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Block AM, Wiegert PC, Namugenyi SB, Tischler AD. Transposon sequencing reveals metabolic pathways essential for Mycobacterium tuberculosis infection. PLoS Pathog 2024; 20:e1011663. [PMID: 38498580 PMCID: PMC10977890 DOI: 10.1371/journal.ppat.1011663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/28/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
New drugs are needed to shorten and simplify treatment of tuberculosis caused by Mycobacterium tuberculosis. Metabolic pathways that M. tuberculosis requires for growth or survival during infection represent potential targets for anti-tubercular drug development. Genes and metabolic pathways essential for M. tuberculosis growth in standard laboratory culture conditions have been defined by genome-wide genetic screens. However, whether M. tuberculosis requires these essential genes during infection has not been comprehensively explored because mutant strains cannot be generated using standard methods. Here we show that M. tuberculosis requires the phenylalanine (Phe) and de novo purine and thiamine biosynthetic pathways for mammalian infection. We used a defined collection of M. tuberculosis transposon (Tn) mutants in essential genes, which we generated using a custom nutrient-rich medium, and transposon sequencing (Tn-seq) to identify multiple central metabolic pathways required for fitness in a mouse infection model. We confirmed by individual retesting and complementation that mutations in pheA (Phe biosynthesis) or purF (purine and thiamine biosynthesis) cause death of M. tuberculosis in the absence of nutrient supplementation in vitro and strong attenuation in infected mice. Our findings show that Tn-seq with defined Tn mutant pools can be used to identify M. tuberculosis genes required during mouse lung infection. Our results also demonstrate that M. tuberculosis requires Phe and purine/thiamine biosynthesis for survival in the host, implicating these metabolic pathways as prime targets for the development of new antibiotics to combat tuberculosis.
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Affiliation(s)
- Alisha M. Block
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, United States of America
| | - Parker C. Wiegert
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, United States of America
| | - Sarah B. Namugenyi
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, United States of America
| | - Anna D. Tischler
- Department of Microbiology and Immunology, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, United States of America
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Woodhead AJ, Erlanson DA, de Esch IJP, Holvey RS, Jahnke W, Pathuri P. Fragment-to-Lead Medicinal Chemistry Publications in 2022. J Med Chem 2024; 67:2287-2304. [PMID: 38289623 DOI: 10.1021/acs.jmedchem.3c02070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
This Perspective is the eighth in an annual series that summarizes successful fragment-to-lead (F2L) case studies published each year. A tabulated summary of relevant articles published in 2022 is provided, and features such as target class, screening methods, and ligand efficiency are discussed both for the 2022 examples and for the combined examples over the years 2015-2022. In addition, trends and new developments in the field are summarized. In 2022, 18 publications described successful fragment-to-lead studies, including the development of three clinical compounds (MTRX1719, MK-8189, and BI-823911).
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Affiliation(s)
- Andrew J Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Blvd., South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rhian S Holvey
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Wolfgang Jahnke
- Novartis Biomedical Research, Discovery Sciences, 4002 Basel, Switzerland
| | - Puja Pathuri
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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Ayoub N, Gedeon A, Munier-Lehmann H. A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis. Front Pharmacol 2024; 15:1329011. [PMID: 38444943 PMCID: PMC10912719 DOI: 10.3389/fphar.2024.1329011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
De novo purine nucleotide biosynthesis (DNPNB) consists of sequential reactions that are majorly conserved in living organisms. Several regulation events take place to maintain physiological concentrations of adenylate and guanylate nucleotides in cells and to fine-tune the production of purine nucleotides in response to changing cellular demands. Recent years have seen a renewed interest in the DNPNB enzymes, with some being highlighted as promising targets for therapeutic molecules. Herein, a review of two newly revealed modes of regulation of the DNPNB pathway has been carried out: i) the unprecedent allosteric regulation of one of the limiting enzymes of the pathway named inosine 5'-monophosphate dehydrogenase (IMPDH), and ii) the supramolecular assembly of DNPNB enzymes. Moreover, recent advances that revealed the therapeutic potential of DNPNB enzymes in bacteria could open the road for the pharmacological development of novel antibiotics.
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Affiliation(s)
- Nour Ayoub
- Institut Pasteur, Université Paris Cité, INSERM UMRS-1124, Paris, France
| | - Antoine Gedeon
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS UMR7203, Laboratoire des Biomolécules, LBM, Paris, France
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Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2023; 12:antibiotics12020315. [PMID: 36830226 PMCID: PMC9951956 DOI: 10.3390/antibiotics12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (KD ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.
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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:ijms231810669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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Prejanò M, Škerlová J, Stenmark P, Himo F. Reaction Mechanism of Human PAICS Elucidated by Quantum Chemical Calculations. J Am Chem Soc 2022; 144:14258-14268. [PMID: 35914774 PMCID: PMC9376930 DOI: 10.1021/jacs.2c05072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Human PAICS is a bifunctional enzyme that is involved
in the de novo purine biosynthesis, catalyzing the
conversion of
aminoimidazole ribonucleotide (AIR) into N-succinylcarboxamide-5-aminoimidazole
ribonucleotide (SAICAR). It comprises two distinct active sites, AIR
carboxylase (AIRc) where the AIR is initially converted to carboxyaminoimidazole
ribonucleotide (CAIR) by reaction with CO2 and SAICAR synthetase
(SAICARs) in which CAIR then reacts with an aspartate to form SAICAR,
in an ATP-dependent reaction. Human PAICS is a promising target for
the treatment of various types of cancer, and it is therefore of high
interest to develop a detailed understanding of its reaction mechanism.
In the present work, density functional theory calculations are employed
to investigate the PAICS reaction mechanism. Starting from the available
crystal structures, two large models of the AIRc and SAICARs active
sites are built and different mechanistic proposals for the carboxylation
and phosphorylation–condensation mechanisms are examined. For
the carboxylation reaction, it is demonstrated that it takes place
in a two-step mechanism, involving a C–C bond formation followed
by a deprotonation of the formed tetrahedral intermediate (known as
isoCAIR) assisted by an active site histidine residue. For the phosphorylation–condensation
reaction, it is shown that the phosphorylation of CAIR takes place
before the condensation reaction with the aspartate. It is further
demonstrated that the three active site magnesium ions are involved
in binding the substrates and stabilizing the transition states and
intermediates of the reaction. The calculated barriers are in good
agreement with available experimental data.
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Affiliation(s)
- Mario Prejanò
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 160 00 Prague, Czech Republic
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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Andreu JM, Huecas S, Araújo-Bazán L, Vázquez-Villa H, Martín-Fontecha M. The Search for Antibacterial Inhibitors Targeting Cell Division Protein FtsZ at Its Nucleotide and Allosteric Binding Sites. Biomedicines 2022; 10:biomedicines10081825. [PMID: 36009372 PMCID: PMC9405007 DOI: 10.3390/biomedicines10081825] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
The global spread of bacterial antimicrobial resistance is associated to millions of deaths from bacterial infections per year, many of which were previously treatable. This, combined with slow antibiotic deployment, has created an urgent need for developing new antibiotics. A still clinically unexploited mode of action consists in suppressing bacterial cell division. FtsZ, an assembling GTPase, is the key protein organizing division in most bacteria and an attractive target for antibiotic discovery. Nevertheless, developing effective antibacterial inhibitors targeting FtsZ has proven challenging. Here we review our decade-long multidisciplinary research on small molecule inhibitors of bacterial division, in the context of global efforts to discover FtsZ-targeting antibiotics. We focus on methods to characterize synthetic inhibitors that either replace bound GTP from the FtsZ nucleotide binding pocket conserved across diverse bacteria or selectively bind into the allosteric site at the interdomain cleft of FtsZ from Bacillus subtilis and the pathogen Staphylococcus aureus. These approaches include phenotype screening combined with fluorescence polarization screens for ligands binding into each site, followed by detailed cytological profiling, and biochemical and structural studies. The results are analyzed to design an optimized workflow to identify effective FtsZ inhibitors, and new approaches for the discovery of FtsZ-targeting antibiotics are discussed.
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Affiliation(s)
- José M. Andreu
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
- Correspondence: (J.M.A.); (M.M.-F.)
| | - Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
| | - Lidia Araújo-Bazán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain;
| | - Mar Martín-Fontecha
- Departamento de Química Orgánica, Facultad de Óptica y Optometría, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain
- Correspondence: (J.M.A.); (M.M.-F.)
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Ethyl Acetate Fraction of Bixa orellana and Its Component Ellagic Acid Exert Antibacterial and Anti-Inflammatory Properties against Mycobacterium abscessus subsp. massiliense. Antibiotics (Basel) 2022; 11:antibiotics11060817. [PMID: 35740223 PMCID: PMC9220277 DOI: 10.3390/antibiotics11060817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium abscessus subsp. massiliense (Mabs) causes chronic infections, which has led to the need for new antimycobacterial agents. In this study, we investigated the antimycobacterial and anti-inflammatory activities of the ethyl acetate fraction of Bixa orellana leaves (BoEA) and ellagic acid (ElAc). In silico analysis predicted that ElAc had low toxicity, was not mutagenic or carcinogenic, and had antimicrobial and anti-inflammatory activities. Apparently, ElAc can interact with COX2 and Dihydrofolate reductase (DHFR) enzymes, which could explain both activities. In vitro analysis showed that BoEA and ElAc exerted antimicrobial activity against Mabs (minimum inhibitory concentration of 1.56, 1.56 mg/mL and bactericidal concentration of 6.25, 3.12 mg/mL, respectively. Clarithromycin showed MIC and MBC of 1 and 6 µg/mL). Treatment with BoEA or ElAc increased survival of Tenebrio molitor larvae after lethal infection with Mabs and reduced carrageenan-induced paw edema in mice, around 40% of edema volume after the fourth hour, similarly to diclofenac. In conclusion, BoEA and ElAc exert antimicrobial effects against Mabs and have anti-inflammatory effects, making them potential sources of antimycobacterial drugs. The biological activities of ElAc may be due to its high binding affinities predicted for COX2 and DHFR enzymes.
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