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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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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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3
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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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Improving Antimicrobial Activity and Physico-Chemical Properties by Isosteric Replacement of 2-Aminothiazole with 2-Aminooxazole. Pharmaceuticals (Basel) 2022; 15:ph15050580. [PMID: 35631406 PMCID: PMC9143880 DOI: 10.3390/ph15050580] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 02/01/2023] Open
Abstract
Antimicrobial drug resistance is currently one of the most critical health issues. Pathogens resistant to last-resort antibiotics are increasing, and very few effective antibacterial agents have been introduced in recent years. The promising drug candidates are often discontinued in the primary stages of the drug discovery pipeline due to their unspecific reactivity (PAINS), toxicity, insufficient stability, or low water solubility. In this work, we investigated a series of substituted N-oxazolyl- and N-thiazolylcarboxamides of various pyridinecarboxylic acids. Final compounds were tested against several microbial species. In general, oxazole-containing compounds showed high activity against mycobacteria, especially Mycobacterium tuberculosis (best MICH37Ra = 3.13 µg/mL), including the multidrug-resistant strains. Promising activities against various bacterial and fungal strains were also observed. None of the compounds was significantly cytotoxic against the HepG2 cell line. Experimental measurement of lipophilicity parameter log k’w and water solubility (log S) confirmed significantly (typically two orders in logarithmic scale) increased hydrophilicity/water solubility of oxazole derivatives in comparison with their thiazole isosteres. Mycobacterial β-ketoacyl-acyl carrier protein synthase III (FabH) was suggested as a probable target by molecular docking and molecular dynamics simulations.
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5
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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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6
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Abstract
Aim: Tumor cells adapt to hypoxic microenvironments by releasing the key transcription factor HIF-1α, which promotes angiogenesis, glycolytic phenotype, metastasis and erythropoiesis, allowing proliferation amid low oxygen levels. Therefore, therapeutic targeting of HIF-1α represents a viable strategy for cancer therapy. Methods & Results: The authors synthesized a series of novel tetrahydroquinazoline derivatives in six steps and demonstrated that their development had a unique ability to suppress HIF-1α expression through proteasomal degradation. Conclusion: Among these compounds, CDMP-TQZ (8bf) exhibited the highest antiproliferative potency in human cancer cells, in part through downregulation of HIF-1α.
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Swain A, Gnanasekar P, Prava J, Rajeev AC, Kesarwani P, Lahiri C, Pan A. A Comparative Genomics Approach for Shortlisting Broad-Spectrum Drug Targets in Nontuberculous Mycobacteria. Microb Drug Resist 2020; 27:212-226. [PMID: 32936741 DOI: 10.1089/mdr.2020.0161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Many members of nontuberculous mycobacteria (NTM) are opportunistic pathogens causing several infections in animals. The incidence of NTM infections and emergence of drug-resistant NTM strains are rising worldwide, emphasizing the need to develop novel anti-NTM drugs. The present study is aimed to identify broad-spectrum drug targets in NTM using a comparative genomics approach. The study identified 537 core proteins in NTM of which 45 were pathogen specific and essential for the survival of pathogens. Furthermore, druggability analysis indicated that 15 were druggable among those 45 proteins. These 15 proteins, which were core proteins, pathogen-specific, essential, and druggable, were considered as potential broad-spectrum candidates. Based on their locations in cytoplasm and membrane, targets were classified as drug and vaccine targets. The identified 15 targets were different enzymes, carrier proteins, transcriptional regulator, two-component system protein, ribosomal, and binding proteins. The identified targets could further be utilized by researchers to design inhibitors for the discovery of antimicrobial agents.
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Affiliation(s)
- Aishwarya Swain
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Jyoti Prava
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Athira C Rajeev
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Pragya Kesarwani
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Archana Pan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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8
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McDowell LL, Quinn CL, Leeds JA, Silverman JA, Silver LL. Perspective on Antibacterial Lead Identification Challenges and the Role of Hypothesis-Driven Strategies. SLAS DISCOVERY 2020; 24:440-456. [PMID: 30890054 DOI: 10.1177/2472555218818786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
For the past three decades, the pharmaceutical industry has undertaken many diverse approaches to discover novel antibiotics, with limited success. We have witnessed and personally experienced many mistakes, hurdles, and dead ends that have derailed projects and discouraged scientists and business leaders. Of the many factors that affect the outcomes of screening campaigns, a lack of understanding of the properties that drive efflux and permeability requirements across species has been a major barrier for advancing hits to leads. Hits that possess bacterial spectrum have seldom also possessed druglike properties required for developability and safety. Persistence in solving these two key barriers is necessary for the reinvestment into discovering antibacterial agents. This perspective narrates our experience in antibacterial discovery-our lessons learned about antibacterial challenges as well as best practices for screening strategies. One of the tenets that guides us is that drug discovery is a hypothesis-driven science. Application of this principle, at all steps in the antibacterial discovery process, should improve decision making and possibly the odds of what has become, in recent decades, an increasingly challenging endeavor with dwindling success rates.
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Affiliation(s)
- Laura L McDowell
- 1 Novartis Institutes for Biomedical Research, Emeryville, CA, USA
| | | | - Jennifer A Leeds
- 1 Novartis Institutes for Biomedical Research, Emeryville, CA, USA
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9
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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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10
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Awuni E. Status of Targeting MreB for the Development of Antibiotics. Front Chem 2020; 7:884. [PMID: 31998684 PMCID: PMC6965359 DOI: 10.3389/fchem.2019.00884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Although many prospective antibiotic targets are known, bacterial infections and resistance to antibiotics remain a threat to public health partly because the druggable potentials of most of these targets have yet to be fully tapped for the development of a new generation of therapeutics. The prokaryotic actin homolog MreB is one of the important antibiotic targets that are yet to be significantly exploited. MreB is a bacterial cytoskeleton protein that has been widely studied and is associated with the determination of rod shape as well as important subcellular processes including cell division, chromosome segregation, cell wall morphogenesis, and cell polarity. Notwithstanding that MreB is vital and conserved in most rod-shaped bacteria, no approved antibiotics targeting it are presently available. Here, the status of targeting MreB for the development of antibiotics is concisely summarized. Expressly, the known therapeutic targets and inhibitors of MreB are presented, and the way forward in the search for a new generation of potent inhibitors of MreB briefly discussed.
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Affiliation(s)
- Elvis Awuni
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
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11
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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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12
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Konaklieva MI. Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies. SLAS DISCOVERY 2018; 24:419-439. [PMID: 30523713 DOI: 10.1177/2472555218812657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.
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13
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Kumar A, Zhang KYJ. Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Front Chem 2018; 6:315. [PMID: 30090808 PMCID: PMC6068280 DOI: 10.3389/fchem.2018.00315] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Affiliation(s)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
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14
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Lamoree B, Hubbard RE. Using Fragment-Based Approaches to Discover New Antibiotics. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2018; 23:495-510. [PMID: 29923463 PMCID: PMC6024353 DOI: 10.1177/2472555218773034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/16/2018] [Accepted: 04/05/2018] [Indexed: 12/29/2022]
Abstract
Fragment-based lead discovery has emerged over the past two decades as a successful approach to generate novel lead candidates in drug discovery programs. The two main advantages over conventional high-throughput screening (HTS) are more efficient sampling of chemical space and tighter control over the physicochemical properties of the lead candidates. Antibiotics are a class of drugs with particularly strict property requirements for efficacy and safety. The development of novel antibiotics has slowed down so much that resistance has now evolved against every available antibiotic drug. Here we give an overview of fragment-based approaches in screening and lead discovery projects for new antibiotics. We discuss several successful hit-to-lead development examples. Finally, we highlight the current challenges and opportunities for fragment-based lead discovery toward new antibiotics.
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Affiliation(s)
- Bas Lamoree
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
| | - Roderick E. Hubbard
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
- Vernalis Research, Granta Park, Abington, Cambridge, UK
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15
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Gao J, Liang L, Chen Q, Zhang L, Huang T. Insight into the molecular mechanism of yeast acetyl-coenzyme A carboxylase mutants F510I, N485G, I69E, E477R, and K73R resistant to soraphen A. J Comput Aided Mol Des 2018; 32:547-557. [PMID: 29464467 DOI: 10.1007/s10822-018-0108-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/16/2018] [Indexed: 11/25/2022]
Abstract
Acetyl-coenzyme A carboxylases (ACCs) is the first committed enzyme of fatty acid synthesis pathway. The inhibition of ACC is thought to be beneficial not only for diseases related to metabolism, such as type-2 diabetes, but also for infectious disease like bacterial infection disease. Soraphen A, a potent allosteric inhibitor of BC domain of yeast ACC, exhibit lower binding affinities to several yeast ACC mutants and the corresponding drug resistance mechanisms are still unknown. We report here a theoretical study of binding of soraphen A to wild type and yeast ACC mutants (including F510I, N485G, I69E, E477R, and K73R) via molecular dynamic simulation and molecular mechanics/generalized Born surface area free energy calculations methods. The calculated binding free energies of soraphen A to yeast ACC mutants are weaker than to wild type, which is highly consistent with the experimental results. The mutant F510I weakens the binding affinity of soraphen A to yeast ACC mainly by decreasing the van der Waals contributions, while the weaker binding affinities of Soraphen A to other yeast ACC mutants including N485G, I69E, E477R, and K73R are largely attributed to the decreased net electrostatic (ΔEele + ΔGGB) interactions. Our simulation results could provide important insights for the development of more potent ACC inhibitors.
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Affiliation(s)
- Jian Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, People's Republic of China.
| | - Li Liang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, People's Republic of China
| | - Qingqing Chen
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, People's Republic of China
| | - Ling Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, People's Republic of China
| | - Tonghui Huang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, People's Republic of China.
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16
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Harit T, Bellaouchi R, Rokni Y, Riahi A, Malek F, Asehraou A. Synthesis, Characterization, Antimicrobial Activity, and Docking Studies of New Triazolic Tripodal Ligands. Chem Biodivers 2017; 14. [DOI: 10.1002/cbdv.201700351] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/04/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Tarik Harit
- Laboratory of Organic, Macromolecular Chemistry and Natural Products - URAC 25; Faculty of Sciences; Mohammed First University; B Mohamed VI, BP: 717 Oujda 60000 Morocco
| | - Reda Bellaouchi
- Laboratory of Biochemistry and Biotechnology; Faculty of Sciences; Mohammed First University; Bd Mohamed VI, BP: 717BP 717 Oujda 60000 Morocco
| | - Yahya Rokni
- Laboratory of Biochemistry and Biotechnology; Faculty of Sciences; Mohammed First University; Bd Mohamed VI, BP: 717BP 717 Oujda 60000 Morocco
| | - Abdelkhalek Riahi
- CNRS UMR 6229; Institut de Chimie Moléculaire de Reims (ICMR)-Groupe Méthodologie en Synthèse Organique; Université de Reims Champagne-Ardenne; Bat. Europol'Agro-Moulin de la Housse, BP 1039 Reims Cedex 2 51687 France
| | - Fouad Malek
- Laboratory of Organic, Macromolecular Chemistry and Natural Products - URAC 25; Faculty of Sciences; Mohammed First University; B Mohamed VI, BP: 717 Oujda 60000 Morocco
| | - Abdeslam Asehraou
- Laboratory of Biochemistry and Biotechnology; Faculty of Sciences; Mohammed First University; Bd Mohamed VI, BP: 717BP 717 Oujda 60000 Morocco
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17
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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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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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Beheshti A, Babadi SS, Nozarian K, Heidarizadeh F, Ghamari N, Mayer P, Motamedi H. Crystal structure, microbiological activity and theoretical studies of Ag(I) and Cu(I) coordination polymers with 1,1′-(butane-1,4-diyl)bis(3-methylimidazoline-2-thione) ligand. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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The Role of Biotin in Bacterial Physiology and Virulence: a Novel Antibiotic Target for
Mycobacterium tuberculosis. Microbiol Spectr 2016; 4. [DOI: 10.1128/microbiolspec.vmbf-0008-2015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
Biotin is an essential cofactor for enzymes present in key metabolic pathways such as fatty acid biosynthesis, replenishment of the tricarboxylic acid cycle, and amino acid metabolism. Biotin is synthesized
de novo
in microorganisms, plants, and fungi, but this metabolic activity is absent in mammals, making biotin biosynthesis an attractive target for antibiotic discovery. In particular, biotin biosynthesis plays important metabolic roles as the sole source of biotin in all stages of the
Mycobacterium tuberculosis
life cycle due to the lack of a transporter for scavenging exogenous biotin. Biotin is intimately associated with lipid synthesis where the products form key components of the mycobacterial cell membrane that are critical for bacterial survival and pathogenesis. In this review we discuss the central role of biotin in bacterial physiology and highlight studies that demonstrate the importance of its biosynthesis for virulence. The structural biology of the known biotin synthetic enzymes is described alongside studies using structure-guided design, phenotypic screening, and fragment-based approaches to drug discovery as routes to new antituberculosis agents.
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21
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Zhang J, Zhao J, Wang L, Liu J, Ren D, Ma Y. Design, synthesis and docking studies of some spiro-oxindole dihydroquinazolinones as antibacterial agents. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.055] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Hubbard RE. The Role of Fragment-based Discovery in Lead Finding. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch01] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Fadda AA, Bayoumy NM, El-Sherbiny IM. Nanoformulation and antimicrobial evaluation of newly synthesized thiouracil derivatives. Drug Dev Ind Pharm 2015; 42:1094-109. [PMID: 26559404 DOI: 10.3109/03639045.2015.1108331] [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] [Indexed: 11/13/2022]
Abstract
The present work reports the synthesis of a new series of pyridopyrimidine derivatives. The newly synthesized compounds were characterized by various analytical and spectral techniques. In addition, their antimicrobial activity was evaluated as well as modeling studies were performed to investigate their ability to recognize and bind to the biotin carboxylase (BC)-active site. The results showed a broad spectrum antibacterial and antifungal profile of the synthesized derivatives. Docking results demonstrated that all members of this class of new derivatives were able to recognize the active site of Escherichia coli BC and form different types of bonding interactions with key active site amino acid residues. Besides the compounds with promising antimicrobial activity in addition to 6-aminothiouracil, as control, were incorporated into polycaprolactone nanoparticles to improve their water solubility, permeability through physiological barriers and consequently enhanced therapeutic efficacy. The compounds-loaded nanoparticles were prepared using single emulsion-solvent evaporation technique, and their diameters were found to be in the range 136 ± 30 to 213 ± 28 nm. Transmission electron microscopy (TEM) showed a spherical and dense morphology of the nanoparticles. The results also showed high entrapment efficiency of the synthesized bioactive compounds in the nanoparticles (85 ± 5% to 91 ± 2%) with a desirable in vitro biodegradation and release profiles.
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Affiliation(s)
- Ahmed A Fadda
- a Chemistry Department , Faculty of Science, Mansoura University , Mansoura , ET , Egypt
| | - Nesma M Bayoumy
- b Chemistry Department , Faculty of Oral and Dental Medicine, Delta University for Science and Technology , Gamasa , Egypt
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24
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Ma Y, Ren D, Zhang J, Liu J, Zhao J, Wang L, Zhang F. Synthesis, antibacterial activities evaluation, and docking studies of some 2-substituted-3-(phenylamino)-dihydroquinazolin-4(1 H )-ones. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.05.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Broussard TC, Pakhomova S, Neau DB, Bonnot R, Waldrop GL. Structural Analysis of Substrate, Reaction Intermediate, and Product Binding in Haemophilus influenzae Biotin Carboxylase. Biochemistry 2015; 54:3860-70. [PMID: 26020841 DOI: 10.1021/acs.biochem.5b00340] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gram-negative and Gram-positive bacteria, the enzyme is composed of three proteins: biotin carboxylase, a biotin carboxyl carrier protein (BCCP), and carboxyltransferase. The reaction mechanism involves two half-reactions with biotin carboxylase catalyzing the ATP-dependent carboxylation of biotin-BCCP in the first reaction. In the second reaction, carboxyltransferase catalyzes the transfer of the carboxyl group from biotin-BCCP to acetyl-CoA to form malonyl-CoA. In this report, high-resolution crystal structures of biotin carboxylase from Haemophilus influenzae were determined with bicarbonate, the ATP analogue AMPPCP; the carboxyphosphate intermediate analogues, phosphonoacetamide and phosphonoformate; the products ADP and phosphate; and the carboxybiotin analogue N1'-methoxycarbonyl biotin methyl ester. The structures have a common theme in that bicarbonate, phosphate, and the methyl ester of the carboxyl group of N1'-methoxycarbonyl biotin methyl ester all bound in the same pocket in the active site of biotin carboxylase and as such utilize the same set of amino acids for binding. This finding suggests a catalytic mechanism for biotin carboxylase in which the binding pocket that binds tetrahedral phosphate also accommodates and stabilizes a tetrahedral dianionic transition state resulting from direct transfer of CO₂ from the carboxyphosphate intermediate to biotin.
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Affiliation(s)
- Tyler C Broussard
- †Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Svetlana Pakhomova
- †Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - David B Neau
- ‡Department of Chemistry and Chemical Biology, Cornell University, Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Ross Bonnot
- †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
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26
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Kumar A, Zhang KYJ. Hierarchical virtual screening approaches in small molecule drug discovery. Methods 2015; 71:26-37. [PMID: 25072167 PMCID: PMC7129923 DOI: 10.1016/j.ymeth.2014.07.007] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023] Open
Abstract
Virtual screening has played a significant role in the discovery of small molecule inhibitors of therapeutic targets in last two decades. Various ligand and structure-based virtual screening approaches are employed to identify small molecule ligands for proteins of interest. These approaches are often combined in either hierarchical or parallel manner to take advantage of the strength and avoid the limitations associated with individual methods. Hierarchical combination of ligand and structure-based virtual screening approaches has received noteworthy success in numerous drug discovery campaigns. In hierarchical virtual screening, several filters using ligand and structure-based approaches are sequentially applied to reduce a large screening library to a number small enough for experimental testing. In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets. Several virtual screening studies are discussed to demonstrate the successful application of hierarchical virtual screening in small molecule drug discovery.
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Affiliation(s)
- Ashutosh Kumar
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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27
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Silvers MA, Robertson GT, Taylor CM, Waldrop GL. Design, Synthesis, and Antibacterial Properties of Dual-Ligand Inhibitors of Acetyl-CoA Carboxylase. J Med Chem 2014; 57:8947-59. [DOI: 10.1021/jm501082n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Molly A. Silvers
- Division
of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Gregory T. Robertson
- Department
of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Carol M. Taylor
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Grover L. Waldrop
- Division
of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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28
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Brylinski M, Waldrop GL. Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 2014; 19:4021-45. [PMID: 24699146 PMCID: PMC6271951 DOI: 10.3390/molecules19044021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/19/2014] [Accepted: 03/25/2014] [Indexed: 01/22/2023] Open
Abstract
As the spread of antibiotic resistant bacteria steadily increases, there is an urgent need for new antibacterial agents. Because fatty acid synthesis is only used for membrane biogenesis in bacteria, the enzymes in this pathway are attractive targets for antibacterial agent development. Acetyl-CoA carboxylase catalyzes the committed and regulated step in fatty acid synthesis. In bacteria, the enzyme is composed of three distinct protein components: biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase. Fragment-based screening revealed that amino-oxazole inhibits biotin carboxylase activity and also exhibits antibacterial activity against Gram-negative organisms. In this report, we redesigned previously identified lead inhibitors to expand the spectrum of bacteria sensitive to the amino-oxazole derivatives by including Gram-positive species. Using 9,411 small organic building blocks, we constructed a diverse combinatorial library of 1.2×10⁸ amino-oxazole derivatives. A subset of 9×10⁶ of these compounds were subjected to structure-based virtual screening against seven biotin carboxylase isoforms using similarity-based docking by eSimDock. Potentially broad-spectrum antibiotic candidates were selected based on the consensus ranking by several scoring functions including non-linear statistical models implemented in eSimDock and traditional molecular mechanics force fields. The analysis of binding poses of the top-ranked compounds docked to biotin carboxylase isoforms suggests that: (1) binding of the amino-oxazole anchor is stabilized by a network of hydrogen bonds to residues 201, 202 and 204; (2) halogenated aromatic moieties attached to the amino-oxazole scaffold enhance interactions with a hydrophobic pocket formed by residues 157, 169, 171 and 203; and (3) larger substituents reach deeper into the binding pocket to form additional hydrogen bonds with the side chains of residues 209 and 233. These structural insights into drug-biotin carboxylase interactions will be tested experimentally in in vitro and in vivo systems to increase the potency of amino-oxazole inhibitors towards both Gram-negative as well as Gram-positive species.
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Affiliation(s)
- Michal Brylinski
- Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Grover L Waldrop
- Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, USA.
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29
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Identification through structure-based methods of a bacterial NAD+-dependent DNA ligase inhibitor that avoids known resistance mutations. Bioorg Med Chem Lett 2014; 24:360-6. [DOI: 10.1016/j.bmcl.2013.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/04/2013] [Indexed: 12/14/2022]
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30
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Rouhana J, Hoh F, Estaran S, Henriquet C, Boublik Y, Kerkour A, Trouillard R, Martinez J, Pugnière M, Padilla A, Chavanieu A. Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors. J Med Chem 2013; 56:8497-511. [PMID: 24112024 DOI: 10.1021/jm4009357] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
By virtual screening using a fragment-based drug design (FBDD) approach, 33 fragments were selected within small pockets around interaction hot spots on the Sec7 surface of the nucleotide exchange factor Arno, and then their ability to interfere with the Arno-catalyzed nucleotide exchange on the G-protein Arf1 was evaluated. By use of SPR, NMR, and fluorescence assays, the direct binding of three of the identified fragments to Arno Sec7 domain was demonstrated and the promiscuous aggregate behavior evaluated. Then the binding mode of one fragment and of a more active analogue was solved by X-ray crystallography. This highlighted the role of stable and transient pockets at the Sec7 domain surface in the discovery and binding of interfering compounds. These results provide structural information on how small organic compounds can interfere with the Arf1-Arno Sec7 domain interaction and may guide the rational drug design of competitive inhibitors of Arno enzymatic activity.
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Affiliation(s)
- Jad Rouhana
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Universités Montpellier 1 et 2, Faculté de Pharmacie, 15 Avenue Charles Flahault BP14491, 34093 Montpellier Cedex 5, France
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31
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Silver LL. Antibacterial Discovery: Problems and Possibilities. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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Pon CL, Fabbretti A, Brandi L. Antibiotics Targeting Translation Initiation in Prokaryotes. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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33
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Škedelj V, Perdih A, Brvar M, Kroflič A, Dubbée V, Savage V, O'Neill AJ, Solmajer T, Bešter-Rogač M, Blanot D, Hugonnet JE, Magnet S, Arthur M, Mainardi JL, Stojan J, Zega A. Discovery of the first inhibitors of bacterial enzyme d-aspartate ligase from Enterococcus faecium (Aslfm). Eur J Med Chem 2013; 67:208-20. [DOI: 10.1016/j.ejmech.2013.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 06/01/2013] [Accepted: 06/02/2013] [Indexed: 01/24/2023]
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34
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Walsh CT, Wencewicz TA. Prospects for new antibiotics: a molecule-centered perspective. J Antibiot (Tokyo) 2013; 67:7-22. [DOI: 10.1038/ja.2013.49] [Citation(s) in RCA: 272] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/22/2013] [Accepted: 05/01/2013] [Indexed: 12/12/2022]
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35
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Broussard TC, Price AE, Laborde SM, Waldrop GL. Complex Formation and Regulation of Escherichia coli Acetyl-CoA Carboxylase. Biochemistry 2013; 52:3346-57. [DOI: 10.1021/bi4000707] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tyler C. Broussard
- Division
of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana
70803, United States
| | - Amanda E. Price
- Division
of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana
70803, United States
| | - Susan M. Laborde
- Division
of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana
70803, United States
| | - Grover L. Waldrop
- Division
of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana
70803, United States
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36
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Broussard TC, Kobe MJ, Pakhomova S, Neau DB, Price AE, Champion TS, Waldrop GL. The three-dimensional structure of the biotin carboxylase-biotin carboxyl carrier protein complex of E. coli acetyl-CoA carboxylase. Structure 2013; 21:650-7. [PMID: 23499019 DOI: 10.1016/j.str.2013.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 02/07/2023]
Abstract
Acetyl-coenzyme A (acetyl-CoA) carboxylase is a biotin-dependent, multifunctional enzyme that catalyzes the regulated step in fatty acid synthesis. The Escherichia coli enzyme is composed of a homodimeric biotin carboxylase (BC), biotinylated biotin carboxyl carrier protein (BCCP), and an α2β2 heterotetrameric carboxyltransferase. This enzyme complex catalyzes two half-reactions to form malonyl-coenzyme A. BC and BCCP participate in the first half-reaction, whereas carboxyltransferase and BCCP are involved in the second. Three-dimensional structures have been reported for the individual subunits; however, the structural basis for how BCCP reacts with the carboxylase or transferase is unknown. Therefore, we report here the crystal structure of E. coli BCCP complexed with BC to a resolution of 2.49 Å. The protein-protein complex shows a unique quaternary structure and two distinct interfaces for each BCCP monomer. These BCCP binding sites are unique compared to phylogenetically related biotin-dependent carboxylases and therefore provide novel targets for developing antibiotics against bacterial acetyl-CoA carboxylase.
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Affiliation(s)
- Tyler C Broussard
- Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, USA
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37
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Waldrop GL, Holden HM, St Maurice M. The enzymes of biotin dependent CO₂ metabolism: what structures reveal about their reaction mechanisms. Protein Sci 2013; 21:1597-619. [PMID: 22969052 DOI: 10.1002/pro.2156] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotin-dependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO₂ carrier. A complete understanding of biotin-dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for anti-obesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a dearth of information regarding the molecular architectures of biotin-dependent enzymes. In recent years there has been an explosion in the number of three-dimensional structures reported for these proteins. Here we review our current understanding of the structures and functions of biotin-dependent enzymes. In addition, we provide a critical analysis of what these structures have and have not revealed about biotin-dependent catalysis.
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Affiliation(s)
- Grover L Waldrop
- Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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38
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A capillary electrophoretic assay for acetyl coenzyme A carboxylase. Anal Biochem 2013; 437:32-8. [PMID: 23435309 DOI: 10.1016/j.ab.2013.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 01/24/2013] [Accepted: 02/07/2013] [Indexed: 01/18/2023]
Abstract
A simple off-column capillary electrophoretic (CE) assay for measuring acetyl coenzyme A carboxylase holoenzyme (holo-ACC) activity and inhibition was developed. The two reactions catalyzed by the holo-ACC components, biotin carboxylase (BC) and carboxyltransferase (CT), were simultaneously monitored in this assay. Acetyl coenzyme A (CoA), malonyl-CoA, adenosine triphosphate (ATP), and adenosine diphosphate (ADP) were separated by capillary electrophoresis, and the depletion of ATP and acetyl-CoA as well as the production of ADP and malonyl-CoA were monitored. Inhibition of holo-ACC by the BC inhibitor, 2-amino-N,N-dibenzyloxazole-5-carboxamide, and the carboxyltransferase inhibitor, andrimid, was confirmed using this assay. A previously reported off-column CE assay for only the CT component of ACC was optimized, and an off-column CE assay for the BC component of ACC also was developed.
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39
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Chopra I. The 2012 Garrod lecture: discovery of antibacterial drugs in the 21st century. J Antimicrob Chemother 2012; 68:496-505. [PMID: 23134656 DOI: 10.1093/jac/dks436] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The discovery and development of antibacterial drugs in the twentieth century were major scientific and medical achievements that have had profound benefits for human society. However, in the twenty-first century the widespread global occurrence of bacteria resistant to the antibiotics and synthetic drugs discovered in the previous century threatens to reverse our ability to treat infectious diseases. Although some new drugs are in development they do not adequately cover growing medical needs. Furthermore, these drugs are mostly derivatives of older classes already in use and therefore prone to existing bacterial resistance mechanisms. Thus, new drug classes are urgently needed. Despite investment in antibacterial drug discovery, no new drug class has been discovered in the past 20 years. In this review, based upon my career as a research scientist in the field of antibacterial drug discovery, I consider some of the technical reasons for the recent failure and look to the future developments that may help to reverse the poor current success rate. Diversification of screening libraries to include new natural products will be important as well as ensuring that the promising drug hits arising from structure-based drug design can achieve effective concentrations at their target sites within the bacterial cell.
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Affiliation(s)
- Ian Chopra
- School of Molecular and Cellular Biology and Antimicrobial Research Centre, University of Leeds, Leeds LS2 9JT, UK.
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40
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Wu C, Dunaway-Mariano D, Mariano PS. Design, synthesis, and evaluation of inhibitors of pyruvate phosphate dikinase. J Org Chem 2012; 78:1910-22. [PMID: 23094589 DOI: 10.1021/jo3018473] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pyruvate phosphate dikinase (PPDK) catalyzes the phosphorylation reaction of pyruvate that forms phosphoenolpyruvate (PEP) via two partial reactions: PPDK + ATP + P(i) → PPDK-P + AMP + PP(i) and PPDK-P + pyruvate → PEP + PPDK. Based on its role in the metabolism of microbial human pathogens, PPDK is a potential drug target. A screen of substances that bind to the PPDK ATP-grasp domain active site revealed that flavone analogues are potent inhibitors of the Clostridium symbiosum PPDK. In silico modeling studies suggested that placement of a 3–6 carbon-tethered ammonium substituent at the 3′- or 4′-positions of 5,7-dihydroxyflavones would result in favorable electrostatic interactions with the PPDK Mg-ATP binding site. As a result, polymethylene-tethered amine derivatives of 5,7-dihydroxyflavones were prepared. Steady-state kinetic analysis of these substances demonstrates that the 4′-aminohexyl-5,7-dyhydroxyflavone 10 is a potent competitive PPDK inhibitor (K(i) = 1.6 ± 0.1 μM). Single turnover experiments were conducted using 4′-aminopropyl-5,7-dihydroxyflavone 7 to show that this flavone specifically targets the ATP binding site and inhibits catalysis of only the PPDK + ATP + P(i) → PPDK-P + AMP PP(i) partial reaction. Finally, the 4′-aminopbutyl-5,7-dihydroxyflavone 8 displays selectivity for inhibition of PPDK versus other enzymes that utilize ATP and NAD.
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Affiliation(s)
- Chun Wu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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41
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Klein T, Henn C, de Jong JC, Zimmer C, Kirsch B, Maurer CK, Pistorius D, Müller R, Steinbach A, Hartmann RW. Identification of small-molecule antagonists of the Pseudomonas aeruginosa transcriptional regulator PqsR: biophysically guided hit discovery and optimization. ACS Chem Biol 2012; 7:1496-501. [PMID: 22765028 DOI: 10.1021/cb300208g] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The Gram-negative pathogen Pseudomonas aeruginosa produces an intercellular alkyl quinolone signaling molecule, the Pseudomonas quinolone signal. The pqs quorum sensing communication system that is characteristic for P. aeruginosa regulates the production of virulence factors. Therefore, we consider the pqs system a novel target to limit P. aeruginosa pathogenicity. Here, we present small molecules targeting a key player of the pqs system, PqsR. A rational design strategy in combination with surface plasmon resonance biosensor analysis led to the identification of PqsR binders. Determination of thermodynamic binding signatures and functional characterization in E. coli guided the hit optimization, resulting in the potent hydroxamic acid derived PqsR antagonist 11 (IC(50) = 12.5 μM). Remarkably it displayed a comparable potency in P. aeruginosa (IC(50) = 23.6 μM) and reduced the production of the virulence factor pyocyanin. Beyond this, site-directed mutagenesis together with thermodynamic analysis provided insights into the energetic characteristics of protein-ligand interactions. Thus the identified PqsR antagonists are promising scaffolds for further drug design efforts against this important pathogen.
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Affiliation(s)
- Tobias Klein
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Claudia Henn
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Johannes C. de Jong
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Christina Zimmer
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Benjamin Kirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Christine K. Maurer
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Dominik Pistorius
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Anke Steinbach
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus
C2.3, 66123 Saarbrücken, Germany
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42
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Fabbretti A, Brandi L, Petrelli D, Pon CL, Castañedo NR, Medina R, Gualerzi CO. The antibiotic Furvina® targets the P-site of 30S ribosomal subunits and inhibits translation initiation displaying start codon bias. Nucleic Acids Res 2012; 40:10366-74. [PMID: 22941660 PMCID: PMC3488254 DOI: 10.1093/nar/gks822] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Furvina®, also denominated G1 (MW 297), is a synthetic nitrovinylfuran [2-bromo-5-(2-bromo-2-nitrovinyl)-furan] antibiotic with a broad antimicrobial spectrum. An ointment (Dermofural®) containing G1 as the only active principle is currently marketed in Cuba and successfully used to treat dermatological infections. Here we describe the molecular target and mechanism of action of G1 in bacteria and demonstrate that in vivo G1 preferentially inhibits protein synthesis over RNA, DNA and cell wall synthesis. Furthermore, we demonstrate that G1 targets the small ribosomal subunit, binds at or near the P-decoding site and inhibits its function interfering with the ribosomal binding of fMet-tRNA during 30S initiation complex (IC) formation ultimately inhibiting translation. Notably, this G1 inhibition displays a bias for the nature (purine vs. pyrimidine) of the 3′-base of the codon, occurring efficiently only when the mRNA directing 30S IC formation and translation contains the canonical AUG initiation triplet or the rarely found AUA triplet, but hardly occurs when the mRNA start codon is either one of the non-canonical triplets AUU or AUC. This codon discrimination by G1 is reminiscent, though of opposite type of that displayed by IF3 in its fidelity function, and remarkably does not occur in the absence of this factor.
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Affiliation(s)
- Attilio Fabbretti
- Laboratory of Genetics, Department of Biosciences & Biotechnology, University of Camerino, 62032 Camerino, MC, Italy.
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43
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Structure and function of biotin-dependent carboxylases. Cell Mol Life Sci 2012; 70:863-91. [PMID: 22869039 DOI: 10.1007/s00018-012-1096-0] [Citation(s) in RCA: 258] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 12/14/2022]
Abstract
Biotin-dependent carboxylases include acetyl-CoA carboxylase (ACC), propionyl-CoA carboxylase (PCC), 3-methylcrotonyl-CoA carboxylase (MCC), geranyl-CoA carboxylase, pyruvate carboxylase (PC), and urea carboxylase (UC). They contain biotin carboxylase (BC), carboxyltransferase (CT), and biotin-carboxyl carrier protein components. These enzymes are widely distributed in nature and have important functions in fatty acid metabolism, amino acid metabolism, carbohydrate metabolism, polyketide biosynthesis, urea utilization, and other cellular processes. ACCs are also attractive targets for drug discovery against type 2 diabetes, obesity, cancer, microbial infections, and other diseases, and the plastid ACC of grasses is the target of action of three classes of commercial herbicides. Deficiencies in the activities of PCC, MCC, or PC are linked to serious diseases in humans. Our understanding of these enzymes has been greatly enhanced over the past few years by the crystal structures of the holoenzymes of PCC, MCC, PC, and UC. The structures reveal unanticipated features in the architectures of the holoenzymes, including the presence of previously unrecognized domains, and provide a molecular basis for understanding their catalytic mechanism as well as the large collection of disease-causing mutations in PCC, MCC, and PC. This review will summarize the recent advances in our knowledge on the structure and function of these important metabolic enzymes.
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44
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Scott DE, Coyne AG, Hudson SA, Abell C. Fragment-Based Approaches in Drug Discovery and Chemical Biology. Biochemistry 2012; 51:4990-5003. [DOI: 10.1021/bi3005126] [Citation(s) in RCA: 324] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Duncan E. Scott
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Sean A. Hudson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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45
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Synthesis and evaluation of anti-tubercular and antibacterial activities of new 4-(2,6-dichlorobenzyloxy)phenyl thiazole, oxazole and imidazole derivatives. Part 2. Eur J Med Chem 2012; 49:164-71. [DOI: 10.1016/j.ejmech.2012.01.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 11/20/2022]
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46
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Polyak SW, Abell AD, Wilce MCJ, Zhang L, Booker GW. Structure, function and selective inhibition of bacterial acetyl-coa carboxylase. Appl Microbiol Biotechnol 2011; 93:983-92. [PMID: 22183085 DOI: 10.1007/s00253-011-3796-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/21/2011] [Accepted: 11/24/2011] [Indexed: 11/24/2022]
Abstract
Acetyl-CoA carboxylase (ACC) catalyses the first committed step in fatty acid biosynthesis: a metabolic pathway required for several important biological processes including the synthesis and maintenance of cellular membranes. ACC employs a covalently attached biotin moiety to bind a carboxyl anion and then transfer it to acetyl-CoA, yielding malonyl-CoA. These activities occur at two different subsites: the biotin carboxylase (BC) and carboxyltransferase (CT). Structural biology, together with small molecule inhibitor studies, has provided new insights into the molecular mechanisms that govern ACC catalysis, specifically the BC and CT subunits. Here, we review these recent findings and highlight key differences between the bacterial and eukaryotic isozymes with a view to establish those features that provide an opportunity for selective inhibition. Especially important are examples of highly selective small molecule inhibitors capable of differentiating between ACCs from different phyla. The implications for early stage antibiotic discovery projects, stemming from these studies, are discussed.
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Affiliation(s)
- S W Polyak
- School of Molecular and Biomedical Science, University of Adelaide, North Tce, Adelaide, South Australia 5005, Australia.
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47
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Fawaz MV, Topper M, Firestine SM. The ATP-grasp enzymes. Bioorg Chem 2011; 39:185-91. [PMID: 21920581 PMCID: PMC3243065 DOI: 10.1016/j.bioorg.2011.08.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/12/2011] [Accepted: 08/13/2011] [Indexed: 12/17/2022]
Abstract
The ATP-grasp enzymes consist of a superfamily of 21 proteins that contain an atypical ATP-binding site, called the ATP-grasp fold. The ATP-grasp fold is comprised of two α+β domains that "grasp" a molecule of ATP between them and members of the family typically have an overall structural design containing three common conserved focal domains. The founding members of the family consist of biotin carboxylase, d-ala-d-ala ligase and glutathione synthetase, all of which catalyze the ATP-assisted reaction of a carboxylic acid with a nucleophile via the formation of an acylphosphate intermediate. While most members of the superfamily follow this mechanistic pathway, studies have demonstrated that two enzymes catalyze only the phosphoryl transfer step and thus are kinases instead of ligases. Members of the ATP-grasp superfamily are found in several metabolic pathways including de novo purine biosynthesis, gluconeogenesis, and fatty acid synthesis. Given the critical nature of these enzymes, researchers have actively sought the development of potent inhibitors of several members of the superfamily as antibacterial and anti-obseity agents. In this review, we will discuss the structure, function, mechanism, and inhibition of the ATP-grasp enzymes.
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Affiliation(s)
| | | | - Steven M. Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201
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48
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Wencewicz TA, Yang B, Rudloff JR, Oliver AG, Miller MJ. N-O chemistry for antibiotics: discovery of N-alkyl-N-(pyridin-2-yl)hydroxylamine scaffolds as selective antibacterial agents using nitroso Diels-Alder and ene chemistry. J Med Chem 2011; 54:6843-58. [PMID: 21859126 PMCID: PMC3188665 DOI: 10.1021/jm200794r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The discovery, syntheses, and structure-activity relationships (SAR) of a new family of heterocyclic antibacterial compounds based on N-alkyl-N-(pyridin-2-yl)hydroxylamine scaffolds are described. A structurally diverse library of ∼100 heterocyclic molecules generated from Lewis acid-mediated nucleophilic ring-opening reactions with nitroso Diels-Alder cycloadducts and nitroso ene reactions with substituted alkenes was evaluated in whole cell antibacterial assays. Compounds containing the N-alkyl-N-(pyridin-2-yl)hydroxylamine structure demonstrated selective and potent antibacterial activity against the Gram-positive bacterium Micrococcus luteus ATCC 10240 (MIC(90) = 2.0 μM or 0.41 μg/mL) and moderate activity against other Gram-positive strains including antibiotic resistant strains of Staphylococcus aureus (MRSA) and Enterococcus faecalis (VRE). A new synthetic route to the active core was developed using palladium-catalyzed Buchwald-Hartwig amination reactions of N-alkyl-O-(4-methoxybenzyl)hydroxylamines with 2-halo-pyridines that facilitated SAR studies and revealed the simplest active structural fragment. This work shows the value of using a combination of diversity-oriented synthesis (DOS) and parallel synthesis for identifying new antibacterial scaffolds.
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Affiliation(s)
- Timothy A. Wencewicz
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Baiyuan Yang
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - James R. Rudloff
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Allen G. Oliver
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Marvin J. Miller
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
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49
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Evaluation of pharmacokinetic/pharmacodynamic relationships of PD-0162819, a biotin carboxylase inhibitor representing a new class of antibacterial compounds, using in vitro infection models. Antimicrob Agents Chemother 2011; 56:124-9. [PMID: 21986824 DOI: 10.1128/aac.00090-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present study investigated the pharmacokinetic/pharmacodynamic (PK/PD) relationships of a prototype biotin carboxylase (BC) inhibitor, PD-0162819, against Haemophilus influenzae 3113 in static concentration time-kill (SCTK) and one-compartment chemostat in vitro infection models. H. influenzae 3113 was exposed to PD-0162819 concentrations of 0.5 to 16× the MIC (MIC = 0.125 μg/ml) and area-under-the-curve (AUC)/MIC ratios of 1 to 1,100 in SCTK and chemostat experiments, respectively. Serial samples were collected over 24 h. For efficacy driver analysis, a sigmoid maximum-effect (E(max)) model was fitted to the relationship between bacterial density changes over 24 h and corresponding PK/PD indices. A semimechanistic PK/PD model describing the time course of bacterial growth and death was developed. The AUC/MIC ratio best explained efficacy (r(2) = 0.95) compared to the peak drug concentration (C(max))/MIC ratio (r(2) = 0.76) and time above the MIC (T>MIC) (r(2) = 0.88). Static effects and 99.9% killing were achieved at AUC/MIC values of 500 and 600, respectively. For time course analysis, the net bacterial growth rate constant, maximum bacterial density, and maximum kill rate constant were similar in SCTK and chemostat studies, but PD-0162819 was more potent in SCTK than in the chemostat (50% effective concentration [EC(50)] = 0.046 versus 0.34 μg/ml). In conclusion, basic PK/PD relationships for PD-0162819 were established using in vitro dynamic systems. Although the bacterial growth parameters and maximum drug effects were similar in SCTK and the chemostat system, PD-0162819 appeared to be more potent in SCTK, illustrating the importance of understanding the differences in preclinical models. Additional studies are needed to determine the in vivo relevance of these results.
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50
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Barry CE. Lessons from seven decades of antituberculosis drug discovery. Curr Top Med Chem 2011; 11:1216-25. [PMID: 21401509 DOI: 10.2174/156802611795429158] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 11/25/2010] [Indexed: 12/31/2022]
Abstract
Despite massive global efforts tuberculosis rates continue to climb and drug-resistance rates are rising to alarming levels. Discovering new agents for treating this bacterial pathogen poses unique challenges, but these challenges have been faced throughout the entire modern history of research into anti-infectives. This review looks back at every decade since the 1940s and summarizes the most important drugs developed during each decade highlighting the lessons learned during these successful medicinal chemistry programs. Looking forward we must accelerate the integration of these past lessons with the impressive advances that have been made in the basic understanding of the biology of this disease.
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Affiliation(s)
- Clifton E Barry
- Tuberculosis Research Section, LCID, NIAID, NIH, Bethesda, MD, USA.
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