well as two practical examples using freely available web tools. The first case presents a virtual screening study of drugs developed from microbial products using Caver Web, a web tool that performs docking along a tunnel. The second case comprises a comparative analysis between a wild type isocitrate dehydrogenase 1 and a mutant that results in cancer, using the recently developed web tool PredictSNPOnco. In summary, this review provides the basic and essential background information necessary for virtual screening experiments, which may accelerate the discovery of novel anticancer drugs.
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Affiliation(s)
- Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, Brno, 656 91, Czech Republic
| | - Natalie M Hendrikse
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, Brno, 656 91, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, Brno, 656 91, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno, 625 00, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, Brno, 656 91, Czech Republic.
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7
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Zhang R, Li X, Zhang X, Qin H, Xiao W. Machine learning approaches for elucidating the biological effects of natural products. Nat Prod Rep 2021; 38:346-361. [PMID: 32869826 DOI: 10.1039/d0np00043d] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2000 to 2020 Machine learning (ML) is an efficient tool for the prediction of bioactivity and the study of structure-activity relationships. Over the past decade, an emerging trend for combining these approaches with the study of natural products (NPs) has developed in order to manage the challenge of the discovery of bioactive NPs. In the present review, we will introduce the basic principles and protocols for using the ML approach to investigate the bioactivity of NPs, citing a series of practical examples regarding the study of anti-microbial, anti-cancer, and anti-inflammatory NPs, etc. ML algorithms manage a variety of classification and regression problems associated with bioactive NPs, from those that are linear to non-linear and from pure compounds to plant extracts. Inspired by cases reported in the literature and our own experience, a number of key points have been emphasized for reducing modeling errors, including dataset preparation and applicability domain analysis.
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Affiliation(s)
- Ruihan Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, 2 Rd Cuihubei, P. R. China.
| | - Xiaoli Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, 2 Rd Cuihubei, P. R. China.
| | - Xingjie Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, 2 Rd Cuihubei, P. R. China.
| | - Huayan Qin
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, 2 Rd Cuihubei, P. R. China.
| | - Weilie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, School of Chemical Science and Technology, Yunnan University, 2 Rd Cuihubei, P. R. China.
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8
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Xu T, Chen W, Zhou J, Dai J, Li Y, Zhao Y. NPBS database: a chemical data resource with relational data between natural products and biological sources. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6031002. [PMID: 33306802 PMCID: PMC7731925 DOI: 10.1093/database/baaa102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/19/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023]
Abstract
NPBS (Natural Products & Biological Sources) database is a chemical data resource with relational data between natural products and biological sources, manually curated from literatures of natural product researches. The relational data link a specific species and all the natural products derived from it and contrarily link a specific natural product and all the biological sources. The biological sources cover diverse species of plant, bacterial, fungal and marine organisms; the natural molecules have proper chemical structure data and computable molecular properties and all the relational data have corresponding references. NPBS database provides a wider choice of biological sources and can be used for dereplication to prevent re-isolation and re-characterization of already known natural products. Database URL: http://www.organchem.csdb.cn/scdb/NPBS
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Affiliation(s)
- Tingjun Xu
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China
| | - Weiming Chen
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China
| | - Junhong Zhou
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China
| | - Jingfang Dai
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China
| | - Yingyong Li
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China
| | - Yingli Zhao
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China
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9
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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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10
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Gupta MK, Vemula S, Donde R, Gouda G, Behera L, Vadde R. In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. J Biomol Struct Dyn 2020; 39:2617-2627. [PMID: 32238078 PMCID: PMC7171389 DOI: 10.1080/07391102.2020.1751300] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent outbreak of Coronavirus disease (COVID-19) pandemic around the world is associated with ‘severe acute respiratory syndrome’ (SARS-CoV2) in humans. SARS-CoV2 is an enveloped virus and E proteins present in them are reported to form ion channels, which is mainly associated with pathogenesis. Thus, there is always a quest to inhibit these ion channels, which in turn may help in controlling diseases caused by SARS-CoV2 in humans. Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human ‘SARS-CoV2 E’ protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. However, after binding with Belachinal, Macaflavanone E, and Vibsanol B, the random motion of the human ‘SARS-CoV2 E’ protein gets reduced, this, in turn, inhibits the function of the ‘SARS-CoV2 E’ protein. It is pertinent to note that two amino acids, namely VAL25 and PHE26, play a key role while interacting with these three phytochemicals. As these three phytochemicals, namely, Belachinal, Macaflavanone E & Vibsanol B, have passed the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) property as well as ‘Lipinski’s Rule of 5s’, they may be utilized as drugs in controlling disease caused via SARS-COV2, after further investigation. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Sarojamma Vemula
- Department of Microbiology, Government Medical College, Anantapur, Andhra Pradesh, India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
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11
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Gupta MK, Vadde R. A computational structural biology study to understand the impact of mutation on structure-function relationship of inward-rectifier potassium ion channel Kir6.2 in human. J Biomol Struct Dyn 2020; 39:1447-1460. [PMID: 32089084 DOI: 10.1080/07391102.2020.1733666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Type 2 diabetes (T2D) is clinically characterized via hyperglycemia. Polymorphism rs5219 in the KCNJ11 gene is a risk factor for developing T2D in humans. KCNJ11 encodes the 'inward-rectifier potassium ion channel (Kir6.2)'. However, because of the absence of the complete crystal/NMR structures of Kir6.2 proteins, insight into its structure and function and its interaction with diverse ligands remain elusive to date. Therefore, a computational approach was employed for predicting the best plausible 'three-dimensional' structure of Kir6.2 as well as for studying the influence of mutation (p. GLU23LYS) on both architectures as well as the function of Kir6.2 employing simulation studies. Results obtained revealed that though, with increased time, 'Gibbs free energy' becomes positive, residues in wild type Kir6.2 experiences less random movement as compared to mutant Kir6.2. The less random movement of residues in wild type Kir6.2 represents the standard coupling between open and closing of 'KATP channel' and thus the normal secretion of insulin. The more dispersed motion of mutant Kir6.2 residues represents 'overactivity' of the 'KATP channel' and thus insulin 'under-secretion'. Further, molecular docking and simulation studies identified two phytochemicals/drugs, namely, A-348441 and chushizisin I, which retains the wild type property of Kir6.2 after binding with mutant protein. Unlike A-348441, this is for the first time, the present study is reporting about the plausible anti-diabetic property of chushizisin I. As these two phytochemicals/drugs, namely, A-348441 and chushizisin I, have passed ADMET test, in the near future, they may be utilized as anti-diabetic drugs after further investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
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12
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Nguyen-Vo TH, Nguyen L, Do N, Nguyen TN, Trinh K, Cao H, Le L. Plant Metabolite Databases: From Herbal Medicines to Modern Drug Discovery. J Chem Inf Model 2020; 60:1101-1110. [PMID: 31873010 DOI: 10.1021/acs.jcim.9b00826] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Traditional herbal medicine has been an inseparable part of the traditional medical science in many countries throughout history. Nowadays, the popularity of using herbal medicines in daily life, as well as clinical practices, has gradually expanded to numerous Western countries with positive impacts and acceptance. The continuous growth of the herbal consumption market has promoted standardization and modernization of herbal-derived products with present pharmacological criteria. To store and extensively share this knowledge with the community and serve scientific research, various herbal metabolite databases have been developed with diverse focuses under the support of modern advances. The advent of these databases has contributed to accelerating research on pharmaceuticals of natural origins. In the scope of this study, we critically review 30 herbal metabolite databases, discuss different related perspectives, and provide a comparative analysis of 18 accessible noncommercial ones. We hope to provide you with fundamental information and multidimensional perspectives from herbal medicines to modern drug discovery.
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Affiliation(s)
- Thanh-Hoang Nguyen-Vo
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Loc Nguyen
- Computational Biology Center, International University-VNU HCMC, Ho Chi Minh City 700000, Vietnam
| | - Nguyet Do
- Computational Biology Center, International University-VNU HCMC, Ho Chi Minh City 700000, Vietnam
| | - Thien-Ngan Nguyen
- Computational Biology Center, International University-VNU HCMC, Ho Chi Minh City 700000, Vietnam
| | - Khang Trinh
- Computational Biology Center, International University-VNU HCMC, Ho Chi Minh City 700000, Vietnam
| | - Hung Cao
- The Henry Samueli School of Engineering, University of California at Irvine, Irvine, California 92697, United States
| | - Ly Le
- Computational Biology Center, International University-VNU HCMC, Ho Chi Minh City 700000, Vietnam.,Vingroup Big Data Institute, Ha Noi 100000, Vietnam
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13
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Cockroft NT, Cheng X, Fuchs JR. STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products. J Chem Inf Model 2019; 59:4906-4920. [PMID: 31589422 DOI: 10.1021/acs.jcim.9b00489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Target fishing is the process of identifying the protein target of a bioactive small molecule. To do so experimentally requires a significant investment of time and resources, which can be expedited with a reliable computational target fishing model. The development of computational target fishing models using machine learning has become very popular over the last several years because of the increased availability of large amounts of public bioactivity data. Unfortunately, the applicability and performance of such models for natural products has not yet been comprehensively assessed. This is, in part, due to the relative lack of bioactivity data available for natural products compared to synthetic compounds. Moreover, the databases commonly used to train such models do not annotate which compounds are natural products, which makes the collection of a benchmarking set difficult. To address this knowledge gap, a data set composed of natural product structures and their associated protein targets was generated by cross-referencing 20 publicly available natural product databases with the bioactivity database ChEMBL. This data set contains 5589 compound-target pairs for 1943 unique compounds and 1023 unique targets. A synthetic data set comprising 107 190 compound-target pairs for 88 728 unique compounds and 1907 unique targets was used to train k-nearest neighbors, random forest, and multilayer perceptron models. The predictive performance of each model was assessed by stratified 10-fold cross-validation and benchmarking on the newly collected natural product data set. Strong performance was observed for each model during cross-validation with area under the receiver operating characteristic (AUROC) scores ranging from 0.94 to 0.99 and Boltzmann-enhanced discrimination of receiver operating characteristic (BEDROC) scores from 0.89 to 0.94. When tested on the natural product data set, performance dramatically decreased with AUROC scores ranging from 0.70 to 0.85 and BEDROC scores from 0.43 to 0.59. However, the implementation of a model stacking approach, which uses logistic regression as a meta-classifier to combine model predictions, dramatically improved the ability to correctly predict the protein targets of natural products and increased the AUROC score to 0.94 and BEDROC score to 0.73. This stacked model was deployed as a web application, called STarFish, and has been made available for use to aid in target identification for natural products.
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Affiliation(s)
- Nicholas T Cockroft
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy , The Ohio State University , Columbus , Ohio 43210 , United States
| | - James R Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy , The Ohio State University , Columbus , Ohio 43210 , United States
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14
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Gupta MK, Vadde R. Insights into the structure–function relationship of both wild and mutant zinc transporter ZnT8 in human: a computational structural biology approach. J Biomol Struct Dyn 2019; 38:137-151. [DOI: 10.1080/07391102.2019.1567391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, India
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15
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Chen Y, Stork C, Hirte S, Kirchmair J. NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules. Biomolecules 2019; 9:biom9020043. [PMID: 30682850 PMCID: PMC6406893 DOI: 10.3390/biom9020043] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 01/11/2023] Open
Abstract
Natural products (NPs) remain the most prolific resource for the development of small-molecule drugs. Here we report a new machine learning approach that allows the identification of natural products with high accuracy. The method also generates similarity maps, which highlight atoms that contribute significantly to the classification of small molecules as a natural product or synthetic molecule. The method can hence be utilized to (i) identify natural products in large molecular libraries, (ii) quantify the natural product-likeness of small molecules, and (iii) visualize atoms in small molecules that are characteristic of natural products or synthetic molecules. The models are based on random forest classifiers trained on data sets consisting of more than 265,000 to 322,000 natural products and synthetic molecules. Two-dimensional molecular descriptors, MACCS keys and Morgan2 fingerprints were explored. On an independent test set the models reached areas under the receiver operating characteristic curve (AUC) of 0.997 and Matthews correlation coefficients (MCCs) of 0.954 and higher. The method was further tested on data from the Dictionary of Natural Products, ChEMBL and other resources. The best-performing models are accessible as a free web service at http://npscout.zbh.uni-hamburg.de/npscout.
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Affiliation(s)
- Ya Chen
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.
| | - Conrad Stork
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.
| | - Steffen Hirte
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.
- Department of Chemistry, University of Bergen, 5007 Bergen, Norway.
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, 5008 Bergen, Norway.
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16
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Gupta MK, Vadde R. In silico identification of natural product inhibitors for γ‐secretase activating protein, a therapeutic target for Alzheimer's disease. J Cell Biochem 2018; 120:10323-10336. [PMID: 30565717 DOI: 10.1002/jcb.28316] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology & Bioinformatics Yogi Vemana University, Kadapa Andhra Pradesh India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics Yogi Vemana University, Kadapa Andhra Pradesh India
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17
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Rampogu S, Zeb A, Baek A, Park C, Son M, Lee KW. Discovery of Potential Plant-Derived Peptide Deformylase (PDF) Inhibitors for Multidrug-Resistant Bacteria Using Computational Studies. J Clin Med 2018; 7:jcm7120563. [PMID: 30563019 PMCID: PMC6306950 DOI: 10.3390/jcm7120563] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 12/16/2022] Open
Abstract
Bacterial peptide deformylase (PDF) is an attractive target for developing novel inhibitors against several types of multidrug-resistant bacteria. The objective of the current study is to retrieve potential phytochemicals as prospective drugs against Staphylococcus aureus peptide deformylase (SaPDF). The current study focuses on applying ligand-based pharmacophore model (PharmL) and receptor-based pharmacophore (PharmR) approaches. Utilizing 20 known active compounds, pharmL was built and validated using Fischer's randomization, test set method and the decoy set method. PharmR was generated from the knowledge imparted by the Interaction Generation protocol implemented on the Discovery Studio (DS) v4.5 and was validated using the decoy set that was employed for pharmL. The selection of pharmR was performed based upon the selectivity score and further utilizing the Pharmacophore Comparison module available on the DS. Subsequently, the validated pharmacophore models were escalated for Taiwan Indigenous Plants (TIP) database screening and furthermore, a drug-like evaluation was performed. Molecular docking was initiated for the resultant compounds, employing CDOCKER (available on the DS) and GOLD. Eventually, the stability of the final PDF⁻hit complexes was affirmed using molecular dynamics (MD) simulation conducted by GROMACS v5.0.6. The redeemed hits demonstrated a similar binding mode and stable intermolecular interactions with the key residues, as determined by no aberrant behaviour for 50 ns. Taken together, it can be stated that the hits can act as putative scaffolds against SaPDF, with a higher therapeutic value. Furthermore, they can act as fundamental structures for designing new drug candidates.
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Affiliation(s)
- Shailima Rampogu
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju 52828, Korea.
| | - Amir Zeb
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju 52828, Korea.
| | - Ayoung Baek
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju 52828, Korea.
| | - Chanin Park
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju 52828, Korea.
| | - Minky Son
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju 52828, Korea.
| | - Keun Woo Lee
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju 52828, Korea.
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18
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Chen Y, Garcia de Lomana M, Friedrich NO, Kirchmair J. Characterization of the Chemical Space of Known and Readily Obtainable Natural Products. J Chem Inf Model 2018; 58:1518-1532. [DOI: 10.1021/acs.jcim.8b00302] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ya Chen
- Center for Bioinformatics, Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany
| | - Marina Garcia de Lomana
- Center for Bioinformatics, Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany
| | - Nils-Ole Friedrich
- Center for Bioinformatics, Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics, Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany
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19
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Chen Y, de Bruyn Kops C, Kirchmair J. Data Resources for the Computer-Guided Discovery of Bioactive Natural Products. J Chem Inf Model 2017; 57:2099-2111. [DOI: 10.1021/acs.jcim.7b00341] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ya Chen
- Center
for Bioinformatics, Department of Computer Science, Faculty of Mathematics,
Informatics and Natural Sciences, Universität Hamburg, Hamburg 20146, Germany
| | - Christina de Bruyn Kops
- Center
for Bioinformatics, Department of Computer Science, Faculty of Mathematics,
Informatics and Natural Sciences, Universität Hamburg, Hamburg 20146, Germany
| | - Johannes Kirchmair
- Center
for Bioinformatics, Department of Computer Science, Faculty of Mathematics,
Informatics and Natural Sciences, Universität Hamburg, Hamburg 20146, Germany
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20
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Computational evaluation of phytocompounds for combating drug resistant tuberculosis by multi-targeted therapy. J Mol Model 2015; 21:247. [PMID: 26323856 DOI: 10.1007/s00894-015-2785-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
The cell wall of Mycobacterium tuberculosis interacts with the host counterpart during the pathogenesis of tuberculosis. L-rhamnosyl (L-Rha) residue, a linker connects the arabinogalactan and peptidoglycan moieties in the bacterial cell wall. The biosynthesis of L-rhamnose utilizes four successive enzymes RmlA, RmlB, RmlC and RmlD. Neither rhamnose nor the genes responsible for its synthesis are observed in humans. Thus, drugs inhibiting enzymes of this pathway are unlikely to interfere with metabolic pathways in humans. The adverse drug effects of first and second line drugs along with the development of multi-drug resistance tuberculosis have stimulated the research in search of new therapeutic drugs. Thus, it is attractive to hypothesize that inhibition of the biosynthesis of L-Rha would be lethal to the mycobacteria. Nature provides innumerable secondary metabolites with novel structural architectures with reported activity against M. tuberculosis. Combination of structure based virtual screening with physicochemical and pharmacokinetic studies against rhamnose pathway enzymes identified potential leads. The crucial screening studies recognized four phytocompounds butein, diospyrin, indicanine, and rumexneposide A with good binding affinity towards the rhamnose pathway proteins. Furthermore, the high throughput screening methods recognized butein, a secondary metabolite from Butea monosperma with strong anti-tubercular bioactive spectrum. Butein displayed promising anti-mycobacterial activity which is validated by Microplate alamar blue assay (MABA). The focus on novel agents like these phytocompounds which exhibit preference toward the successive enzymes of a single pathway can prevent the development of bacterial resistance.
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21
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Leyva-Peralta MA, Robles-Zepeda RE, Garibay-Escobar A, Ruiz-Bustos E, Alvarez-Berber LP, Gálvez-Ruiz JC. In vitro anti-proliferative activity of Argemone gracilenta and identification of some active components. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 15:13. [PMID: 25652581 PMCID: PMC4321710 DOI: 10.1186/s12906-015-0532-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 01/19/2015] [Indexed: 11/19/2022]
Abstract
Background Cancer is one of the leading causes of death worldwide. Natural products have been regarded as important sources of potential chemotherapeutic agents. In this study, we evaluated the anti-proliferative activity of Argemone gracilenta’s methanol extract and its fractions. We identified those compounds of the most active fractions that displayed anti-proliferative activity. Methods The anti-proliferative activity on different cancerous cell lines (M12.C3F6, RAW 264.7, HeLa) was evaluated in vitro using the MTT colorimetric method. Identification of the active compounds present in the fractions with the highest activity was achieved by nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS) analyses. Results Both argemonine and berberine alkaloids, isolated from the ethyl acetate fraction, displayed high anti-proliferative activity with IC50 values of 2.8, 2.5, 12.1, and 2.7, 2.4, 79.5 μg/mL on M12.C3F6, RAW 264.7, and HeLa cancerous cell lines, respectively. No activity was shown on the normal L-929 cell line. From the hexane fraction, a mixture of fatty acids and fatty acid esters of 16 or more carbon atoms with anti-proliferative activity was identified, showing a range of IC50 values of 16.8-24.9, 34.1-35.4, and 67.6-91.8 μg/mL on M12.C3F6, RAW 264.7, and HeLa cancerous cell lines, respectively. On the normal L-929 cell line, this mixture showed a range of IC50 values of 85.1 to 100 μg/mL. Conclusion This is the first study that relates argemonine, berberine, and a mixture of fatty acids and fatty acid esters with the anti-proliferative activity displayed by Argemone gracilenta.
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22
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Neves BJ, Andrade CH, Cravo PVL. Natural products as leads in schistosome drug discovery. Molecules 2015; 20:1872-903. [PMID: 25625682 PMCID: PMC6272663 DOI: 10.3390/molecules20021872] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 12/31/2014] [Accepted: 01/14/2015] [Indexed: 11/16/2022] Open
Abstract
Schistosomiasis is a neglected parasitic tropical disease that claims around 200,000 human lives every year. Praziquantel (PZQ), the only drug recommended by the World Health Organization for the treatment and control of human schistosomiasis, is now facing the threat of drug resistance, indicating the urgent need for new effective compounds to treat this disease. Therefore, globally, there is renewed interest in natural products (NPs) as a starting point for drug discovery and development for schistosomiasis. Recent advances in genomics, proteomics, bioinformatics, and cheminformatics have brought about unprecedented opportunities for the rapid and more cost-effective discovery of new bioactive compounds against neglected tropical diseases. This review highlights the main contributions that NP drug discovery and development have made in the treatment of schistosomiasis and it discusses how integration with virtual screening (VS) strategies may contribute to accelerating the development of new schistosomidal leads, especially through the identification of unexplored, biologically active chemical scaffolds and structural optimization of NPs with previously established activity.
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Affiliation(s)
- Bruno J Neves
- LabMol-Laboratory for Drug Design and Molecular Modeling, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia 74605-170, Brazil.
| | - Carolina H Andrade
- LabMol-Laboratory for Drug Design and Molecular Modeling, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia 74605-170, Brazil.
| | - Pedro V L Cravo
- GenoBio-Laboratory of Genomics and Biotechnology, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia 74605-050, Brazil.
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23
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Tung CW, Lin YC, Chang HS, Wang CC, Chen IS, Jheng JL, Li JH. TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau055. [PMID: 24930145 PMCID: PMC4057645 DOI: 10.1093/database/bau055] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure–activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein–ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb.
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Affiliation(s)
- Chun-Wei Tung
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Ying-Chi Lin
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Hsun-Shuo Chang
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Chia-Chi Wang
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Ih-Sheng Chen
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Jhao-Liang Jheng
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Jih-Heng Li
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, TaiwanSchool of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, PhD Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan and National Environmental Health Research Center, National Health Research Institutes, Miaoli County 35053, Taiwan
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