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Basmadjian C, Zhao Q, Bentouhami E, Djehal A, Nebigil CG, Johnson RA, Serova M, de Gramont A, Faivre S, Raymond E, Désaubry LG. Cancer wars: natural products strike back. Front Chem 2014; 2:20. [PMID: 24822174 PMCID: PMC4013484 DOI: 10.3389/fchem.2014.00020] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/04/2014] [Indexed: 12/14/2022] Open
Abstract
Natural products have historically been a mainstay source of anticancer drugs, but in the 90's they fell out of favor in pharmaceutical companies with the emergence of targeted therapies, which rely on antibodies or small synthetic molecules identified by high throughput screening. Although targeted therapies greatly improved the treatment of a few cancers, the benefit has remained disappointing for many solid tumors, which revitalized the interest in natural products. With the approval of rapamycin in 2007, 12 novel natural product derivatives have been brought to market. The present review describes the discovery and development of these new anticancer drugs and highlights the peculiarities of natural product and new trends in this exciting field of drug discovery.
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Affiliation(s)
- Christine Basmadjian
- Therapeutic Innovation Laboratory, UMR7200, CNRS/University of StrasbourgIllkirch, France
- AAREC Filia ResearchClichy, France
| | - Qian Zhao
- Therapeutic Innovation Laboratory, UMR7200, CNRS/University of StrasbourgIllkirch, France
- AAREC Filia ResearchClichy, France
| | - Embarek Bentouhami
- L.C.I.M.N Laboratory, Department of Process Engineering, Faculty of Technology, University Ferhat AbbasSétif, Algeria
| | - Amel Djehal
- Therapeutic Innovation Laboratory, UMR7200, CNRS/University of StrasbourgIllkirch, France
- L.C.I.M.N Laboratory, Department of Process Engineering, Faculty of Technology, University Ferhat AbbasSétif, Algeria
| | - Canan G. Nebigil
- Biotechnology and Cell Signaling Laboratory, UMR 7242, CNRS/ University of StrasbourgIllkirch, France
| | - Roger A. Johnson
- Department of Physiology and Biophysics, State University of New YorkStony Brook, NY, USA
| | | | | | - Sandrine Faivre
- AAREC Filia ResearchClichy, France
- Department of Medical Oncology, Beaujon University Hospital, INSERM U728/AP-HPClichy, France
| | - Eric Raymond
- AAREC Filia ResearchClichy, France
- Department of Medical Oncology, Beaujon University Hospital, INSERM U728/AP-HPClichy, France
| | - Laurent G. Désaubry
- Therapeutic Innovation Laboratory, UMR7200, CNRS/University of StrasbourgIllkirch, France
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Montalbano F, Cal PMSD, Carvalho MABR, Gonçalves LM, Lucas SD, Guedes RC, Veiros LF, Moreira R, Gois PMP. Discovery of new heterocycles with activity against human neutrophile elastase based on a boron promoted one-pot assembly reaction. Org Biomol Chem 2014; 11:4465-72. [PMID: 23715243 DOI: 10.1039/c3ob40614h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Herein we demonstrate for the first time that a boron promoted one-pot assembly reaction may be used to discover novel enzyme inhibitors. Inhibitors for HNE were simply assembled in excellent yields, high diastereoselectivities and IC50 up to 1.10 μM, based on components like salicylaldehyde, aryl boronic acids and amino acids. The combination of synthetic, biochemical, analytical and theoretical studies allowed the identification of the 4-methoxy or the 4-diethyl amino substituent of the salicylaldehyde as the most important recognition moiety and the imine alkylation, lactone ring opening as key events in the mechanism of inhibition.
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Affiliation(s)
- Francesco Montalbano
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
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Ntie-Kang F, Lifongo LL, Simoben CV, Babiaka SB, Sippl W, Mbaze LM. The uniqueness and therapeutic value of natural products from West African medicinal plants, part II: terpenoids, geographical distribution and drug discovery. RSC Adv 2014. [DOI: 10.1039/c4ra04543b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this review series, an attempt has been made to give indepth coverage of natural products derived from West African medicinal plants with diverse biological activities.
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Affiliation(s)
- Fidele Ntie-Kang
- Chemical and Bioactivity Information Centre
- Department of Chemistry
- Faculty of Science
- University of Buea
- Buea, Cameroon
| | - Lydia L. Lifongo
- Chemical and Bioactivity Information Centre
- Department of Chemistry
- Faculty of Science
- University of Buea
- Buea, Cameroon
| | - Conrad V. Simoben
- Chemical and Bioactivity Information Centre
- Department of Chemistry
- Faculty of Science
- University of Buea
- Buea, Cameroon
| | - Smith B. Babiaka
- Chemical and Bioactivity Information Centre
- Department of Chemistry
- Faculty of Science
- University of Buea
- Buea, Cameroon
| | - Wolfgang Sippl
- Department of Pharmaceutical Sciences
- Martin-Luther University of Halle-Wittenberg
- Halle, Germany
| | - Luc Meva'a Mbaze
- Department of Chemistry
- Faculty of Science
- University of Douala
- Douala, Cameroon
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Abstract
The chemical diversity, binding specificity and propensity to interact with biological targets has inspired many researchers to utilize natural products as molecular probes. Almost all reported carbonic anhydrase inhibitors comprise a zinc binding group in their structure of which the primary sulfonamide moiety (-SO2NH2) is the foremost example and to a lesser extent the primary sulfamate (-O-SO2NH2) and sulfamide (-NH-SO2NH2) groups. Natural products that comprise these zinc binding groups in their structure are however rare and relatively few natural products have been explored as a source for novel carbonic anhydrase inhibitors. This chapter will highlight the recent and growing interest in carbonic anhydrase inhibitors sourced from nature, demonstrating that natural product chemical space presents a rich source of potential alternate chemotypes for the discovery of novel drug-like carbonic anhydrase inhibitors.
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105
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Ntie-Kang F, Onguéné PA, Scharfe M, Owono Owono LC, Megnassan E, Mbaze LM, Sippl W, Efange SMN. ConMedNP: a natural product library from Central African medicinal plants for drug discovery. RSC Adv 2014. [DOI: 10.1039/c3ra43754j] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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New antimalarial hits from Dacryodes edulis (Burseraceae)--part I: isolation, in vitro activity, in silico "drug-likeness" and pharmacokinetic profiles. PLoS One 2013; 8:e79544. [PMID: 24282507 PMCID: PMC3836662 DOI: 10.1371/journal.pone.0079544] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/21/2013] [Indexed: 11/19/2022] Open
Abstract
The aims of the present study were to identify the compounds responsible for the anti-malarial activity of Dacryoedes edulis (Burseraceae) and to investigate their suitability as leads for the treatment of drug resistant malaria. Five compounds were isolated from ethyl acetate and hexane extracts of D. edulis stem bark and tested against 3D7 (chloroquine-susceptible) and Dd2 (multidrug-resistant) strains of Plasmodium falciparum, using the parasite lactate dehydrogenase method. Cytotoxicity studies were carried out on LLC-MK2 monkey kidney epithelial cell-line. In silico analysis was conducted by calculating molecular descriptors using the MOE software running on a Linux workstation. The “drug-likeness” of the isolated compounds was assessed using Lipinski criteria, from computed molecular properties of the geometry optimized structures. Computed descriptors often used to predict absorption, distribution, metabolism, elimination and toxicity (ADMET) were used to assess the pharmacokinetic profiles of the isolated compounds. Antiplasmodial activity was demonstrated for the first time in five major natural products previously identified in D. edulis, but not tested against malaria parasites. The most active compound identified was termed DES4. It had IC50 values of 0.37 and 0.55 µg/mL, against 3D7 and Dd2 respectively. In addition, this compound was shown to act in synergy with quinine, satisfied all criteria of “Drug-likeness” and showed considerable probability of providing an antimalarial lead. The remaining four compounds also showed antiplasmodial activity, but were less effective than DES4. None of the tested compounds was cytotoxicity against LLC-MK2 cells, suggesting their selective activities on malaria parasites. Based on the high in vitro activity, low toxicity and predicted “Drug-likeness” DES4 merits further investigation as a possible drug lead for the treatment of malaria.
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108
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Ntie-Kang F, Zofou D, Babiaka SB, Meudom R, Scharfe M, Lifongo LL, Mbah JA, Mbaze LM, Sippl W, Efange SMN. AfroDb: a select highly potent and diverse natural product library from African medicinal plants. PLoS One 2013; 8:e78085. [PMID: 24205103 PMCID: PMC3813505 DOI: 10.1371/journal.pone.0078085] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/06/2013] [Indexed: 11/22/2022] Open
Abstract
Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We assess the bioactivity and "drug-likeness" of a relatively small but structurally diverse dataset (containing >1,000 compounds) from African medicinal plants, which have been tested and proven a wide range of biological activities. The geographical regions of collection of the medicinal plants cover the entire continent of Africa, based on data from literature sources and information from traditional healers. For each isolated compound, the three dimensional (3D) structure has been used to calculate physico-chemical properties used in the prediction of oral bioavailability on the basis of Lipinski's "Rule of Five". A comparative analysis has been carried out with the "drug-like", "lead-like", and "fragment-like" subsets, as well as with the Dictionary of Natural Products. A diversity analysis has been carried out in comparison with the ChemBridge diverse database. Furthermore, descriptors related to absorption, distribution, metabolism, excretion and toxicity (ADMET) have been used to predict the pharmacokinetic profile of the compounds within the dataset. Our results prove that drug discovery, beginning with natural products from the African flora, could be highly promising. The 3D structures are available and could be useful for virtual screening and natural product lead generation programs.
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Affiliation(s)
- Fidele Ntie-Kang
- Chemical and Bioactivity Information Centre, Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
- Center Atomic Molecular Physics, Optics and Quantum, Faculty of Science, University of Douala, Douala, Cameroon
- Department of Pharmaceutical Sciences, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Denis Zofou
- Biotechnology Unit, Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Smith B. Babiaka
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
| | - Rolande Meudom
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
| | - Michael Scharfe
- Department of Pharmaceutical Sciences, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Lydia L. Lifongo
- Chemical and Bioactivity Information Centre, Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
| | - James A. Mbah
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
| | - Luc Meva’a Mbaze
- Department of Chemistry, Faculty of Science, University of Douala, Douala, Cameroon
| | - Wolfgang Sippl
- Department of Pharmaceutical Sciences, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Simon M. N. Efange
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
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Lahore S, Narkhede U, Merlini L, Dallavalle S. Total Synthesis of the Natural Product Benzo[j]fluoranthene-4,9-diol: An Approach to the Synthesis of Oxygenated Benzo[j]fluoranthenes. J Org Chem 2013; 78:10860-6. [DOI: 10.1021/jo401887t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Santosh Lahore
- Department of Food, Environmental
and Nutritional Sciences, Division of Chemistry and Molecular Biology, Università di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Umesh Narkhede
- Department of Food, Environmental
and Nutritional Sciences, Division of Chemistry and Molecular Biology, Università di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Lucio Merlini
- Department of Food, Environmental
and Nutritional Sciences, Division of Chemistry and Molecular Biology, Università di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Sabrina Dallavalle
- Department of Food, Environmental
and Nutritional Sciences, Division of Chemistry and Molecular Biology, Università di Milano, Via Celoria 2, 20133 Milano, Italy
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Ntie-Kang F, Mbah JA, Lifongo LL, Owono Owono LC, Megnassan E, Meva'a Mbaze L, Judson PN, Sippl W, Efange SM. Assessing the pharmacokinetic profile of the CamMedNP natural products database: an in silico approach. Org Med Chem Lett 2013; 3:10. [PMID: 24229455 PMCID: PMC3767462 DOI: 10.1186/2191-2858-3-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/15/2013] [Indexed: 12/19/2022] Open
Abstract
Background Drug metabolism and pharmacokinetic (DMPK) assessment has come to occupy a place of interest during the early stages of drug discovery today. Computer-based methods are slowly gaining ground in this area and are often used as initial tools to eliminate compounds likely to present uninteresting pharmacokinetic profiles and unacceptable levels of toxicity from the list of potential drug candidates, hence cutting down the cost of the discovery of a drug. Results In the present study, we present an in silico assessment of the DMPK profile of our recently published natural products database of 1,859 unique compounds derived from 224 species of medicinal plants from the Cameroonian forest. In this analysis, we have used 46 computed physico-chemical properties or molecular descriptors to predict the absorption, distribution, metabolism and elimination (ADME) of the compounds. This survey demonstrated that about 50% of the compounds within the Cameroonian medicinal plant and natural products (CamMedNP) database are compliant, having properties which fall within the range of ADME properties of >95% of currently known drugs, while >73% of the compounds have ≤2 violations. Moreover, about 72% of the compounds within the corresponding ‘drug-like’ subset showed compliance. Conclusions In addition to the previously verified levels of ‘drug-likeness’ and the diversity and the wide range of measured biological activities, the compounds in the CamMedNP database show interesting DMPK profiles and, hence, could represent an important starting point for hit/lead discovery from medicinal plants in Africa.
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Affiliation(s)
- Fidele Ntie-Kang
- CEPAMOQ, Faculty of Science, University of Douala, P,O, Box 8580, Douala, Cameroon.
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Cheng TR, Chan T, Tsou E, Chang S, Yun W, Yang P, Wu Y, Cheng W. From Natural Product‐Inspired Pyrrolidine Scaffolds to the Development of New Human Golgi α‐Mannosidase II Inhibitors. Chem Asian J 2013; 8:2600-4. [DOI: 10.1002/asia.201300680] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Ting‐Jen R. Cheng
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Ting‐Hao Chan
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - En‐Lun Tsou
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Shang‐Yu Chang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Wen‐Yi Yun
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Pei‐Jung Yang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Ying‐Ta Wu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Wei‐Chieh Cheng
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
- Department of Chemistry, National Cheng‐Kung University, 1, University Road, Tainan (Taiwan), Fax: (+886) 2 27899931
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112
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Ntie-Kang F, Lifongo LL, Mbah JA, Owono Owono LC, Megnassan E, Mbaze LM, Judson PN, Sippl W, Efange SMN. In silico drug metabolism and pharmacokinetic profiles of natural products from medicinal plants in the Congo basin. In Silico Pharmacol 2013; 1:12. [PMID: 25505657 PMCID: PMC4230438 DOI: 10.1186/2193-9616-1-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/06/2013] [Indexed: 01/05/2023] Open
Abstract
Purpose Drug metabolism and pharmacokinetics (DMPK) assessment has come to occupy a place of interest during the early stages of drug discovery today. The use of computer modelling to predict the DMPK and toxicity properties of a natural product library derived from medicinal plants from Central Africa (named ConMedNP). Material from some of the plant sources are currently employed in African Traditional Medicine. Methods Computer-based methods are slowly gaining ground in this area and are often used as preliminary criteria for the elimination of compounds likely to present uninteresting pharmacokinetic profiles and unacceptable levels of toxicity from the list of potential drug candidates, hence cutting down the cost of discovery of a drug. In the present study, we present an in silico assessment of the DMPK and toxicity profile of a natural product library containing ~3,200 compounds, derived from 379 species of medicinal plants from 10 countries in the Congo Basin forests and savannas, which have been published in the literature. In this analysis, we have used 46 computed physico-chemical properties or molecular descriptors to predict the absorption, distribution, metabolism and elimination and toxicity (ADMET) of the compounds. Results This survey demonstrated that about 45% of the compounds within the ConMedNP compound library are compliant, having properties which fall within the range of ADME properties of 95% of currently known drugs, while about 69% of the compounds have ≤ 2 violations. Moreover, about 73% of the compounds within the corresponding “drug-like” subset showed compliance. Conclusions In addition to the verified levels of “drug-likeness”, diversity and the wide range of measured biological activities, the compounds from medicinal plants in Central Africa show interesting DMPK profiles and hence could represent an important starting point for hit/lead discovery. Electronic supplementary material The online version of this article (doi:10.1186/2193-9616-1-12) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fidele Ntie-Kang
- CEPAMOQ, Faculty of Science, University of Douala, P.O. Box 8580, Douala, Cameroon ; Chemical and Bioactivity Information Centre, Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea, Cameroon ; Department of Pharmaceutical Sciences, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck Str. 4, 06120 Halle (Saale), Germany
| | - Lydia L Lifongo
- Chemical and Bioactivity Information Centre, Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea, Cameroon
| | - James A Mbah
- Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Luc C Owono Owono
- CEPAMOQ, Faculty of Science, University of Douala, P.O. Box 8580, Douala, Cameroon ; Laboratory for Simulations and Biomolecular Physics, Advanced Teachers Training College, University of Yaoundé, I, P.O. Box 47, Yaoundé, Cameroon
| | - Eugene Megnassan
- Laboratory of Fundamental and Applied Physics, University of Abobo-Adjame, Abidjan, 02 BP 801 Cote d'Ivoire
| | - Luc Meva'a Mbaze
- Department of Chemistry, Faculty of Science, University of Douala, P. O. Box 24157, Douala, Cameroon
| | - Philip N Judson
- Chemical and Bioactivity Information Centre, 22-23 Blenheim Terrace, Woodhouse Lane, Leeds LS2 9HD UK
| | - Wolfgang Sippl
- Department of Pharmaceutical Sciences, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck Str. 4, 06120 Halle (Saale), Germany
| | - Simon M N Efange
- Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea, Cameroon
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Addla D, Jallapally A, Kanwal A, Sridhar B, Banerjee SK, Kantevari S. Design, synthesis and evaluation of novel 2-hydroxypyrrolobenzodiazepine-5,11-dione analogues as potent angiotensin converting enzyme (ACE) inhibitors. Bioorg Med Chem 2013; 21:4485-93. [DOI: 10.1016/j.bmc.2013.05.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 12/19/2022]
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Gu J, Gui Y, Chen L, Yuan G, Lu HZ, Xu X. Use of natural products as chemical library for drug discovery and network pharmacology. PLoS One 2013; 8:e62839. [PMID: 23638153 PMCID: PMC3636197 DOI: 10.1371/journal.pone.0062839] [Citation(s) in RCA: 234] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 03/28/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Natural products have been an important source of lead compounds for drug discovery. How to find and evaluate bioactive natural products is critical to the achievement of drug/lead discovery from natural products. METHODOLOGY We collected 19,7201 natural products structures, reported biological activities and virtual screening results. Principal component analysis was employed to explore the chemical space, and we found that there was a large portion of overlap between natural products and FDA-approved drugs in the chemical space, which indicated that natural products had large quantity of potential lead compounds. We also explored the network properties of natural product-target networks and found that polypharmacology was greatly enriched to those compounds with large degree and high betweenness centrality. In order to make up for a lack of experimental data, high throughput virtual screening was employed. All natural products were docked to 332 target proteins of FDA-approved drugs. The most potential natural products for drug discovery and their indications were predicted based on a docking score-weighted prediction model. CONCLUSIONS Analysis of molecular descriptors, distribution in chemical space and biological activities of natural products was conducted in this article. Natural products have vast chemical diversity, good drug-like properties and can interact with multiple cellular target proteins.
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Affiliation(s)
- Jiangyong Gu
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yuanshen Gui
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
- Institute of Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Lirong Chen
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Hui-Zhe Lu
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
- Institute of Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Xiaojie Xu
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
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Kell DB. Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it. FEBS J 2013; 280:5957-80. [PMID: 23552054 DOI: 10.1111/febs.12268] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/20/2013] [Accepted: 03/26/2013] [Indexed: 12/16/2022]
Abstract
Despite the sequencing of the human genome, the rate of innovative and successful drug discovery in the pharmaceutical industry has continued to decrease. Leaving aside regulatory matters, the fundamental and interlinked intellectual issues proposed to be largely responsible for this are: (a) the move from 'function-first' to 'target-first' methods of screening and drug discovery; (b) the belief that successful drugs should and do interact solely with single, individual targets, despite natural evolution's selection for biochemical networks that are robust to individual parameter changes; (c) an over-reliance on the rule-of-5 to constrain biophysical and chemical properties of drug libraries; (d) the general abandoning of natural products that do not obey the rule-of-5; (e) an incorrect belief that drugs diffuse passively into (and presumably out of) cells across the bilayers portions of membranes, according to their lipophilicity; (f) a widespread failure to recognize the overwhelmingly important role of proteinaceous transporters, as well as their expression profiles, in determining drug distribution in and between different tissues and individual patients; and (g) the general failure to use engineering principles to model biology in parallel with performing 'wet' experiments, such that 'what if?' experiments can be performed in silico to assess the likely success of any strategy. These facts/ideas are illustrated with a reasonably extensive literature review. Success in turning round drug discovery consequently requires: (a) decent systems biology models of human biochemical networks; (b) the use of these (iteratively with experiments) to model how drugs need to interact with multiple targets to have substantive effects on the phenotype; (c) the adoption of polypharmacology and/or cocktails of drugs as a desirable goal in itself; (d) the incorporation of drug transporters into systems biology models, en route to full and multiscale systems biology models that incorporate drug absorption, distribution, metabolism and excretion; (e) a return to 'function-first' or phenotypic screening; and (f) novel methods for inferring modes of action by measuring the properties on system variables at all levels of the 'omes. Such a strategy offers the opportunity of achieving a state where we can hope to predict biological processes and the effect of pharmaceutical agents upon them. Consequently, this should both lower attrition rates and raise the rates of discovery of effective drugs substantially.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester, UK; Manchester Institute of Biotechnology, The University of Manchester, UK
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Yu MJ. Druggable chemical space and enumerative combinatorics. J Cheminform 2013; 5:19. [PMID: 23594604 PMCID: PMC3641967 DOI: 10.1186/1758-2946-5-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/07/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a growing body of literature describing the properties of marketed drugs, the concept of drug-likeness and the vastness of chemical space. In that context, enumerative combinatorics with simple atomic components may be useful in the conception and design of structurally novel compounds for expanding and enhancing high-throughput screening (HTS) libraries. RESULTS A random combination of mono- and diatomic carbon, hydrogen, nitrogen, and oxygen containing components in the absence of molecular weight constraints but with the ability to form rings affords virtual compounds that fall in bulk physicochemical space typically associated with drugs, but whose ring assemblies fall in new or under-represented areas of chemical shape space. When compared against compounds in the ChEMBL_14, MDDR, Drug Bank and Dictionary of Natural Products, the percentage of virtual compounds with a Tanimoto index of 1.0 (ECFP_4) was found to be as high as 0.21. Depending on therapeutic target, this value may be in range of what might be expected from an experimental HTS campaign in terms of a true hit rate. CONCLUSION Virtual compounds derived through enumerative combinatorics of simple atomic components have drug-like properties with ring assemblies that fall in new or under-represented areas of shape space. Structures derived in this manner could provide the starting point or inspiration for the design of structurally novel scaffolds in an unbiased fashion.
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Affiliation(s)
- Melvin J Yu
- Eisai Inc,, 4 Corporate, Dr, Andover, MA, 01810, USA.
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117
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Li D, Xu S, Cai H, Pei L, Wang L, Wu X, Yao H, Jiang J, Sun Y, Xu J. Library Construction and Biological Evaluation of Enmein-Type Diterpenoid Analogues as Potential Anticancer Agents. ChemMedChem 2013; 8:812-8. [DOI: 10.1002/cmdc.201200559] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/26/2013] [Indexed: 11/10/2022]
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118
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Patil NT, Shinde VS, Sridhar B. Relay Catalytic Branching Cascade: A Technique to Access Diverse Molecular Scaffolds. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208738] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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119
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Patil NT, Shinde VS, Sridhar B. Relay Catalytic Branching Cascade: A Technique to Access Diverse Molecular Scaffolds. Angew Chem Int Ed Engl 2013; 52:2251-5. [DOI: 10.1002/anie.201208738] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/20/2023]
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120
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Patil NT, Konala A, Sravanti S, Singh A, Ummanni R, Sridhar B. Electrophile induced branching cascade: a powerful approach to access various molecular scaffolds and their exploration as novel anti-mycobacterial agents. Chem Commun (Camb) 2013; 49:10109-11. [DOI: 10.1039/c3cc45289a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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121
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Titarenko Z, Vasilevich N, Zernov V, Kirpichenok M, Genis D. Oxygen-containing fragments in natural products. J Comput Aided Mol Des 2012; 27:125-60. [PMID: 23271273 DOI: 10.1007/s10822-012-9629-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/17/2012] [Indexed: 01/08/2023]
Abstract
An analysis of the chemical environment of the oxygen atoms in the DNP database compared to the CMC and SCD databases was performed. Some structural clusters were identified which are predominant among the natural products and can be considered as distinctive features of NPs. Fifty-three oxygen-containing structural fragments that are distinctive for the DNP (distinctive set of fragments DSF) in comparison with the SCD have been identified. A new descriptor Mc was introduced for describing the ratio of atoms involved in the DSF to the total number of heavy atoms. A significant difference in the Mc values among the reference databases allowed the use of a specific cluster of the DSF as a tool for performing similarity searches for oxygen-containing NP molecules, or for evaluation or comparison of databases according to their NP-likeness. An example illustrating that the suggested approach could allow not only estimating the NP-likeness, but also serve as a tool for designing new NP-like compounds is provided. The suggested approach for NP-likeness evaluation moves away from the traditional ideas of scaffolds, cycles, linkers and substituents.
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Affiliation(s)
- Zoya Titarenko
- ASINEX, 20 Geroev Panfilovtsev Str., Moscow 125480, Russia
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122
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Natural-product-derived fragments for fragment-based ligand discovery. Nat Chem 2012; 5:21-8. [DOI: 10.1038/nchem.1506] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 10/19/2012] [Indexed: 12/11/2022]
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123
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Brown JB. Staying Grounded in Reality - an Opinion on Why Informatics Students Should Have Laboratory Experience. Mol Inform 2012; 31:777-81. [PMID: 27476733 DOI: 10.1002/minf.201200096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- J B Brown
- Kyoto University Graduate School of Pharmaceutical Sciences, Department of Systems Bioscience for Drug Discovery, Kyoto, Japan.
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124
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Choomuenwai V, Andrews KT, Davis RA. Synthesis and antimalarial evaluation of a screening library based on a tetrahydroanthraquinone natural product scaffold. Bioorg Med Chem 2012; 20:7167-74. [DOI: 10.1016/j.bmc.2012.09.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/18/2012] [Accepted: 09/25/2012] [Indexed: 10/27/2022]
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125
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A minimalist fragment approach for the design of natural-product-like synthetic scaffolds. Drug Discov Today 2012; 17:1170-4. [DOI: 10.1016/j.drudis.2012.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 05/12/2012] [Accepted: 05/22/2012] [Indexed: 11/22/2022]
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126
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Brandi L, Maffioli S, Donadio S, Quaglia F, Sette M, Milón P, Gualerzi CO, Fabbretti A. Structural and functional characterization of the bacterial translocation inhibitor GE82832. FEBS Lett 2012; 586:3373-8. [PMID: 22841550 DOI: 10.1016/j.febslet.2012.07.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 10/28/2022]
Abstract
The structure of GE82832, a translocation inhibitor produced by a soil microorganism, is shown to be highly related to that of dityromycin, a bicyclodecadepsipeptide antibiotic discovered long ago whose characterization had never been pursued beyond its structural elucidation. GE82832 and dityromycin were shown to interfere with both aminoacyl-tRNA and mRNA movement and with the Pi release occurring after ribosome- and EF-G-dependent GTP hydrolysis. These findings and the unusual ribosomal localization of GE82832/dityromycin near protein S13 suggest that the mechanism of inhibition entails an interference with the rotation of the 30S subunit "head" which accompanies the ribosome-unlocking step of translocation.
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Affiliation(s)
- Letizia Brandi
- Department of Biosciences & Biotechnology, University of Camerino, Camerino (MC), Italy
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127
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Fleury-Brégeot N, Raushel J, Sandrock DL, Dreher SD, Molander GA. Rapid and efficient access to secondary arylmethylamines. Chemistry 2012; 18:9564-70. [PMID: 22767518 DOI: 10.1002/chem.201200831] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Indexed: 11/07/2022]
Abstract
Ammoniomethyl trifluoroborates are very powerful reagents that can be used to access biologically relevant aryl- and heteroaryl-methylamine motifs via Suzuki-Miyaura cross-couplings. Until now, this method was limited to the production of tertiary and primary amines. The synthesis of a large array of secondary ammoniomethyltrifluoroborates has been achieved through a one step nucleophilic substitution reaction on the potassium bromomethyltrifluoroborate. Smooth cross-coupling conditions have been designed, based on the use of an aminobiphenyl palladium precatalyst, to couple these trifluoroborates efficiently with aryl bromides. This strategy offers a new way to access biologically relevant motifs and allows, with the previously developed methods, access to all three classes of aminomethylarenes.
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Affiliation(s)
- Nicolas Fleury-Brégeot
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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128
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Vasilevich NI, Kombarov RV, Genis DV, Kirpichenok MA. Lessons from Natural Products Chemistry Can Offer Novel Approaches for Synthetic Chemistry in Drug Discovery. J Med Chem 2012; 55:7003-9. [DOI: 10.1021/jm300344v] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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129
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Kato N, Takahashi S, Nogawa T, Saito T, Osada H. Construction of a microbial natural product library for chemical biology studies. Curr Opin Chem Biol 2012; 16:101-8. [DOI: 10.1016/j.cbpa.2012.02.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/12/2012] [Accepted: 02/13/2012] [Indexed: 10/28/2022]
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130
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Montalbano F, Candeias NR, Veiros LF, André V, Duarte MT, Bronze MR, Moreira R, Gois PMP. Four-component assembly of chiral N-B heterocycles with a natural product-like framework. Org Lett 2012; 14:988-91. [PMID: 22316104 DOI: 10.1021/ol203224n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dative N-B bond was used to simply assemble heterocycles with a skeleton akin to the 5-oxofuro[2,3-b]furan motif. Twenty-five new N-B heterocycles were prepared via a highly efficient one-pot four-component reaction in yields and diastereoselectivities up to 95% and >97%, respectively. Several reaction intermediates were discovered using electrospray ionization mass spectroscopy which set the basis for the mechanism elucidation using DFT calculations.
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Affiliation(s)
- Francesco Montalbano
- Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
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131
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Peptide Scaffolds: Flexible Molecular Structures With Diverse Therapeutic Potentials. Int J Pept Res Ther 2012. [DOI: 10.1007/s10989-011-9286-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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132
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Barnes EC, Choomuenwai V, Andrews KT, Quinn RJ, Davis RA. Design and synthesis of screening libraries based on the muurolane natural product scaffold. Org Biomol Chem 2012; 10:4015-23. [DOI: 10.1039/c2ob00029f] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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133
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Kirst HA. Recent derivatives from smaller classes of fermentation-derived antibacterials. Expert Opin Ther Pat 2011; 22:15-35. [DOI: 10.1517/13543776.2012.642370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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134
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135
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Wetzel S, Bon RS, Kumar K, Waldmann H. Biology-Oriented Synthesis. Angew Chem Int Ed Engl 2011; 50:10800-26. [DOI: 10.1002/anie.201007004] [Citation(s) in RCA: 396] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Indexed: 12/22/2022]
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136
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Langdon SR, Brown N, Blagg J. Scaffold diversity of exemplified medicinal chemistry space. J Chem Inf Model 2011; 51:2174-85. [PMID: 21877753 PMCID: PMC3180201 DOI: 10.1021/ci2001428] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Indexed: 11/28/2022]
Abstract
The scaffold diversity of 7 representative commercial and proprietary compound libraries is explored for the first time using both Murcko frameworks and Scaffold Trees. We show that Level 1 of the Scaffold Tree is useful for the characterization of scaffold diversity in compound libraries and offers advantages over the use of Murcko frameworks. This analysis also demonstrates that the majority of compounds in the libraries we analyzed contain only a small number of well represented scaffolds and that a high percentage of singleton scaffolds represent the remaining compounds. We use Tree Maps to clearly visualize the scaffold space of representative compound libraries, for example, to display highly populated scaffolds and clusters of structurally similar scaffolds. This study further highlights the need for diversification of compound libraries used in hit discovery by focusing library enrichment on the synthesis of compounds with novel or underrepresented scaffolds.
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Affiliation(s)
- Sarah R. Langdon
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K
| | - Nathan Brown
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K
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137
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Imhoff JF, Labes A, Wiese J. Bio-mining the microbial treasures of the ocean: New natural products. Biotechnol Adv 2011; 29:468-82. [DOI: 10.1016/j.biotechadv.2011.03.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 02/25/2011] [Accepted: 03/09/2011] [Indexed: 01/10/2023]
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138
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Schuffenhauer A, Varin T. Rule-Based Classification of Chemical Structures by Scaffold. Mol Inform 2011; 30:646-64. [PMID: 27467257 DOI: 10.1002/minf.201100078] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/14/2011] [Indexed: 01/25/2023]
Abstract
Databases for small organic chemical molecules usually contain millions of structures. The screening decks of pharmaceutical companies contain more than a million of structures. Nevertheless chemical substructure searching in these databases can be performed interactively in seconds. Because of this nobody has really missed structural classification of these databases for the purpose of finding data for individual chemical substructures. However, a full deck high-throughput screen produces also activity data for more than a million of substances. How can this amount of data be analyzed? Which are the active scaffolds identified by an assays? To answer such questions systematic classifications of molecules by scaffolds are needed. In this review it is described how molecules can be hierarchically classified by their scaffolds. It is explained how such classifications can be used to identify active scaffolds in an HTS data set. Once active classes are identified, they need to be visualized in the context of related scaffolds in order to understand SAR. Consequently such visualizations are another topic of this review. In addition scaffold based diversity measures are discussed and an outlook is given about the potential impact of structural classifications on a chemically aware semantic web.
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Affiliation(s)
- Ansgar Schuffenhauer
- Novartis Institutes for BioMedical Research, CPC/LFP, WSJ-88.11.11, Postfach, Basel, Switzerland, CH-4002; phone:+41 61 32 45385.
| | - Thibault Varin
- Novartis Institutes for BioMedical Research, CPC/LFP, WSJ-88.11.11, Postfach, Basel, Switzerland, CH-4002; phone:+41 61 32 45385
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139
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Liu W, Khedkar V, Baskar B, Schürmann M, Kumar K. Branching Cascades: A Concise Synthetic Strategy Targeting Diverse and Complex Molecular Frameworks. Angew Chem Int Ed Engl 2011; 50:6900-5. [DOI: 10.1002/anie.201102440] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 05/12/2011] [Indexed: 01/01/2023]
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140
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Liu W, Khedkar V, Baskar B, Schürmann M, Kumar K. Branching Cascades: A Concise Synthetic Strategy Targeting Diverse and Complex Molecular Frameworks. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102440] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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141
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Varin T, Schuffenhauer A, Ertl P, Renner S. Mining for bioactive scaffolds with scaffold networks: improved compound set enrichment from primary screening data. J Chem Inf Model 2011; 51:1528-38. [PMID: 21615076 DOI: 10.1021/ci2000924] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of meaningful chemical patterns in the increasing amounts of high-throughput-generated bioactivity data available today is an increasingly important challenge for successful drug discovery. Herein, we present the scaffold network as a novel approach for mapping and navigation of chemical and biological space. A scaffold network represents the chemical space of a library of molecules consisting of all molecular scaffolds and smaller "parent" scaffolds generated therefrom by the pruning of rings, effectively leading to a network of common scaffold substructure relationships. This algorithm provides an extension of the scaffold tree algorithm that, instead of a network, generates a tree relationship between a heuristically rule-based selected subset of parent scaffolds. The approach was evaluated for the identification of statistically significantly active scaffolds from primary screening data for which the scaffold tree approach has already been shown to be successful. Because of the exhaustive enumeration of smaller scaffolds and the full enumeration of relationships between them, about twice as many statistically significantly active scaffolds were identified compared to the scaffold-tree-based approach. We suggest visualizing scaffold networks as islands of active scaffolds.
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Affiliation(s)
- Thibault Varin
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, CH-4056 Basel, Switzerland
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142
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Sequential Transformations to Access Polycyclic Chemotypes: Asymmetric Crotylation and Metal Carbenoid Reactions. Angew Chem Int Ed Engl 2011; 50:5938-42. [DOI: 10.1002/anie.201101366] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Indexed: 01/07/2023]
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143
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Wu J, Becerril J, Lian Y, Davies HML, Porco JA, Panek JS. Sequential Transformations to Access Polycyclic Chemotypes: Asymmetric Crotylation and Metal Carbenoid Reactions. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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144
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Kingston DGI. Modern natural products drug discovery and its relevance to biodiversity conservation. JOURNAL OF NATURAL PRODUCTS 2011; 74:496-511. [PMID: 21138324 PMCID: PMC3061248 DOI: 10.1021/np100550t] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Natural products continue to provide a diverse and unique source of bioactive lead compounds for drug discovery, but maintaining their continued eminence as source compounds is challenging in the face of the changing face of the pharmaceutical industry and the changing nature of biodiversity prospecting brought about by the Convention on Biological Diversity. This review provides an overview of some of these challenges and suggests ways in which they can be addressed so that natural products research can remain a viable and productive route to drug discovery. Results from International Cooperative Biodiversity Groups (ICBGs) working in Madagascar, Panama, and Suriname are used as examples of what can be achieved when biodiversity conservation is linked to drug discovery.
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Affiliation(s)
- David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States.
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145
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Zhang YL, Zhang J, Jiang N, Lu YH, Wang L, Xu SH, Wang W, Zhang GF, Xu Q, Ge HM, Ma J, Song YC, Tan RX. Immunosuppressive polyketides from mantis-associated Daldinia eschscholzii. J Am Chem Soc 2011; 133:5931-40. [PMID: 21434637 DOI: 10.1021/ja110932p] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Polyketides with unknown architectures are highly desired for the discovery of new drugs and agrochemicals. Here, the mantis-associated Daldinia eschscholzii, a fungus known to produce immunosuppressants dalesconols A and B, was found to simultaneously generate four novel skeletons capable of shaping the unusual chemistry of the fungal polyketides, of which seven were structurally unique and substantially immunosuppressive. In particular, the scaled-up fermentation of the microbe enabled the structural characterization of minor or "transitional" intermediate polyketides that allowed the reasonable recognition of the four biosynthetic pathways initiated by condensations of four, five, six and eight acetate units, respectively. Furthermore, the decarbonylation reaction of triketone, as in the case of daeschol A, was described for the first time, in addition to the structural correction of sporothrin C and nodulone. The work provided a set of novel immunosuppressive molecules that are of significance to drug discovery.
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Affiliation(s)
- Ying L Zhang
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
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146
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Ginsburg H, Deharo E. A call for using natural compounds in the development of new antimalarial treatments - an introduction. Malar J 2011; 10 Suppl 1:S1. [PMID: 21411010 PMCID: PMC3059457 DOI: 10.1186/1475-2875-10-s1-s1] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural compounds, mostly from plants, have been the mainstay of traditional medicine for thousands of years. They have also been the source of lead compounds for modern medicine, but the extent of mining of natural compounds for such leads decreased during the second half of the 20th century. The advantage of natural compounds for the development of drugs derives from their innate affinity for biological receptors. Natural compounds have provided the best anti-malarials known to date. Recent surveys have identified many extracts of various organisms (mostly plants) as having antiplasmodial activity. Huge libraries of fractionated natural compounds have been screened with impressive hit rates. Importantly, many cases are known where the crude biological extract is more efficient pharmacologically than the most active purified compound from this extract. This could be due to synergism with other compounds present in the extract, that as such have no pharmacological activity. Indeed, such compounds are best screened by cell-based assay where all potential targets in the cell are probed and possible synergies identified. Traditional medicine uses crude extracts. These have often been shown to provide many concoctions that deal better with the overall disease condition than with the causative agent itself. Traditional medicines are used by ~80 % of Africans as a first response to ailment. Many of the traditional medicines have demonstrable anti-plasmodial activities. It is suggested that rigorous evaluation of traditional medicines involving controlled clinical trials in parallel with agronomical development for more reproducible levels of active compounds could improve the availability of drugs at an acceptable cost and a source of income in malaria endemic countries.
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Affiliation(s)
- Hagai Ginsburg
- Dept, Biol, Chem, Inst, Life Sci, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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147
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Back to the Roots: Prediction of Biologically Active Natural Products from Ayurveda Traditional Medicine. Mol Inform 2011; 30:181-7. [DOI: 10.1002/minf.201000163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 12/20/2010] [Indexed: 11/07/2022]
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148
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Abstract
This chapter provides a brief overview of chemoinformatics and its applications to chemical library design. It is meant to be a quick starter and to serve as an invitation to readers for more in-depth exploration of the field. The topics covered in this chapter are chemical representation, chemical data and data mining, molecular descriptors, chemical space and dimension reduction, quantitative structure-activity relationship, similarity, diversity, and multiobjective optimization.
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149
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Odendaal AY, Trader DJ, Carlson EE. Chemoselective enrichment for natural products discovery. Chem Sci 2011; 2:760-764. [PMID: 24926410 DOI: 10.1039/c0sc00620c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Natural products account for a significant proportion of modern day therapeutic agents. However, the discovery of novel compounds is hindered by the isolation process, which often relies upon extraction and chromatographic separation techniques. These methods, which are dependent upon the physicochemical properties of the compounds, have a limited ability to both purify and concentrate the minor components of a biological extract. We have devised an isolation strategy based upon an orthogonal chemical feature, namely, functional group composition. Development of a functional group-targeted method is expected to achieve exceptional resolution given the large number of distinct moieties present in natural product extracts. Here, we describe the generation of controllably reversible covalent enrichment tags for the chemoselective isolation of alcohol-containing natural products from complex mixtures.
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Affiliation(s)
- Antoinette Y Odendaal
- Department of Chemistry, Indiana University, 212 S. Hawthorne Dr, Bloomington, IN, 47401, USA
| | - Darci J Trader
- Department of Chemistry, Indiana University, 212 S. Hawthorne Dr, Bloomington, IN, 47401, USA
| | - Erin E Carlson
- Department of Chemistry, Indiana University, 212 S. Hawthorne Dr, Bloomington, IN, 47401, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Dr, Bloomington, IN, 47401, USA
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Wei Y, Chen YT, Shi L, Gao LX, Liu S, Cui YM, Zhang W, Shen Q, Li J, Nan FJ. Discovery and structural modification of novel inhibitors of PTP1B inspired by the ACT fragment of scleritodermin A. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00153a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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