1
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Junior DBC, Lacerda PS, de Pilla Varotti F, Leite FHA. Towards development of new antimalarial compounds through in silico and in vitro assays. Comput Biol Chem 2024; 111:108093. [PMID: 38772047 DOI: 10.1016/j.compbiolchem.2024.108093] [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: 12/18/2023] [Revised: 02/17/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Malaria is one of most widespread infectious disease in world. The antimalarial therapy presents a series of limitations, such as toxicity and the emergence of resistance, which makes the search for new drugs urgent. Thus, it becomes necessary to explore essential and exclusive therapeutic targets of the parasite to achieve selective inhibition. Enoyl-ACP reductase is an enzyme of the type II fatty acid biosynthetic pathway and is responsible for the rate-limiting step in the fatty acid elongation cycle. In this work, we use hierarchical virtual screening and drug repositioning strategies to prioritize compounds for phenotypic assays and molecular dynamics studies. The molecules were tested against chloroquine-resistant W2 strain of Plasmodium falciparum (EC50 between 330.05 and 13.92 µM). Nitrofurantoin was the best antimalarial activity at low micromolar range (EC50 = 13.92 µM). However, a hit compound against malaria must have a biological activity value below 1 µM. A large number of molecules present problems with permeability in biological membranes and reaching an effective concentration in their target's microenvironment. Nitrofurantoin derivatives with inclusions of groups which confer increased lipid solubility (methyl groups, halogens and substituted and unsubstituted aromatic rings) have been proposed. These derivatives were pulled through the lipid bilayer in molecular dynamics simulations. Molecules 14, 18 and 21 presented lower free energy values than nitrofurantoin when crossing the lipid bilayer.
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Affiliation(s)
| | - Pedro Sousa Lacerda
- Laboratório de Bioinformática e Modelagem Molecular, Universidade Federal da Bahia, Brazil
| | | | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil; Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Brazil; Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Brazil.
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2
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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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3
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Egu SA, Ali I, Khan KM, Chigurupati S, Qureshi U, Salar U, Ul-Haq Z, Almahmoud SA, Felemban SG, Ali M, Taha M. Rhodanine-benzamides as potential hits for α-amylase enzyme inhibitors and radical (DPPH and ABTS) scavengers. Mol Divers 2024:10.1007/s11030-024-10813-z. [PMID: 38446373 DOI: 10.1007/s11030-024-10813-z] [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: 11/13/2022] [Accepted: 01/19/2024] [Indexed: 03/07/2024]
Abstract
A series of 3-substituted and 3,5-disubstituted rhodanine-based derivatives were synthesized from 3-aminorhodanine and examined for α-amylase inhibitory, DPPH (1,1-diphenyl-2-picrylhydrazyl) and ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical scavenging activities in vitro. These derivatives displayed significant α-amylase inhibitory potential with IC50 values of 11.01-56.04 µM in comparison to standard acarbose (IC50 = 9.08 ± 0.07 µM). Especially, compounds 7 (IC50 = 11.01 ± 0.07 µM) and 8 (IC50 = 12.01 ± 0.07 µM) showed highest α-amylase inhibitory activities among the whole series. In addition to α-amylase inhibitory activity, all compounds also demonstrated significant scavenging activities against DPPH and ABTS radicals, with IC50 values ranging from 12.24 to 57.33 and 13.29-59.09 µM, respectively, as compared to the standard ascorbic acid (IC50 = 15.08 ± 0.03 µM for DPPH; IC50 = 16.09 ± 0.17 µM for ABTS). These findings reveal that the nature and position of the substituents on the phenyl ring(s) are crucial for variation in the activities. The structure-activity relationship (SAR) revealed that the compounds bearing an electron-withdrawing group (EWG) at para substitution possessed the highest activity. In kinetic studies, only the km value was changed, with no observed changes in Vmax, indicating a competitive inhibition. Molecular docking studies revealed important interactions between compounds and the α-amylase active pocket. Further advanced research needs to perform on the identified compounds in order to obtain potential antidiabetic agents.
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Affiliation(s)
- Samuel Attah Egu
- Department of Pure and Industrial Chemistry, Kogi State University, Anyigba, Kogi State, Nigeria
- International Center for Chemical and Biological Sciences, H. E. J. Research Institute of Chemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Irfan Ali
- International Center for Chemical and Biological Sciences, H. E. J. Research Institute of Chemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Khalid Mohammed Khan
- International Center for Chemical and Biological Sciences, H. E. J. Research Institute of Chemistry, University of Karachi, Karachi, 75270, Pakistan.
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations [IRMC], Imam Abdulrahman Bin Faisal University, P.O. Box 31441, Dammam, Kingdom of Saudi Arabia.
- Pakistan Academy of Science, 3-Constitution Avenue, G-5/2, Islamabad, 44000, Pakistan.
| | - Sridevi Chigurupati
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah, 52571, Kingdom of Saudi Arabia
| | - Urooj Qureshi
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Uzma Salar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Suliman A Almahmoud
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah, 52571, Kingdom of Saudi Arabia
| | - Shatha Ghazi Felemban
- Department of Medical Laboratory Science, Fakeeh College for Medical Sciences, Jeddah, 21461, Kingdom of Saudi Arabia
| | - Mohsin Ali
- Department of Chemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Taha
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations [IRMC], Imam Abdulrahman Bin Faisal University, P.O. Box 31441, Dammam, Kingdom of Saudi Arabia
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Bieri C, Esmel A, Keita M, Owono LCO, Dali B, Megnassan E, Miertus S, Frecer V. Structure-Based Design and Pharmacophore-Based Virtual Screening of Combinatorial Library of Triclosan Analogues Active against Enoyl-Acyl Carrier Protein Reductase of Plasmodium falciparum with Favourable ADME Profiles. Int J Mol Sci 2023; 24:ijms24086916. [PMID: 37108083 PMCID: PMC10139228 DOI: 10.3390/ijms24086916] [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: 03/12/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Cost-effective therapy of neglected and tropical diseases such as malaria requires everlasting drug discovery efforts due to the rapidly emerging drug resistance of the plasmodium parasite. We have carried out computational design of new inhibitors of the enoyl-acyl carrier protein reductase (ENR) of Plasmodium falciparum (PfENR) using computer-aided combinatorial and pharmacophore-based molecular design. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) complexation QSAR model was developed for triclosan-based inhibitors (TCL) and a significant correlation was established between the calculated relative Gibbs free energies of complex formation (∆∆Gcom) between PfENR and TCL and the observed inhibitory potencies of the enzyme (IC50exp) for a training set of 20 known TCL analogues. Validation of the predictive power of the MM-PBSA QSAR model was carried out with the generation of 3D QSAR pharmacophore (PH4). We obtained a reasonable correlation between the relative Gibbs free energy of complex formation ∆∆Gcom and IC50exp values, which explained approximately 95% of the PfENR inhibition data: pIC50exp=-0.0544×∆∆Gcom+6.9336,R2=0.95. A similar agreement was established for the PH4 pharmacophore model of the PfENR inhibition (pIC50exp=0.9754×pIC50pre+0.1596, R2=0.98). Analysis of enzyme-inhibitor binding site interactions suggested suitable building blocks to be used in a virtual combinatorial library of 33,480 TCL analogues. Structural information derived from the complexation model and the PH4 pharmacophore guided us through in silico screening of the virtual combinatorial library of TCL analogues to finally identify potential new TCL inhibitors effective at low nanomolar concentrations. Virtual screening of the library by PfENR-PH4 led to a predicted IC50pre value for the best inhibitor candidate as low as 1.9 nM. Finally, the stability of PfENR-TCLx complexes and the flexibility of the active conformation of the inhibitor for selected top-ranking TCL analogues were checked with the help of molecular dynamics. This computational study resulted in a set of proposed new potent inhibitors with predicted antimalarial effects and favourable pharmacokinetic profiles that act on a novel pharmacological target, PfENR.
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Affiliation(s)
- Cecile Bieri
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Akori Esmel
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Luc Calvin Owono Owono
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P.O. Box 47, Yaoundé 1, Cameroon
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
| | - Brice Dali
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
- International Centre for Theoretical Physics, Strada Costiera 11, I-34151 Trieste, Italy
- Laboratoire de Cristallographie-Physique Moléculaire, Université De Cocody, Abidjan 22, Côte d'Ivoire
- Laboratoire de Chimie Organique Structurale et Théorique, Université De Cocody, Abidjan 22, Côte d'Ivoire
| | - Stanislav Miertus
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
| | - Vladimir Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, SK-83232 Bratislava, Slovakia
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5
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Manhas A, Ghosh A, Verma Y, Das T, Jha PC. Identification of natural products against enoyl-acyl-carrier-protein reductase in malaria via combined pharmacophore modeling, molecular docking and simulations studies. J Biomol Struct Dyn 2023; 41:2002-2015. [PMID: 35043754 DOI: 10.1080/07391102.2022.2027819] [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: 02/02/2023]
Abstract
Plasmodium falciparum is counted as one of the deadly species causing malaria. In that respect, enoyl acyl carrier protein reductase is recognized as one of the attractive druggable targets for the identification of antimalarials. Thus, from the structural proteome of ENR, common feature pharmacophores were constructed. To identify the representative models, all the hypotheses were subjected to validation methods, like, test set, enrichment factor, and Güner-Henry method, and the selected representative hypotheses were used to screen out the drug-like natural products. Further, the screened candidates were advanced to molecular docking calculations. Based on the docking score criteria and presence of essential interaction with Tyr277, seven candidates were shortlisted to conduct the HYDE and QSAR assessment. Further, the stability of these complexes was evaluated by employing molecular dynamics simulations, molecular mechanics-generalized born surface area approach-based free binding energy calculations with the residue-wise contribution of PfENR to the total binding free energy of the complex. On comparing the root mean square deviation, and fluctuation plots of the docked candidates with the reference, all the candidates displayed stable behavior, and the same outcome was depicted from the secondary structure element. However, from the free energy calculations, and residue-wise contribution conducted after dynamics, it was observed that out of seven, only five candidates sustain the binding with Tyr277 and cofactor of PfENR. Therefore, in the current work, the hybrid study of screening and stability lead to the identification of five structurally diverse candidates that can be employed for the design of novel antimalarials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anu Manhas
- Department of Chemistry, Pandit Deendayal Energy University (former PDPU), Gandhinagar, Gujarat, India
| | - Amar Ghosh
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Yogesh Verma
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Tanay Das
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
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Katiki M, Neetu N, Pratap S, Kumar P. Biochemical and structural basis for Moraxella catarrhalis enoyl-acyl carrier protein reductase (FabI) inhibition by triclosan and estradiol. Biochimie 2022; 198:8-22. [PMID: 35276316 DOI: 10.1016/j.biochi.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 02/06/2022] [Accepted: 02/22/2022] [Indexed: 11/02/2022]
Abstract
The enoyl-acyl carrier protein reductase (ENR) is an established drug target and catalyzes the last reduction step of the fatty acid elongation cycle. Here, we report the crystal structures of FabI from Moraxella catarrhalis (McFabI) in the apo form, binary complex with NAD+ and ternary complex with NAD + -triclosan (TCL) determined at 2.36, 2.12 and 2.22 Å resolutions, respectively. The comparative study of these three structures revealed three different conformational states for the substrate-binding loop (SBL), including an unstructured intermediate, a structured intermediate and a closed conformation in the apo, binary and ternary complex forms, respectively; indicating the flexibility of SBL during the ligand binding. Virtual screening has suggested that estradiol cypionate may be a potential inhibitor of McFabI. Subsequently, estradiol (EST), the natural form of estradiol cypionate, was assessed for its FabI-binding and -inhibition properties. In vitro studies demonstrated that TCL and EST bind to McFabI with high affinity (KD = 0.038 ± 0.004 and 5 ± 0.06 μM respectively) and inhibit its activity (Ki = 62.93 ± 3.95 nM and 25.97 ± 1.93 μM respectively) and suppress the growth of M. catarrhalis. These findings reveal that TCL and EST inhibit the McFabI activity and thereby affect cell growth. This study suggests that estradiol may be exploited as a novel scaffold for the designing and development of more potential FabI inhibitors.
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Affiliation(s)
- Madhusudhanarao Katiki
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Neetu Neetu
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shivendra Pratap
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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7
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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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8
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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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9
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Plasmodium dihydrofolate reductase is a second enzyme target for the antimalarial action of triclosan. Sci Rep 2018; 8:1038. [PMID: 29348637 PMCID: PMC5773535 DOI: 10.1038/s41598-018-19549-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/29/2017] [Indexed: 12/19/2022] Open
Abstract
Malaria, caused by parasites of the genus Plasmodium, leads to over half a million deaths per year, 90% of which are caused by Plasmodium falciparum. P. vivax usually causes milder forms of malaria; however, P. vivax can remain dormant in the livers of infected patients for weeks or years before re-emerging in a new bout of the disease. The only drugs available that target all stages of the parasite can lead to severe side effects in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency; hence, there is an urgent need to develop new drugs active against blood and liver stages of the parasite. Different groups have demonstrated that triclosan, a common antibacterial agent, targets the Plasmodium liver enzyme enoyl reductase. Here, we provide 4 independent lines of evidence demonstrating that triclosan specifically targets both wild-type and pyrimethamine-resistant P. falciparum and P. vivax dihydrofolate reductases, classic targets for the blood stage of the parasite. This makes triclosan an exciting candidate for further development as a dual specificity antimalarial, which could target both liver and blood stages of the parasite.
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10
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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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11
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Ghattas MA, Mansour RA, Atatreh N, Bryce RA. Analysis of Enoyl-Acyl Carrier Protein Reductase Structure and Interactions Yields an Efficient Virtual Screening Approach and Suggests a Potential Allosteric Site. Chem Biol Drug Des 2015; 87:131-42. [PMID: 26259619 DOI: 10.1111/cbdd.12635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/14/2015] [Accepted: 07/31/2015] [Indexed: 11/28/2022]
Abstract
Enoyl-acyl carrier protein reductases have an important role in fatty acid biosynthesis and are considered essential for bacterial and protozoal survival. Here, we perform a computational assessment of enoyl-acyl carrier protein reductase structures, providing insights for inhibitor design that we incorporate into a virtual screening approach. Firstly, we analyse 80 crystal structures of 16 different enoyl-acyl carrier protein reductases for their active site characteristics and druggability, finding these sites contain a readily druggable pocket, of varying size and shape. Interestingly, a high affinity, potentially allosteric site was identified for pfFabl. Analysis of the ligand-protein interactions of four enoyl-acyl carrier protein reductases from different micro-organisms (InhA, pfFabl, saFabl and ecFabl), involving 59 available crystal structures, found three commonly shared interactions; constraining these interactions in docking improved enrichment of enoyl-acyl carrier protein reductase virtual screens, by up to 60% in the top 3% of the ranked library. This docking protocol also improved pose prediction, decreasing the root-mean-square deviation to crystallographic pose by up to 75% on average. The binding site analysis and knowledge-based docking protocol presented here can potentially assist in the structure-based design of new enoyl-acyl carrier protein reductase inhibitors.
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Affiliation(s)
- Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, United Arab Emirates
| | - Ramez A Mansour
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, United Arab Emirates
| | - Richard A Bryce
- Manchester Pharmacy School, University of Manchester, Manchester, M13 9PT, UK
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12
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Rajkhowa S, Jha AN, Deka RC. Anti-tubercular drug development: computational strategies to identify potential compounds. J Mol Graph Model 2015; 62:56-68. [PMID: 26386453 DOI: 10.1016/j.jmgm.2015.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/13/2015] [Accepted: 09/05/2015] [Indexed: 10/23/2022]
Abstract
InhA is an attractive target to combat tuberculosis (TB), which is targeted by many pro-drugs (isoniazid, etc.) and drugs such as triclosan. However, triclosan is less useful as an antitubercular drug due to its low bioavailability and therefore, in order to overcome this difficulty, many derivatives of triclosan were prepared. Here, we have combined various computational techniques to virtually screen out four potential triclosan derivatives. Molecular docking methods have been employed to screen out 32 out of 62 triclosan derivatives considering the mode of binding and the top re-rank scores. A comparative study on the chemical properties of triclosan and some of its derivatives has been performed using density functional theory (DFT) calculations. DFT based global reactivity descriptors (GRD), such as hardness, chemical potential, chemical softness, electrophilicity index, Fukui function, and local philicity calculated at the optimized geometries were used to investigate the usefulness of these descriptors for understanding the reactive nature and sites of the molecules. QSAR equations were built using these descriptors considering these 32 compounds. Four common compounds showing the best correlation and the best docking scores were considered for the ADMET property calculations and their dynamical movements have been studied using molecular dynamics simulations. Our results showed that these four compounds are chemically more active than triclosan and have the potential to inhibit the Mycobacterium tuberculosis enoyl acyl carrier protein reductase. This work shows that combination of different computational techniques may help to screen out potential drug candidates from a list of possible ones.
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Affiliation(s)
- Sanchaita Rajkhowa
- Department of Chemical Sciences, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Anupam Nath Jha
- Department of Molecular Biology & Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Ramesh Chandra Deka
- Department of Chemical Sciences, Tezpur University, Napaam, Tezpur 784028, Assam, India.
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13
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Owono Owono LC, Ntie-Kang F, Keita M, Megnassan E, Frecer V, Miertus S. Virtually Designed Triclosan-Based Inhibitors of Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis and of Plasmodium falciparum. Mol Inform 2015; 34:292-307. [PMID: 27490275 DOI: 10.1002/minf.201400141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/04/2014] [Indexed: 11/12/2022]
Abstract
We report here new chemical structures of predicted nanomolar triclosan-based inhibitors (TCLs) of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) virtually proposed by computer-assisted molecular design. 3D models of InhA-TCL complexes were prepared by in situ modifications of the reference crystal structure (PDB entry 1P45) for a training set of 15 TCLs with known InhA inhibitory activities. A QSAR model was built leading to linear correlation between the calculated free energies of complexation (ΔΔGcom ) and experimental values IC50 (exp) : pIC50 =-0.0657×ΔΔGcom +3.0502, R(2) =0.96. In addition, ligand-based quantitative pharmacophore model (PH4) was built from bound conformations of the training set compounds and confirmed the correlation between molecular models and observed activities: pIC50 (exp=) 0.8929×pIC50 (pre) -0.441, R(2) =0.95. Structural information from both models helped us to propose new TCL analogues. A virtual library of TCLs with known predicted activities against enoyl-acyl carrier protein reductase of Plasmodium falciparum (PfENR) was evaluated, revealing dual target TCLs. Moreover, analysis of binding site interactions suggested enriching substitutions, which led to more potent TCLs with predicted pIC50 (pre) as low as 7 nM. The computational approach, which used both free energy estimated from molecular modeling and 3D-QSAR pharmacophore model, was helpful in virtually proposing the dual-targeted drugs and provided valuable information for the design of novel potential antituberculotic agents.
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Affiliation(s)
- Luc C Owono Owono
- University of Yaoundé I, Advanced Teacher Training College, Laboratory for Simulation and Molecular Biophysics, P.O. Box 47 Yaoundé, Cameroon.,University of Douala, Centre for Atomic Molecular Physics and Quantum Optics (CEPAMOQ), P.O. Box 8580 Douala, Cameroon.,International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, Trieste, I-34012, Italy phone:+22502363008
| | - Fidele Ntie-Kang
- University of Douala, Centre for Atomic Molecular Physics and Quantum Optics (CEPAMOQ), P.O. Box 8580 Douala, Cameroon.,International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, Trieste, I-34012, Italy phone:+22502363008.,University of Buea, Chemical and Bioactivity Information Centre, Department of Chemistry, P.O. Box 63, Buea, Cameroon
| | - Melalie Keita
- International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, Trieste, I-34012, Italy phone:+22502363008.,University of Abobo Adjamé, UFR SFA, Laboratoire de Physique Fondamentale et Appliquée, 02 BP 801, Abidjan 02, Cote D'Ivoire
| | - Eugene Megnassan
- International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, Trieste, I-34012, Italy phone:+22502363008. .,University of Abobo Adjamé, UFR SFA, Laboratoire de Physique Fondamentale et Appliquée, 02 BP 801, Abidjan 02, Cote D'Ivoire.
| | - Vladimir Frecer
- International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, Trieste, I-34012, Italy phone:+22502363008.,Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, SK-83232 Bratislava, Slovakia.,International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
| | - Stanislav Miertus
- International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, Trieste, I-34012, Italy phone:+22502363008.,International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia.,Faculty of Natural Sciences, University of Ss. Cyril and Methodius, SK-91701 Trnava, Slovakia
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14
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Kumar SP, George LB, Jasrai YT, Pandya HA. Prioritization of active antimalarials using structural interaction profile of Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR)-triclosan derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:61-77. [PMID: 25567142 DOI: 10.1080/1062936x.2014.984628] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An empirical relationship between the experimental inhibitory activities of triclosan derivatives and its computationally predicted Plasmodium falciparum enoyl-acyl carrier protein (ACP) reductase (PfENR) dock poses was developed to model activities of known antimalarials. A statistical model was developed using 57 triclosan derivatives with significant measures (r = 0.849, q(2) = 0.619, s = 0.481) and applied on structurally related and structurally diverse external datasets. A substructure-based search on ChEMBL malaria dataset (280 compounds) yielded only two molecules with significant docking energy, whereas eight active antimalarials (EC(50) < 100 nM, tested on 3D7 strain) with better predicted activities (pIC(50) ~ 7) from Open Access Malaria Box (400 compounds) were prioritized. Further, calculations on the structurally diverse rhodanine molecules (known PfENR inhibitors) distinguished actives (experimental IC(50) = 0.035 μM; predicted pIC(50) = 6.568) and inactives (experimental IC(50) = 50 μM; predicted pIC50 = -4.078), which showed that antimalarials possessing dock poses similar to experimental interaction profiles can be used as leads to test experimentally on enzyme assays.
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Affiliation(s)
- S P Kumar
- a Department of Bioinformatics, Applied Botany Centre (ABC) , University School of Sciences, Gujarat University , Ahmedabad , India
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15
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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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16
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Tallorin LC, Durrant JD, Nguyen QG, McCammon JA, Burkart MD. Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. Bioorg Med Chem 2014; 22:6053-6061. [PMID: 25284249 PMCID: PMC4807855 DOI: 10.1016/j.bmc.2014.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/25/2014] [Accepted: 09/02/2014] [Indexed: 01/29/2023]
Abstract
Enoyl-acyl carrier protein reductase (ENR), a critical enzyme in type II fatty acid biosynthesis, is a promising target for drug discovery against hepatocyte-stage Plasmodium falciparum. In order to identify PfENR-specific inhibitors, we docked 70 FDA-approved, bioactive, and/or natural product small molecules known to inhibit the growth of whole-cell blood-stage P. falciparum into several PfENR crystallographic structures. Subsequent in vitro activity assays identified a noncompetitive low-micromolar PfENR inhibitor, celastrol, from this set of compounds.
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17
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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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18
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Kumar SP, Pandya HA, Desai VH, Jasrai YT. Compound prioritization from inverse docking experiment using receptor-centric and ligand-centric methods: a case study onPlasmodium falciparumFab enzymes. J Mol Recognit 2014; 27:215-29. [DOI: 10.1002/jmr.2353] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/16/2013] [Accepted: 12/16/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Sivakumar Prasanth Kumar
- Department of Bioinformatics, Applied Botany Centre (ABC); Gujarat University; Ahmedabad 380009 Gujarat India
| | - Himanshu A. Pandya
- Department of Bioinformatics, Applied Botany Centre (ABC); Gujarat University; Ahmedabad 380009 Gujarat India
| | - Vishal H. Desai
- Department of Bioinformatics, Applied Botany Centre (ABC); Gujarat University; Ahmedabad 380009 Gujarat India
| | - Yogesh T. Jasrai
- Department of Bioinformatics, Applied Botany Centre (ABC); Gujarat University; Ahmedabad 380009 Gujarat India
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19
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Integrating molecular docking, CoMFA analysis, and machine-learning classification with virtual screening toward identification of novel scaffolds as Plasmodium falciparum enoyl acyl carrier protein reductase inhibitor. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0910-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Zhang F, Wen Q, Wang SF, Shahla Karim B, Yang YS, Liu JJ, Zhang WM, Zhu HL. Design, synthesis and antibacterial activities of 5-(pyrazin-2-yl)-4H-1,2,4-triazole-3-thiol derivatives containing Schiff base formation as FabH inhibitory. Bioorg Med Chem Lett 2014; 24:90-5. [DOI: 10.1016/j.bmcl.2013.11.079] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 11/04/2013] [Accepted: 11/27/2013] [Indexed: 11/26/2022]
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21
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Afanador GA, Muench SP, McPhillie M, Fomovska A, Schön A, Zhou Y, Cheng G, Stec J, Freundlich JS, Shieh HM, Anderson JW, Jacobus DP, Fidock DA, Kozikowski AP, Fishwick CW, Rice DW, Freire E, McLeod R, Prigge ST. Discrimination of potent inhibitors of Toxoplasma gondii enoyl-acyl carrier protein reductase by a thermal shift assay. Biochemistry 2013; 52:9155-66. [PMID: 24295325 DOI: 10.1021/bi400945y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many microbial pathogens rely on a type II fatty acid synthesis (FASII) pathway that is distinct from the type I pathway found in humans. Enoyl-acyl carrier protein reductase (ENR) is an essential FASII pathway enzyme and the target of a number of antimicrobial drug discovery efforts. The biocide triclosan is established as a potent inhibitor of ENR and has been the starting point for medicinal chemistry studies. We evaluated a series of triclosan analogues for their ability to inhibit the growth of Toxoplasma gondii, a pervasive human pathogen, and its ENR enzyme (TgENR). Several compounds that inhibited TgENR at low nanomolar concentrations were identified but could not be further differentiated because of the limited dynamic range of the TgENR activity assay. Thus, we adapted a thermal shift assay (TSA) to directly measure the dissociation constant (Kd) of the most potent inhibitors identified in this study as well as inhibitors from previous studies. Furthermore, the TSA allowed us to determine the mode of action of these compounds in the presence of the reduced nicotinamide adenine dinucleotide (NADH) or nicotinamide adenine dinucleotide (NAD⁺) cofactor. We found that all of the inhibitors bind to a TgENR-NAD⁺ complex but that they differed in their dependence on NAD⁺ concentration. Ultimately, we were able to identify compounds that bind to the TgENR-NAD⁺ complex in the low femtomolar range. This shows how TSA data combined with enzyme inhibition, parasite growth inhibition data, and ADMET predictions allow for better discrimination between potent ENR inhibitors for the future development of medicine.
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Affiliation(s)
- Gustavo A Afanador
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore, Maryland 21205, United States
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22
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In vitro and in silico antimalarial activity of 2-(2-hydrazinyl)thiazole derivatives. Eur J Pharm Sci 2013; 52:138-45. [PMID: 24231338 DOI: 10.1016/j.ejps.2013.11.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 10/04/2013] [Accepted: 11/01/2013] [Indexed: 11/21/2022]
Abstract
A series of 2-(2-hydrazinyl)thiazole derivatives with a wide range of substitutions at 2-, 4- and 5-positions were synthesized, characterized and evaluated their inhibitory potentials against plasmodium falciparum, NF54, by in vitro blood stage assay. The compounds, ethyl-4-methyl-2-[(E)-2-[1-(pyridin-2-yl)ethylidene]hydrazin-1-yl]-1,3-thiazole-5-carboxylate, 4d, and 1-{4-methyl-2-[(E)-2-[1-(pyridin-2-yl)ethylidene]hydrazin-1-yl]-1,3-thiazol-5-yl}ethan-1-one, 5d showed significant antimalarial activity with IC50 values of 0.725 μM and 0.648 μM respectively. To understand the mechanism, the binding interactions between 2-(2-hydrazinyl)thiazole derivatives and trans-2-enoyl acyl carrier protein reductase of P. falciparum were studied through docking studies. The half maximal inhibitory concentration (IC50) through docking studies for the compounds, 4d and 5d were found to be 22.88 μM and 631.84 μM respectively.
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23
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Wang Y, Ma S. Recent Advances in Inhibitors of Bacterial Fatty Acid Synthesis Type II (FASII) System Enzymes as Potential Antibacterial Agents. ChemMedChem 2013; 8:1589-608. [DOI: 10.1002/cmdc.201300209] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/30/2013] [Indexed: 12/25/2022]
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24
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Hu X, Compton JR, Abdulhameed MDM, Marchand CL, Robertson KL, Leary DH, Jadhav A, Hershfield JR, Wallqvist A, Friedlander AM, Legler PM. 3-substituted indole inhibitors against Francisella tularensis FabI identified by structure-based virtual screening. J Med Chem 2013; 56:5275-87. [PMID: 23815100 DOI: 10.1021/jm4001242] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we describe novel inhibitors against Francisella tularensis SchuS4 FabI identified from structure-based in silico screening with integrated molecular dynamics simulations to account for induced fit of a flexible loop crucial for inhibitor binding. Two 3-substituted indoles, 54 and 57, preferentially bound the NAD(+) form of the enzyme and inhibited growth of F. tularensis SchuS4 at concentrations near that of their measured Ki. While 57 was species-specific, 54 showed a broader spectrum of growth inhibition against F. tularensis , Bacillus anthracis , and Staphylococcus aureus . Binding interaction analysis in conjunction with site-directed mutagenesis revealed key residues and elements that contribute to inhibitor binding and species specificity. Mutation of Arg-96, a poorly conserved residue opposite the loop, was unexpectedly found to enhance inhibitor binding in the R96G and R96M variants. This residue may affect the stability and closure of the flexible loop to enhance inhibitor (or substrate) binding.
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Affiliation(s)
- Xin Hu
- Center of Bio/Molecular Science and Engineering, Naval Research Laboratories , Washington, D.C. 20375, United States
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25
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Lipid synthesis in protozoan parasites: a comparison between kinetoplastids and apicomplexans. Prog Lipid Res 2013; 52:488-512. [PMID: 23827884 DOI: 10.1016/j.plipres.2013.06.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 06/16/2013] [Accepted: 06/17/2013] [Indexed: 12/22/2022]
Abstract
Lipid metabolism is of crucial importance for pathogens. Lipids serve as cellular building blocks, signalling molecules, energy stores, posttranslational modifiers, and pathogenesis factors. Parasites rely on a complex system of uptake and synthesis mechanisms to satisfy their lipid needs. The parameters of this system change dramatically as the parasite transits through the various stages of its life cycle. Here we discuss the tremendous recent advances that have been made in the understanding of the synthesis and uptake pathways for fatty acids and phospholipids in apicomplexan and kinetoplastid parasites, including Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania. Lipid synthesis differs in significant ways between parasites from both phyla and the human host. Parasites have acquired novel pathways through endosymbiosis, as in the case of the apicoplast, have dramatically reshaped substrate and product profiles, and have evolved specialized lipids to interact with or manipulate the host. These differences potentially provide opportunities for drug development. We outline the lipid pathways for key species in detail as they progress through the developmental cycle and highlight those that are of particular importance to the biology of the pathogens and/or are the most promising targets for parasite-specific treatment.
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26
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Development of a triclosan scaffold which allows for adaptations on both the A- and B-ring for transport peptides. Bioorg Med Chem Lett 2013; 23:3551-5. [PMID: 23664871 DOI: 10.1016/j.bmcl.2013.04.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/09/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023]
Abstract
The enoyl acyl-carrier protein reductase (ENR) enzyme is harbored within the apicoplast of apicomplexan parasites providing a significant challenge for drug delivery, which may be overcome through the addition of transductive peptides, which facilitates crossing the apicoplast membranes. The binding site of triclosan, a potent ENR inhibitor, is occluded from the solvent making the attachment of these linkers challenging. Herein, we have produced 3 new triclosan analogs with bulky A- and B-ring motifs, which protrude into the solvent allowing for the future attachment of molecular transporters for delivery.
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27
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Schrader FC, Glinca S, Sattler JM, Dahse HM, Afanador GA, Prigge ST, Lanzer M, Mueller AK, Klebe G, Schlitzer M. Novel type II fatty acid biosynthesis (FAS II) inhibitors as multistage antimalarial agents. ChemMedChem 2013; 8:442-61. [PMID: 23341167 DOI: 10.1002/cmdc.201200407] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Indexed: 11/09/2022]
Abstract
Malaria is a potentially fatal disease caused by Plasmodium parasites and poses a major medical risk in large parts of the world. The development of new, affordable antimalarial drugs is of vital importance as there are increasing reports of resistance to the currently available therapeutics. In addition, most of the current drugs used for chemoprophylaxis merely act on parasites already replicating in the blood. At this point, a patient might already be suffering from the symptoms associated with the disease and could additionally be infectious to an Anopheles mosquito. These insects act as a vector, subsequently spreading the disease to other humans. In order to cure not only malaria but prevent transmission as well, a drug must target both the blood- and pre-erythrocytic liver stages of the parasite. P. falciparum (Pf) enoyl acyl carrier protein (ACP) reductase (ENR) is a key enzyme of plasmodial type II fatty acid biosynthesis (FAS II). It has been shown to be essential for liver-stage development of Plasmodium berghei and is therefore qualified as a target for true causal chemoprophylaxis. Using virtual screening based on two crystal structures of PfENR, we identified a structurally novel class of FAS inhibitors. Subsequent chemical optimization yielded two compounds that are effective against multiple stages of the malaria parasite. These two most promising derivatives were found to inhibit blood-stage parasite growth with IC(50) values of 1.7 and 3.0 μM and lead to a more prominent developmental attenuation of liver-stage parasites than the gold-standard drug, primaquine.
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Affiliation(s)
- Florian C Schrader
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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28
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Novel diaryl ureas with efficacy in a mouse model of malaria. Bioorg Med Chem Lett 2012; 23:1022-5. [PMID: 23313245 PMCID: PMC3746744 DOI: 10.1016/j.bmcl.2012.12.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 11/28/2012] [Accepted: 12/10/2012] [Indexed: 11/23/2022]
Abstract
Exploration of triclosan analogs has led to novel diaryl ureas with significant potency against in vitro cultures of drug-resistant and drug-sensitive strains of the human malaria parasite Plasmodium falciparum. Compound 18 demonstrated EC(50) values of 37 and 55 nM versus in vitro cultured parasite strains and promising in vivo efficacy in a Plasmodium berghei antimalarial mouse model, with >50% survival at day 31 post-treatment when administered subcutaneously at 256 mg/kg. This series of compounds provides a chemical scaffold of novel architecture, as validated by cheminformatics analysis, to pursue antimalarial drug discovery efforts.
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29
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Presence and removal of a contaminating NADH oxidation activity in recombinant maltose-binding protein fusion proteins expressed in Escherichia coli. Biotechniques 2012; 52:247-53. [PMID: 22482440 DOI: 10.2144/0000113822] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 01/26/2012] [Indexed: 11/23/2022] Open
Abstract
We observed the presence of contaminating NADH oxidation activity in maltose binding protein (MBP) fusion proteins expressed in Escherichia coli and purified using conventional amylose resin-based affinity chromatography. This contaminating NADH oxidation activity was detectable with at least four different enzymes from Cryptosporidium parvum expressed as MBP-fusion proteins (i.e., an enoyl-reductase domain from a type I fatty acid synthase, a fatty acyl-CoA binding protein, the acyl-ligase domain from a polyketide synthase, and a putative thioesterase), regardless of their NADH dependence. However, contaminating NADH oxidation activity was not present when fusion proteins were engineered to contain a His-tag and were purified using a Ni-NTA resin-based protocol. Alternatively, for proteins containing only an MBP-tag, the contaminating activity could be eliminated through the addition of 0.1% Triton X-100 and 2% glycerol to the column buffer during homogenization of bacteria and first column wash, followed by an additional wash and elution with regular column and elution buffers. Removal of the artifactual activity is very valuable in the study of enzymes using NADH as a cofactor, particularly when the native activity is low or the recombinant proteins are inactive.
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Qidwai T, Khan F. Antimalarial Drugs and Drug Targets Specific to Fatty Acid Metabolic Pathway of Plasmodium falciparum. Chem Biol Drug Des 2012; 80:155-72. [DOI: 10.1111/j.1747-0285.2012.01389.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mosqueda J, Olvera-Ramirez A, Aguilar-Tipacamu G, Canto GJ. Current advances in detection and treatment of babesiosis. Curr Med Chem 2012; 19:1504-18. [PMID: 22360483 PMCID: PMC3355466 DOI: 10.2174/092986712799828355] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 10/25/2011] [Accepted: 10/26/2011] [Indexed: 01/15/2023]
Abstract
Babesiosis is a disease with a world-wide distribution affecting many species of mammals principally cattle and man. The major impact occurs in the cattle industry where bovine babesiosis has had a huge economic effect due to loss of meat and beef production of infected animals and death. Nowadays to those costs there must be added the high cost of tick control, disease detection, prevention and treatment. In almost a century and a quarter since the first report of the disease, the truth is: there is no a safe and efficient vaccine available, there are limited chemotherapeutic choices and few low-cost, reliable and fast detection methods. Detection and treatment of babesiosis are important tools to control babesiosis. Microscopy detection methods are still the cheapest and fastest methods used to identify Babesia parasites although their sensitivity and specificity are limited. Newer immunological methods are being developed and they offer faster, more sensitive and more specific options to conventional methods, although the direct immunological diagnoses of parasite antigens in host tissues are still missing. Detection methods based on nucleic acid identification and their amplification are the most sensitive and reliable techniques available today; importantly, most of those methodologies were developed before the genomics and bioinformatics era, which leaves ample room for optimization. For years, babesiosis treatment has been based on the use of very few drugs like imidocarb or diminazene aceturate. Recently, several pharmacological compounds were developed and evaluated, offering new options to control the disease. With the complete sequence of the Babesia bovis genome and the B. bigemina genome project in progress, the post-genomic era brings a new light on the development of diagnosis methods and new chemotherapy targets. In this review, we will present the current advances in detection and treatment of babesiosis in cattle and other animals, with additional reference to several apicomplexan parasites.
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Affiliation(s)
- J Mosqueda
- C.A. Salud Animal y Microbiología Ambiental. Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Mexico.
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Botté CY, Dubar F, McFadden GI, Maréchal E, Biot C. Plasmodium falciparum apicoplast drugs: targets or off-targets? Chem Rev 2011; 112:1269-83. [PMID: 22026508 DOI: 10.1021/cr200258w] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Cyrille Y Botté
- Laboratoire de Physiologie Cellulaire Végétale, UMR 5168, CNRS, CEA, INRA, Université Joseph Fourier, Grenoble, France
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Maity K, Banerjee T, Prabakaran N, Surolia N, Surolia A, Suguna K. Effect of substrate binding loop mutations on the structure, kinetics, and inhibition of enoyl acyl carrier protein reductase from Plasmodium falciparum. IUBMB Life 2011; 63:30-41. [PMID: 21280175 DOI: 10.1002/iub.412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 11/30/2010] [Indexed: 11/06/2022]
Abstract
Enoyl acyl carrier protein reductase (ENR), which catalyzes the final and rate limiting step of fatty acid elongation, has been validated as a potential drug target. Triclosan is known to be an effective inhibitor for this enzyme. We mutated the substrate binding site residue Ala372 of the ENR of Plasmodium falciparum (PfENR) to Methionine and Valine which increased the affinity of the enzyme towards triclosan to almost double, close to that of Escherichia coli ENR (EcENR) which has a Methionine at the structurally similar position of Ala372 of PfENR. Kinetic studies of the mutants of PfENR and the crystal structure analysis of the A372M mutant revealed that a more hydrophobic environment enhances the affinity of the enzyme for the inhibitor. A triclosan derivative showed a threefold increase in the affinity towards the mutants compared to the wild type, due to additional interactions with the A372M mutant as revealed by the crystal structure. The enzyme has a conserved salt bridge which stabilizes the substrate binding loop and appears to be important for the active conformation of the enzyme. We generated a second set of mutants to check this hypothesis. These mutants showed loss of function, except in one case, where the crystal structure showed that the substrate binding loop is stabilized by a water bridge network.
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Affiliation(s)
- Koustav Maity
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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34
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Burrows JN, Waterson D. Discovering New Medicines to Control and Eradicate Malaria. TOPICS IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1007/7355_2011_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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35
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Kim KH, Ha BH, Kim SJ, Hong SK, Hwang KY, Kim EE. Crystal structures of Enoyl-ACP reductases I (FabI) and III (FabL) from B. subtilis. J Mol Biol 2010; 406:403-15. [PMID: 21185310 DOI: 10.1016/j.jmb.2010.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/25/2010] [Accepted: 12/01/2010] [Indexed: 12/22/2022]
Abstract
Enoyl-[acyl carrier protein] (ACP) reductase (ENR) is a key enzyme in type II fatty acid synthesis that catalyzes the last step in each elongation cycle. Therefore, it has been considered as a target for antibiotics. However, recent studies indicate that some pathogens have more than one ENR; in particular, Bacillus subtilis has two ENRs, FabI and FabL. The crystal structures of the ternary complexes of BsFaBI and BsFabL are found as a homotetramer showing the same overall structure despite a sequence identity of only 24%. The positions of the catalytic dyad of Tyr-(Xaa)(6)-Lys in FabL are almost identical to that of FabI, but a detailed structural analysis shows that FabL shares more structural similarities with FabG and other members of the SDR (short-chain alcohol dehydrogenase/reductase) family. The apo FabL structure shows significantly different conformations at the cofactor and the substrate-binding regions, and this resulted in a totally different tetrameric arrangement reflecting the flexibility of these regions in the absence of the cofactor and substrate/inhibitor.
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Affiliation(s)
- Kook-Han Kim
- Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolkok-dong, Sungbuk-gu, Seoul 136-791, South Korea
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36
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Maity K, Bhargav SP, Sankaran B, Surolia N, Surolia A, Suguna K. X-ray crystallographic analysis of the complexes of enoyl acyl carrier protein reductase of Plasmodium falciparum with triclosan variants to elucidate the importance of different functional groups in enzyme inhibition. IUBMB Life 2010; 62:467-76. [PMID: 20503440 DOI: 10.1002/iub.327] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Triclosan, a well-known inhibitor of Enoyl Acyl Carrier Protein Reductase (ENR) from several pathogenic organisms, is a promising lead compound to design effective drugs. We have solved the X-ray crystal structures of Plasmodium falciparum ENR in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations. The structures revealed that 4 and 2' substituted compounds have more interactions with the protein, cofactor, and solvents when compared with triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2' position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water-based inhibitor design. 2' and 4' unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensate for the lost interactions due to the unsubstitution at 2' and 4'. In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2' and 4' positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors.
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Affiliation(s)
- Koustav Maity
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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37
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Shah P, Siddiqi MI. 3D-QSAR studies on triclosan derivatives as Plasmodium falciparum enoyl acyl carrier reductase inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2010; 21:527-545. [PMID: 20818586 DOI: 10.1080/1062936x.2010.502297] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
3D-QSAR studies were carried out on a training set of 53 structurally highly diverse analogues of triclosan to investigate the correlation of the structural properties of triclosan derivatives with the inhibition of the activity of enoyl acyl carrier protein reductase in Plasmodium falciparum (PfENR) by employing Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The crystal structure bound conformation of triclosan, was used as a template for aligning molecules. The probable binding mode conformations of other inhibitors were explored according to molecular docking and molecular mechanics poisson-boltzmann surface area (MM/PBSA) solvation free energy estimation methods using grid based linear Poisson-Boltzmann calculations. Predictive 3D-QSAR models, established using routine database alignment rule based on crystallographic-bound conformation of template molecule, produced statistically significant results with cross-validated r2 cv values of 0.64 and 0.54 and non-cross-validated r2 ncv values of 0.96 and 0.97 for CoMFA and CoMSIA models, respectively. The statistically significant models were validated by a test set of nine compounds with predictive r(2) values of 0.534 and 0.765 for CoMFA and CoMSIA respectively. Our QSAR model is able to successfully explain the geometric and electrostatic complementarities between ligands and receptor and provides useful guidelines to design novel triclosan derivatives as Plasmodium falciparum enoyl acyl carrier reductase inhibitors.
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Affiliation(s)
- P Shah
- Molecular and Structural Biology Division, Central Drug Research Institute, Lucknow 226 001, India
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38
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Coppens I, Sullivan DJ, Prigge ST. An update on the rapid advances in malaria parasite cell biology. Trends Parasitol 2010; 26:305-10. [PMID: 20382563 DOI: 10.1016/j.pt.2010.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 03/10/2010] [Accepted: 03/12/2010] [Indexed: 01/05/2023]
Abstract
Recent years have seen rapid advances in our understanding of malaria parasite cell biology. Some of this progress has been the result of developments in genetic techniques, advances in imaging technology, and new molecular tools. We focus on three aspects of parasite cell biology: (i) plastid metabolism, (ii) sporozoite biology, and (iii) protein transport to and from the host erythrocyte. In each case recent work has led to a deeper understanding of parasite biology, often at the expense of previously accepted paradigms. These studies also highlight the impediments, technical and otherwise, that will have to be overcome for continued rapid progress in these fields.
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Affiliation(s)
- Isabelle Coppens
- Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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39
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Priyadarshi A, Kim EE, Hwang KY. Structural insights into Staphylococcus aureus enoyl-ACP reductase (FabI), in complex with NADP and triclosan. Proteins 2010; 78:480-6. [PMID: 19768684 DOI: 10.1002/prot.22581] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Amit Priyadarshi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, South Korea
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40
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Kumar G, Banerjee T, Kapoor N, Surolia N, Surolia A. SAR and pharmacophore models for the rhodanine inhibitors of Plasmodium falciparum enoyl-acyl carrier protein reductase. IUBMB Life 2010; 62:204-13. [DOI: 10.1002/iub.306] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Pillai AD, Pain M, Solomon T, Bokhari AAB, Desai SA. A cell-based high-throughput screen validates the plasmodial surface anion channel as an antimalarial target. Mol Pharmacol 2010; 77:724-33. [PMID: 20101003 DOI: 10.1124/mol.109.062711] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The plasmodial surface anion channel (PSAC) is an unusual small-conductance ion channel induced on erythrocytes infected with plasmodia, including parasites responsible for human malaria. Although broadly available inhibitors produce microscopic clearance of parasite cultures at high concentrations and suggest that PSAC is an antimalarial target, they have low affinity for the channel and may interfere with other parasite activities. To address these concerns, we developed a miniaturized assay for PSAC activity and carried out a high-throughput inhibitor screen. Approximately 70,000 compounds from synthetic and natural product libraries were screened, revealing inhibitors from multiple structural classes including two novel and potent heterocyclic scaffolds. Single-channel patch-clamp studies indicated that these compounds act directly on PSAC, further implicating a proposed role in transport of diverse solutes. A statistically significant correlation between channel inhibition and in vitro parasite killing by a family of compounds provided chemical validation of PSAC as a drug target. These new inhibitors should be important research tools and may be starting points for much-needed antimalarial drugs.
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Affiliation(s)
- Ajay D Pillai
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852-8132, USA
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42
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Prediction of potential antimalarial targets of artemisinin based on protein information from whole genome of Plasmodium falciparum. CHINESE SCIENCE BULLETIN-CHINESE 2009. [DOI: 10.1007/s11434-009-0634-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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Wells TNC, Alonso PL, Gutteridge WE. New medicines to improve control and contribute to the eradication of malaria. Nat Rev Drug Discov 2009; 8:879-91. [DOI: 10.1038/nrd2972] [Citation(s) in RCA: 244] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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44
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Lee PJ, Bhonsle JB, Gaona HW, Huddler DP, Heady TN, Kreishman-Deitrick M, Bhattacharjee A, McCalmont WF, Gerena L, Lopez-Sanchez M, Roncal NE, Hudson TH, Johnson JD, Prigge ST, Waters NC. Targeting the fatty acid biosynthesis enzyme, beta-ketoacyl-acyl carrier protein synthase III (PfKASIII), in the identification of novel antimalarial agents. J Med Chem 2009; 52:952-63. [PMID: 19191586 DOI: 10.1021/jm8008103] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of fatty acids to the human malaria parasite, Plasmodium falciparum, and differences due to a type I fatty acid synthesis (FAS) pathway in the parasite, make it an attractive drug target. In the present study, we developed and a utilized a pharmacophore to select compounds for testing against PfKASIII, the initiating enzyme of FAS. This effort identified several PfKASIII inhibitors that grouped into various chemical classes of sulfides, sulfonamides, and sulfonyls. Approximately 60% of the submicromolar inhibitors of PfKASIII inhibited in vitro growth of the malaria parasite. These compounds inhibited both drug sensitive and resistant parasites and testing against a mammalian cell line revealed an encouraging in vitro therapeutic index for the most active compounds. Docking studies into the active site of PfKASIII suggest a potential binding mode that exploits amino acid residues at the mouth of the substrate tunnel.
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Affiliation(s)
- Patricia J Lee
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
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45
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Functional expression of Francisella tularensis FabH and FabI, potential antibacterial targets. Protein Expr Purif 2009; 65:83-91. [DOI: 10.1016/j.pep.2008.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 11/12/2008] [Accepted: 11/17/2008] [Indexed: 11/19/2022]
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46
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Freundlich JS, Wang F, Vilchèze C, Gulten G, Langley R, Schiehser GA, Jacobus DP, Jacobs WR, Sacchettini JC. Triclosan derivatives: towards potent inhibitors of drug-sensitive and drug-resistant Mycobacterium tuberculosis. ChemMedChem 2009; 4:241-8. [PMID: 19130456 PMCID: PMC3541007 DOI: 10.1002/cmdc.200800261] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Indexed: 11/08/2022]
Abstract
Triclosan has been previously shown to inhibit InhA, an essential enoyl acyl carrier protein reductase involved in mycolic acid biosynthesis, the inhibition of which leads to the lysis of Mycobacterium tuberculosis. Using a structure-based drug design approach, a series of 5-substituted triclosan derivatives was developed. Two groups of derivatives with alkyl and aryl substituents, respectively, were identified with dramatically enhanced potency against purified InhA. The most efficacious inhibitor displayed an IC(50) value of 21 nM, which was 50-fold more potent than triclosan. X-ray crystal structures of InhA in complex with four triclosan derivatives revealed the structural basis for the inhibitory activity. Six selected triclosan derivatives were tested against isoniazid-sensitive and resistant strains of M. tuberculosis. Among those, the best inhibitor had an MIC value of 4.7 microg mL(-1) (13 microM), which represents a tenfold improvement over the bacteriocidal activity of triclosan. A subset of these triclosan analogues was more potent than isoniazid against two isoniazid-resistant M. tuberculosis strains, demonstrating the significant potential for structure-based design in the development of next generation antitubercular drugs.
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Affiliation(s)
- Joel S. Freundlich
- Dr. J. S. Freundlich, F. Wang, G. Gulten, R. Langley, Prof. Dr. J. C. Sacchettini, Texas A&M University Department of Biochemistry and Biophysics, College Station, TX 77843-2128 (USA)
- Dr. G. A. Schiehser, Dr. D. P. Jacobus, Jacobus Pharmaceutical Company, Princeton, NJ 08540 (USA)
| | - Feng Wang
- Dr. J. S. Freundlich, F. Wang, G. Gulten, R. Langley, Prof. Dr. J. C. Sacchettini, Texas A&M University Department of Biochemistry and Biophysics, College Station, TX 77843-2128 (USA)
| | - Catherine Vilchèze
- Dr. C. Vilchèze, Prof. Dr. W. R. Jacobs, Jr., Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461 (USA)
| | - Gulcin Gulten
- Dr. J. S. Freundlich, F. Wang, G. Gulten, R. Langley, Prof. Dr. J. C. Sacchettini, Texas A&M University Department of Biochemistry and Biophysics, College Station, TX 77843-2128 (USA)
| | - Robert Langley
- Dr. J. S. Freundlich, F. Wang, G. Gulten, R. Langley, Prof. Dr. J. C. Sacchettini, Texas A&M University Department of Biochemistry and Biophysics, College Station, TX 77843-2128 (USA)
| | - Guy A. Schiehser
- Dr. G. A. Schiehser, Dr. D. P. Jacobus, Jacobus Pharmaceutical Company, Princeton, NJ 08540 (USA)
| | - David P. Jacobus
- Dr. G. A. Schiehser, Dr. D. P. Jacobus, Jacobus Pharmaceutical Company, Princeton, NJ 08540 (USA)
| | - William R. Jacobs
- Dr. C. Vilchèze, Prof. Dr. W. R. Jacobs, Jr., Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461 (USA)
| | - James C. Sacchettini
- Dr. J. S. Freundlich, F. Wang, G. Gulten, R. Langley, Prof. Dr. J. C. Sacchettini, Texas A&M University Department of Biochemistry and Biophysics, College Station, TX 77843-2128 (USA)
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47
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The fatty acid biosynthesis enzyme FabI plays a key role in the development of liver-stage malarial parasites. Cell Host Microbe 2009; 4:567-78. [PMID: 19064257 DOI: 10.1016/j.chom.2008.11.001] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 11/03/2008] [Accepted: 11/05/2008] [Indexed: 01/01/2023]
Abstract
The fatty acid synthesis type II pathway has received considerable interest as a candidate therapeutic target in Plasmodium falciparum asexual blood-stage infections. This apicoplast-resident pathway, distinct from the mammalian type I process, includes FabI. Here, we report synthetic chemistry and transfection studies concluding that Plasmodium FabI is not the target of the antimalarial activity of triclosan, an inhibitor of bacterial FabI. Disruption of fabI in P. falciparum or the rodent parasite P. berghei does not impede blood-stage growth. In contrast, mosquito-derived, FabI-deficient P. berghei sporozoites are markedly less infective for mice and typically fail to complete liver-stage development in vitro. This defect is characterized by an inability to form intrahepatic merosomes that normally initiate blood-stage infections. These data illuminate key differences between liver- and blood-stage parasites in their requirements for host versus de novo synthesized fatty acids, and create new prospects for stage-specific antimalarial interventions.
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48
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Ben Mamoun C, Prigge ST, Vial H. Targeting the Lipid Metabolic Pathways for the Treatment of Malaria. Drug Dev Res 2009; 71:44-55. [PMID: 20559451 DOI: 10.1002/ddr.20347] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The control and eventual eradication of human malaria is considered one of the most important global public health goals of the 21st Century. Malaria, caused by intraerythrocytic protozoan parasites of the genus Plasmodium, is by far the most lethal and among the most prevalent of the infectious diseases. Four species of Plasmodium (P. falciparum, P. malariae, P. ovale, and P. vivax) are known to be infectious to humans, and more recent cases of infection due to P. knowlesi also have been reported. These species cause approximately 300 million annual cases of clinical malaria resulting in around one million deaths mostly caused by P. falciparum. The rapid emergence of drug-resistant Plasmodium strains has severely reduced the potency of medicines commonly used to treat and block the transmission of malaria and threatens the effectiveness of combination therapy in the field. New drugs that target important parasite functions, which are not the target of current antimalarial drugs, and have the potential to act against multi-drug-resistant Plasmodium strains are urgently needed. Recent studies in P. falciparum have unraveled new metabolic pathways for the synthesis of the parasite phospholipids and fatty acids. The present review summarizes our current understanding of these pathways in Plasmodium development and pathogenesis, and provides an update on the efforts underway to characterize their importance using genetic means and to develop antimalarial therapies targeting lipid metabolic pathways.
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Affiliation(s)
- Choukri Ben Mamoun
- Section of Infectious Disease, Yale University School of Medicine, New Haven, Connecticut
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49
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Tipparaju SK, Mulhearn DC, Klein GM, Chen Y, Tapadar S, Bishop MH, Yang S, Chen J, Ghassemi M, Santarsiero BD, Cook JL, Johlfs M, Mesecar AD, Johnson ME, Kozikowski AP. Design and synthesis of aryl ether inhibitors of the Bacillus anthracis enoyl-ACP reductase. ChemMedChem 2008; 3:1250-68. [PMID: 18663709 PMCID: PMC2693028 DOI: 10.1002/cmdc.200800047] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Indexed: 11/11/2022]
Abstract
The problem of increasing bacterial resistance to the current generation of antibiotics is well documented. Known resistant pathogens such as methicillin-resistant Staphylococcus aureus are becoming more prevalent, while the potential exists for developing drug-resistant pathogens for use as bioweapons, such as Bacillus anthracis. The biphenyl ether antibacterial agent, triclosan, exhibits broad-spectrum activity by targeting the fatty acid biosynthetic pathway through inhibition of enoyl-acyl carrier protein reductase (ENR) and provides a potential scaffold for the development of new, broad-spectrum antibiotics. We used a structure-based approach to develop novel aryl ether analogues of triclosan that target ENR, the product of the fabI gene, from B. anthracis (BaENR). Structure-based design methods were used for the expansion of the compound series including X-ray crystal structure determination, molecular docking, and QSAR methods. Structural modifications were made to both phenyl rings of the 2-phenoxyphenyl core. A number of compounds exhibited improved potency against BaENR and increased efficacy against both the Sterne strain of B. anthracis and the methicillin-resistant strain of S. aureus. X-ray crystal structures of BaENR in complex with triclosan and two other compounds help explain the improved efficacy of the new compounds and suggest future rounds of optimization that might be used to improve their potency.
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Affiliation(s)
- Suresh K. Tipparaju
- Dr. S. K. Tipparaju, Dr. Y. Chen, Dr. S. Tapadar, Prof. Dr. A. P. Kozikowski, Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA Fax: (312) 413 0577
| | - Debbie C. Mulhearn
- Dr. D. C. Mulhearn, G. M. Klein, M. H. Bishop, S. Yang, Dr. B. D. Santarsiero, Dr. M. Johlfs, Dr. A. D. Mesecar, Prof. Dr. M. E. Johnson, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607–7173, USA, Fax: (312) 413 9303
| | - Gary M. Klein
- Dr. S. K. Tipparaju, Dr. Y. Chen, Dr. S. Tapadar, Prof. Dr. A. P. Kozikowski, Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA Fax: (312) 413 0577
- Dr. D. C. Mulhearn, G. M. Klein, M. H. Bishop, S. Yang, Dr. B. D. Santarsiero, Dr. M. Johlfs, Dr. A. D. Mesecar, Prof. Dr. M. E. Johnson, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607–7173, USA, Fax: (312) 413 9303
| | - Yufeng Chen
- Dr. S. K. Tipparaju, Dr. Y. Chen, Dr. S. Tapadar, Prof. Dr. A. P. Kozikowski, Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA Fax: (312) 413 0577
| | - Subhasish Tapadar
- Dr. S. K. Tipparaju, Dr. Y. Chen, Dr. S. Tapadar, Prof. Dr. A. P. Kozikowski, Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA Fax: (312) 413 0577
| | - Molly H. Bishop
- Dr. D. C. Mulhearn, G. M. Klein, M. H. Bishop, S. Yang, Dr. B. D. Santarsiero, Dr. M. Johlfs, Dr. A. D. Mesecar, Prof. Dr. M. E. Johnson, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607–7173, USA, Fax: (312) 413 9303
| | - Shuo Yang
- Dr. D. C. Mulhearn, G. M. Klein, M. H. Bishop, S. Yang, Dr. B. D. Santarsiero, Dr. M. Johlfs, Dr. A. D. Mesecar, Prof. Dr. M. E. Johnson, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607–7173, USA, Fax: (312) 413 9303
| | - Juan Chen
- Dr. J. Chen, Dr. M. Ghassemi, Dr. J. L. Cook, Department of Medicine, University of Illinois at Chicago, 808 S. Wood St., Chicago IL 60612, USA
| | - Mahmood Ghassemi
- Dr. J. Chen, Dr. M. Ghassemi, Dr. J. L. Cook, Department of Medicine, University of Illinois at Chicago, 808 S. Wood St., Chicago IL 60612, USA
| | - Bernard D. Santarsiero
- Dr. D. C. Mulhearn, G. M. Klein, M. H. Bishop, S. Yang, Dr. B. D. Santarsiero, Dr. M. Johlfs, Dr. A. D. Mesecar, Prof. Dr. M. E. Johnson, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607–7173, USA, Fax: (312) 413 9303
| | - James L. Cook
- Dr. J. Chen, Dr. M. Ghassemi, Dr. J. L. Cook, Department of Medicine, University of Illinois at Chicago, 808 S. Wood St., Chicago IL 60612, USA
| | - Mary Johlfs
- Dr. D. C. Mulhearn, G. M. Klein, M. H. Bishop, S. Yang, Dr. B. D. Santarsiero, Dr. M. Johlfs, Dr. A. D. Mesecar, Prof. Dr. M. E. Johnson, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607–7173, USA, Fax: (312) 413 9303
| | - Andrew D. Mesecar
- Dr. S. K. Tipparaju, Dr. Y. Chen, Dr. S. Tapadar, Prof. Dr. A. P. Kozikowski, Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA Fax: (312) 413 0577
- Dr. D. C. Mulhearn, G. M. Klein, M. H. Bishop, S. Yang, Dr. B. D. Santarsiero, Dr. M. Johlfs, Dr. A. D. Mesecar, Prof. Dr. M. E. Johnson, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607–7173, USA, Fax: (312) 413 9303
| | - Michael E. Johnson
- Dr. D. C. Mulhearn, G. M. Klein, M. H. Bishop, S. Yang, Dr. B. D. Santarsiero, Dr. M. Johlfs, Dr. A. D. Mesecar, Prof. Dr. M. E. Johnson, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607–7173, USA, Fax: (312) 413 9303
| | - Alan P. Kozikowski
- Dr. S. K. Tipparaju, Dr. Y. Chen, Dr. S. Tapadar, Prof. Dr. A. P. Kozikowski, Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA Fax: (312) 413 0577
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Lu H, Tonge PJ. Inhibitors of FabI, an enzyme drug target in the bacterial fatty acid biosynthesis pathway. Acc Chem Res 2008; 41:11-20. [PMID: 18193820 DOI: 10.1021/ar700156e] [Citation(s) in RCA: 184] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The modern age of drug discovery, which had been slowly gathering momentum during the early part of the twentieth century, exploded into life in the 1940s with the isolation of penicillin and streptomycin. The immense success of these early drug discovery efforts prompted the general view that many infectious diseases would now be effectively controlled and even eradicated. However this initial optimism was misplaced, and pathogens such as multidrug-resistant Mycobacterium tuberculosis and methicillin-resistant Staphylococcus aureus present a major current threat to human health. Drug resistance arises through the unrelenting pressure of natural selection, and there is thus a continuing need to identify novel drug targets and develop chemotherapeutics that circumvent existing drug resistance mechanisms. In this Account, we summarize current progress in developing inhibitors of FabI, the NADH-dependent enoyl reductase from the type II bacterial fatty acid biosynthesis pathway (FAS-II), a validated but currently underexploited target for drug discovery. The FabI inhibitors have been divided into two groups, based on whether they form a covalent adduct with the NAD (+) cofactor. Inhibitors that form a covalent adduct include the diazaborines, as well as the front-line tuberculosis drug isoniazid. The NAD adducts formed with these compounds are formally bisubstrate enzyme inhibitors, and we summarize progress in developing novel leads based on these pharmacophores. Inhibitors that do not form covalent adducts form a much larger group, although generally these compounds also require the cofactor to be bound to the enzyme. Using structure-based approaches, we have developed a series of alkyl diphenyl ethers that are nanomolar inhibitors of InhA, the FabI from M. tuberculosis, and that are active against INH-resistant strains of M. tuberculosis. This rational approach to inhibitor development is based on the proposal that high-affinity inhibition of the FabI enzymes is coupled to the ordering of a loop of amino acids close to the active site. Compounds that promote loop ordering are slow onset FabI inhibitors with increased residence time on the enzyme. The diphenyl ether skeleton has also been used as a framework by us and others to develop potent inhibitors of the FabI enzymes from other pathogens such as Escherichia coli, S. aureus, and Plasmodium falciparum. Meanwhile chemical optimization of compounds identified in high-throughput screening programs has resulted in the identification of several classes of heteroaromatic FabI inhibitors with potent activity both in vitro and in vivo. Finally, screening of natural product libraries may provide useful chemical entities for the development of novel agents with low toxicity. While the discovery that not all pathogens contain FabI homologues has led to reduced industrial interest in FabI as a broad spectrum target, there is substantial optimism that FabI inhibitors can be developed for disease-specific applications. In addition, the availability of genome sequencing data, improved methods for target identification and validation, and the development of novel approaches for determining the mode of action of current drugs will all play critical roles in the road ahead and in exploiting other components of the FAS-II pathway.
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Affiliation(s)
- Hao Lu
- Department of Chemistry and Institute for Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400
| | - Peter J. Tonge
- Department of Chemistry and Institute for Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400
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