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A R Oliveira G, G D V Morales B, M O Sousa R, S Pereira S, Antunes D, Caffarena ER, Zanchi FB. Exploring Novel Antimalarial Compounds Targeting Plasmodium falciparum Enoyl-ACP Reductase: Computational and Experimental Insights. ACS OMEGA 2024; 9:22777-22793. [PMID: 38826533 PMCID: PMC11137734 DOI: 10.1021/acsomega.3c09893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/06/2024] [Accepted: 04/15/2024] [Indexed: 06/04/2024]
Abstract
Malaria, caused by Plasmodium protozoa with Plasmodium falciparum as the most virulent species, continues to pose significant health challenges. Despite the availability of effective antimalarial drugs, the emergence of resistance has heightened the urgency for developing novel therapeutic compounds. In this study, we investigated the enoyl-ACP reductase enzyme of P. falciparum (PfENR) as a promising target for antimalarial drug discovery. Through a comprehensive analysis, we conducted a comparative evaluation of two lead compounds, LD1 (CID: 44405336, lead compounds 1) and LD2 (CID: 72703246, lead compounds 2), obtained from the PubChem/NCBI ligand database, to serve as reference molecules in the identification of potential derivatives using virtual screening assays. Among the newly identified candidates, Ligand 1 (LG1) and Ligand 2 (LG2) exhibited intriguing characteristics and underwent further investigation through docking and molecular dynamics simulations. Ligand 1 (LG1) demonstrated interactions similar to LD1, including hydrogen bonding with Asp218, while Ligand 2 (LG2) displayed superior binding energy comparable to LD1 and LD2, despite lacking hydrogen bonding interactions observed in the control compounds triclosan and its derivative 7-(4-chloro-2-hydroxyphenoxy)-4-methyl-2H-chromen-2-one (CHJ). Following computational validation using the MM/GBSA method to estimate binding free energy, commercially acquired LG1 and LG2 ligands were subjected to in vitro testing. Inhibition assays were performed to evaluate their potential as PfENR inhibitors alongside triclosan as a control compound. LG1 exhibited no inhibitory effects, while LG2 demonstrated inhibitory effects like triclosan. In conclusion, this study contributes valuable insights into developing novel antimalarial drugs by identifying LG2 as a potential ligand and employing a comprehensive approach integrating computational and experimental methodologies.
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Affiliation(s)
- George A R Oliveira
- Laboratório
de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz, CEP: 76812-245 Porto Velho-RO, Brazil
- Programa
de Pós-graduação Stricto sensu em Biologia Computacional
e Sistemas do Instituto Oswaldo Cruz, CEP: 21040-360 Rio de Janeiro-RJ, Brazil
| | - Bruno G D V Morales
- Laboratório
de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz, CEP: 76812-245 Porto Velho-RO, Brazil
- Programa
de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia
(UNIR), CEP: 76801-974 Porto Velho-RO, Brazil
| | - Rosa M O Sousa
- Laboratório
de Engenharia de Anticorpos, Fundação
Oswaldo Cruz de Rondônia, CEP: 76812-245 Porto Velho-RO, Brazil
| | - Soraya S Pereira
- Programa
de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia
(UNIR), CEP: 76801-974 Porto Velho-RO, Brazil
- Laboratório
de Engenharia de Anticorpos, Fundação
Oswaldo Cruz de Rondônia, CEP: 76812-245 Porto Velho-RO, Brazil
- Programa
de Pós-graduação Stricto sensu em Biologia Computacional
e Sistemas do Instituto Oswaldo Cruz, CEP: 21040-360 Rio de Janeiro-RJ, Brazil
| | - Deborah Antunes
- Laboratório
de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fundação Oswaldo
Cruz (FIOCRUZ), CEP: 21040-900 Rio de Janeiro-RJ, Brazil
| | - Ernesto R. Caffarena
- Programa
de Pós-graduação Stricto sensu em Biologia Computacional
e Sistemas do Instituto Oswaldo Cruz, CEP: 21040-360 Rio de Janeiro-RJ, Brazil
- Programa
de Computação Científica—PROCC, Fundação
Oswaldo Cruz, CEP: 21040-900 Rio de Janeiro-RJ, Brazil
| | - Fernando B. Zanchi
- Laboratório
de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz, CEP: 76812-245 Porto Velho-RO, Brazil
- Programa
de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia
(UNIR), CEP: 76801-974 Porto Velho-RO, Brazil
- Instituto
Nacional de Epidemiologia na Amazônia Ocidental—EPIAMO, CEP: 76812-245 Porto Velho-RO, Brazil
- Programa
de Pós-graduação Stricto sensu em Biologia Computacional
e Sistemas do Instituto Oswaldo Cruz, CEP: 21040-360 Rio de Janeiro-RJ, Brazil
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Jain A, Sharma R, Gautam L, Shrivastava P, Singh KK, Vyas SP. Biomolecular interactions between Plasmodium and human host: A basis of targeted antimalarial therapy. ANNALES PHARMACEUTIQUES FRANÇAISES 2024; 82:401-419. [PMID: 38519002 DOI: 10.1016/j.pharma.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024]
Abstract
Malaria is one of the serious health concerns worldwide as it remains a clinical challenge due to the complex life cycle of the malaria parasite and the morphological changes it undergoes during infection. The malaria parasite multiplies rapidly and spreads in the population by changing its alternative hosts. These various morphological stages of the parasite in the human host cause clinical symptoms (anemia, fever, and coma). These symptoms arise due to the preprogrammed biology of the parasite in response to the human pathophysiological response. Thus, complete elimination becomes one of the major health challenges. Although malaria vaccine(s) are available in the market, they still contain to cause high morbidity and mortality. Therefore, an approach for eradication is needed through the exploration of novel molecular targets by tracking the epidemiological changes the parasite adopts. This review focuses on the various novel molecular targets.
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Affiliation(s)
- Anamika Jain
- Drug Delivery and Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, M.P., 470003, India
| | - Rajeev Sharma
- Amity Institute of Pharmacy, Amity University Madhya Pradesh, Gwalior, M.P., 474005, India.
| | - Laxmikant Gautam
- Babulal Tarabai Institute of Pharmaceutical Science, Sagar, M.P., 470228, India
| | - Priya Shrivastava
- Drug Delivery and Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, M.P., 470003, India
| | - Kamalinder K Singh
- School of Pharmacy and Biomedical Sciences, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Suresh P Vyas
- Drug Delivery and Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, M.P., 470003, India.
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3
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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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Costa Júnior DB, Araújo JSC, Oliveira LDM, Neri FSM, Moreira POL, Taranto AG, Fonseca AL, Varotti FDP, Leite FHA. A novel antiplasmodial compound: integration of in silico and in vitro assays. J Biomol Struct Dyn 2021; 40:6295-6307. [PMID: 33554762 DOI: 10.1080/07391102.2021.1882339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Malaria is a disease caused by Plasmodium genus. which P. falciparum is responsible for the most severe form of the disease, cerebral malaria. In 2018, 405,000 people died of malaria. Antimalarial drugs have serious adverse effects and limited efficacy due to multidrug-resistant strains. One way to overcome these limitations is the use of computational approaches for prioritizing candidates to phenotypic assays and/or in vitro assays against validated targets. Plasmodium falciparum Enoyl-ACP reductase (PfENR) is noteworthy because it catalyzes the rate-limiting step of the biosynthetic pathway of fatty acid. Thus, the study aimed to identify potential PfENR inhibitors by ligand (2D molecular similarity and pharmacophore models) and structure-based virtual screening (molecular docking). 2D similarity-based virtual screening using Tanimoto Index (> 0.45) selected 29,236 molecules from natural products subset available in ZINC database (n = 181,603). Next, 10 pharmacophore models for PfENR inhibitors were generated and evaluated based on the internal statistical parameters from GALAHAD™ and ROC/AUC curve. These parameters selected a suitable pharmacophore model with one hydrophobic center and two hydrogen bond acceptors. The alignment of the filtered molecules on best pharmacophore model resulted in the selection of 10,977 molecules. These molecules were directed to the docking-based virtual screening by AutoDock Vina 1.1.2 program. These strategies selected one compound to phenotypic assays against parasite. ZINC630259 showed EC50 = 0.12 ± 0.018 µM in antiplasmodial assays and selective index similar to other antimalarial drugs. Finally, MM/PBSA method showed stability of molecule within PfENR binding site (ΔGbinding=-57.337 kJ/mol).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- David Bacelar Costa Júnior
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Larissa de Mattos Oliveira
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Flávio Simas Moreira Neri
- Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Alex Gutterres Taranto
- Laboratório de Bioinformática e Desenho de Fármacos, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Amanda Luisa Fonseca
- Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Fernando de Pilla Varotti
- Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Laboratório de Qumioinformática e Avaliação Biológica, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
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Yang LS, Wang Y, Wang EH, Yang J, Pan X, Liao X, Yang XS. Polyphosphoric acid-promoted synthesis of coumarins lacking substituents at positions 3 and 4. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1792498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Li-Shou Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - Yu Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - En-Hua Wang
- Department of Medicine and Food, Guizhou Vocational College of Agriculture, Guiyang, PR China
| | - Jan Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - Xiong Pan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - Xiu Liao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - Xiao-Sheng Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
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6
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Rana P, Ghouse SM, Akunuri R, Madhavi YV, Chopra S, Nanduri S. FabI (enoyl acyl carrier protein reductase) - A potential broad spectrum therapeutic target and its inhibitors. Eur J Med Chem 2020; 208:112757. [PMID: 32883635 DOI: 10.1016/j.ejmech.2020.112757] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/30/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Development of new anti-bacterial agents acting upon underexploited targets and thus evading known mechanisms of resistance is the need of the hour. The highly conserved and distinct bacterial fatty acid biosynthesis pathway (FAS-II), presents a validated and yet relatively underexploited target for drug discovery. FabI and its isoforms (FabL, FabK, FabV and InhA) are essential enoyl-ACP reductases present in several microorganisms. In addition, the components of the FAS-II pathway are distinct from the multi-enzyme FAS-I complex found in mammals. Thus, inhibition of FabI and its isoforms is anticipated to result in broad-spectrum antibacterial activity. Several research groups from industry and academic laboratories have devoted significant efforts to develop effective FabI-targeting antibiotics, which are currently in various stages of clinical development for the treatment of multi-drug resistant bacterial infections. This review summarizes all the natural as well as synthetic inhibitors of gram-positive and gram-negative enoyl ACP reductases (FabI). The knowledge of the reported inhibitors can aid in the development of broad-spectrum antibacterials specifically targeting FabI enzymes from S. aureus, S. epidermidis, B. anthracis, B. cereus, E. coli, P. aeruginosa, P. falciparum and M. tuberculosis.
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Affiliation(s)
- Preeti Rana
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Shaik Mahammad Ghouse
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Ravikumar Akunuri
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Y V Madhavi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Janakipuram Extension, Lucknow, 226 031, Uttar Pradesh, India.
| | - Srinivas Nanduri
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India.
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7
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Trevisan DAC, da Silva PV, Farias ABP, Campanerut-Sá PAZ, Ribeiro TDVR, Faria DR, de Mendonça PSB, de Mello JCP, Seixas FAV, Mikcha JMG. Antibacterial activity of Barbatimão (Stryphnodendron adstringens) against Staphylococcus aureus: in vitro and in silico studies. Lett Appl Microbiol 2020; 71:259-271. [PMID: 32412089 DOI: 10.1111/lam.13317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 12/23/2022]
Abstract
We evaluated the activity of the aqueous fraction and the ethyl acetate fraction of Stryphnodendron adstringens against Staphylococcus aureus and proposed their mechanism of action. The antibacterial activity of S. adstringens fractions was evaluated against S. aureus and the cell targets were rated by docking. The fractions showed moderate antibacterial activity against S. aureus without toxicity on two mammalian cell lines. They also showed synergistic antibacterial activity with tannic acid (TA). In silico assays indicated FabG, FabZ and FabI as probable targets. The metabolic pathway for fatty acid biosynthesis in S. aureus was affected by components of S. adstringens. The synergistic effect when combining TA with S. adstringens fractions suggests a natural alternative to S. aureus control. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study describing the possible targets of action of Stryphnodendron adstringens on Staphylococcus aureus. Molecular dynamics simulations showed that the components of S. adstringens affected the metabolic pathway for fatty acid biosynthesis (FAS II) in S. aureus, inhibiting the FabI, FabG and FabZ enzymes. As tannic acid (TA) is a known inhibitor of some targets identified, we showed synergistic antibacterial activity of S. adstringens in combination with TA. This combination did not show toxicity against HaCaT and Vero cells and based on all these results we suggest that S. adstringens can be a natural and sustainable alternative to S. aureus control.
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Affiliation(s)
- D A C Trevisan
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Brazil
| | - P V da Silva
- Department of Technology, State University of Maringá, Maringá, Umuarama, PR, Brazil
| | - A B P Farias
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Brazil
| | - P A Z Campanerut-Sá
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Brazil
| | - T D V R Ribeiro
- Department of Pharmacy, State University of Maringá, Maringá, PR, Brazil
| | - D R Faria
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Brazil
| | - P S B de Mendonça
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Brazil
| | - J C P de Mello
- Department of Pharmacy, State University of Maringá, Maringá, PR, Brazil
| | - F A V Seixas
- Department of Technology, State University of Maringá, Maringá, Umuarama, PR, Brazil
| | - J M G Mikcha
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Brazil
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Radka CD, Frank MW, Yao J, Seetharaman J, Miller DJ, Rock CO. The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI). J Biol Chem 2020; 295:7635-7652. [PMID: 32317282 PMCID: PMC7261799 DOI: 10.1074/jbc.ra120.013336] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/20/2020] [Indexed: 01/07/2023] Open
Abstract
Enoyl-acyl carrier protein reductase (FabI) catalyzes a rate-controlling step in bacterial fatty-acid synthesis and is a target for antibacterial drug development. A phylogenetic analysis shows that FabIs fall into four divergent clades. Members of clades 1-3 have been structurally and biochemically characterized, but the fourth clade, found in members of phylum Bacteroidetes, is uncharacterized. Here, we identified the unique structure and conformational changes that distinguish clade 4 FabIs. Alistipes finegoldii is a prototypical Bacteroidetes inhabitant of the gut microbiome. We found that A. finegoldii FabI (AfFabI) displays cooperative kinetics and uses NADH as a cofactor, and its crystal structure at 1.72 Å resolution showed that it adopts a Rossmann fold as do other characterized FabIs. It also disclosed a carboxyl-terminal extension that forms a helix-helix interaction that links the protomers as a unique feature of AfFabI. An AfFabI·NADH crystal structure at 1.86 Å resolution revealed that this feature undergoes a large conformational change to participate in covering the NADH-binding pocket and establishing the water channels that connect the active site to the central water well. Progressive deletion of these interactions led to catalytically compromised proteins that fail to bind NADH. This unique conformational change imparted a distinct shape to the AfFabI active site that renders it refractory to a FabI drug that targets clade 1 and 3 pathogens. We conclude that the clade 4 FabI, found in the Bacteroidetes inhabitants of the gut, have several structural features and conformational transitions that distinguish them from other bacterial FabIs.
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Affiliation(s)
- Christopher D. Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Matthew W. Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Darcie J. Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Charles O. Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, To whom correspondence should be addressed:
262 Danny Thomas Place, Memphis, TN 38105. Tel.:
901-595-3491; E-mail:
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9
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Du Y, Valenciano AL, Dai Y, Zheng Y, Zhang F, Zhang Y, Clement J, Goetz M, Kingston DGI, Cassera MB. Anibamine and Its Analogues: Potent Antiplasmodial Agents from Aniba citrifolia. JOURNAL OF NATURAL PRODUCTS 2020; 83:569-577. [PMID: 31577436 PMCID: PMC7103529 DOI: 10.1021/acs.jnatprod.9b00724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In our continuing search for novel natural products with antiplasmodial activity, an extract of Aniba citrifolia was found to have good activity, with an IC50 value less than 1.25 μg/mL. After bioassay-directed fractionation, the known indolizinium alkaloid anibamine (1) and the new indolizinium alkaloid anibamine B (2) were isolated as the major bioactive constituents, with antiplasmodial IC50 values of 0.170 and 0.244 μM against the drug-resistant Dd2 strain of Plasmodium falciparum. The new coumarin anibomarin A (3), the new norneolignan anibignan A (5), and six known neolignans (7-12) were also obtained. The structures of all the isolated compounds were determined based on analyses of 1D and 2D NMR spectroscopic and mass spectrometric data, and the absolute configuration of anibignan A (5) was assigned from its ECD spectrum. Evaluation of a library of 28 anibamine analogues (13-40) indicated that quaternary charged analogues had IC50 values as low as 58 nM, while uncharged analogues were inactive or significantly less active. Assessment of the potential effects of anibamine and its analogues on the intraerythrocytic stages and morphological development of P. falciparum revealed substantial activity against ring stages for compounds with two C-10 side chains, while those with only one C-10 side chain exhibited substantial activity against trophozoite stages, suggesting different mechanisms of action.
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Affiliation(s)
- Yongle Du
- Department of Chemistry and Virginia Tech Center for Drug Discovery, M/C 0212, Virginia Tech, Blacksburg, VA 24061, United States
| | - Ana Lisa Valenciano
- Department of Biochemistry and Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, Georgia 30602, United States
| | - Yumin Dai
- Department of Chemistry and Virginia Tech Center for Drug Discovery, M/C 0212, Virginia Tech, Blacksburg, VA 24061, United States
| | - Yi Zheng
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA 23298, United States
| | - Feng Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA 23298, United States
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA 23298, United States
| | - Jason Clement
- Natural Products Discovery Institute, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Michael Goetz
- Natural Products Discovery Institute, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - David G. I. Kingston
- Department of Chemistry and Virginia Tech Center for Drug Discovery, M/C 0212, Virginia Tech, Blacksburg, VA 24061, United States
| | - Maria B. Cassera
- Department of Biochemistry and Molecular Biology, and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, Georgia 30602, United States
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10
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Reddy TS, Moon H, Choi MS. Coumarin–tetraphenylethylene regioisomers: synthesis, photophysical and aggregation-induced emission properties. NEW J CHEM 2020. [DOI: 10.1039/d0nj00037j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coumarin–tetraphenylethylene (CTPE) regioisomers with different linkage types and substitution positions (coumarin C5, C6, C7) were synthesized, characterized, photophysical and aggregation-induced emission properties reported.
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Affiliation(s)
| | - Hyungkyu Moon
- Division of Chemical Engineering
- Konkuk University
- Seoul
- South Korea
| | - Myung-Seok Choi
- Division of Chemical Engineering
- Konkuk University
- Seoul
- South Korea
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11
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Feng Z, Yu Y, Yang X, Zhong D, Song D, Yang H, Chen X, Zhou G, Wu Z. Isomers of Coumarin-Based Cyclometalated Ir(III) Complexes with Easily Tuned Phosphorescent Color and Features for Highly Efficient Organic Light-Emitting Diodes. Inorg Chem 2019; 58:7393-7408. [DOI: 10.1021/acs.inorgchem.9b00534] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Yue Yu
- School of Physics and Optoelectronic Engineering, Xidian University, Xi’an 710071, PR China
| | | | | | | | | | | | | | - Zhaoxin Wu
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, PR China
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12
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Manhas A, Patel A, Lone MY, Jha PK, Jha PC. Identification of
Pf
ENR inhibitors: A hybrid structure‐based approach in conjunction with molecular dynamics simulations. J Cell Biochem 2018; 119:8490-8500. [DOI: 10.1002/jcb.27075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/26/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Anu Manhas
- School of Chemical Sciences Central University of Gujarat Gandhinagar Gujarat India
| | - Anjali Patel
- Department of Physics M. S. University of Baroda Vadodara Gujarat India
| | - Mohsin Y. Lone
- School of Chemical Sciences Central University of Gujarat Gandhinagar Gujarat India
- Department of Chemistry Indian Institute of Technology Gandhinagar Gujarat India
| | - Prafulla K. Jha
- Department of Physics M. S. University of Baroda Vadodara Gujarat India
| | - Prakash C. Jha
- Centre for Applied Chemistry Central University of Gujarat Gandhinagar Gujarat India
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Negi A, Bhandari N, Shyamlal BRK, Chaudhary S. Inverse docking based screening and identification of protein targets for Cassiarin alkaloids against Plasmodium falciparum. Saudi Pharm J 2018; 26:546-567. [PMID: 29844728 PMCID: PMC5961758 DOI: 10.1016/j.jsps.2018.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/31/2018] [Indexed: 12/21/2022] Open
Abstract
Various reports have shown Cassiarin alkaloids, selective in vitro activities against various strains of Plasmodium falciparum with low cytotoxicity, which indicates their possible candidature as antimalarial drug. However, poor recognition of their protein targets and molecular binding behaviour, certainly limits their exploration as antimalarial drug candidature. To address this, we utilises inverse screening, based on three different docking methodologies in order to find their most putative protein targets. In our study, we screened 1047 protein structures from protein data bank, which belongs to 147 different proteins. Our investigation identified 16 protein targets for Cassiarins. In few cases of identified protein targets, the binding site was poorly studied, which encouraged us to perform comparative sequence and structural studies with their homologous proteins, like as in case of Kelch motif associated protein, Armadillo repeats only protein and Methionine aminopeptidase 1b. In our study, we also found Tryptophanyl-tRNA synthetase and 1-Deoxy-D-Xylose-5-phosphate reductoisomerase proteins are the most common targets for Cassiarins.
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Affiliation(s)
- Arvind Negi
- School of Chemistry, National University of Ireland, University Road, Galway H91 TK33, Ireland
| | - Nitisha Bhandari
- School of Biotechnology, Graphic Era University, Dehradun, Bell Road, Society Area, Clement Town, Dehradun, Uttarakhand 248002, India
| | - Bharti Rajesh Kumar Shyamlal
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, National Institute of Technology Jaipur, Jawaharlal Nehru Marg, Jaipur 302017, India
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, National Institute of Technology Jaipur, Jawaharlal Nehru Marg, Jaipur 302017, India
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14
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Alencar N, Sola I, Linares M, Juárez-Jiménez J, Pont C, Viayna A, Vílchez D, Sampedro C, Abad P, Pérez-Benavente S, Lameira J, Bautista JM, Muñoz-Torrero D, Luque FJ. First homology model of Plasmodium falciparum glucose-6-phosphate dehydrogenase: Discovery of selective substrate analog-based inhibitors as novel antimalarial agents. Eur J Med Chem 2018; 146:108-122. [PMID: 29407943 DOI: 10.1016/j.ejmech.2018.01.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/27/2017] [Accepted: 01/15/2018] [Indexed: 01/07/2023]
Abstract
In Plasmodium falciparum the bifunctional enzyme glucose-6-phosphate dehydrogenase‒6-phosphogluconolactonase (PfG6PD‒6PGL) is involved in the catalysis of the first reaction of the pentose phosphate pathway. Since this enzyme has a key role in parasite development, its unique structure represents a potential target for the discovery of antimalarial drugs. Here we describe the first 3D structural model of the G6PD domain of PfG6PD‒6PGL. Compared to the human enzyme (hG6PD), the 3D model has enabled the identification of a key difference in the substrate-binding site, which involves the replacement of Arg365 in hG6PD by Asp750 in PfG6PD. In a prospective validation of the model, this critical change has been exploited to rationally design a novel family of substrate analog-based inhibitors that can display the necessary selectivity towards PfG6PD. A series of glucose derivatives featuring an α-methoxy group at the anomeric position and different side chains at position 6 bearing distinct basic functionalities has been synthesized, and their PfG6PD and hG6PD inhibitory activities and their toxicity against parasite and mammalian cells have been assessed. Several compounds displayed micromolar affinity (Ki up to 23 μM), favorable selectivity (up to > 26-fold), and low cytotoxicity. Phenotypic assays with P. falciparum cultures revealed high micromolar IC50 values, likely as a result of poor internalization of the compounds in the parasite cell. Overall, these results endorse confidence to the 3D model of PfG6PD, paving the way for the use of target-based drug design approaches in antimalarial drug discovery studies around this promising target.
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Affiliation(s)
- Nelson Alencar
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - Irene Sola
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences and IBUB, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - María Linares
- Research Institute Hospital 12 de Octubre, Avda. de Cordoba s/n, 28041 Madrid, Spain
| | - Jordi Juárez-Jiménez
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences and IBUB, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Antonio Viayna
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - David Vílchez
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - Cristina Sampedro
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences and IBUB, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Paloma Abad
- Research Institute Hospital 12 de Octubre, Avda. de Cordoba s/n, 28041 Madrid, Spain; Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Facultad de Veterinaria, Ciudad Universitaria, 28040 Madrid, Spain
| | - Susana Pérez-Benavente
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Facultad de Veterinaria, Ciudad Universitaria, 28040 Madrid, Spain
| | - Jerónimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos-LPDF, Instituto de Ciências Exatas e Naturais- ICEN, Universidade Federal do Pará - UFPA, Av. Augusto Correa, Nº 1- Bairro: Guamá, Cep: 66.075-900 Belém-Pará, Brazil
| | - José M Bautista
- Research Institute Hospital 12 de Octubre, Avda. de Cordoba s/n, 28041 Madrid, Spain; Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Facultad de Veterinaria, Ciudad Universitaria, 28040 Madrid, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences and IBUB, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain.
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16
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Magwenzi FN, Khanye SD, Veale CG. Unexpected transformations of 3-(bromoacetyl)coumarin provides new evidence for the mechanism of thiol mediated dehalogenation of α-halocarbonyls. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.01.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Wang T, Guan G, Korhonen PK, Koehler AV, Hall RS, Young ND, Yin H, Gasser RB. The apicoplast genomes of two taxonomic units of Babesia from sheep. Vet Parasitol 2016; 233:123-128. [PMID: 27916258 DOI: 10.1016/j.vetpar.2016.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/31/2016] [Accepted: 11/05/2016] [Indexed: 02/07/2023]
Abstract
The apicoplast (ap) is a unique, non-photosynthetic organelle found in most apicomplexan parasites. Due to the essential roles that this organelle has, it has been widely considered as target for drugs against diseases caused by apicomplexans. Exploring the ap genomes of such parasites would provide a better understanding of their systematics and their basic molecular biology for therapeutics. However, there is limited information available on the ap genomes of apicomplexan parasites. In the present study, the ap genomes of two operational taxonomic units of Babesia (known as Babesia sp. Lintan [Bl] and Babesia sp. Xinjiang [Bx]) from sheep were sequenced, assembled and annotated using a massive parallel sequencing-based approach. Then, the gene content and gene order in these ap genomes (∼30.7kb in size) were defined and compared, and the genetic differences were assessed. In addition, a phylogenetic analysis of ap genomic data sets was carried out to assess the relationships of these taxonomic units with other apicomplexan parasites for which complete ap genomic data sets were publicly available. The results showed that the ap genomes of Bl and Bx encode 59 and 57 genes, respectively, including 2 ribosomal RNA genes, 25 transfer RNA genes and 30-32 protein-encoding genes, being similar in content to those of Babesia bovis and B. orientalis. Ap gene regions that might serve as markers for future epidemiological and population genetic studies of Babesia species were identified. Using sequence data for a subset of six protein-encoding genes, a close relationship of Bl and Bx with Babesia bovis from cattle and B. orientalis from water buffalo was inferred. Although the focus of the present study was on Babesia, we propose that the present sequencing-bioinformatic approach should be applicable to organellar genomes of a wide range of apicomplexans of veterinary importance.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China; Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China
| | - Pasi K Korhonen
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Anson V Koehler
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Ross S Hall
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China.
| | - Robin B Gasser
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia.
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18
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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19
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Chakraborty A. Understanding the biology of the Plasmodium falciparum apicoplast; an excellent target for antimalarial drug development. Life Sci 2016; 158:104-10. [DOI: 10.1016/j.lfs.2016.06.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 11/29/2022]
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20
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Gobbi S, Hu Q, Zimmer C, Engel M, Belluti F, Rampa A, Hartmann RW, Bisi A. Exploiting the Chromone Scaffold for the Development of Inhibitors of Corticosteroid Biosynthesis. J Med Chem 2016; 59:2468-77. [DOI: 10.1021/acs.jmedchem.5b01609] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Silvia Gobbi
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro,
6, I-40126 Bologna, Italy
| | - Qingzhong Hu
- Pharmaceutical
and Medicinal Chemistry, Saarland University and Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Universitätscampus E8 1, 66123 Saarbrücken, Germany
| | - Christina Zimmer
- Pharmaceutical
and Medicinal Chemistry, Saarland University and Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Universitätscampus E8 1, 66123 Saarbrücken, Germany
| | - Matthias Engel
- Pharmaceutical
and Medicinal Chemistry, Saarland University and Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Universitätscampus E8 1, 66123 Saarbrücken, Germany
| | - Federica Belluti
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro,
6, I-40126 Bologna, Italy
| | - Angela Rampa
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro,
6, I-40126 Bologna, Italy
| | - Rolf W. Hartmann
- Pharmaceutical
and Medicinal Chemistry, Saarland University and Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Universitätscampus E8 1, 66123 Saarbrücken, Germany
| | - Alessandra Bisi
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro,
6, I-40126 Bologna, Italy
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21
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Berenstein AJ, Magariños MP, Chernomoretz A, Agüero F. A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PLoS Negl Trop Dis 2016; 10:e0004300. [PMID: 26735851 PMCID: PMC4703370 DOI: 10.1371/journal.pntd.0004300] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/21/2015] [Indexed: 12/16/2022] Open
Abstract
Drug development for neglected diseases has been historically hampered due to lack of market incentives. The advent of public domain resources containing chemical information from high throughput screenings is changing the landscape of drug discovery for these diseases. In this work we took advantage of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to develop a novel integrative network model to prioritize and identify candidate drug targets in neglected pathogen proteomes, and bioactive drug-like molecules. We modeled genomic (proteins) and chemical (bioactive compounds) data as a multilayer weighted network graph that takes advantage of bioactivity data across 221 species, chemical similarities between 1.7 105 compounds and several functional relations among 1.67 105 proteins. These relations comprised orthology, sharing of protein domains, and shared participation in defined biochemical pathways. We showcase the application of this network graph to the problem of prioritization of new candidate targets, based on the information available in the graph for known compound-target associations. We validated this strategy by performing a cross validation procedure for known mouse and Trypanosoma cruzi targets and showed that our approach outperforms classic alignment-based approaches. Moreover, our model provides additional flexibility as two different network definitions could be considered, finding in both cases qualitatively different but sensible candidate targets. We also showcase the application of the network to suggest targets for orphan compounds that are active against Plasmodium falciparum in high-throughput screens. In this case our approach provided a reduced prioritization list of target proteins for the query molecules and showed the ability to propose new testable hypotheses for each compound. Moreover, we found that some predictions highlighted by our network model were supported by independent experimental validations as found post-facto in the literature. Neglected tropical diseases are human infectious diseases that are often associated with poverty. Historically, lack of interest from the pharmaceutical industry resulted in the lack of good drugs to combat the majority of the pathogens that cause these diseases. Recently, the availability of open chemical information has increased with the advent of public domain chemical resources and the release of data from high throughput screening assays. Our aim in this work was to make use of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to prioritize and identify candidate drug targets in neglected pathogen proteomes, and drug-like bioactive molecules to foster drug development against neglected diseases. Our approach to the problem relied on applying bioinformatics and computational biology strategies to model large datasets spanning complete proteomes and extensive chemical information from publicly available sources. As a result, we were able to prioritize drug targets and identify potential targets for orphan bioactive drugs.
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Affiliation(s)
- Ariel José Berenstein
- Laboratorio de Bioinformática, Fundación Instituto Leloir, Buenos Aires, Argentina
- Departamento de Física, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Paula Magariños
- Laboratorio de Genómica y Bioinformática, Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico de Chascomús, Universidad de San Martín–CONICET, Sede San Martín, San Martín, Buenos Aires, Argentina
| | - Ariel Chernomoretz
- Laboratorio de Bioinformática, Fundación Instituto Leloir, Buenos Aires, Argentina
- Departamento de Física, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fernán Agüero
- Laboratorio de Genómica y Bioinformática, Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico de Chascomús, Universidad de San Martín–CONICET, Sede San Martín, San Martín, Buenos Aires, Argentina
- * E-mail: ,
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22
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Aneja B, Kumar B, Jairajpuri MA, Abid M. A structure guided drug-discovery approach towards identification of Plasmodium inhibitors. RSC Adv 2016. [DOI: 10.1039/c5ra19673f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This article provides a comprehensive review of inhibitors from natural, semisynthetic or synthetic sources against key targets ofPlasmodium falciparum.
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Affiliation(s)
- Babita Aneja
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Bhumika Kumar
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohammad Abid
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
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23
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Wang B, Chen H, Wu Y, Liu B. Synthesis of Two Coumarins Isolated from Aster praealtus. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201500295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Fatty acid metabolism in the Plasmodium apicoplast: Drugs, doubts and knockouts. Mol Biochem Parasitol 2015; 199:34-50. [DOI: 10.1016/j.molbiopara.2015.03.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 12/25/2022]
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25
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In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. J Comput Aided Mol Des 2014; 29:79-87. [PMID: 25344312 DOI: 10.1007/s10822-014-9806-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
The need for novel therapeutics against Plasmodium falciparum is urgent due to recent emergence of multi-drug resistant malaria parasites. Since fatty acids are essential for both the liver and blood stages of the malarial parasite, targeting fatty acid biosynthesis is a promising strategy for combatting P. falciparum. We present a combined computational and experimental study to identify novel inhibitors of enoyl-acyl carrier protein reductase (PfENR) in the fatty acid biosynthesis pathway. A small-molecule database from ChemBridge was docked into three distinct PfENR crystal structures that provide multiple receptor conformations. Two different docking algorithms were used to generate a consensus score in order to rank possible small molecule hits. Our studies led to the identification of five low-micromolar pyrimidine dione inhibitors of PfENR.
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Abstract
Despite a century of control and eradication campaigns, malaria remains one of the world's most devastating diseases. Our once-powerful therapeutic weapons are losing the war against the Plasmodium parasite, whose ability to rapidly develop and spread drug resistance hamper past and present malaria-control efforts. Finding new and effective treatments for malaria is now a top global health priority, fuelling an increase in funding and promoting open-source collaborations between researchers and pharmaceutical consortia around the world. The result of this is rapid advances in drug discovery approaches and technologies, with three major methods for antimalarial drug development emerging: (i) chemistry-based, (ii) target-based, and (iii) cell-based. Common to all three of these approaches is the unique ability of structural biology to inform and accelerate drug development. Where possible, SBDD (structure-based drug discovery) is a foundation for antimalarial drug development programmes, and has been invaluable to the development of a number of current pre-clinical and clinical candidates. However, as we expand our understanding of the malarial life cycle and mechanisms of resistance development, SBDD as a field must continue to evolve in order to develop compounds that adhere to the ideal characteristics for novel antimalarial therapeutics and to avoid high attrition rates pre- and post-clinic. In the present review, we aim to examine the contribution that SBDD has made to current antimalarial drug development efforts, covering hit discovery to lead optimization and prevention of parasite resistance. Finally, the potential for structural biology, particularly high-throughput structural genomics programmes, to identify future targets for drug discovery are discussed.
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