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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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2
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Abstract
Antibiotic resistance is a serious public health concern, and new drugs are needed to ensure effective treatment of many bacterial infections. Bacterial type II fatty acid synthesis (FASII) is a vital aspect of bacterial physiology, not only for the formation of membranes but also to produce intermediates used in vitamin production. Nature has evolved a repertoire of antibiotics inhibiting different aspects of FASII, validating these enzymes as potential targets for new antibiotic discovery and development. However, significant obstacles have been encountered in the development of FASII antibiotics, and few FASII drugs have advanced beyond the discovery stage. Most bacteria are capable of assimilating exogenous fatty acids. In some cases they can dispense with FASII if fatty acids are present in the environment, making the prospects for identifying broad-spectrum drugs against FASII targets unlikely. Single-target, pathogen-specific FASII drugs appear the best option, but a major drawback to this approach is the rapid acquisition of resistance via target missense mutations. This complication can be mitigated during drug development by optimizing the compound design to reduce the potential impact of on-target missense mutations at an early stage in antibiotic discovery. The lessons learned from the difficulties in FASII drug discovery that have come to light over the last decade suggest that a refocused approach to designing FASII inhibitors has the potential to add to our arsenal of weapons to combat resistance to existing antibiotics.
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Affiliation(s)
- Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
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3
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Zhou Y, Liang YQ, Wang XY, Chang HY, Hu SP, Sun J. Design, Synthesis and Antibacterial Activities of Novel Amide Derivatives Bearing Dioxygenated Rings as Potential β-Ketoacyl-acyl Carrier Protein Synthase III (FabH) Inhibitors. Chem Pharm Bull (Tokyo) 2022; 70:544-549. [DOI: 10.1248/cpb.c22-00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yang Zhou
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology
| | - Yin-Qiu Liang
- Zhejiang International Scientific and Technological Cooperative Base of Biomedical Materials and Technology, Zhejiang Engineering Research Center for Biomedical Materials, Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences
| | - Xin-Yu Wang
- Zhejiang International Scientific and Technological Cooperative Base of Biomedical Materials and Technology, Zhejiang Engineering Research Center for Biomedical Materials, Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences
| | - Hao-Yun Chang
- Zhejiang International Scientific and Technological Cooperative Base of Biomedical Materials and Technology, Zhejiang Engineering Research Center for Biomedical Materials, Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences
| | - Su-Pei Hu
- Department of Medical Research, Hwa Mei Hospital, University of Chinese Academy of Sciences
| | - Juan Sun
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology
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4
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Iakovenko RO, Chrenko D, Kristek J, Desmedt E, Zálešák F, De Vleeschouwer F, Pospíšil J. Heteroaryl sulfonamide synthesis: scope and limitations. Org Biomol Chem 2022; 20:3154-3159. [PMID: 35343994 DOI: 10.1039/d2ob00345g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Heteroaryl sulfonamides are important structural motifs in the medicinal and agrochemical industries. However, their synthesis often relies on the use of heteroaryl sulfonyl chlorides, which are unstable and toxic reagents. Herein, we report a protocol that allows direct oxidative coupling of heteroaryl thiols and primary amines, readily available and inexpensive commodity chemicals. The transformation proceeds under mild reaction conditions and yields the desired N-alkylated sulfonamides in good yields. N-alkyl heteroaryl sulfonamides can be further transformed using a microwave-promoted Fukuyama-Mitsunobu reaction to N,N-dialkyl heteroaryl sulfonamides. The developed protocols thus enable the preparation of previously difficult to prepare sulfonamides (toxic reagents, harsh conditions, and low yields) under mild conditions.
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Affiliation(s)
- Roman O Iakovenko
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, and Faculty of Science, Palacky University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic.
| | - Daniel Chrenko
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, and Faculty of Science, Palacky University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic. .,Department of Chemical Biology, Faculty of Science, Palacky University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic
| | - Jozef Kristek
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, Olomouc CZ-771 46, Czech Republic
| | - Eline Desmedt
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - František Zálešák
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, Olomouc CZ-771 46, Czech Republic
| | - Freija De Vleeschouwer
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Jiří Pospíšil
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, and Faculty of Science, Palacky University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic. .,Department of Chemical Biology, Faculty of Science, Palacky University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, Olomouc CZ-771 46, Czech Republic
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5
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Li B, Chen C, Jia J, He L. Research progress on antineoplastic, antibacterial, and anti-inflammatory activities of seven-membered heterocyclic derivatives. Curr Med Chem 2022; 29:5076-5096. [PMID: 35345989 DOI: 10.2174/0929867329666220328123953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Seven-membered heterocyclic compounds are important drug scaffolds, because of their unique chemical structures. They widely exist in natural products and show a variety of biological activities. They have commonly been used in central nervous system drugs in the past 30 years. In the past decade, there are many studies on the activities of antitumor, antibacterial, etc. Herein, we summarize the research advances in different kinds of seven-membered heterocyclic compounds containing nitrogen, oxygen, and sulfur heteroatoms with antitumor, antisepsis, and anti-inflammation activities in the past ten years, which is expected to be beneficial to the development and design of novel drugs for the corresponding indications.
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Affiliation(s)
- Bin Li
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Chen Chen
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Jingjing Jia
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ling He
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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Shinde R, Suvarna V. Fatty Acid Biosynthesis: An Updated Review on KAS Inhibitors. Curr Drug Discov Technol 2022; 19:e110122200137. [PMID: 35021976 DOI: 10.2174/1570163819666220111113032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
Since the early twentieth century, with the isolation of penicillin and streptomycin in the 1940s, the modern era of anti-infective drug development has gained momentum. Due to the enormous success of early drug discovery, many infectious diseases were successfully prevented and eradicated. However, this initial hope was wrongheaded, and pathogens evolved as a significant threat to human health. Drug resistance develops as a result of natural selection's relentless pressure, necessitating the identification of new drug targets and the creation of chemotherapeutics that bypass existing drug resistance mechanisms. Fatty acid biosynthesis (FAS) is a crucial metabolic mechanism for bacteria during their growth and development. Several crucial enzymes involved in this biosynthetic pathway have been identified as potential targets for new antibacterial agents. In Escherichia coli (E. coli), this pathway has been extensively investigated. The present review focuses on progress in the development of Kas A, Kas B, and Fab H inhibitors as mono-therapeutic antibiotics.
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Affiliation(s)
- Rani Shinde
- Department of Quality Assurance, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai University, Mumbai, India
| | - Vasanti Suvarna
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai University, Mumbai, India
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Zálešák F, Kováč O, Lachetová E, Št'astná N, Pospíšil J. Unified Approach to Benzo[ d]thiazol-2-yl-Sulfonamides. J Org Chem 2021; 86:11291-11309. [PMID: 34479409 DOI: 10.1021/acs.joc.1c00317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, we report a unified approach to N-substituted and N,N-disubstituted benzothiazole (BT) sulfonamides. Our approach to BT-sulfonamides starts from simple commercially available building blocks (benzo[d]thiazole-2-thiol and primary and secondary amines) that are connected via (a) a S oxidation/S-N coupling approach, (b) a S-N coupling/S-oxidation sequence, or via (c) a S-oxidation/S-F bond formation/SuFEx approach. The labile N-H bond in N-monoalkylated BT-sulfonamides (pKa (BTSO2N(H)Bn) = 3.34 ± 0.05) further allowed us to develop a simple weak base-promoted N-alkylation method and a stereoselective microwave-promoted Fukuyama-Mitsunobu reaction. N-Alkyl-N-aryl BT-sulfonamides were accessed with the help of the Chan-Lam coupling reaction. Developed methods were further used in stereo and chemoselective transformations of podophyllotoxin and several amino alcohols.
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Affiliation(s)
- František Zálešák
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
| | - Ondřej Kováč
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
| | - Eliška Lachetová
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
| | - Nikola Št'astná
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic
| | - Jiří Pospíšil
- Department of Organic Chemistry, Faculty of Science, Palacky University, tř. 17. listopadu 1192/12, CZ-771 46 Olomouc, Czech Republic.,Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany AS CR, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
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8
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Jia B, Ma YM, Liu B, Chen P, Hu Y, Zhang R. Synthesis, Antimicrobial Activity, Structure-Activity Relationship, and Molecular Docking Studies of Indole Diketopiperazine Alkaloids. Front Chem 2019; 7:837. [PMID: 31850323 PMCID: PMC6897290 DOI: 10.3389/fchem.2019.00837] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
Strategies for the synthesis of indole diketopiperazine alkaloids (indole DKPs) have been described and involve three analogs of indole DKPs. The antimicrobial activity and structure-activity relationship (SAR) of 24 indole DKPs were explored. Compounds 3b and 3c were found to be the most active, with minimum inhibitory concentrations (MIC) values in the range of 0.94–3.87 μM (0.39–1.56 μg/mL) against the four tested bacteria (Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, and Escherichia coli). Furthermore, compounds 4a and 4b displayed broad-spectrum antimicrobial activity with MIC values of 1.10–36.9 μM (0.39–12.5 μg/mL) against all tested bacteria and plant pathogenic fungi (Colletotrichum gloeosporioides, Valsa mali, Alternaria alternata and Alternaria brassicae). According to the in silico study, compounds 3c showed significant binding affinity to the FabH protein from Escherichia coli, which has been identified as the key target enzyme of fatty acid synthesis (FAS) in bacteria. Therefore, these compounds are not only promising new antibacterial agents but also potential FabH inhibitors.
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Affiliation(s)
- Bin Jia
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yang-Min Ma
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Bin Liu
- School of Pharmacy, Shaanxi Institute of International Trade and Commerce, Xi'an, China.,Collaborative Innovation Center of Green Manufacturing Technology for Traditional Chinese Medicine in Shaanxi Province, Xi'an, China
| | - Pu Chen
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yan Hu
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Rui Zhang
- School of Arts and Sciences, Shaanxi University of Science and Technology, Xi'an, China
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9
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Zheng C, Hou W, Liu J, Xu X, Lin J, Sun P, Chen W. Design and synthesis of 2‐hydroxyl‐4‐methoxyl‐3‐(3‐methylbut‐2‐en‐1‐yl)‐6‐(4‐phenylbenzoylamino)benzoic acid derivatives as antibacterial agents based on cajaninstilbene acid scaffold hopping. Drug Dev Res 2019; 80:750-757. [DOI: 10.1002/ddr.21556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 04/25/2019] [Accepted: 05/19/2019] [Indexed: 01/25/2023]
Affiliation(s)
- Chang Zheng
- College of PharmacyJinan University Guangzhou People's Republic of China
| | - Wen Hou
- College of PharmacyJinan University Guangzhou People's Republic of China
| | - Jun Liu
- College of PharmacyJinan University Guangzhou People's Republic of China
| | - Xiao‐Fang Xu
- College of PharmacyJinan University Guangzhou People's Republic of China
| | - Jing Lin
- College of PharmacyJinan University Guangzhou People's Republic of China
| | - Ping‐Hua Sun
- College of PharmacyJinan University Guangzhou People's Republic of China
| | - Wei‐Min Chen
- College of PharmacyJinan University Guangzhou People's Republic of China
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10
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Sun J, He W, Liu HY, Qin J, Ye CL. Design, synthesis and molecular docking of 1,4-benzodioxane thiazolidinedione piperazine derivatives as FabH inhibitors. Bioorg Chem 2019; 88:102958. [PMID: 31054434 DOI: 10.1016/j.bioorg.2019.102958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/17/2019] [Accepted: 04/28/2019] [Indexed: 10/26/2022]
Abstract
A series of novel 1,4-benzodioxane thiazolidinedione piperazine derivatives targeting FabH were designed and synthesized. The compounds exhibited better inhibitory activity against Gram-negative bacteria by computer-assisted screening, antibacterial activity test and E. coli FabH inhibitory activity test, wherein compound 6j exhibited the most significant inhibitory activity (MIC = 1.80 μΜ for P. aeruginosa, MIC = 1.56 μΜ for E. coli). Besides, compound 6j still showed the best E. coli FabH inhibitory activity (IC50 = 0.06 μΜ). Moreover, the antibacterial activities of all compounds were strongly correlated with the inhibitory ability of FabH, with a correlation coefficient of 0.954. Computational docking studies also showed that compound 6j has interacting with FabH key residues in the active site.
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Affiliation(s)
- Juan Sun
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou 310023, People's Republic of China
| | - Wen He
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou 310023, People's Republic of China
| | - Han-Yu Liu
- School of Life Science, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Jie Qin
- School of Life Science, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Chun-Lin Ye
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou 310023, People's Republic of China.
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. MEDCHEMCOMM 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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12
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Suchand B, Satyanarayana G. Palladium-Catalyzed Acylation Reactions: A One-Pot Diversified Synthesis of Phthalazines, Phthalazinones and Benzoxazinones. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800159] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Basuli Suchand
- Indian Institute of Technology (IIT) Hyderabad; 502 285, Sangareddy District Kandi - Telangana India
| | - Gedu Satyanarayana
- Indian Institute of Technology (IIT) Hyderabad; 502 285, Sangareddy District Kandi - Telangana India
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13
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Ekström AG, Kelly V, Marles-Wright J, Cockroft SL, Campopiano DJ. Structural evidence for the covalent modification of FabH by 4,5-dichloro-1,2-dithiol-3-one (HR45). Org Biomol Chem 2018; 15:6310-6313. [PMID: 28715001 PMCID: PMC5708339 DOI: 10.1039/c7ob01396e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We use mass spectrometry analysis and molecular modelling to show the established antimicrobial inhibitor 4,5-dichloro-1,2-dithiol-3-one (HR45) acts by forming a covalent adduct with the target β-ketoacyl-ACP synthase III (FabH). The 5-chloro substituent directs attack of the essential active site thiol (C112) via a Michael-type addition elimination reaction mechanism.
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Affiliation(s)
- Alexander G Ekström
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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14
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Ekström AG, Wang JT, Bella J, Campopiano DJ. Non-invasive 19F NMR analysis of a protein-templated N-acylhydrazone dynamic combinatorial library. Org Biomol Chem 2018; 16:8144-8149. [DOI: 10.1039/c8ob01918e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful tool to identify ligands for biological targets.
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Affiliation(s)
| | | | - Juraj Bella
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh
- UK
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15
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Qiu L, Tian K, Pan J, Jiang L, Yang H, Zhu X, Shen B, Duan Y, Huang Y. A Facile Semi-Synthetic Approach towards Halogen-Substituted Aminobenzoic Acid Analogues of Platensimycin. Tetrahedron 2017; 73:771-775. [PMID: 28626267 PMCID: PMC5471356 DOI: 10.1016/j.tet.2016.12.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Platensimycin (PTM), produced by several strains of Streptomyces platensis, is a promising drug lead for infectious diseases and diabetes. The recent pilot-scale production of PTM from S. platensis SB12026 has set the stage for the facile semi-synthesis of a focused library of PTM analogues. In this study, gram-quantity of platensic acid (PTMA) was prepared by the sulfuric acid-catalyzed ethanolysis of PTM, followed by a mild hydrolysis in aqueous lithium hydroxide. Three PTMA esters were also obtained in near quantitative yields in a single step, suggesting a facile route to make PTMA aliphatic esters. 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (HATU)-catalyzed coupling of PTMA and 33 aminobenzoates resulted in the synthesis of 28 substituted aminobenzoate analogues of PTM, among which 26 of them were reported for the first time. Several of the PTM analogues showed weak antibacterial activity against methicillin-resistant Staphylococcus aureus. Our study supported the potential utility to integrate natural product biosynthetic and semi-synthetic approaches for structure diversification.
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Affiliation(s)
- Lin Qiu
- Xiangya International Academy of Translational Medicine, Central South University, Tongzipo Road, #172, Yuelu District, Changsha, Hunan 410013, China
| | - Kai Tian
- Xiangya International Academy of Translational Medicine, Central South University, Tongzipo Road, #172, Yuelu District, Changsha, Hunan 410013, China
| | - Jian Pan
- Xiangya International Academy of Translational Medicine, Central South University, Tongzipo Road, #172, Yuelu District, Changsha, Hunan 410013, China
| | - Lin Jiang
- Xiangya International Academy of Translational Medicine, Central South University, Tongzipo Road, #172, Yuelu District, Changsha, Hunan 410013, China
| | - Hu Yang
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410013, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Tongzipo Road, #172, Yuelu District, Changsha, Hunan 410013, China
- Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410013, China
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
- Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Tongzipo Road, #172, Yuelu District, Changsha, Hunan 410013, China
- Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410013, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410013, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Tongzipo Road, #172, Yuelu District, Changsha, Hunan 410013, China
- Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410013, China
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16
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Docking and molecular dynamics studies on triclosan derivatives binding to FabI. J Mol Model 2017; 23:25. [DOI: 10.1007/s00894-016-3192-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
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17
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Zhou Y, Yang YS, Song XD, Lu L, Zhu HL. Study of Schiff-Base-Derived with Dioxygenated Rings and Nitrogen Heterocycle as Potential β-Ketoacyl-acyl Carrier Protein Synthase III (FabH) Inhibitors. Chem Pharm Bull (Tokyo) 2017; 65:178-185. [DOI: 10.1248/cpb.c16-00772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Xiao-Da Song
- School of Life Science and Technology, China Pharmaceutical University
| | - Liang Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
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18
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Kamal AAM, Maurer CK, Allegretta G, Haupenthal J, Empting M, Hartmann RW. Quorum Sensing Inhibitors as Pathoblockers for Pseudomonas aeruginosa Infections: A New Concept in Anti-Infective Drug Discovery. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2017_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Alam MS, Jebin S, Rahman MM, Bari ML, Lee DU. Biological and quantitative-SAR evaluations, and docking studies of (E)-N -benzylidenebenzohydrazide analogues as potential antibacterial agents. EXCLI JOURNAL 2016; 15:350-61. [PMID: 27540348 PMCID: PMC4983803 DOI: 10.17179/excli2016-388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/09/2016] [Indexed: 11/10/2022]
Abstract
A series of 15 (E)-N'-benzylidenebenzohydrazide analogues were evaluated for their antimicrobial activities against eleven pathogenic and food-borne microbes, namely, S. aureus (G(+)), L. monocytogenes (G(+)), B. subtilis (G(+)), K. pneumonia (G¯), C. sakazakii (G¯), C. freundii (G¯), S. enterica (G¯), S. enteritidis (G¯), E. coli (G¯), Y. pestis (G¯), and P. aeruginosa (G¯). Most of the compounds exhibited selective activity against some Gram-negative bacterial strains. Of the compounds tested (3a-o), 3b and 3g were most active against C. freundii (MIC = ~19 µg mL(-1)). Whereas, compounds 3d, 3i, 3k and 3n exhibited MIC values ranging from 37.5 to 75 μg mL(-1) against C. freundii, and compounds 3e, 3l and 3n had MIC values of ~75 μg mL(-1) against K. pneumonia. Quantitative structure-antibacterial activity relationships were studied using physicochemical parameters and a good correlation was found between calculated octanol-water partition coefficients (clogP; a lipophilic parameter) and antibacterial activities. In silico screening was also performed by docking high (3b and 3g) and low (3n) activity compounds on the active site of E. coli FabH receptor, which is an important therapeutic target. The findings of these in silico screening studies provide a theoretical basis for the design and synthesis of novel benzylidenebenzohydrazide analogues that inhibit bacterial FabH.
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Affiliation(s)
- Mohammad Sayed Alam
- Division of Bioscience, Dongguk University, Gyeongju 780-714, Republic of Korea; Department of Chemistry, Jagannath University, Dhaka 1100, Bangladesh
| | - Sefat Jebin
- Department of Chemistry, Jagannath University, Dhaka 1100, Bangladesh
| | | | - Md Latiful Bari
- Food analysis and Research laboratory, Centre for Advance Research in Sciences, University of Dhaka, Dhaka-1000, Bangladesh
| | - Dong-Ung Lee
- Division of Bioscience, Dongguk University, Gyeongju 780-714, Republic of Korea
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20
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Segretti ND, Serafim RA, Segretti MC, Miyata M, Coelho FR, Augusto O, Ferreira EI. New antibacterial agents: Hybrid bioisoster derivatives as potential E. coli FabH inhibitors. Bioorg Med Chem Lett 2016; 26:3988-93. [DOI: 10.1016/j.bmcl.2016.06.089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 11/30/2022]
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21
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McKinney DC, Eyermann CJ, Gu RF, Hu J, Kazmirski SL, Lahiri SD, McKenzie AR, Shapiro AB, Breault G. Antibacterial FabH Inhibitors with Mode of Action Validated in Haemophilus influenzae by in Vitro Resistance Mutation Mapping. ACS Infect Dis 2016; 2:456-64. [PMID: 27626097 DOI: 10.1021/acsinfecdis.6b00053] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fatty acid biosynthesis is essential to bacterial growth in Gram-negative pathogens. Several small molecules identified through a combination of high-throughput and fragment screening were cocrystallized with FabH (β-ketoacyl-acyl carrier protein synthase III) from Escherichia coli and Streptococcus pneumoniae. Structure-based drug design was used to merge several scaffolds to provide a new class of inhibitors. After optimization for Gram-negative enzyme inhibitory potency, several compounds demonstrated antimicrobial activity against an efflux-negative strain of Haemophilus influenzae. Mutants resistant to these compounds had mutations in the FabH gene near the catalytic triad, validating FabH as a target for antimicrobial drug discovery.
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Affiliation(s)
- David C. McKinney
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Charles J. Eyermann
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Rong-Fang Gu
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jun Hu
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Steven L. Kazmirski
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sushmita D. Lahiri
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Andrew R. McKenzie
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Adam B. Shapiro
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Gloria Breault
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
- Structure and Biophysics and #Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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22
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Zhou Y, Luo Y, Yang YS, Lu L, Zhu HL. Study of acylhydrazone derivatives with deoxygenated seven-membered rings as potential β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00263c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fatty acid biosynthesis is essential for bacterial survival.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Yin Luo
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Liang Lu
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing 210023
- People's Republic of China
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Composing compound libraries for hit discovery--rationality-driven preselection or random choice by structural diversity? Future Med Chem 2015; 6:2057-72. [PMID: 25531968 DOI: 10.4155/fmc.14.142] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
AIMS In order to identify new scaffolds for drug discovery, surface plasmon resonance is frequently used to screen structurally diverse libraries. Usually, hit rates are low and identification processes are time consuming. Hence, approaches which improve hit rates and, thus, reduce the library size are required. METHODS In this work, we studied three often used strategies for their applicability to identify inhibitors of PqsD. In two of them, target-specific aspects like inhibition of a homologous protein or predicted binding determined by virtual screening were used for compound preselection. Finally, a fragment library, covering a large chemical space, was screened and served as comparison. RESULTS & CONCLUSION Indeed, higher hit rates were observed for methods employing preselected libraries indicating that target-oriented compound selection provides a time-effective alternative.
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Discovery of bacterial fatty acid synthase type II inhibitors using a novel cellular bioluminescent reporter assay. Antimicrob Agents Chemother 2015; 59:5775-87. [PMID: 26169404 DOI: 10.1128/aac.00686-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/06/2015] [Indexed: 12/11/2022] Open
Abstract
Novel, cellular, gain-of-signal, bioluminescent reporter assays for fatty acid synthesis type II (FASII) inhibitors were constructed in an efflux-deficient strain of Pseudomonas aeruginosa and based on the discovery that FASII genes in P. aeruginosa are coordinately upregulated in response to pathway disruption. A screen of 115,000 compounds identified a series of sulfonamidobenzamide (SABA) analogs, which generated strong luminescent signals in two FASII reporter strains but not in four control reporter strains designed to respond to inhibitors of pathways other than FASII. The SABA analogs selectively inhibited lipid biosynthesis in P. aeruginosa and exhibited minimal cytotoxicity to mammalian cells (50% cytotoxic concentration [CC50] ≥ 80 μM). The most potent SABA analogs had MICs of 0.5 to 7.0 μM (0.2 to 3.0 μg/ml) against an efflux-deficient Escherichia coli (ΔtolC) strain but had no detectable MIC against efflux-proficient E. coli or against P. aeruginosa (efflux deficient or proficient). Genetic, molecular genetic, and biochemical studies revealed that SABA analogs target the enzyme (AccC) catalyzing the biotin carboxylase half-reaction of the acetyl coenzyme A (acetyl-CoA) carboxylase step in the initiation phase of FASII in E. coli and P. aeruginosa. These results validate the capability and the sensitivity of this novel bioluminescent reporter screen to identify inhibitors of E. coli and P. aeruginosa FASII.
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25
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Shamim A, Abbasi SW, Azam SS. Structural and dynamical aspects of Streptococcus gordonii FabH through molecular docking and MD simulations. J Mol Graph Model 2015; 60:180-96. [PMID: 26059477 DOI: 10.1016/j.jmgm.2015.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 01/01/2023]
Abstract
β-Ketoacyl-ACP-synthase III (FabH or KAS III) has become an attractive target for the development of new antibacterial agents which can overcome the multidrug resistance. Unraveling the fatty acid biosynthesis (FAB) metabolic pathway and understanding structural coordinates of FabH will provide valuable insights to target Streptococcus gordonii for curing oral infection. In this study, we designed inhibitors against therapeutic target FabH, in order to block the FAB pathway. As compared to other targets, FabH has more interactions with other proteins, located on the leading strand with higher codon adaptation index value and associated with lipid metabolism category of COG. Current study aims to gain in silico insights into the structural and dynamical aspect of S. gordonii FabH via molecular docking and molecular dynamics (MD) simulations. The FabH protein is catalytically active in dimerization while it can lock in monomeric state. Current study highlights two residues Pro88 and Leu315 that are close to each other by dimerization. The active site of FabH is composed of the catalytic triad formed by residues Cys112, His249, and Asn279 in which Cys112 is involved in acetyl transfer, while His249 and Asn279 play an active role in decarboxylation. Docking analysis revealed that among the studied compounds, methyl-CoA disulfide has highest GOLD score (82.75), binding affinity (-11 kcal/mol) and exhibited consistently better interactions. During MD simulations, the FabH structure remained stable with the average RMSD value of 1.7 Å and 1.6 Å for undocked protein and docked complex, respectively. Further, crucial hydrogen bonding of the conserved catalytic triad for exhibiting high affinity between the FabH protein and ligand is observed by RDF analysis. The MD simulation results clearly demonstrated that binding of the inhibitor with S. gordonii FabH enhanced the structure and stabilized the dimeric FabH protein. Therefore, the inhibitor has the potential to become a lead compound.
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Affiliation(s)
- Amen Shamim
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sumra Wajid Abbasi
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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26
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Mittal A, Johnson ME. Conformational diversity of bacterial FabH: implications for molecular recognition specificity. J Mol Graph Model 2014; 55:115-22. [PMID: 25437098 DOI: 10.1016/j.jmgm.2014.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 09/22/2014] [Accepted: 11/07/2014] [Indexed: 11/25/2022]
Abstract
The molecular basis of variable substrate and inhibitor specificity of the highly conserved bacterial fatty acid synthase enzyme, FabH, across different bacterial species remains poorly understood. In the current work, we explored the conformational diversity of FabH enzymes to understand the determinants of diverse interaction specificity across Gram-positive and Gram-negative bacteria. Atomistic molecular dynamics simulations reveal that FabH from E. coli and E. faecalis exhibit distinct native state conformational ensembles and dynamic behaviors. Despite strikingly similar substrate binding pockets, hot spot assessment using computational solvent mapping identified quite different favorable binding interactions between the two homologs. Our data suggest that FabH utilizes protein dynamics and seemingly minor sequence and structural differences to modulate its molecular recognition and substrate specificity across bacterial species. These insights will potentially facilitate the rational design and development of antibacterial inhibitors against FabH enzymes.
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Affiliation(s)
- Anuradha Mittal
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave-m/c 870, Chicago, IL 60607-7173, USA
| | - Michael E Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave-m/c 870, Chicago, IL 60607-7173, USA.
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27
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Qin YJ, Wang PF, Makawana JA, Wang ZC, Wang ZN, Yan-Gu, Jiang AQ, Zhu HL. Design, synthesis and biological evaluation of metronidazole-thiazole derivatives as antibacterial inhibitors. Bioorg Med Chem Lett 2014; 24:S0960-894X(14)01007-5. [PMID: 25318998 DOI: 10.1016/j.bmcl.2014.09.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 09/11/2014] [Accepted: 09/18/2014] [Indexed: 10/24/2022]
Abstract
A series of metronidazole-thiazole derivatives has been designed, synthesized and evaluated as potential antibacterial inhibitors. All the synthesized compounds were determined by elemental analysis, 1H NMR and MS. They were also tested for antibacterial activity against Escherichia coli, Bacillus thuringiensis, Bacillus subtilis and Pseudomonas aeruginosa as well as for the inhibition to FabH. The results showed that compound 5e exhibited the most potent inhibitory activity against E. coli FabH with IC50 of 4.9μM. Molecular modeling simulation studies were performed in order to predict the biological activity of proposed compounds. Toxicity assay of compounds 5a, 5b, 5d, 5e, 5g and 5i showed that they were noncytotoxic against human macrophage. The results revealed that these compounds offered remarkable viability.
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Affiliation(s)
- Ya-Juan Qin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Peng-Fei Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Jigar A Makawana
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Zhong-Chang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Ze-Nan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Yan-Gu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China
| | - Ai-Qin Jiang
- School of Medicine, Nanjing University, Nanjing 210093, People's Republic of China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science Nanjing University, Nanjing 210093, People's Republic of China.
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28
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Shinohara H, Sonoda M, Hayagane N, Kita S, Tanimori S, Ogawa A. Silica gel-promoted convenient synthesis of 2-bromo-3-hydroxybenzoate derivatives. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.07.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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29
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Toward the computer-aided discovery of FabH inhibitors. Do predictive QSAR models ensure high quality virtual screening performance? Mol Divers 2014; 18:637-54. [PMID: 24671521 DOI: 10.1007/s11030-014-9513-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
Abstract
Antibiotic resistance has increased over the past two decades. New approaches for the discovery of novel antibacterials are required and innovative strategies will be necessary to identify novel and effective candidates. Related to this problem, the exploration of bacterial targets that remain unexploited by the current antibiotics in clinical use is required. One of such targets is the β-ketoacyl-acyl carrier protein synthase III (FabH). Here, we report a ligand-based modeling methodology for the virtual-screening of large collections of chemical compounds in the search of potential FabH inhibitors. QSAR models are developed for a diverse dataset of 296 FabH inhibitors using an in-house modeling framework. All models showed high fitting, robustness, and generalization capabilities. We further investigated the performance of the developed models in a virtual screening scenario. To carry out this investigation, we implemented a desirability-based algorithm for decoys selection that was shown effective in the selection of high quality decoys sets. Once the QSAR models were validated in the context of a virtual screening experiment their limitations arise. For this reason, we explored the potential of ensemble modeling to overcome the limitations associated to the use of single classifiers. Through a detailed evaluation of the virtual screening performance of ensemble models it was evidenced, for the first time to our knowledge, the benefits of this approach in a virtual screening scenario. From all the obtained results, we could arrive to a significant main conclusion: at least for FabH inhibitors, virtual screening performance is not guaranteed by predictive QSAR models.
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30
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Li JR, Li DD, Wang RR, Sun J, Dong JJ, Du QR, Fang F, Zhang WM, Zhu HL. Design and synthesis of thiazole derivatives as potent FabH inhibitors with antibacterial activity. Eur J Med Chem 2014; 75:438-47. [DOI: 10.1016/j.ejmech.2013.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 11/02/2013] [Accepted: 11/14/2013] [Indexed: 10/25/2022]
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Khanfar MA, Quinti L, Wang H, Choi SH, Kazantsev AG, Silverman RB. Development and characterization of 3-(benzylsulfonamido)benzamides as potent and selective SIRT2 inhibitors. Eur J Med Chem 2014; 76:414-26. [PMID: 24602787 DOI: 10.1016/j.ejmech.2014.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/23/2014] [Accepted: 02/05/2014] [Indexed: 10/25/2022]
Abstract
Inhibitors of sirtuin-2 deacetylase (SIRT2) have been shown to be protective in various models of Huntington's disease (HD) by decreasing polyglutamine aggregation, a hallmark of HD pathology. The present study was directed at optimizing the potency of SIRT2 inhibitors containing the neuroprotective sulfobenzoic acid scaffold and improving their pharmacology. To achieve that goal, 176 analogues were designed, synthesized, and tested in deacetylation assays against the activities of major human sirtuins SIRT1-3. This screen yielded 15 compounds with enhanced potency for SIRT2 inhibition and 11 compounds having SIRT2 inhibition equal to reference compound AK-1. The newly synthesized compounds also demonstrated higher SIRT2 selectivity over SIRT1 and SIRT3. These candidates were subjected to a dose-response bioactivity assay, measuring an increase in α-tubulin K40 acetylation in two neuronal cell lines, which yielded five compounds bioactive in both cell lines and eight compounds bioactive in at least one of the cell lines tested. These bioactive compounds were subsequently tested in a tertiary polyglutamine aggregation assay, which identified five inhibitors. ADME properties of the bioactive SIRT2 inhibitors were assessed, which revealed a significant improvement of the pharmacological properties of the new entities, reaching closer to the goal of a clinically-viable candidate.
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Affiliation(s)
- Mohammad A Khanfar
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA; Department of Pharmaceutical Sciences, The University of Jordan, Amman, Jordan
| | - Luisa Quinti
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA 02129-4404, USA
| | - Hua Wang
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Soo Hyuk Choi
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Aleksey G Kazantsev
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA 02129-4404, USA.
| | - Richard B Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA.
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Panjkovich A, Gibert I, Daura X. antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation. BMC Genomics 2014; 15:36. [PMID: 24438389 PMCID: PMC3932961 DOI: 10.1186/1471-2164-15-36] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/11/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Development of novel antibacterial drugs is both an urgent healthcare necessity and a partially neglected field. The last decades have seen a substantial decrease in the discovery of novel antibiotics, which combined with the recent thrive of multi-drug-resistant pathogens have generated a scenario of general concern. The procedures involved in the discovery and development of novel antibiotics are economically challenging, time consuming and lack any warranty of success. Furthermore, the return-on-investment for an antibacterial drug is usually marginal when compared to other therapeutics, which in part explains the decrease of private investment. RESULTS In this work we present antibacTR, a computational pipeline designed to aid researchers in the selection of potential drug targets, one of the initial steps in antibacterial-drug discovery. The approach was designed and implemented as part of two publicly funded initiatives aimed at discovering novel antibacterial targets, mechanisms and drugs for a priority list of Gram-negative pathogens: Acinetobacter baumannii, Escherichia coli, Helicobacter pylori, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. However, at present this list has been extended to cover a total of 74 fully sequenced Gram-negative pathogens. antibacTR is based on sequence comparisons and queries to multiple databases (e.g. gene essentiality, virulence factors) to rank proteins according to their potential as antibacterial targets. The dynamic ranking of potential drug targets can easily be executed, customized and accessed by the user through a web interface which also integrates computational analyses performed in-house and visualizable on-site. These include three-dimensional modeling of protein structures and prediction of active sites among other functionally relevant ligand-binding sites. CONCLUSIONS Given its versatility and ease-of-use at integrating both experimental annotation and computational analyses, antibacTR may effectively assist microbiologists, medicinal-chemists and other researchers working in the field of antibacterial drug-discovery. The public web-interface for antibacTR is available at 'http://bioinf.uab.cat/antibactr'.
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Affiliation(s)
| | | | - Xavier Daura
- Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
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33
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Song X, Yang Y, Zhao J, Chen Y. Synthesis and Antibacterial Activity of Cinnamaldehyde Acylhydrazone with a 1,4-Benzodioxan Fragment as a Novel Class of Potent β-Ketoacyl–Acyl Carrier Protein Synthase III (FabH) Inhibitor. Chem Pharm Bull (Tokyo) 2014; 62:1110-8. [DOI: 10.1248/cpb.c14-00485] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Xiaoda Song
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
- School of Life Science and Technology, China Pharmaceutical University
| | - Yushun Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Jing Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Yangjian Chen
- School of Life Science and Technology, China Pharmaceutical University
- School of Biology and Pharmaceutics, Zhejiang Pharmaceutical College
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34
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Hinsberger S, Hüsecken K, Groh M, Negri M, Haupenthal J, Hartmann RW. Discovery of Novel Bacterial RNA Polymerase Inhibitors: Pharmacophore-Based Virtual Screening and Hit Optimization. J Med Chem 2013; 56:8332-8. [DOI: 10.1021/jm400485e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan Hinsberger
- Helmholtz-Institute for Pharmaceutical
Research Saarland, Department
of Drug Design and Optimization, and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
| | - Kristina Hüsecken
- Helmholtz-Institute for Pharmaceutical
Research Saarland, Department
of Drug Design and Optimization, and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
| | - Matthias Groh
- Helmholtz-Institute for Pharmaceutical
Research Saarland, Department
of Drug Design and Optimization, and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
| | - Matthias Negri
- Helmholtz-Institute for Pharmaceutical
Research Saarland, Department
of Drug Design and Optimization, and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Helmholtz-Institute for Pharmaceutical
Research Saarland, Department
of Drug Design and Optimization, and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz-Institute for Pharmaceutical
Research Saarland, Department
of Drug Design and Optimization, and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
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35
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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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36
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Weidel E, de Jong JC, Brengel C, Storz MP, Braunshausen A, Negri M, Plaza A, Steinbach A, Müller R, Hartmann RW. Structure optimization of 2-benzamidobenzoic acids as PqsD inhibitors for Pseudomonas aeruginosa infections and elucidation of binding mode by SPR, STD NMR, and molecular docking. J Med Chem 2013; 56:6146-55. [PMID: 23834469 DOI: 10.1021/jm4006302] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pseudomonas aeruginosa employs a characteristic pqs quorum sensing (QS) system that functions via the signal molecules PQS and its precursor HHQ. They control the production of a number of virulence factors and biofilm formation. Recently, we have shown that sulfonamide substituted 2-benzamidobenzoic acids, which are known FabH inhibitors, are also able to inhibit PqsD, the enzyme catalyzing the last and key step in the biosynthesis of HHQ. Here, we describe the further optimization and characterization of this class of compounds as PqsD inhibitors. Structural modifications showed that both the carboxylic acid ortho to the amide and 3'-sulfonamide are essential for binding. Introduction of substituents in the anthranilic part of the molecule resulted in compounds with IC50 values in the low micromolar range. Binding mode investigations by SPR with wild-type and mutated PqsD revealed that this compound class does not bind into the active center of PqsD but in the ACoA channel, preventing the substrate from accessing the active site. This binding mode was further confirmed by docking studies and STD NMR.
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Affiliation(s)
- Elisabeth Weidel
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Department of Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
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37
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Holler TP, Evdokimov AG, Narasimhan L. Structural biology approaches to antibacterial drug discovery. Expert Opin Drug Discov 2013; 2:1085-101. [PMID: 23484874 DOI: 10.1517/17460441.2.8.1085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antibacterial drug discovery has undertaken a major experiment in the 12 years since the first bacterial genomes were sequenced. Genome mining has identified hundreds of potential targets that have been distilled to a relatively small number of broad-spectrum targets ('low-hanging fruit') using the genetics tools of modern microbiology. Prosecuting these targets with high-throughput screens has led to a disappointingly small number of lead series that have mostly evaporated under closer scrutiny. In the meantime, multi-drug resistant pathogens are becoming a serious challenge in the clinic and the community and the number of pharmaceutical firms pursuing antibacterial discovery has declined. Filling the antibacterial development pipeline with novel chemical series is a significant challenge that will require the collaboration of scientists from many disciplines. Fortunately, advancements in the tools of structural biology and of in silico modeling are opening up new avenues of research that may help deal with the problems associated with discovering novel antibiotics.
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Affiliation(s)
- Tod P Holler
- Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA +1 734 622 5954 ; +1 734 622 2963 ; Tod.Holler@pfizer. com
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38
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Potentiating 1-(2-hydroxypropyl)-2-styryl-5-nitroimidazole derivatives against antibacterial agents: Design, synthesis and biology analysis. Eur J Med Chem 2013; 65:456-63. [DOI: 10.1016/j.ejmech.2013.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/03/2013] [Accepted: 05/05/2013] [Indexed: 11/24/2022]
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39
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Cheng K, Xue JY, Zhu HL. Design, synthesis and antibacterial activity studies of thiazole derivatives as potent ecKAS III inhibitors. Bioorg Med Chem Lett 2013; 23:4235-8. [PMID: 23731945 DOI: 10.1016/j.bmcl.2013.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/27/2013] [Accepted: 05/02/2013] [Indexed: 10/26/2022]
Abstract
Two series of thiazole derivatives containing amide skeleton were synthesized and developed as potent Escherichia coli β-ketoacyl-(acyl-carrier-protein) synthase III (ecKAS III) inhibitors. All the 24 new synthesized compounds were assayed for antibacterial activity against the respective Gram-negative and Gram-positive bacterial strains, including E. coli, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus. In which, 10 compounds with broad-spectrum antibacterial activities were further tested for their ecKAS III inhibitory activity. Last, we have successfully found that compound 4e showed both the promising broad antibacterial activity with MIC of 1.56-6.25μg/mL against the representative bacterial stains, and also processed the most potent ecKAS III inhibitory activity with IC50 of 5.3μM. In addition, docking simulation also carried out in this study to give a potent prediction binding mode between the small molecule and ecKAS III (PDB code: 1hnj) protein.
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Affiliation(s)
- Kui Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
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40
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Zhou Y, Du QR, Sun J, Li JR, Fang F, Li DD, Qian Y, Gong HB, Zhao J, Zhu HL. Novel Schiff-base-derived FabH inhibitors with dioxygenated rings as antibiotic agents. ChemMedChem 2013; 8:433-41. [PMID: 23401291 DOI: 10.1002/cmdc.201200587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Indexed: 11/10/2022]
Abstract
Fatty acid biosynthesis plays a vital role in bacterial survival and several key enzymes involved in this biosynthetic pathway have been identified as attractive targets for the development of new antibacterial agents. Of these promising targets, β-ketoacyl-acyl carrier protein (ACP) synthase III (FabH) is the most attractive target that could trigger the initiation of fatty acid biosynthesis and is highly conserved among Gram-positive and -negative bacteria. Designing small molecules with FabH inhibitory activity displays great significance for developing antibiotic agents, which should be highly selective, nontoxic and broad-spectrum. In this manuscript, a series of novel Schiff base compounds were designed and synthesized, and their biological activities were evaluated as potential inhibitors. Among these 21 new compounds, (E)-N-((3,4-dihydro-2H-benzo[b][1,4]dioxepin-7-yl)methylene)hexadecan-1-amine (10) showed the most potent antibacterial activity with a MIC value of 3.89-7.81 μM(-1) against the tested bacterial strains and exhibited the most potent E. coli FabH inhibitory activity with an IC(50) value of 1.6 μM. Docking simulation was performed to position compound 10 into the E. coli FabH active site to determine the probable binding conformation.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Hankou Road, Nanjing 210093, PR China
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41
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Wang XL, Zhang YB, Tang JF, Yang YS, Chen RQ, Zhang F, Zhu HL. Design, synthesis and antibacterial activities of vanillic acylhydrazone derivatives as potential β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. Eur J Med Chem 2012; 57:373-82. [DOI: 10.1016/j.ejmech.2012.09.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/24/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
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42
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Inhibitors of fatty acid synthesis in prokaryotes and eukaryotes as anti-infective, anticancer and anti-obesity drugs. Future Med Chem 2012; 4:1113-51. [PMID: 22709254 DOI: 10.4155/fmc.12.62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is a large range of diseases, such diabetes and cancer, which are connected to abnormal fatty acid metabolism in human cells. Therefore, inhibitors of human fatty acid synthase have great potential to manage or treat these diseases. In prokaryotes, fatty acid synthesis is important for signaling, as well as providing starting materials for the synthesis of phospholipids, which are required for the formation of the cell membrane. Recently, there has been renewed interest in the development of new molecules that target bacterial fatty acid synthases for the treatment of bacterial diseases. In this review, we look at the differences and similarities between fatty acid synthesis in humans and bacteria and highlight various small molecules that have been shown to inhibit either the mammalian or bacterial fatty acid synthase or both.
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Luo Y, Yang YS, Fu J, Zhu HL. Novel FabH inhibitors: a patent and article literature review (2000--2012). Expert Opin Ther Pat 2012; 22:1325-36. [PMID: 22998551 DOI: 10.1517/13543776.2012.727798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The traditional antimicrobial chemotherapy drugs play their effects mostly via bacterial interference with in vivo amino acids, nucleotides, amino sugars and other small molecule synthesis, or interfering the biochemical processes of these small molecules to synthesize nucleic acids, peptidoglycan and other biological macromolecules. In recent years, enzymes with single function in bacterial fatty acid synthetase system have become the genome-driven novel antibacterial drug targets. Among inhibitors of these targets, FabH inhibitors are distinguished, for their target is different from that of existing antibiotics. Therefore, discovery of FabH inhibitors might be a potential orientation to overcome bacterial resistance. AREAS COVERED This review summarized new patents and articles published on FabH inhibitors from 2000 to 2012. EXPERT OPINION The review gives a brief understanding about the background and development in the area of FabH inhibitors that aims to solve the bacterial resistance problem. This review puts emphasis on some typical small molecules, which participate in the process of FabH inhibition. Overall, the research scopes of antibacterial agents are getting broad. Fatty acid synthase (FAS) pathway has been proved to be a promising target for the therapy. However, claim of novel antibacterial agents with more active and higher specificity is still continued.
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Affiliation(s)
- Yin Luo
- Nanjing University, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing 210093, People's Republic of China
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Luo Y, Zhang LR, Hu Y, Zhang S, Fu J, Wang XM, Zhu HL. Synthesis and Antimicrobial Activities of Oximes Derived from O-Benzylhydroxylamine as FabH Inhibitors. ChemMedChem 2012; 7:1587-93. [DOI: 10.1002/cmdc.201200225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/12/2012] [Indexed: 11/07/2022]
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45
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Yang YS, Zhang F, Gao C, Zhang YB, Wang XL, Tang JF, Sun J, Gong HB, Zhu HL. Discovery and modification of sulfur-containing heterocyclic pyrazoline derivatives as potential novel class of β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. Bioorg Med Chem Lett 2012; 22:4619-24. [DOI: 10.1016/j.bmcl.2012.05.091] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/14/2012] [Accepted: 05/28/2012] [Indexed: 01/18/2023]
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Fatty acid biosynthesis in Pseudomonas aeruginosa is initiated by the FabY class of β-ketoacyl acyl carrier protein synthases. J Bacteriol 2012; 194:5171-84. [PMID: 22753059 DOI: 10.1128/jb.00792-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The prototypical type II fatty acid synthesis (FAS) pathway in bacteria utilizes two distinct classes of β-ketoacyl synthase (KAS) domains to assemble long-chain fatty acids, the KASIII domain for initiation and the KASI/II domain for elongation. The central role of FAS in bacterial viability and virulence has stimulated significant effort toward developing KAS inhibitors, particularly against the KASIII domain of the β-acetoacetyl-acyl carrier protein (ACP) synthase FabH. Herein, we show that the opportunistic pathogen Pseudomonas aeruginosa does not utilize a FabH ortholog but rather a new class of divergent KAS I/II enzymes to initiate the FAS pathway. When a P. aeruginosa cosmid library was used to rescue growth in a fabH downregulated strain of Escherichia coli, a single unannotated open reading frame, PA5174, complemented fabH depletion. While deletion of all four KASIII domain-encoding genes in the same P. aeruginosa strain resulted in a wild-type growth phenotype, deletion of PA5174 alone specifically attenuated growth due to a defect in de novo FAS. Siderophore secretion and quorum-sensing signaling, particularly in the rhl and Pseudomonas quinolone signal (PQS) systems, was significantly muted in the absence of PA5174. The defect could be repaired by intergeneric complementation with E. coli fabH. Characterization of recombinant PA5174 confirmed a preference for short-chain acyl coenzyme A (acyl-CoA) substrates, supporting the identification of PA5174 as the predominant enzyme catalyzing the condensation of acetyl coenzyme A with malonyl-ACP in P. aeruginosa. The identification of the functional role for PA5174 in FAS defines the new FabY class of β-ketoacyl synthase KASI/II domain condensation enzymes.
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Hamilton JJ, Reed JL. Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. PLoS One 2012; 7:e34670. [PMID: 22666308 PMCID: PMC3359066 DOI: 10.1371/journal.pone.0034670] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 03/08/2012] [Indexed: 11/20/2022] Open
Abstract
Genome-scale network reconstructions are useful tools for understanding cellular metabolism, and comparisons of such reconstructions can provide insight into metabolic differences between organisms. Recent efforts toward comparing genome-scale models have focused primarily on aligning metabolic networks at the reaction level and then looking at differences and similarities in reaction and gene content. However, these reaction comparison approaches are time-consuming and do not identify the effect network differences have on the functional states of the network. We have developed a bilevel mixed-integer programming approach, CONGA, to identify functional differences between metabolic networks by comparing network reconstructions aligned at the gene level. We first identify orthologous genes across two reconstructions and then use CONGA to identify conditions under which differences in gene content give rise to differences in metabolic capabilities. By seeking genes whose deletion in one or both models disproportionately changes flux through a selected reaction (e.g., growth or by-product secretion) in one model over another, we are able to identify structural metabolic network differences enabling unique metabolic capabilities. Using CONGA, we explore functional differences between two metabolic reconstructions of Escherichia coli and identify a set of reactions responsible for chemical production differences between the two models. We also use this approach to aid in the development of a genome-scale model of Synechococcus sp. PCC 7002. Finally, we propose potential antimicrobial targets in Mycobacterium tuberculosis and Staphylococcus aureus based on differences in their metabolic capabilities. Through these examples, we demonstrate that a gene-centric approach to comparing metabolic networks allows for a rapid comparison of metabolic models at a functional level. Using CONGA, we can identify differences in reaction and gene content which give rise to different functional predictions. Because CONGA provides a general framework, it can be applied to find functional differences across models and biological systems beyond those presented here.
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Affiliation(s)
| | - Jennifer L. Reed
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America,
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Xu Z, Ma L, Chen H, Zhou R. In silico identification of potential drug targets in swine pathogen Haemophilus parasuis. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Discovery of novel selective inhibitors of Staphylococcus aureus β-ketoacyl acyl carrier protein synthase III. Eur J Med Chem 2011; 47:261-9. [PMID: 22104972 DOI: 10.1016/j.ejmech.2011.10.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/22/2011] [Accepted: 10/28/2011] [Indexed: 11/22/2022]
Abstract
β-Ketoacyl-acyl carrier protein synthase III (KAS III) is a condensing enzyme in bacterial fatty acid synthesis and a potential target while designing novel antibiotics. In our previous report, we discovered the lead compound YKAs3003, which serves as an inhibitor of Escherichia coli KAS III (ecKAS III), and determined a reliable pharmacophore map from in silico screening. In this study, we determined two pharmacophore maps from receptor-oriented pharmacophore-based in silico screening of the x-ray structure of Staphylococcus aureus KAS III (saKAS III) to identify potent saKAS III inhibitors. We discovered a new potential inhibitor (6) with broad-spectrum antimicrobial activity and 0.8 nM binding affinity for saKAS III, proving the reliability of our pharmacophore map. Using optimization procedures, we identified three new antimicrobial saKAS III inhibitors: 6c (2,4-dichloro-benzoic acid (2,3,4-trihydroxy-benzylidene)-hydrazide), 6e (4-[(3-chloro-pyrazin-2-yl)-hydrazonomethyl]-benzene-1,3-diol), and 6 (4-[(5-trifluoromethyl-pyridin-2-yl)-hydrazonomethyl]-benzene-1,3-diol). All three inhibitors have a novel 4-hydrazonomethyl-benzene-1,3-diol core structure. These inhibitors exhibited high binding affinity to saKAS III and highly selective antimicrobial activities against S. aureus and methicillin-resistant S. aureus, with minimal inhibitory concentration values of 1-2 μg/mL.
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Zhang HJ, Qin X, Liu K, Zhu DD, Wang XM, Zhu HL. Synthesis, antibacterial activities and molecular docking studies of Schiff bases derived from N-(2/4-benzaldehyde-amino) phenyl-N′-phenyl-thiourea. Bioorg Med Chem 2011; 19:5708-15. [DOI: 10.1016/j.bmc.2011.06.077] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/24/2011] [Accepted: 06/25/2011] [Indexed: 10/17/2022]
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