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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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2
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Khomenko TM, Korchagina DV, Baev DS, Vassiliev PM, Volcho KP, Salakhutdinov NF. Antimicrobial Activity of Substituted Benzopentathiepin-6-amines. J Antibiot (Tokyo) 2019; 72:590-599. [PMID: 31118480 DOI: 10.1038/s41429-019-0191-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 11/09/2022]
Abstract
A number of substituted benzopentathiepin-6-amines and their analogues without a polysulfur ring were synthesized and evaluated in vitro for antimicrobial activity against a panel of reference bacterial and fungal strains. Trifluoroacetamide 14 demonstrated high antibacterial activity against Staphylococcus aureus (MRSA strain) with a MIC of 4 μg/mL, which was four-fold higher than the activity of a reference drug amoxicillin. This compound was also most active against the Candida albicans fungus (MIC of 1 μg ml-1), whereas amide 17 containing a morpholine substituent was most active against the Cryptococcus neoformans fungus (MIC of 2 μg ml-1). These compounds have no hemolytic activity and are low cytotoxic. Replacement of the pentathiepine ring with 1,3-dithiolan-2-one or 1,3-dithiolane moieties leads to loss of antimicrobial activity. Based on the QSAR analysis and molecular docking data, bacterial DNA ligase might be one of the targets for the antibacterial activity of substituted benzopentathiepin-6-amines against S. aureus.
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Affiliation(s)
- Tatyana M Khomenko
- Novosibirsk Institute of Organic Chemistry, Lavrentjev av. 9, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova st. 1, Novosibirsk, 630090, Russia
| | - Dina V Korchagina
- Novosibirsk Institute of Organic Chemistry, Lavrentjev av. 9, Novosibirsk, 630090, Russia
| | - Dmitry S Baev
- Novosibirsk Institute of Organic Chemistry, Lavrentjev av. 9, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova st. 1, Novosibirsk, 630090, Russia
| | - Pavel M Vassiliev
- Volgograd State Medical University, Pavshikh Bortsov Sq. 1, Volgograd, 400131, Russia
| | - Konstantin P Volcho
- Novosibirsk Institute of Organic Chemistry, Lavrentjev av. 9, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova st. 1, Novosibirsk, 630090, Russia.
| | - Nariman F Salakhutdinov
- Novosibirsk Institute of Organic Chemistry, Lavrentjev av. 9, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova st. 1, Novosibirsk, 630090, Russia
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Rationale redesign of type III secretion systems: toward the development of non-pathogenic E. coli for in vivo delivery of therapeutic payloads. Curr Opin Microbiol 2017; 41:1-7. [PMID: 29141238 DOI: 10.1016/j.mib.2017.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 12/12/2022]
Abstract
Transkingdom secretion systems that bacteria use to inject proteins directly into the cytosol of mammalian host cells play an essential role in the virulence of many Gram-negative bacterial pathogens. Current efforts are underway to repurpose these machines as novel therapeutics; type III secretion systems as vectors for the delivery of proteins of therapeutic value including heterologous antigens for vaccine development and type IV secretion systems as vectors for DNA. While initial studies focused on the use of attenuated or replication incompetent pathogens, the recent development of non-pathogenic Escherichia coli that encode programmable type III secretion systems expands possibilities for the in vivo directed delivery of therapeutic payloads.
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Sethi G, Chopra G, Samudrala R. Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform. Mini Rev Med Chem 2016; 15:705-17. [PMID: 25694071 DOI: 10.2174/1389557515666150219145148] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 10/30/2014] [Accepted: 11/25/2014] [Indexed: 01/27/2023]
Abstract
We have examined the effect of eight different protein classes (channels, GPCRs, kinases, ligases, nuclear receptors, proteases, phosphatases, transporters) on the benchmarking performance of the CANDO drug discovery and repurposing platform (http://protinfo.org/cando). The first version of the CANDO platform utilizes a matrix of predicted interactions between 48278 proteins and 3733 human ingestible compounds (including FDA approved drugs and supplements) that map to 2030 indications/diseases using a hierarchical chem and bio-informatic fragment based docking with dynamics protocol (> one billion predicted interactions considered). The platform uses similarity of compound-proteome interaction signatures as indicative of similar functional behavior and benchmarking accuracy is calculated across 1439 indications/diseases with more than one approved drug. The CANDO platform yields a significant correlation (0.99, p-value < 0.0001) between the number of proteins considered and benchmarking accuracy obtained indicating the importance of multitargeting for drug discovery. Average benchmarking accuracies range from 6.2 % to 7.6 % for the eight classes when the top 10 ranked compounds are considered, in contrast to a range of 5.5 % to 11.7 % obtained for the comparison/control sets consisting of 10, 100, 1000, and 10000 single best performing proteins. These results are generally two orders of magnitude better than the average accuracy of 0.2% obtained when randomly generated (fully scrambled) matrices are used. Different indications perform well when different classes are used but the best accuracies (up to 11.7% for the top 10 ranked compounds) are achieved when a combination of classes are used containing the broadest distribution of protein folds. Our results illustrate the utility of the CANDO approach and the consideration of different protein classes for devising indication specific protocols for drug repurposing as well as drug discovery.
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Affiliation(s)
| | | | - Ram Samudrala
- Department of Biomedical Informatics, School of Medicine and Biomedical Sciences, State University of New York (SUNY), 923 Main Street, Buffalo, NY 14203, USA.
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Ravishankar S, Ambady A, Ramu H, Mudugal NV, Tunduguru R, Anbarasu A, Sharma UK, Sambandamurthy VK, Ramaiah S. An IPTG Inducible Conditional Expression System for Mycobacteria. PLoS One 2015; 10:e0134562. [PMID: 26247874 PMCID: PMC4527713 DOI: 10.1371/journal.pone.0134562] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/12/2015] [Indexed: 12/21/2022] Open
Abstract
Conditional expression strains serve as a valuable tool to study the essentiality and to establish the vulnerability of a target under investigation in a drug discovery program. While essentiality implies an absolute requirement of a target function, vulnerability provides valuable information on the extent to which a target function needs to be depleted to achieve bacterial growth inhibition followed by cell death. The critical feature of an ideal conditional expression system is its ability to tightly regulate gene expression to achieve the full spectrum spanning from a high level of expression in order to support growth and near zero level of expression to mimic conditions of gene knockout. A number of bacterial conditional expression systems have been reported for use in mycobacteria. The utility of an isopropylthiogalactoside (IPTG) inducible system in mycobacteria has been reported for protein overexpression and anti-sense gene expression from a replicating multi-copy plasmid. Herein, we report the development of a versatile set of non-replicating IPTG inducible vectors for mycobacteria which can be used for generation of conditional expression strains through homologous recombination. The role of a single lac operator versus a double lac operator to regulate gene expression was evaluated by monitoring the expression levels of β-galactosidase in Mycobacterium smegmatis. These studies indicated a significant level of leaky expression from the vector with a single lac operator but none from the vector with double lac operator. The significance of the double lac operator vector for target validation was established by monitoring the growth kinetics of an inhA, a rpoB and a ftsZ conditional expression strain grown in the presence of different concentrations of IPTG. The utility of this inducible system in identifying target specific inhibitors was established by screening a focussed library of small molecules using an inhA and a rpoB conditional expression strain.
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Affiliation(s)
- Sudha Ravishankar
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
- * E-mail:
| | - Anisha Ambady
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | - Haripriya Ramu
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | - Naina Vinay Mudugal
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | | | - Anand Anbarasu
- School of Biosciences & Technology, VIT University, Vellore, Tamil Nadu, India
| | - Umender K. Sharma
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | | | - Sudha Ramaiah
- School of Biosciences & Technology, VIT University, Vellore, Tamil Nadu, India
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Howard S, Amin N, Benowitz AB, Chiarparin E, Cui H, Deng X, Heightman TD, Holmes DJ, Hopkins A, Huang J, Jin Q, Kreatsoulas C, Martin ACL, Massey F, McCloskey L, Mortenson PN, Pathuri P, Tisi D, Williams PA. Fragment-based discovery of 6-azaindazoles as inhibitors of bacterial DNA ligase. ACS Med Chem Lett 2013; 4:1208-12. [PMID: 24900632 DOI: 10.1021/ml4003277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/10/2013] [Indexed: 02/06/2023] Open
Abstract
Herein we describe the application of fragment-based drug design to bacterial DNA ligase. X-ray crystallography was used to guide structure-based optimization of a fragment-screening hit to give novel, nanomolar, AMP-competitive inhibitors. The lead compound 13 showed antibacterial activity across a range of pathogens. Data to demonstrate mode of action was provided using a strain of S. aureus, engineered to overexpress DNA ligase.
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Affiliation(s)
- Steven Howard
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Nader Amin
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Andrew B. Benowitz
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Elisabetta Chiarparin
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Haifeng Cui
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Xiaodong Deng
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Tom D. Heightman
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - David J. Holmes
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Anna Hopkins
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Jianzhong Huang
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Qi Jin
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Constantine Kreatsoulas
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Agnes C. L. Martin
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Frances Massey
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lynn McCloskey
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Paul N. Mortenson
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Puja Pathuri
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Dominic Tisi
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Pamela A. Williams
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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The kinetic mechanism of S. pneumoniae DNA ligase and inhibition by adenosine-based antibacterial compounds. Biochem Pharmacol 2012; 84:654-60. [PMID: 22743594 DOI: 10.1016/j.bcp.2012.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/07/2012] [Accepted: 06/18/2012] [Indexed: 11/23/2022]
Abstract
The NAD-dependent DNA ligase is an excellent target for the discovery of antibacterial agents with a novel mode of action. In this work the DNA ligase from Streptococcus pneumoniae was investigated for its steady-state kinetic parameters and inhibition by compounds with an adenosine substructure. Inhibition by substrate DNA that was observed in the enzyme turnover experiments was verified by direct binding measurements using isothermal titration calorimetry (ITC). The substrate-inhibited enzyme form was identified as deadenylated DNA ligase. The binding potencies of 2-(butylsulfanyl) adenosine and 2-(cyclopentyloxy) adenosine were not significantly affected by the presence of the enzyme-bound DNA substrate. Finally, a mutant protein was prepared that was known to confer resistance to the adenosine compounds' antibacterial activity. The mutant protein was shown to have little catalytic impairment yet it was less susceptible to adenosine compound inhibition.
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Mechanistic assessment of DNA ligase as an antibacterial target in Staphylococcus aureus. Antimicrob Agents Chemother 2012; 56:4095-102. [PMID: 22585221 DOI: 10.1128/aac.00215-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We report the use of a known pyridochromanone inhibitor with antibacterial activity to assess the validity of NAD(+)-dependent DNA ligase (LigA) as an antibacterial target in Staphylococcus aureus. Potent inhibition of purified LigA was demonstrated in a DNA ligation assay (inhibition constant [K(i)] = 4.0 nM) and in a DNA-independent enzyme adenylation assay using full-length LigA (50% inhibitory concentration [IC(50)] = 28 nM) or its isolated adenylation domain (IC(50) = 36 nM). Antistaphylococcal activity was confirmed against methicillin-susceptible and -resistant S. aureus (MSSA and MRSA) strains (MIC = 1.0 μg/ml). Analysis of spontaneous resistance potential revealed a high frequency of emergence (4 × 10(-7)) of high-level resistant mutants (MIC > 64) with associated ligA lesions. There were no observable effects on growth rate in these mutants. Of 22 sequenced clones, 3 encoded point substitutions within the catalytic adenylation domain and 19 in the downstream oligonucleotide-binding (OB) fold and helix-hairpin-helix (HhH) domains. In vitro characterization of the enzymatic properties of four selected mutants revealed distinct signatures underlying their resistance to inhibition. The infrequent adenylation domain mutations altered the kinetics of adenylation and probably elicited resistance directly. In contrast, the highly represented OB fold domain mutations demonstrated a generalized resistance mechanism in which covalent LigA activation proceeds normally and yet the parameters of downstream ligation steps are altered. A resulting decrease in substrate K(m) and a consequent increase in substrate occupancy render LigA resistant to competitive inhibition. We conclude that the observed tolerance of staphylococcal cells to such hypomorphic mutations probably invalidates LigA as a viable target for antistaphylococcal chemotherapy.
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Brötz-Oesterhelt H, Sass P. Postgenomic strategies in antibacterial drug discovery. Future Microbiol 2010; 5:1553-79. [DOI: 10.2217/fmb.10.119] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
During the last decade the field of antibacterial drug discovery has changed in many aspects including bacterial organisms of primary interest, discovery strategies applied and pharmaceutical companies involved. Target-based high-throughput screening had been disappointingly unsuccessful for antibiotic research. Understanding of this lack of success has increased substantially and the lessons learned refer to characteristics of targets, screening libraries and screening strategies. The ‘genomics’ approach was replaced by a diverse array of discovery strategies, for example, searching for new natural product leads among previously abandoned compounds or new microbial sources, screening for synthetic inhibitors by targeted approaches including structure-based design and analyses of focused libraries and designing resistance-breaking properties into antibiotics of established classes. Furthermore, alternative treatment options are being pursued including anti-virulence strategies and immunotherapeutic approaches. This article summarizes the lessons learned from the genomics era and describes discovery strategies resulting from that knowledge.
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Affiliation(s)
- Heike Brötz-Oesterhelt
- AiCuris, Wuppertal, Germany, Institute for Pharmaceutical Biology, University of Duesseldorf, Universitätsstrasse 1, Building 26.23.U1, Germany
| | - Peter Sass
- Institute of Medical Microbiology, Immunology & Parasitology, Pharmaceutical Microbiology Section, University of Bonn, Germany
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Swoboda JG, Campbell J, Meredith TC, Walker S. Wall teichoic acid function, biosynthesis, and inhibition. Chembiochem 2010; 11:35-45. [PMID: 19899094 DOI: 10.1002/cbic.200900557] [Citation(s) in RCA: 282] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jonathan G Swoboda
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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