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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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Hans AC, Becker PM, Haußmann J, Suhr S, Wanner DM, Lederer V, Willig F, Frey W, Sarkar B, Kästner J, Peters R. A Practical and Robust Zwitterionic Cooperative Lewis Acid/Acetate/Benzimidazolium Catalyst for Direct 1,4-Additions. Angew Chem Int Ed Engl 2023; 62:e202217519. [PMID: 36651714 DOI: 10.1002/anie.202217519] [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: 11/28/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/19/2023]
Abstract
A catalyst type is disclosed allowing for exceptional efficiency in direct 1,4-additions. The catalyst is a zwitterionic entity, in which acetate binds to CuII , which is formally negatively charged and serving as counterion for benzimidazolium. All 3 functionalities are involved in the catalytic activation. For maleimides productivity was increased by a factor >300 compared to literature (TONs up to 6700). High stereoselectivity and productivity was attained for a broad range of other Michael acceptors as well. The polyfunctional catalyst is accessible in only 4 steps from N-Ph-benzimidazole with an overall yield of 96 % and robust during catalysis. This allowed to reuse the same catalyst multiple times with nearly constant efficiency. Mechanistic studies, in particular by DFT, give a detailed picture how the catalyst operates. The benzimidazolium unit stabilizes the coordinated enolate nucleophile and prevents that acetate/acetic acid dissociate from the catalyst.
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Affiliation(s)
- Andreas C Hans
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Patrick M Becker
- Universität Stuttgart, Institut für Theoretische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Johanna Haußmann
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Simon Suhr
- Universität Stuttgart, Institut für Anorganische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Daniel M Wanner
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Vera Lederer
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Felix Willig
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Wolfgang Frey
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Biprajit Sarkar
- Universität Stuttgart, Institut für Anorganische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Johannes Kästner
- Universität Stuttgart, Institut für Theoretische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - René Peters
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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Cifone MT, He Y, Basu R, Wang N, Davoodi S, Spagnuolo LA, Si Y, Daryaee T, Stivala CE, Walker SG, Tonge PJ. Heterobivalent Inhibitors of Acetyl-CoA Carboxylase: Drug Target Residence Time and Time-Dependent Antibacterial Activity. J Med Chem 2022; 65:16510-16525. [PMID: 36459397 PMCID: PMC10303036 DOI: 10.1021/acs.jmedchem.2c01380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The relationship between drug-target residence time and the post-antibiotic effect (PAE) provides insights into target vulnerability. To probe the vulnerability of bacterial acetyl-CoA carboxylase (ACC), a series of heterobivalent inhibitors were synthesized based on pyridopyrimidine 1 and moiramide B (3) which bind to the biotin carboxylase and carboxyltransferase ACC active sites, respectively. The heterobivalent compound 17, which has a linker of 50 Å, was a tight binding inhibitor of Escherichia coli ACC (Kiapp 0.2 nM) and could be displaced from ACC by a combination of both 1 and 3 but not just by 1. In agreement with the prolonged occupancy of ACC resulting from forced proximity binding, the heterobivalent inhibitors produced a PAE in E. coli of 1-4 h in contrast to 1 and 3 in combination or alone, indicating that ACC is a vulnerable target and highlighting the utility of kinetic, time-dependent effects in the drug mechanism of action.
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Affiliation(s)
- Matthew T Cifone
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - YongLe He
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Rajeswari Basu
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Nan Wang
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Shabnam Davoodi
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Lauren A Spagnuolo
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Yuanyuan Si
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Taraneh Daryaee
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Craig E Stivala
- Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Stephen G Walker
- Department of Oral Biology and Pathology, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Peter J Tonge
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Radiology, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
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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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Ali I, Khan A, Fa Z, Khan T, Wei DQ, Zheng J. Crystal structure of Acetyl-CoA carboxylase (AccB) from Streptomyces antibioticus and insights into the substrate-binding through in silico mutagenesis and biophysical investigations. Comput Biol Med 2022; 145:105439. [PMID: 35344865 DOI: 10.1016/j.compbiomed.2022.105439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/14/2022] [Accepted: 03/20/2022] [Indexed: 11/18/2022]
Abstract
Acetyl-CoA carboxylase (ACC) is crucial for polyketides biosynthesis and acts as an essential metabolic checkpoint. It is also an attractive drug target against obesity, cancer, microbial infections, and diabetes. However, the lack of knowledge, particularly sequence-structure function relationship to narrate ligand-enzyme binding, has hindered the progress of ACC-specific therapeutics and unnatural "natural" polyketides. Structural characterization of such enzymes will boost the opportunity to understand the substrate binding, designing new inhibitors and information regarding the molecular rules which control the substrate specificity of ACCs. To understand the substrate specificity, we determined the crystal structure of AccB (Carboxyl-transferase, CT) from Streptomyces antibioticus with a resolution of 2.3 Å and molecular modeling approaches were employed to unveil the molecular mechanism of acetyl-CoA recognition and processing. The CT domain of S. antibioticus shares a similar structural organization with the previous structures and the two steps reaction was confirmed by enzymatic assay. Furthermore, to reveal the key hotspots required for the substrate recognition and processing, in silico mutagenesis validated only three key residues (V223, Q346, and Q514) that help in the fixation of the substrate. Moreover, we also presented atomic level knowledge on the mechanism of the substrate binding, which unveiled the terminal loop (500-514) function as an opening and closing switch and pushes the substrate inside the cavity for stable binding. A significant decline in the hydrogen bonding half-life was observed upon the alanine substitution. Consequently, the presented structural data highlighted the potential key interacting residues for substrate recognition and will also help to re-design ACCs active site for proficient substrate specificity to produce diverse polyketides.
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Affiliation(s)
- Imtiaz Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Zhang Fa
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, PR China.
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Craft MK, Waldrop GL. Mechanism of biotin carboxylase inhibition by ethyl 4-[[2-chloro-5-(phenylcarbamoyl)phenyl]sulphonylamino]benzoate. J Enzyme Inhib Med Chem 2021; 37:100-108. [PMID: 34894987 PMCID: PMC8667948 DOI: 10.1080/14756366.2021.1994558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The rise of antibacterial-resistant bacteria is a major problem in the United States of America and around the world. Millions of patients are infected with antimicrobial resistant bacteria each year. Novel antibacterial agents are needed to combat the growing and present crisis. Acetyl-CoA carboxylase (ACC), the multi-subunit complex which catalyses the first committed step in fatty acid synthesis, is a validated target for antibacterial agents. However, there are at present, no commercially available antibiotics that target ACC. Ethyl 4-[[2-chloro-5-(phenylcarbamoyl)phenyl]sulfonylamino]benzoate (SABA1) is a compound that has been shown to have antibacterial properties against Pseudomonas aeruginosa and Escherichia coli. SABA1 inhibits biotin carboxylase (BC), the enzyme that catalyses the first half reaction of ACC. SABA1 inhibits BC via an atypical mechanism. It binds in the biotin binding site in the presence of ADP. SABA1 represents a potentially new class of antibiotics that can be used to combat the antibacterial resistance crisis.
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Affiliation(s)
- Matthew K Craft
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Grover L Waldrop
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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Vikram V, Amperayani KR, Umadevi P. 3-(Methoxycarbonyl)thiophene Thiourea Derivatives as Potential Potent Bacterial Acetyl-CoA Carboxylase Inhibitors. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021080145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Landeros JM, Cruz‐Hernández C, Juaristi E. α‐Amino Acids and α,β‐Dipeptides Intercalated into Hydrotalcite: Efficient Catalysts in the Asymmetric Michael Addition Reaction of Aldehydes to
N
‐Substituted Maleimides. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100877] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- José M. Landeros
- Departamento de Química, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional Avenida IPN #2508 07360 Ciudad de México Mexico
| | - Carlos Cruz‐Hernández
- Departamento de Química, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional Avenida IPN #2508 07360 Ciudad de México Mexico
| | - Eusebio Juaristi
- Departamento de Química, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional Avenida IPN #2508 07360 Ciudad de México Mexico
- El Colegio Nacional Luis González Obregón 23, Centro Histórico 06020 Ciudad de México Mexico
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Liang Y, He D, Zhou D, Li J, Tang L, Wang Z. Synthesis, Antibacterial and Pharmacokinetic Evaluation of Novel Derivatives of Harmine N 9-Cinnamic Acid. Molecules 2021; 26:4842. [PMID: 34443429 PMCID: PMC8400480 DOI: 10.3390/molecules26164842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
A series of 16 new derivatives of harmine N9-Cinnamic acid were synthesized and fully characterized using NMR and MS. The in vitro antibacterial evaluation revealed that most of the synthesized harmine derivatives displayed better antibacterial activities against Gram-positive strains (S. aureus, S. albus and MRSA) than Gram-negative strains (E. coli and PA). In particular, compound 3c showed the strongest bactericidal activity with a minimum inhibitory concentration of 13.67 μg/mL. MTT assay showed that compound 3c displayed weaker cytotoxicity than harmine with IC50 of 340.30, 94.86 and 161.67 μmol/L against WI-38, MCF-7 and HepG2 cell lines, respectively. The pharmacokinetic study revealed that the distribution and elimination of 3c in vivo were rapid in rats with an oral bioavailability of 6.9%.
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Affiliation(s)
- Yan Liang
- School of Pharmacy, Lanzhou University, West Donggang Road No. 199, Lanzhou 730000, China; (Y.L.); (D.H.)
| | - Dian He
- School of Pharmacy, Lanzhou University, West Donggang Road No. 199, Lanzhou 730000, China; (Y.L.); (D.H.)
| | - Deshun Zhou
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, No. 335, Qilihe District, Lanzhou 730050, China; (D.Z.); (J.L.); (L.T.)
| | - Junshuai Li
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, No. 335, Qilihe District, Lanzhou 730050, China; (D.Z.); (J.L.); (L.T.)
| | - Lei Tang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, No. 335, Qilihe District, Lanzhou 730050, China; (D.Z.); (J.L.); (L.T.)
| | - Zhen Wang
- School of Pharmacy, Lanzhou University, West Donggang Road No. 199, Lanzhou 730000, China; (Y.L.); (D.H.)
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Zhirnov VV, Velihina YS, Mitiukhin OP, Brovarets VS. Intrinsic drug potential of oxazolo[5,4-d]pyrimidines and oxazolo[4,5-d]pyrimidines. Chem Biol Drug Des 2021; 98:561-581. [PMID: 34148293 DOI: 10.1111/cbdd.13911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/12/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022]
Abstract
The oxazole and pyrimidine rings are widely displayed in natural products and synthetic molecules. They are known as the prime skeletons for drug discovery. On the account of structural and chemical diversity, oxazole and pyrimidine-based molecules, as central scaffolds, not only provide different types of interactions with various receptors and enzymes, showing broad biological activities, but also occupy a core position in medicinal chemistry, showing their importance for development and discovery of newer potential therapeutic agents (Curr Top Med Chem, 16, 2016, 3133; Int J Pharm Pharm Sci, 8, 2016, 8; BMC Chem, 13, 2019, 44). For a long time, relatively little attention has been paid to their fused rings that are oxazolopyrimidines, whose chemical structure is similar to that of natural purines because probably none of these compounds were found in natural products or their biological activities turned out to be unexpressed (Bull Chem Soc Jpn, 43, 1970, 187). Recently, however, a significant number of studies have been published on the biological properties of oxazolo[5,4-d]pyrimidines, showing their significant activity as agonists and antagonists of signaling pathways involved in the regulation of the cell life cycle, whereas oxazolo[4,5-d]pyrimidines, on the contrary, represent a poorly studied class of compounds. Limited access to this scaffold has resulted in a corresponding lack of biological research (Eur J Organ Chem, 18, 2018, 2148). Actually, oxazolo[5,4-d]pyrimidine is a versatile scaffold used for the design of bioactive ligands against enzymes and receptors. This review focuses on biological targets and associated pathogenetic mechanisms, as well as pathological disorders that can be modified by well-known oxazolopyrimidines that have been proven to date. Many molecular details of these processes are omitted here, which the interested reader will find in the cited literature. This work also does not cover the methods for the synthesis of the oxazolopyrimidines, which are exhaustively described by De Coen et al. (Eur J Organ Chem, 18, 2018, 2148). The review as well does not discuss the structure-activity relationship, which is described in detail in the original works and deliberately, whenever possible, cites not primary sources, but mostly relevant review articles, so that the reader who wants to delve into a particular problem will immediately receive more complete information. It is expected that the information presented in this review will help readers better understand the purpose of the development of oxazolopyrimidines and the possibility of their development as drugs for the treatment of a wide range of diseases.
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Affiliation(s)
- Victor V Zhirnov
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Bases, Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Yevheniia S Velihina
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Bases, Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Oleg P Mitiukhin
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Bases, Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
| | - Volodymyr S Brovarets
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Bases, Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kyiv, Ukraine
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Zhao Z, Yue J, Ji X, Nian M, Kang K, Qiao H, Zheng X. Research progress in biological activities of succinimide derivatives. Bioorg Chem 2020; 108:104557. [PMID: 33376010 DOI: 10.1016/j.bioorg.2020.104557] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
Succinimides are well recognized heterocyclic compounds in drug discovery which produce diverse therapeutically related applications in pharmacological practices. Researches in medicinal chemistry field have isolated and synthesized succinimide derivatives with multiple medicinal properties including anticonvulsant, anti-inflammatory, antitumor and antimicrobial agents, 5-HT receptor ligands and enzyme inhibitors. Simultaneously, SAR (Structure-Activity Relationship) analysis has been gradually possessed, along with a great deal of derivatives have been derived for potential targets. In this article, we comprehensively summarize the biological activities and SAR for succinimide derivatives, along with the featuring bioactive molecules reported in patents, wishing to provide an overall retrospect and prospect on the succinimide analogues.
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Affiliation(s)
- Zefeng Zhao
- College of Acupuncture & Massage, Shaanxi University of Chinese Medicine, Xixian New Area, Shaanxi Province 712046, PR China; Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China; School of Pharmacy, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, 229 Taibai Road, Xi'an 710069, PR China
| | - Jiangxin Yue
- Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China
| | - Xiaotong Ji
- Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China
| | - Meng Nian
- Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China
| | - Kaiwen Kang
- Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China
| | - Haifa Qiao
- College of Acupuncture & Massage, Shaanxi University of Chinese Medicine, Xixian New Area, Shaanxi Province 712046, PR China; Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China.
| | - Xiaohui Zheng
- School of Pharmacy, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, 229 Taibai Road, Xi'an 710069, PR China
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12
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Huang T, Wu X, Yan S, Liu T, Yin X. Synthesis and in vitro evaluation of novel spiroketopyrazoles as acetyl-CoA carboxylase inhibitors and potential antitumor agents. Eur J Med Chem 2020; 212:113036. [PMID: 33276990 DOI: 10.1016/j.ejmech.2020.113036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/06/2020] [Accepted: 11/14/2020] [Indexed: 12/19/2022]
Abstract
Acetyl-CoA carboxylase (ACC) is a rate-limiting enzyme in de novo fatty acid synthesis, which plays a critical role in the growth and survival of cancer cells. In this study, a series of spiroketopyrazole derivatives bearing quinoline moieties were synthesized, and in vitro anticancer activities of these compounds as ACC inhibitors were evaluated. The biological evaluation showed that compound 7j exhibited the strongest enzyme inhibitory activity (IC50 = 1.29 nM), while compound 7m displayed the most potent anti-proliferative activity against A549, HepG2, and MDA-MB-231 cells with corresponding IC50 values of 0.55, 0.38, and 1.65 μM, respectively. The preliminary pharmacological studies confirmed that compound 7m reduced the intracellular malonyl-CoA and TG levels in a dose-dependent manner. Moreover, it could down-regulate cyclin D1 and CDK4 to disturb the cell cycle and up-regulate Bax, caspase-3, and PARP along with the suppression of Bcl-2 to induce apoptosis. Notably, the combination of 7m with doxorubicin synergistically decreased the HepG2 cell viability. These results indicated that compound 7m as a single agent, or in combination with other antitumor drugs, might be a promising therapeutic agent for the treatment of hepatocellular carcinoma.
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Affiliation(s)
- Tonghui Huang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 221004, Xuzhou, Jiangsu, China; Xuzhou Medical University Science Park, 221000, Xuzhou, Jiangsu, People's Republic of China.
| | - Xin Wu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 221004, Xuzhou, Jiangsu, China
| | - Shirong Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 221004, Xuzhou, Jiangsu, China
| | - Tianya Liu
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, 221002, Xuzhou, Jiangsu, China
| | - Xiaoxing Yin
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 221004, Xuzhou, Jiangsu, China.
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Recent development in acetyl-CoA carboxylase inhibitors and their potential as novel drugs. Future Med Chem 2020; 12:533-561. [PMID: 32048880 DOI: 10.4155/fmc-2019-0312] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Acetyl-CoA carboxylase (ACC), a critical enzyme in the regulation of fatty acid synthesis and metabolism, has emerged as an attractive target for a plethora of emerging diseases, such as diabetes mellitus, nonalcoholic fatty liver disease, cancer, bacterial infections and so on. With decades of efforts in medicinal chemistry, significant progress has been made toward the design and discovery of a considerable number of inhibitors of this enzyme. In this review, we not only clarify the role of ACC in emerging diseases, but also summarize recent developments of potent ACC inhibitors and discuss their molecular mechanisms of action and potentials as novel drugs as well as future perspectives toward the design and discovery of novel ACC inhibitors.
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14
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Andrews LD, Kane TR, Dozzo P, Haglund CM, Hilderbrandt DJ, Linsell MS, Machajewski T, McEnroe G, Serio AW, Wlasichuk KB, Neau DB, Pakhomova S, Waldrop GL, Sharp M, Pogliano J, Cirz RT, Cohen F. Optimization and Mechanistic Characterization of Pyridopyrimidine Inhibitors of Bacterial Biotin Carboxylase. J Med Chem 2019; 62:7489-7505. [PMID: 31306011 DOI: 10.1021/acs.jmedchem.9b00625] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A major challenge for new antibiotic discovery is predicting the physicochemical properties that enable small molecules to permeate Gram-negative bacterial membranes. We have applied physicochemical lessons from previous work to redesign and improve the antibacterial potency of pyridopyrimidine inhibitors of biotin carboxylase (BC) by up to 64-fold and 16-fold against Escherichia coli and Pseudomonas aeruginosa, respectively. Antibacterial and enzyme potency assessments in the presence of an outer membrane-permeabilizing agent or in efflux-compromised strains indicate that penetration and efflux properties of many redesigned BC inhibitors could be improved to various extents. Spontaneous resistance to the improved pyridopyrimidine inhibitors in P. aeruginosa occurs at very low frequencies between 10-8 and 10-9. However, resistant isolates had alarmingly high minimum inhibitory concentration shifts (16- to >128-fold) compared to the parent strain. Whole-genome sequencing of resistant isolates revealed that either BC target mutations or efflux pump overexpression can lead to the development of high-level resistance.
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Affiliation(s)
- Logan D Andrews
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Timothy R Kane
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Paola Dozzo
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Cat M Haglund
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Darin J Hilderbrandt
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Martin S Linsell
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Timothy Machajewski
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Glen McEnroe
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Alisa W Serio
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Kenneth B Wlasichuk
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - David B Neau
- Northeastern Collaborative Access Team , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Svetlana Pakhomova
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Grover L Waldrop
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Marc Sharp
- Linnaeus Bioscience Inc. , 3210 Merryfield Row , San Diego , California 92121 , United States
| | - Joe Pogliano
- Linnaeus Bioscience Inc. , 3210 Merryfield Row , San Diego , California 92121 , United States.,University of California, San Diego , 9500 Gilman Drive , La Jolla, San Diego , California 92093 , United States
| | - Ryan T Cirz
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
| | - Frederick Cohen
- Former employee of Achaogen Inc. , 1 Tower Place, Suite 400 , South San Francisco , California 94080 , United States
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15
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Li J, Wei J, Zhu B, Wang T, Jiao N. Cu-catalyzed oxygenation of alkene-tethered amides with O 2 via unactivated C[double bond, length as m-dash]C bond cleavage: a direct approach to cyclic imides. Chem Sci 2019; 10:9099-9103. [PMID: 31827752 PMCID: PMC6889834 DOI: 10.1039/c9sc03175h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/04/2019] [Indexed: 12/15/2022] Open
Abstract
An efficient aerobic unactivated C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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C bond cleavage process was achieved, in which the succinimide or glutarimide derivatives could be prepared directly from alkenyl amides.
The transformations of unactivated alkenes through C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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C bond double cleavage are always attractive but very challenging. We report herein a chemoselective approach to valuable cyclic imides by a novel Cu-catalyzed geminal amino-oxygenation of unactivated C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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C bonds. O2 was successfully employed as the oxidant as well as the O-source and was incorporated into alkenyl amides via C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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C bond cleavage for the efficient preparation of succinimide or glutarimide derivatives. Moreover, the present strategy under simple conditions can be used in the late-stage modification of biologically active compounds and the synthesis of pharmaceuticals, which demonstrated the potential application.
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Affiliation(s)
- Junhua Li
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Xue Yuan Road 38 , Beijing 100191 , China .
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Xue Yuan Road 38 , Beijing 100191 , China .
| | - Bencong Zhu
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Xue Yuan Road 38 , Beijing 100191 , China .
| | - Teng Wang
- School of Chemistry , Beihang University , Xue Yuan Road 37 , Beijing , 100191 , China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Xue Yuan Road 38 , Beijing 100191 , China . .,State Key Laboratory of Organometallic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
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16
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Klahn P, Brönstrup M. Bifunctional antimicrobial conjugates and hybrid antimicrobials. Nat Prod Rep 2017; 34:832-885. [PMID: 28530279 DOI: 10.1039/c7np00006e] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to the end of 2016Novel antimicrobial drugs are continuously needed to counteract bacterial resistance development. An innovative molecular design strategy for novel antibiotic drugs is based on the hybridization of an antibiotic with a second functional entity. Such conjugates can be grouped into two major categories. In the first category (antimicrobial hybrids), both functional elements of the hybrid exert antimicrobial activity. Due to the dual targeting, resistance development can be significantly impaired, the pharmacokinetic properties can be superior compared to combination therapies with the single antibiotics, and the antibacterial potency is often enhanced in a synergistic manner. In the second category (antimicrobial conjugates), one functional moiety controls the accumulation of the other part of the conjugate, e.g. by mediating an active transport into the bacterial cell or blocking the efflux. This approach is mostly applied to translocate compounds across the cell envelope of Gram-negative bacteria through membrane-embedded transporters (e.g. siderophore transporters) that provide nutrition and signalling compounds to the cell. Such 'Trojan Horse' approaches can expand the antibacterial activity of compounds against Gram-negative pathogens, or offer new options for natural products that could not be developed as standalone antibiotics, e.g. due to their toxicity.
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Affiliation(s)
- P Klahn
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany. and Institute for Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
| | - M Brönstrup
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
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17
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Bacterial fatty acid metabolism in modern antibiotic discovery. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1300-1309. [PMID: 27668701 DOI: 10.1016/j.bbalip.2016.09.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 12/28/2022]
Abstract
Bacterial fatty acid synthesis is essential for many pathogens and different from the mammalian counterpart. These features make bacterial fatty acid synthesis a desirable target for antibiotic discovery. The structural divergence of the conserved enzymes and the presence of different isozymes catalyzing the same reactions in the pathway make bacterial fatty acid synthesis a narrow spectrum target rather than the traditional broad spectrum target. Furthermore, bacterial fatty acid synthesis inhibitors are single-targeting, rather than multi-targeting like traditional monotherapeutic, broad-spectrum antibiotics. The single-targeting nature of bacterial fatty acid synthesis inhibitors makes overcoming fast-developing, target-based resistance a necessary consideration for antibiotic development. Target-based resistance can be overcome through multi-targeting inhibitors, a cocktail of single-targeting inhibitors, or by making the single targeting inhibitor sufficiently high affinity through a pathogen selective approach such that target-based mutants are still susceptible to therapeutic concentrations of drug. Many of the pathogens requiring new antibiotic treatment options encode for essential bacterial fatty acid synthesis enzymes. This review will evaluate the most promising targets in bacterial fatty acid metabolism for antibiotic therapeutics development and review the potential and challenges in advancing each of these targets to the clinic and circumventing target-based resistance. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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18
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Silvers MA, Pakhomova S, Neau DB, Silvers WC, Anzalone N, Taylor CM, Waldrop GL. Crystal Structure of Carboxyltransferase from Staphylococcus aureus Bound to the Antibacterial Agent Moiramide B. Biochemistry 2016; 55:4666-74. [PMID: 27471863 DOI: 10.1021/acs.biochem.6b00641] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dramatic increase in the prevalence of antibiotic-resistant bacteria has necessitated a search for new antibacterial agents against novel targets. Moiramide B is a natural product, broad-spectrum antibiotic that inhibits the carboxyltransferase component of acetyl-CoA carboxylase, which catalyzes the first committed step in fatty acid synthesis. Herein, we report the 2.6 Å resolution crystal structure of moiramide B bound to carboxyltransferase. An unanticipated but significant finding was that moiramide B bound as the enol/enolate. Crystallographic studies demonstrate that the (4S)-methyl succinimide moiety interacts with the oxyanion holes of the enzyme, supporting the notion that an anionic enolate is the active form of the antibacterial agent. Structure-activity studies demonstrate that the unsaturated fatty acid tail of moiramide B is needed only for entry into the bacterial cell. These results will allow the design of new antibacterial agents against the bacterial form of carboxyltransferase.
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Affiliation(s)
| | | | - David B Neau
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States.,Northeastern Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - William C Silvers
- Department of Radiology, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
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19
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Hooven TA, Catomeris AJ, Akabas LH, Randis TM, Maskell DJ, Peters SE, Ott S, Santana-Cruz I, Tallon LJ, Tettelin H, Ratner AJ. The essential genome of Streptococcus agalactiae. BMC Genomics 2016; 17:406. [PMID: 27229469 PMCID: PMC4881062 DOI: 10.1186/s12864-016-2741-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/14/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Next-generation sequencing of transposon-genome junctions from a saturated bacterial mutant library (Tn-seq) is a powerful tool that permits genome-wide determination of the contribution of genes to fitness of the organism under a wide range of experimental conditions. We report development, testing, and results from a Tn-seq system for use in Streptococcus agalactiae (group B Streptococcus; GBS), an important cause of neonatal sepsis. METHODS Our method uses a Himar1 mini-transposon that inserts at genomic TA dinucleotide sites, delivered to GBS on a temperature-sensitive plasmid that is subsequently cured from the bacterial population. In order to establish the GBS essential genome, we performed Tn-seq on DNA collected from three independent mutant libraries-with at least 135,000 mutants per library-at serial 24 h time points after outgrowth in rich media. RESULTS After statistical analysis of transposon insertion density and distribution, we identified 13.5 % of genes as essential and 1.2 % as critical, with high levels of reproducibility. Essential and critical genes are enriched for fundamental cellular housekeeping functions, such as acyl-tRNA biosynthesis, nucleotide metabolism, and glycolysis. We further validated our system by comparing fitness assignments of homologous genes in GBS and a close bacterial relative, Streptococcus pyogenes, which demonstrated 93 % concordance. Finally, we used our fitness assignments to identify signal transduction pathway components predicted to be essential or critical in GBS. CONCLUSIONS We believe that our baseline fitness assignments will be a valuable tool for GBS researchers and that our system has the potential to reveal key pathogenesis gene networks and potential therapeutic/preventative targets.
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Affiliation(s)
- Thomas A Hooven
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Andrew J Catomeris
- Department of Pediatrics, Division of Pediatric Infectious Diseases, New York University School of Medicine, 550 First Avenue (MSB 223), New York, NY, 10016, USA
| | - Leor H Akabas
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Tara M Randis
- Department of Pediatrics, Division of Pediatric Infectious Diseases, New York University School of Medicine, 550 First Avenue (MSB 223), New York, NY, 10016, USA
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah E Peters
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sandra Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ivette Santana-Cruz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Adam J Ratner
- Department of Pediatrics, Division of Pediatric Infectious Diseases, New York University School of Medicine, 550 First Avenue (MSB 223), New York, NY, 10016, USA. .,Department of Microbiology, New York University School of Medicine, New York, NY, USA.
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