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Marín M, López M, Gallego-Yerga L, Álvarez R, Peláez R. Experimental structure based drug design (SBDD) applications for anti-leishmanial drugs: A paradigm shift? Med Res Rev 2024; 44:1055-1120. [PMID: 38142308 DOI: 10.1002/med.22005] [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] [Received: 05/04/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Leishmaniasis is a group of neglected tropical diseases caused by at least 20 species of Leishmania protozoa, which are spread by the bite of infected sandflies. There are three main forms of the disease: cutaneous leishmaniasis (CL, the most common), visceral leishmaniasis (VL, also known as kala-azar, the most serious), and mucocutaneous leishmaniasis. One billion people live in areas endemic to leishmaniasis, with an annual estimation of 30,000 new cases of VL and more than 1 million of CL. New treatments for leishmaniasis are an urgent need, as the existing ones are inefficient, toxic, and/or expensive. We have revised the experimental structure-based drug design (SBDD) efforts applied to the discovery of new drugs against leishmaniasis. We have grouped the explored targets according to the metabolic pathways they belong to, and the key achieved advances are highlighted and evaluated. In most cases, SBDD studies follow high-throughput screening campaigns and are secondary to pharmacokinetic optimization, due to the majoritarian belief that there are few validated targets for SBDD in leishmaniasis. However, some SBDD strategies have significantly contributed to new drug candidates against leishmaniasis and a bigger number holds promise for future development.
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Affiliation(s)
- Miguel Marín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Marta López
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
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Hasan ME, Samir A, Khalil MM, Shafaa MW. Bioinformatics approach for prediction and analysis of the Non-Structural Protein 4B (NSP4B) of the Zika virus. J Genet Eng Biotechnol 2024; 22:100336. [PMID: 38494248 PMCID: PMC10860876 DOI: 10.1016/j.jgeb.2023.100336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
BACKGROUND The Nonstructural Protein (NSP) 4B of Zika virus of 251 amino acids from (ZIKV/Human/POLG_ZIKVF) with accession number (A0A024B7W1), Induces the production of Endoplasmic Reticulum ER-derived membrane vesicles, which are the sites of viral replication. To understand the physical basis of how proteins fold in nature and to solve the challenge of protein structure prediction, Ab-initio and comparative modeling are crucial tools. RESULTS The systematic in silico technique, ThreaDom, had only predicted one domain (4 - 190) of NSP4B. I-TASSER, and Alphafold were ranked as the best servers for full-length 3-D protein structure predictions of NSP4B, where the predicted models were evaluated quantitatively using benchmarked metrics including C-score (-3.43), TM-score (0.77949), RMSD (2.73), and Z-score (1.561). The functional and protein binding motifs were realized using motif databases, secondary and surface accessibility predictions combined with Post-Translational Modification Sites (PTMs) prediction. Two highly conserved protein-binding motifs (Flavi NS4B and Bacillus papRprotein), together with three (PTMs) (Casein Kinase II, Myristyl site, and ASN-Glycosylation site) were predicted utilizing the Motif scan and Scanprosite servers. These patterns and PTMs were associated with NSP4B's role in triggering the development of the viral replication complex and its participation in the localization of NS3 and NS5 on the membrane. Only one hit from Structural Classification of Protein (SCOP) matched the protein sequence at positions 10 to 397 and was categorized six-hairpin glycosidases superfamily according to CATH (Class, Architecture, Topology, and Homology). Integrating this NSP4B information with the templates' SCOP and CATH annotations achieves it easier to attribute structure-function/evolution links to both previously known and recently discovered protein structures.
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Affiliation(s)
- Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt.
| | - Aya Samir
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
| | - Magdy M Khalil
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt; School of Biotechnology, Badr University in Cairo, Egypt
| | - Medhat W Shafaa
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
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Sooram B, Mallikarjunachari U, Uddavesh S, Saudagar P. Pharmacophore-guided drug design using LdNMT as a model drug target for leishmaniasis. J Biomol Struct Dyn 2024; 42:863-875. [PMID: 37096664 DOI: 10.1080/07391102.2023.2196695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/22/2023] [Indexed: 04/26/2023]
Abstract
Leishmaniasis is caused by Leishmania genus parasites and has a high mortality rate. The available drugs to treat leishmaniasis fail due to acquired resistance in parasites. Several enzymes of the Leishmania parasite have been used to design new therapeutic molecules against leishmaniasis. This study uses a pharmacophore-guided approach to design the drug candidate by targeting Leishmania N-Myristoyl transferase (LdNMT). From the initial sequence analysis of LdNMT, we have identified a unique 20 amino acid stretch exploited for screening and designing the small molecules. The pharmacophore for the myristate binding site on LdNMT was elucidated, and a heatmap was constructed. The leishmanial NMT pharmacophore has similarities with other pathogenic microorganisms. Moreover, substituting alanine in pharmacophoric residues elevates the affinity of myristate with NMT. Furthermore, a molecular dynamics (MD) simulation study was conducted to ascertain the stability of the mutants and or wild type. The wild-type NMT has a comparatively low affinity to myristate compared to alanine mutants, indicating that hydrophobic residues favor the myristate binding. The molecules were initially designed by using pharmacophore as a sieving mechanism. In subsequent steps, the selected molecules screened against leishmanial unique amino acid stretch and subsequently with human, leishmanial full-size NMTs. The compounds BP5, TYI, DMU, 3PE and 4UL were the top hits and chemical features similar to the myristate. The molecule 4UL was found to be highly specific towards leishmanial NMT over human NMT, suggesting the molecule is a strong leishmanial NMT inhibitor. The molecule can be taken further to assess it in in-vitro conditions.
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Affiliation(s)
- Banesh Sooram
- Department of Biotechnology, National Institute of Technology-Warangal, Warangal, Telangana, India
| | - Uppuladinne Mallikarjunachari
- Department of High Performance Computing-Medical and Bioinformatics Applications, Centre for Development for Advanced Computing (CDAC), Pune, Maharastra, India
| | - Sonavane Uddavesh
- Department of High Performance Computing-Medical and Bioinformatics Applications, Centre for Development for Advanced Computing (CDAC), Pune, Maharastra, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology-Warangal, Warangal, Telangana, India
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Nascimento IJDS, Cavalcanti MDAT, de Moura RO. Exploring N-myristoyltransferase as a promising drug target against parasitic neglected tropical diseases. Eur J Med Chem 2023; 258:115550. [PMID: 37336067 DOI: 10.1016/j.ejmech.2023.115550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Neglected tropical diseases (NTDs) constitute a group of approximately 20 infectious diseases that mainly affect the impoverished population without basic sanitation in tropical countries. These diseases are responsible for many deaths worldwide, costing billions of dollars in public health investment to treat and control these infections. Among them are the diseases caused by protozoa of the Trypanosomatid family, which constitute Trypanosoma cruzi (Chagas disease), Trypanosoma brucei (sleeping sickness), and Leishmaniasis. In addition, there is a classification of other diseases, called the big three, AIDS, tuberculosis, and malaria, which are endemic in countries with tropical conditions. Despite the high mortality rates, there is still a gap in the treatment. The drugs have a high incidence of side effects and protozoan resistance, justifying the investment in developing new alternatives. In fact, the Target-Based Drug Design (TBDD) approach is responsible for identifying several promising compounds, and among the targets explored through this approach, N-myristoyltransferase (NMT) stands out. It is an enzyme related to the co-translational myristoylation of N-terminal glycine in various peptides. The myristoylation process is a co-translation that occurs after removing the initiator methionine. This process regulates the assembly of protein complexes and stability, which justifies its potential as a drug target. In order to propose NMT as a potential target for parasitic diseases, this review will address the entire structure and function of this enzyme and the primary studies demonstrating its promising potential against Leishmaniasis, T. cruzi, T. brucei, and malaria. We hope our information can help researchers worldwide search for potential drugs against these diseases that have been threatening the health of the world's population.
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Affiliation(s)
- Igor José Dos Santos Nascimento
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Cesmac University Center, Pharmacy Departament, Maceió, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil.
| | - Misael de Azevedo Teotônio Cavalcanti
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Ricardo Olimpio de Moura
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
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Shaw S, Roditi I. The sweet and sour sides of trypanosome social motility. Trends Parasitol 2023; 39:242-250. [PMID: 36732111 DOI: 10.1016/j.pt.2023.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Recent studies showed that the formation of elegant geometric patterns by communities of Trypanosoma brucei on semi-solid surfaces, dubbed social motility (SoMo) by its discoverers, is a manifestation of pH taxis. This is caused by procyclic forms generating and responding to pH gradients through glucose metabolism and cAMP signalling. These findings established that trypanosomes can sense and manipulate gradients, potentially helping them to navigate through host tissues. At the same time, the host itself and bystanders such as endosymbionts have the potential to shape the environment and influence the chances of successful transmission. We postulate that the ability to sense and contribute to the gradient landscape may also underlie the tissue tropism and migration of other parasites in their hosts.
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Affiliation(s)
- Sebastian Shaw
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Leroux M, Luquain-Costaz C, Lawton P, Azzouz-Maache S, Delton I. Fatty Acid Composition and Metabolism in Leishmania Parasite Species: Potential Biomarkers or Drug Targets for Leishmaniasis? Int J Mol Sci 2023; 24:ijms24054702. [PMID: 36902138 PMCID: PMC10003364 DOI: 10.3390/ijms24054702] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Fatty acids have received growing interest in Leishmania biology with the characterization of the enzymes allowing the complete fatty acid synthesis of this trypanosomatid parasite. This review presents a comparative analysis of the fatty acid profiles of the major classes of lipids and phospholipids in different species of Leishmania with cutaneous or visceral tropism. Specificities relating to the parasite forms, resistance to antileishmanial drugs, and host/parasite interactions are described as well as comparisons with other trypanosomatids. Emphasis is placed on polyunsaturated fatty acids and their metabolic and functional specificities, in particular, their conversion into oxygenated metabolites that are inflammatory mediators able to modulate metacyclogenesis and parasite infectivity. The impact of lipid status on the development of leishmaniasis and the potential of fatty acids as therapeutic targets or candidates for nutritional interventions are discussed.
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Affiliation(s)
- Marine Leroux
- CNRS 5007, LAGEPP, Université of Lyon, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
| | - Céline Luquain-Costaz
- CNRS 5007, LAGEPP, Université of Lyon, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Department of Biosciences, INSA Lyon, 69100 Villeurbanne, France
| | - Philippe Lawton
- CNRS 5007, LAGEPP, Université of Lyon, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
| | - Samira Azzouz-Maache
- CNRS 5007, LAGEPP, Université of Lyon, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
| | - Isabelle Delton
- CNRS 5007, LAGEPP, Université of Lyon, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
- Department of Biosciences, INSA Lyon, 69100 Villeurbanne, France
- Correspondence:
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Yahiya S, Saunders CN, Hassan S, Straschil U, Fischer OJ, Rueda-Zubiaurre A, Haase S, Vizcay-Barrena G, Famodimu MT, Jordan S, Delves MJ, Tate EW, Barnard A, Fuchter MJ, Baum J. A novel class of sulphonamides potently block malaria transmission by targeting a Plasmodium vacuole membrane protein. Dis Model Mech 2023; 16:dmm049950. [PMID: 36715290 PMCID: PMC9934914 DOI: 10.1242/dmm.049950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/13/2022] [Indexed: 01/31/2023] Open
Abstract
Phenotypic cell-based screens are critical tools for discovering candidate drugs for development, yet identification of the cellular target and mode of action of a candidate drug is often lacking. Using an imaging-based screen, we recently discovered an N-[(4-hydroxychroman-4-yl)methyl]-sulphonamide (N-4HCS) compound, DDD01035881, that blocks male gamete formation in the malaria parasite life cycle and subsequent transmission of the parasite to the mosquito with nanomolar activity. To identify the target(s) of DDD01035881, and of the N-4HCS class of compounds more broadly, we synthesised a photoactivatable derivative, probe 2. Photoaffinity labelling of probe 2 coupled with mass spectrometry identified the 16 kDa Plasmodium falciparum parasitophorous vacuole membrane protein Pfs16 as a potential parasite target. Complementary methods including cellular thermal shift assays confirmed that the parent molecule DDD01035881 stabilised Pfs16 in lysates from activated mature gametocytes. Combined with high-resolution, fluorescence and electron microscopy data, which demonstrated that parasites inhibited with N-4HCS compounds phenocopy the targeted deletion of Pfs16 in gametocytes, these data implicate Pfs16 as a likely target of DDD01035881. This finding establishes N-4HCS compounds as being flexible and effective starting candidates from which transmission-blocking antimalarials can be developed in the future.
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Affiliation(s)
- Sabrina Yahiya
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Charlie N. Saunders
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Sarah Hassan
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Ursula Straschil
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Oliver J. Fischer
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Ainoa Rueda-Zubiaurre
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Silvia Haase
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Gema Vizcay-Barrena
- Centre for Ultrastructural Imaging, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Mufuliat Toyin Famodimu
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Sarah Jordan
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Michael J. Delves
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Anna Barnard
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Matthew J. Fuchter
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Jake Baum
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
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Orabi MAA, Alshahrani MM, Sayed AM, Abouelela ME, Shaaban KA, Abdel-Sattar ES. Identification of Potential Leishmania N-Myristoyltransferase Inhibitors from Withania somnifera (L.) Dunal: A Molecular Docking and Molecular Dynamics Investigation. Metabolites 2023; 13:metabo13010093. [PMID: 36677018 PMCID: PMC9861338 DOI: 10.3390/metabo13010093] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Leishmaniasis is a group of infectious diseases caused by Leishmania protozoa. The ineffectiveness, high toxicity, and/or parasite resistance of the currently available antileishmanial drugs has created an urgent need for safe and effective leishmaniasis treatment. Currently, the molecular-docking technique is used to predict the proper conformations of small-molecule ligands and the strength of the contact between a protein and a ligand, and the majority of research for the development of new drugs is centered on this type of prediction. Leishmania N-myristoyltransferase (NMT) has been shown to be a reliable therapeutic target for investigating new anti-leishmanial molecules through this kind of virtual screening. Natural products provide an incredible source of affordable chemical scaffolds that serve in the development of effective drugs. Withania somnifera leaves, roots, and fruits have been shown to contain withanolide and other phytomolecules that are efficient anti-protozoal agents against Malaria, Trypanosoma, and Leishmania spp. Through a review of previously reported compounds from W. somnifera-afforded 35 alkaloid, phenolic, and steroid compounds and 132 withanolides/derivatives, typical of the Withania genus. These compounds were subjected to molecular docking screening and molecular dynamics against L. major NMT. Calycopteretin-3-rutinoside and withanoside IX showed the highest affinity and binding stability to L. major NMT, implying that these compounds could be used as antileishmanial drugs and/or as a scaffold for the design of related parasite NMT inhibitors with markedly enhanced binding affinity.
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Affiliation(s)
- Mohamed A. A. Orabi
- Department of Pharmacognosy, College of Pharmacy, Najran University, Najran 61441, Saudi Arabia
- Correspondence: or ; Tel.: +966-557398835
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Mohamed E. Abouelela
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt
- Center for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Khaled A. Shaaban
- Center for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - El-Shaymaa Abdel-Sattar
- Department of Medical Microbiology and Immunology, Faculty of Pharmacy, South Valley University, Qena 83523, Egypt
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Omics Approaches in Drug Development against Leishmaniasis: Current Scenario and Future Prospects. Pathogens 2022; 12:pathogens12010039. [PMID: 36678387 PMCID: PMC9866966 DOI: 10.3390/pathogens12010039] [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: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Leishmaniasis is a zoonotic disease transmitted in humans by the bite of Leishmania-infected phlebotomine sandflies. Each year approximately 58,500 cases of leishmaniasis are diagnosed across the globe, with a mortality rate of nearly seven percent. There are over 20 parasitic strains of Leishmania which are known to cause distinct types of leishmaniasis and pose an endemic threat to humans worldwide. Therefore, it is crucial to develop potential medications and vaccines to combat leishmaniasis. However, the task of developing therapeutic solutions is challenging due to Leishmania's digenetic lifecycle. The challenge is further intensified by cases of resistance against the available drugs. Owing to these challenges, the conventional drug development regimen is further limited by target discovery and ligand suitability for the targets. On the other hand, as an added advantage, the emergence of omics-based tools, such as high-end proteomics, transcriptomics and genomics, has hastened the pace of target discovery and target-based drug development. It is now becoming apparent that multi-omics convergence and an inter-connected systems approach is less time-consuming and more cost-effective for any drug-development process. This comprehensive review is an attempt to summarize the current knowledge on the muti-omics approach in drug development against leishmaniasis. In particular, it elaborates the potential target identification from secreted proteins in various stages of Leishmania infection and also illustrates the convergence of transcriptomic and genomic data towards the collective goal of drug discovery. This review also provides an understanding of the potential parasite's drug targets and drug resistance characteristics of the parasite, which can be used in designing effective and specific therapeutics.
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Priyamvada L, Kallemeijn WW, Faronato M, Wilkins K, Goldsmith CS, Cotter CA, Ojeda S, Solari R, Moss B, Tate EW, Satheshkumar PS. Inhibition of vaccinia virus L1 N-myristoylation by the host N-myristoyltransferase inhibitor IMP-1088 generates non-infectious virions defective in cell entry. PLoS Pathog 2022; 18:e1010662. [PMID: 36215331 PMCID: PMC9584500 DOI: 10.1371/journal.ppat.1010662] [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: 06/10/2022] [Revised: 10/20/2022] [Accepted: 08/26/2022] [Indexed: 11/06/2022] Open
Abstract
We have recently shown that the replication of rhinovirus, poliovirus and foot-and-mouth disease virus requires the co-translational N-myristoylation of viral proteins by human host cell N-myristoyltransferases (NMTs), and is inhibited by treatment with IMP-1088, an ultrapotent small molecule NMT inhibitor. Here, we examine the importance of N-myristoylation during vaccinia virus (VACV) infection in primate cells and demonstrate the anti-poxviral effects of IMP-1088. N-myristoylated proteins from VACV and the host were metabolically labelled with myristic acid alkyne during infection using quantitative chemical proteomics. We identified VACV proteins A16, G9 and L1 to be N-myristoylated. Treatment with NMT inhibitor IMP-1088 potently abrogated VACV infection, while VACV gene expression, DNA replication, morphogenesis and EV formation remained unaffected. Importantly, we observed that loss of N-myristoylation resulted in greatly reduced infectivity of assembled mature virus particles, characterized by significantly reduced host cell entry and a decline in membrane fusion activity of progeny virus. While the N-myristoylation of VACV entry proteins L1, A16 and G9 was inhibited by IMP-1088, mutational and genetic studies demonstrated that the N-myristoylation of L1 was the most critical for VACV entry. Given the significant genetic identity between VACV, monkeypox virus and variola virus L1 homologs, our data provides a basis for further investigating the role of N-myristoylation in poxviral infections as well as the potential of selective NMT inhibitors like IMP-1088 as broad-spectrum poxvirus inhibitors.
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Affiliation(s)
- Lalita Priyamvada
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Wouter W. Kallemeijn
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Monica Faronato
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Kimberly Wilkins
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Cynthia S. Goldsmith
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Catherine A. Cotter
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Suany Ojeda
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Clinipace, Morrisville, North Carolina, United States of America
| | - Roberto Solari
- National Heart and Lung Institute, Imperial College of Science, Technology & Medicine, London, United Kingdom
| | - Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Edward W. Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- * E-mail: (EWT); (PSS)
| | - Panayampalli Subbian Satheshkumar
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (EWT); (PSS)
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11
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Moorhouse AJ, Loats AE, Medler KF, Roberts SG. The BASP1 transcriptional corepressor modifies chromatin through lipid-dependent and lipid-independent mechanisms. iScience 2022; 25:104796. [PMID: 35982799 PMCID: PMC9379585 DOI: 10.1016/j.isci.2022.104796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/22/2022] [Accepted: 07/14/2022] [Indexed: 12/01/2022] Open
Abstract
The transcriptional corepressor BASP1 requires N-terminal myristoylation for its activity and functions through interactions with nuclear lipids. Here we determine the role of BASP1 lipidation in histone modification and the modulation of chromatin accessibility. We find that the removal of the active histone modifications H3K9ac and H3K4me3 by BASP1 requires the N-terminal myristoylation of BASP1. In contrast, the placement of the repressive histone modification, H3K27me3, by BASP1 does not require BASP1 lipidation. RNA-seq and ATAC-seq analysis finds that BASP1 regulates the activity of multiple transcription factors and induces extensive changes in chromatin accessibility. We find that ∼50% of BASP1 target genes show lipidation-dependent chromatin compaction and transcriptional repression. Our results suggest that BASP1 elicits both lipid-dependent and lipid-independent functions in histone modification and transcriptional repression. In accordance with this, we find that the tumor suppressor activity of BASP1 is also partially dependent on its myristoylation.
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Affiliation(s)
| | - Amy E. Loats
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Kathryn F. Medler
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Stefan G.E. Roberts
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
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12
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Madeo G, Savojardo C, Luigi Martelli P, Casadio R. SVMyr: a web server detecting co- and post-translational myristoylation in proteins. J Mol Biol 2022; 434:167605. [DOI: 10.1016/j.jmb.2022.167605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/31/2022] [Accepted: 04/19/2022] [Indexed: 12/31/2022]
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13
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Pyne N, Paul S. Screening of medicinal plants unraveled the leishmanicidal credibility of Garcinia cowa; highlighting Norcowanin, a novel anti-leishmanial phytochemical through in-silico study. J Parasit Dis 2022; 46:202-214. [PMID: 35299910 PMCID: PMC8901847 DOI: 10.1007/s12639-021-01441-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/07/2021] [Indexed: 02/04/2023] Open
Abstract
Leishmaniasis, one of the most prevalent yet neglected parasitic causes of death, yearns for therapeutic control and treatment. Severely toxic and inefficient modern-day pentavalent antimonials, caters the search for naturally derived drugs, as efficient alternatives for disease treatment. The anti-promastigote activity of ten different plants selected for their ethnomedicinal properties revealed significant leishmanicidal capacity; the most potent being Garcinia cowa methanolic extract with an IC50 value of 21.4 µg/ml. Garcinia cowa, a plant endemic to North-Eastern India that is of the Clusiaceae family, is replete with such medicinal qualities as antimicrobial, antiviral, antiparasitic, and antiproliferative activities. Computational biology with its tools such as molecular docking has opened new horizons aimed at a better understanding of biological systems, complexes, and their interactions, and subsequently drug discovery via in silico techniques. Therefore, an in-silico study was designed to evaluate the binding capability of six phytochemicals- cowanin, cowanol, cowaxanthone, norcowanin, rubraxanthone, and a basic xanthone, found in Garcinia cowa against Pentamidine, a synthetic anti-leishmanial drug. The active sites of three characteristic enzymes belonging to the Leishmania donovani parasite: O-acetylserine sulfhydrylase (OASS), Trypanothione reductase (TryR), and N-Myristoyltransferase (NMT) were chosen as target proteins. Results revealed lower binding energies and higher affinities, of nearly all the phytochemicals with respect to Pentamidine, indicating their leishmanicidal potential. Norcowanin showed the lowest average binding of - 9.8 kcal/mol against all the three enzymes under study.
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Affiliation(s)
- Nibedita Pyne
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Santanu Paul
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
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14
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Escrivani DO, Charlton RL, Caruso MB, Burle-Caldas GA, Borsodi MPG, Zingali RB, Arruda-Costa N, Palmeira-Mello MV, de Jesus JB, Souza AMT, Abrahim-Vieira B, Freitag-Pohl S, Pohl E, Denny PW, Rossi-Bergmann B, Steel PG. Chalcones identify cTXNPx as a potential antileishmanial drug target. PLoS Negl Trop Dis 2021; 15:e0009951. [PMID: 34780470 PMCID: PMC8664226 DOI: 10.1371/journal.pntd.0009951] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/10/2021] [Accepted: 10/26/2021] [Indexed: 12/31/2022] Open
Abstract
With current drug treatments failing due to toxicity, low efficacy and resistance; leishmaniasis is a major global health challenge that desperately needs new validated drug targets. Inspired by activity of the natural chalcone 2’,6’-dihydroxy-4’-methoxychalcone (DMC), the nitro-analogue, 3-nitro-2’,4’,6’- trimethoxychalcone (NAT22, 1c) was identified as potent broad spectrum antileishmanial drug lead. Structural modification provided an alkyne containing chemical probe that labelled a protein within the parasite that was confirmed as cytosolic tryparedoxin peroxidase (cTXNPx). Crucially, labelling is observed in both promastigote and intramacrophage amastigote life forms, with no evidence of host macrophage toxicity. Incubation of the chalcone in the parasite leads to ROS accumulation and parasite death. Deletion of cTXNPx, by CRISPR-Cas9, dramatically impacts upon the parasite phenotype and reduces the antileishmanial activity of the chalcone analogue. Molecular docking studies with a homology model of in-silico cTXNPx suggest that the chalcone is able to bind in the putative active site hindering access to the crucial cysteine residue. Collectively, this work identifies cTXNPx as an important target for antileishmanial chalcones. Leishmaniasis is an insect vector-borne parasitic disease. With >350 million people world wide considered at risk, 12 million people currently infected and an economic cost that can be estimated in terms of >3.3 million working life years lost, leishmaniasis is a major global health challenge. The disease is of particular importance in Brazil. Current treatment of leishmaniasis is difficult requiring a long, costly course of drug treatment using old drugs with poor safety indications requiring close medical supervision. Moreover, resistance to current antileishmanials is growing, emphasising a major need for new drug targets. In earlier work we had identified a naturally inspired chalcone which had promising antileishmanial activity but with no known mode of action. In this work we use an analogue of this molecule as an activity based probe to identify a protein target of the chalcone. This protein, cTXNPx, has a major role in protecting the parasite against attack by reactive oxygen species in the host cell. By inhibiting this protein the parasite can no longer survive in the host. Collectively this work validates cTXNPx as a drug target with the chalcone as a lead structure for future drug discovery programmes.
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Affiliation(s)
- Douglas O. Escrivani
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Chemistry, Durham University, Science Laboratories, South Road, Durham, United Kingdom
| | - Rebecca L. Charlton
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Chemistry, Durham University, Science Laboratories, South Road, Durham, United Kingdom
| | - Marjolly B. Caruso
- Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriela A. Burle-Caldas
- Department of Biosciences, Durham University, Science Laboratories, South Road, Durham, United Kingdom
| | - Maria Paula G. Borsodi
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Russolina B. Zingali
- Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Natalia Arruda-Costa
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Jéssica B. de Jesus
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Stefanie Freitag-Pohl
- Department of Chemistry, Durham University, Science Laboratories, South Road, Durham, United Kingdom
| | - Ehmke Pohl
- Department of Chemistry, Durham University, Science Laboratories, South Road, Durham, United Kingdom
- Department of Biosciences, Durham University, Science Laboratories, South Road, Durham, United Kingdom
| | - Paul W. Denny
- Department of Biosciences, Durham University, Science Laboratories, South Road, Durham, United Kingdom
| | - Bartira Rossi-Bergmann
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (BR-B); (PGS)
| | - Patrick G. Steel
- Department of Chemistry, Durham University, Science Laboratories, South Road, Durham, United Kingdom
- * E-mail: (BR-B); (PGS)
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15
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Drug discovery in leishmaniasis using protein lipidation as a target. Biophys Rev 2021; 13:1139-1146. [PMID: 35035594 PMCID: PMC8724199 DOI: 10.1007/s12551-021-00855-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
The leishmaniases are infectious diseases caused by a number of species of obligate intracellular protozoa of the genus Leishmania with disease manifesting as cutaneous, mucocutaneous and visceral forms. Despite being endemic in more than 80 countries and its being the cause of high morbidity and mortality, leishmaniasis remains a neglected tropical disease. Chemotherapy is the frontline treatment, but drugs in current use suffer from toxic side effects, difficulties in administration and extended treatment times - moreover, resistance is emerging. New anti-leishmanial drugs are a recognised international priority. Here, we review investigations into N-myristoyltransferase (NMT) as a potential drug target. NMT catalyses the co-translational transfer of a C14 fatty acid from myristoyl-CoA onto the N-terminal glycine residue of a significant subset of proteins in eukaryotic cells. This covalent modification influences the stability and interactions of substrate proteins with lipids and partner proteins. Structure-guided development of new lead compounds emerging from high-throughput screening campaigns targeting Leishmania donovani NMT has led to the discovery of potent inhibitors which have been used to gain insights into the role of protein myristoylation in these parasites and to validate NMT as a drug target.
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16
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Kallemeijn WW, Lanyon-Hogg T, Panyain N, Goya Grocin A, Ciepla P, Morales-Sanfrutos J, Tate EW. Proteome-wide analysis of protein lipidation using chemical probes: in-gel fluorescence visualization, identification and quantification of N-myristoylation, N- and S-acylation, O-cholesterylation, S-farnesylation and S-geranylgeranylation. Nat Protoc 2021; 16:5083-5122. [PMID: 34707257 DOI: 10.1038/s41596-021-00601-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 07/05/2021] [Indexed: 02/08/2023]
Abstract
Protein lipidation is one of the most widespread post-translational modifications (PTMs) found in nature, regulating protein function, structure and subcellular localization. Lipid transferases and their substrate proteins are also attracting increasing interest as drug targets because of their dysregulation in many disease states. However, the inherent hydrophobicity and potential dynamic nature of lipid modifications makes them notoriously challenging to detect by many analytical methods. Chemical proteomics provides a powerful approach to identify and quantify these diverse protein modifications by combining bespoke chemical tools for lipidated protein enrichment with quantitative mass spectrometry-based proteomics. Here, we report a robust and proteome-wide approach for the exploration of five major classes of protein lipidation in living cells, through the use of specific chemical probes for each lipid PTM. In-cell labeling of lipidated proteins is achieved by the metabolic incorporation of a lipid probe that mimics the specific natural lipid, concomitantly wielding an alkyne as a bio-orthogonal labeling tag. After incorporation, the chemically tagged proteins can be coupled to multifunctional 'capture reagents' by using click chemistry, allowing in-gel fluorescence visualization or enrichment via affinity handles for quantitative chemical proteomics based on label-free quantification (LFQ) or tandem mass-tag (TMT) approaches. In this protocol, we describe the application of lipid probes for N-myristoylation, N- and S-acylation, O-cholesterylation, S-farnesylation and S-geranylgeranylation in multiple cell lines to illustrate both the workflow and data obtained in these experiments. We provide detailed workflows for method optimization, sample preparation for chemical proteomics and data processing. A properly trained researcher (e.g., technician, graduate student or postdoc) can complete all steps from optimizing metabolic labeling to data processing within 3 weeks. This protocol enables sensitive and quantitative analysis of lipidated proteins at a proteome-wide scale at native expression levels, which is critical to understanding the role of lipid PTMs in health and disease.
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Affiliation(s)
- Wouter W Kallemeijn
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- The Francis Crick Institute, London, UK
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Nattawadee Panyain
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Global Health Institute, Faculty of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Goya Grocin
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- The Francis Crick Institute, London, UK
| | - Paulina Ciepla
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Julia Morales-Sanfrutos
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Proteomics Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK.
- The Francis Crick Institute, London, UK.
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17
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Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 PMCID: PMC8820976 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
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Affiliation(s)
- Kiall F. Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
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18
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Rashidi S, Tuteja R, Mansouri R, Ali-Hassanzadeh M, Shafiei R, Ghani E, Karimazar M, Nguewa P, Manzano-Román R. The main post-translational modifications and related regulatory pathways in the malaria parasite Plasmodium falciparum: An update. J Proteomics 2021; 245:104279. [PMID: 34089893 DOI: 10.1016/j.jprot.2021.104279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/18/2021] [Accepted: 05/27/2021] [Indexed: 12/14/2022]
Abstract
There are important challenges when investigating individual post-translational modifications (PTMs) or protein interaction network and delineating if PTMs or their changes and cross-talks are involved during infection, disease initiation or as a result of disease progression. Proteomics and in silico approaches now offer the possibility to complement each other to further understand the regulatory involvement of these modifications in parasites and infection biology. Accordingly, the current review highlights key expressed or altered proteins and PTMs are invisible switches that turn on and off the function of most of the proteins. PTMs include phosphorylation, glycosylation, ubiquitylation, palmitoylation, myristoylation, prenylation, acetylation, methylation, and epigenetic PTMs in P. falciparum which have been recently identified. But also other low-abundant or overlooked PTMs that might be important for the parasite's survival, infectivity, antigenicity, immunomodulation and pathogenesis. We here emphasize the PTMs as regulatory pathways playing major roles in the biology, pathogenicity, metabolic pathways, survival, host-parasite interactions and the life cycle of P. falciparum. Further validations and functional characterizations of such proteins might confirm the discovery of therapeutic targets and might most likely provide valuable data for the treatment of P. falciparum, the main cause of severe malaria in human.
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Affiliation(s)
- Sajad Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Renu Tuteja
- Parasite Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Reza Mansouri
- Department of Immunology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Mohammad Ali-Hassanzadeh
- Department of Immunology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Reza Shafiei
- Vector-borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Esmaeel Ghani
- Endocrinology and Metabolism Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammadreza Karimazar
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Paul Nguewa
- University of Navarra, ISTUN Instituto de Salud Tropical, Department of Microbiology and Parasitology, IdiSNA (Navarra Institute for Health Research), c/Irunlarrea 1, 31008 Pamplona, Spain.
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain.
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19
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Zazula R, Moravec M, Pehal F, Nejtek T, Protuš M, Müller M. Myristic Acid Serum Levels and Their Significance for Diagnosis of Systemic Inflammatory Response, Sepsis, and Bacteraemia. J Pers Med 2021; 11:jpm11040306. [PMID: 33923419 PMCID: PMC8074080 DOI: 10.3390/jpm11040306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 01/10/2023] Open
Abstract
Myristic acid is identified as a metabolite with the highest diagnostic sensitivity and specificity in the metabolome of patients with bacteraemia. Its significant decrease has been observed in patients with septic shock not responding to treatment. Another study has reported a close correlation of myristic acid levels with the outcome of severe trauma patients. Myristic acid concentrations were investigated in a cohort of septic patients and patients with Systemic Inflammatory Response Syndrome (SIRS) in 5 consecutive days following diagnosis and compared to healthy controls. The study population groups-Sepsis 34, SIRS 31, and Healthy Control 120 patients were included. Serum samples were analyzed using gas chromatography and mass spectrometry. The myristic acid levels in the Sepsis Group and SIRS Group were found to be significantly higher when compared to healthy controls. The serum concentration of myristic acid in septic patients with bacteraemia was higher than in septic patients without bacteraemia. Most patients with sepsis and SIRS had the highest levels of myristic acid within 24 h after an established diagnosis. Myristic acid should be considered as a new candidate marker of severe inflammation and sepsis. A simplified analysis and sufficient body of validated data are necessary steps towards the introduction of this metabolite into routine clinical practice.
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Affiliation(s)
- Roman Zazula
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer University Hospital, 140 59 Prague, Czech Republic; (M.M.); (F.P.); (T.N.); (M.M.)
- Correspondence: ; Tel.: +420-261-083-811
| | - Michal Moravec
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer University Hospital, 140 59 Prague, Czech Republic; (M.M.); (F.P.); (T.N.); (M.M.)
| | - František Pehal
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer University Hospital, 140 59 Prague, Czech Republic; (M.M.); (F.P.); (T.N.); (M.M.)
| | - Tomáš Nejtek
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer University Hospital, 140 59 Prague, Czech Republic; (M.M.); (F.P.); (T.N.); (M.M.)
| | - Marek Protuš
- Department of Anaesthesiology, Resuscitation and Intensive Care, Institute for Clinical and Experimental Medicine, First Faculty of Medicine, Charles University, 140 21 Prague, Czech Republic;
| | - Martin Müller
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer University Hospital, 140 59 Prague, Czech Republic; (M.M.); (F.P.); (T.N.); (M.M.)
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20
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Denny PW, Kalesh K. How can proteomics overhaul our understanding of Leishmania biology? Expert Rev Proteomics 2021; 17:789-792. [PMID: 33535845 DOI: 10.1080/14789450.2020.1885375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Paul W Denny
- Department of Biosciences, Durham University , Durham, UK
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21
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Losada de la Lastra A, Hassan S, Tate EW. Deconvoluting the biology and druggability of protein lipidation using chemical proteomics. Curr Opin Chem Biol 2021; 60:97-112. [PMID: 33221680 DOI: 10.1016/j.cbpa.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 01/13/2023]
Abstract
Lipids are indispensable cellular building blocks, and their post-translational attachment to proteins makes them important regulators of many biological processes. Dysfunction of protein lipidation is also implicated in many pathological states, yet its systematic analysis presents significant challenges. Thanks to innovations in chemical proteomics, lipidation can now be readily studied by metabolic tagging using functionalized lipid analogs, enabling global profiling of lipidated substrates using mass spectrometry. This has spearheaded the first deconvolution of their full scope in a range of contexts, from cells to pathogens and multicellular organisms. Protein N-myristoylation, S-acylation, and S-prenylation are the most well-studied lipid post-translational modifications because of their extensive contribution to the regulation of diverse cellular processes. In this review, we focus on recent advances in the study of these post-translational modifications, with an emphasis on how novel mass spectrometry methods have elucidated their roles in fundamental biological processes.
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Affiliation(s)
- Ana Losada de la Lastra
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Sarah Hassan
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK.
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22
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Bell AS, Yu Z, Hutton JA, Wright MH, Brannigan JA, Paape D, Roberts SM, Sutherell CL, Ritzefeld M, Wilkinson AJ, Smith DF, Leatherbarrow RJ, Tate EW. Novel Thienopyrimidine Inhibitors of Leishmania N-Myristoyltransferase with On-Target Activity in Intracellular Amastigotes. J Med Chem 2020; 63:7740-7765. [PMID: 32575985 PMCID: PMC7383931 DOI: 10.1021/acs.jmedchem.0c00570] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
The
leishmaniases, caused by Leishmania species
of protozoan parasites, are neglected tropical diseases with millions
of cases worldwide. Current therapeutic approaches are limited by
toxicity, resistance, and cost. N-Myristoyltransferase
(NMT), an enzyme ubiquitous and essential in all eukaryotes, has been
validated via genetic and pharmacological methods as a promising anti-leishmanial
target. Here we describe a comprehensive structure–activity
relationship (SAR) study of a thienopyrimidine series previously identified
in a high-throughput screen against Leishmania NMT,
across 68 compounds in enzyme- and cell-based assay formats. Using
a chemical tagging target engagement biomarker assay, we identify
the first inhibitor in this series with on-target NMT activity in
leishmania parasites. Furthermore, crystal structure analyses of 12
derivatives in complex with Leishmania major NMT revealed key factors important for future structure-guided optimization
delivering IMP-105 (43), a compound with modest activity
against Leishmania donovani intracellular
amastigotes and excellent selectivity (>660-fold) for Leishmania NMT over human NMTs.
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Affiliation(s)
- Andrew S Bell
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ
| | - Zhiyong Yu
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ
| | - Jennie A Hutton
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ
| | - Megan H Wright
- School of Chemistry, University of Leeds, Leeds, U.K. LS2 9JT
| | - James A Brannigan
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York, U.K. YO10 5DD
| | - Daniel Paape
- Centre for Immunology and Infection, York Biomedical Research Institute, Department of Biology, University of York, York, U.K. YO10 5NG
| | - Shirley M Roberts
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York, U.K. YO10 5DD
| | - Charlotte L Sutherell
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ
| | - Markus Ritzefeld
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ
| | - Anthony J Wilkinson
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York, U.K. YO10 5DD
| | - Deborah F Smith
- Centre for Immunology and Infection, York Biomedical Research Institute, Department of Biology, University of York, York, U.K. YO10 5NG
| | - Robin J Leatherbarrow
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ
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23
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Broncel M, Dominicus C, Vigetti L, Nofal SD, Bartlett EJ, Touquet B, Hunt A, Wallbank BA, Federico S, Matthews S, Young JC, Tate EW, Tardieux I, Treeck M. Profiling of myristoylation in Toxoplasma gondii reveals an N-myristoylated protein important for host cell penetration. eLife 2020; 9:e57861. [PMID: 32618271 PMCID: PMC7373427 DOI: 10.7554/elife.57861] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/27/2020] [Indexed: 12/26/2022] Open
Abstract
N-myristoylation is a ubiquitous class of protein lipidation across eukaryotes and N-myristoyl transferase (NMT) has been proposed as an attractive drug target in several pathogens. Myristoylation often primes for subsequent palmitoylation and stable membrane attachment, however, growing evidence suggests additional regulatory roles for myristoylation on proteins. Here we describe the myristoylated proteome of Toxoplasma gondii using chemoproteomic methods and show that a small-molecule NMT inhibitor developed against related Plasmodium spp. is also functional in Toxoplasma. We identify myristoylation on a transmembrane protein, the microneme protein 7 (MIC7), which enters the secretory pathway in an unconventional fashion with the myristoylated N-terminus facing the lumen of the micronemes. MIC7 and its myristoylation play a crucial role in the initial steps of invasion, likely during the interaction with and penetration of the host cell. Myristoylation of secreted eukaryotic proteins represents a substantial expansion of the functional repertoire of this co-translational modification.
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Affiliation(s)
- Malgorzata Broncel
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Caia Dominicus
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Luis Vigetti
- Institute for Advanced Biosciences, Team Membrane Dynamics of Parasite-Host Cell Interactions, CNRS UMR5309, INSERM U1209, Université Grenoble AlpesGrenobleFrance
| | - Stephanie D Nofal
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Edward J Bartlett
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City CampusLondonUnited Kingdom
| | - Bastien Touquet
- Institute for Advanced Biosciences, Team Membrane Dynamics of Parasite-Host Cell Interactions, CNRS UMR5309, INSERM U1209, Université Grenoble AlpesGrenobleFrance
| | - Alex Hunt
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Bethan A Wallbank
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Stefania Federico
- The Peptide Chemistry STP, The Francis Crick InstituteLondonUnited Kingdom
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South KensingtonLondonUnited Kingdom
| | - Joanna C Young
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City CampusLondonUnited Kingdom
| | - Isabelle Tardieux
- Institute for Advanced Biosciences, Team Membrane Dynamics of Parasite-Host Cell Interactions, CNRS UMR5309, INSERM U1209, Université Grenoble AlpesGrenobleFrance
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick InstituteLondonUnited Kingdom
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24
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Fedoryshchak RO, Ocasio CA, Strutton B, Mattocks J, Corran AJ, Tate EW. Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism. RSC Chem Biol 2020; 1:68-78. [PMID: 34458749 PMCID: PMC8341946 DOI: 10.1039/d0cb00020e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022] Open
Abstract
Zymoseptoria tritici is the causative agent of Septoria tritici blotch (STB), which costs billions of dollars annually to major wheat-producing countries in terms of both fungicide use and crop loss. Agricultural pathogenic fungi have acquired resistance to most commercially available fungicide classes, and the rate of discovery and development of new fungicides has stalled, demanding new approaches and insights. Here we investigate a potential mechanism of targeting an important wheat pathogen Z. tritici via inhibition of N-myristoyltransferase (NMT). We characterize Z. tritici NMT biochemically for the first time, profile the in vivo Z. tritici myristoylated proteome and identify and validate the first Z. tritici NMT inhibitors. Proteomic investigation of the downstream effects of NMT inhibition identified an unusual and novel mechanism of defense against chemical toxicity in Z. tritici through the application of comparative bioinformatics to deconvolute function from the previously largely unannotated Z. tritici proteome. Research into novel fungicidal modes-of-action is essential to satisfy an urgent unmet need for novel fungicide targets, and we anticipate that this study will serve as a useful proteomics and bioinformatics resource for researchers studying Z. tritici.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | - Cory A Ocasio
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | | | - Jo Mattocks
- Syngenta AG, Jealott's Hill Research Centre Bracknell UK
| | | | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
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25
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Parthasarathy A, Kalesh K. Defeating the trypanosomatid trio: proteomics of the protozoan parasites causing neglected tropical diseases. RSC Med Chem 2020; 11:625-645. [PMID: 33479664 PMCID: PMC7549140 DOI: 10.1039/d0md00122h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/12/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry-based proteomics enables accurate measurement of the modulations of proteins on a large scale upon perturbation and facilitates the understanding of the functional roles of proteins in biological systems. It is a particularly relevant methodology for studying Leishmania spp., Trypanosoma cruzi and Trypanosoma brucei, as the gene expression in these parasites is primarily regulated by posttranscriptional mechanisms. Large-scale proteomics studies have revealed a plethora of information regarding modulated proteins and their molecular interactions during various life processes of the protozoans, including stress adaptation, life cycle changes and interactions with the host. Important molecular processes within the parasite that regulate the activity and subcellular localisation of its proteins, including several co- and post-translational modifications, are also accurately captured by modern proteomics mass spectrometry techniques. Finally, in combination with synthetic chemistry, proteomic techniques facilitate unbiased profiling of targets and off-targets of pharmacologically active compounds in the parasites. This provides important data sets for their mechanism of action studies, thereby aiding drug development programmes.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology , Thomas H. Gosnell School of Life Sciences , 85 Lomb Memorial Dr , Rochester , NY 14623 , USA
| | - Karunakaran Kalesh
- Department of Chemistry , Durham University , Lower Mount Joy, South Road , Durham DH1 3LE , UK .
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26
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Meinnel T, Dian C, Giglione C. Myristoylation, an Ancient Protein Modification Mirroring Eukaryogenesis and Evolution. Trends Biochem Sci 2020; 45:619-632. [PMID: 32305250 DOI: 10.1016/j.tibs.2020.03.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/02/2020] [Accepted: 03/12/2020] [Indexed: 12/18/2022]
Abstract
N-myristoylation (MYR) is a crucial fatty acylation catalyzed by N-myristoyltransferases (NMTs) that is likely to have appeared over 2 billion years ago. Proteome-wide approaches have now delivered an exhaustive list of substrates undergoing MYR across approximately 2% of any proteome, with constituents, several unexpected, associated with different membrane compartments. A set of <10 proteins conserved in eukaryotes probably represents the original set of N-myristoylated targets, marking major changes occurring throughout eukaryogenesis. Recent findings have revealed unexpected mechanisms and reactivity, suggesting competition with other acylations that are likely to influence cellular homeostasis and the steady state of the modification landscape. Here, we review recent advances in NMT catalysis, substrate specificity, and MYR proteomics, and discuss concepts regarding MYR during evolution.
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Affiliation(s)
- Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Cyril Dian
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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27
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Altamura F, Rajesh R, Catta-Preta CMC, Moretti NS, Cestari I. The current drug discovery landscape for trypanosomiasis and leishmaniasis: Challenges and strategies to identify drug targets. Drug Dev Res 2020; 83:225-252. [PMID: 32249457 DOI: 10.1002/ddr.21664] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
Human trypanosomiasis and leishmaniasis are vector-borne neglected tropical diseases caused by infection with the protozoan parasites Trypanosoma spp. and Leishmania spp., respectively. Once restricted to endemic areas, these diseases are now distributed worldwide due to human migration, climate change, and anthropogenic disturbance, causing significant health and economic burden globally. The current chemotherapy used to treat these diseases has limited efficacy, and drug resistance is spreading. Hence, new drugs are urgently needed. Phenotypic compound screenings have prevailed as the leading method to discover new drug candidates against these diseases. However, the publication of the complete genome sequences of multiple strains, advances in the application of CRISPR/Cas9 technology, and in vivo bioluminescence-based imaging have set the stage for advancing target-based drug discovery. This review analyses the limitations of the narrow pool of available drugs presently used for treating these diseases. It describes the current drug-based clinical trials highlighting the most promising leads. Furthermore, the review presents a focused discussion on the most important biological and pharmacological challenges that target-based drug discovery programs must overcome to advance drug candidates. Finally, it examines the advantages and limitations of modern research tools designed to identify and validate essential genes as drug targets, including genomic editing applications and in vivo imaging.
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Affiliation(s)
- Fernando Altamura
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | - Rishi Rajesh
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | | | - Nilmar S Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Igor Cestari
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
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28
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Paape D, Prendergast CT, Price HP, Doehl JSP, Smith DF. Genetic validation of Leishmania genes essential for amastigote survival in vivo using N-myristoyltransferase as a model. Parasit Vectors 2020; 13:132. [PMID: 32171322 PMCID: PMC7071782 DOI: 10.1186/s13071-020-3999-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/26/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Proving that specific genes are essential for the intracellular viability of Leishmania parasites within macrophages remains a challenge for the identification of suitable targets for drug development. This is especially evident in the absence of a robust inducible expression system or functioning RNAi machinery that works in all Leishmania species. Currently, if a target gene of interest in extracellular parasites can only be deleted from its genomic locus in the presence of ectopic expression from a wild type copy, it is assumed that this gene will also be essential for viability in disease-promoting intracellular parasites. However, functional essentiality must be proven independently in both life-cycle stages for robust validation of the gene of interest as a putative target for chemical intervention. METHODS Here, we have used plasmid shuffle methods in vivo to provide supportive genetic evidence that N-myristoyltransferase (NMT) is essential for Leishmania viability throughout the parasite life-cycle. Following confirmation of NMT essentiality in vector-transmitted promastigotes, a range of mutant parasites were used to infect mice prior to negative selection pressure to test the hypothesis that NMT is also essential for parasite viability in an established infection. RESULTS Ectopically-expressed NMT was only dispensable under negative selection in the presence of another copy. Total parasite burdens in animals subjected to negative selection were comparable to control groups only if an additional NMT copy, not affected by the negative selection, was expressed. CONCLUSIONS NMT is an essential gene in all parasite life-cycle stages, confirming its role as a genetically-validated target for drug development.
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Affiliation(s)
- Daniel Paape
- Centre for Immunology and Infection, Department of Biology, University of York, York, YO10 5DD UK
- Present Address: Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA UK
| | - Catriona T. Prendergast
- Centre for Immunology and Infection, Department of Biology, University of York, York, YO10 5DD UK
- Present Address: Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA UK
| | - Helen P. Price
- Centre for Immunology and Infection, Department of Biology, University of York, York, YO10 5DD UK
- Present Address: Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Newcastle-under-Lyme, ST5 5BG UK
| | - Johannes S. P. Doehl
- Centre for Immunology and Infection, Department of Biology, University of York, York, YO10 5DD UK
| | - Deborah F. Smith
- Centre for Immunology and Infection, Department of Biology, University of York, York, YO10 5DD UK
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29
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Crepaldi F, de Toledo JS, do Carmo AO, Ferreira Marques Machado L, de Brito DDV, Serufo AV, Almeida APM, de Oliveira LG, Ricotta TQN, Moreira DDS, Murta SMF, Diniz AB, Menezes GB, López-Gonzálvez Á, Barbas C, Fernandes AP. Mapping Alterations Induced by Long-Term Axenic Cultivation of Leishmania amazonensis Promastigotes With a Multiplatform Metabolomic Fingerprint Approach. Front Cell Infect Microbiol 2019; 9:403. [PMID: 31867285 PMCID: PMC6904349 DOI: 10.3389/fcimb.2019.00403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/11/2019] [Indexed: 11/16/2022] Open
Abstract
Leishmaniases are widespread neglected diseases with an incidence of 1.6 million new cases and 40 thousand deaths per year. Leishmania parasites may show distinct, species-specific patterns of virulence that lead to different clinical manifestations. It is well known that successive in vitro passages (SIVP) lead to the attenuation of virulence, but neither the metabolism nor the pathways involved in these processes are well understood. Herein, promastigotes of a virulent L. amazonensis strain recently isolated from mice was compared to SIVP derived and attenuated promastigotes, submitted to 10, 40, and 60 axenic passages and named R10, R40, and R60, respectively. In vitro assays and in vivo tests were performed to characterize and confirmed the attenuation profiles. A metabolomic fingerprint comparison of R0, R10, and R60 was performed by means of capillary electrophoresis, liquid and gas chromatography coupled to mass spectrometry. To validate the metabolomic data, qPCR for selected loci, flow cytometry to measure aPS exposure, sensitivity to antimony tartrate and ROS production assays were conducted. The 65 identified metabolites were clustered in biochemical categories and mapped in eight metabolic pathways: ABC transporters; fatty acid biosynthesis; glycine, serine and threonine metabolism; β-alanine metabolism; glutathione metabolism; oxidative phosphorylation; glycerophospholipid metabolism and lysine degradation. The obtained metabolomic data correlated with previous proteomic findings of the SVIP parasites and the gene expression of 13 selected targets. Late SIVP cultures were more sensitive to SbIII produced more ROS and exposed less phosphatidylserine in their surface. The correspondent pathways were connected to build a biochemical map of the most significant alterations involved with the process of attenuation of L. amazonensis. Overall, the reported data pointed out to a very dynamic and continuous metabolic reprogramming process, accompanied by changes in energetic, lipid and redox metabolisms, membrane remodeling and reshaping of parasite-host cells interactions, causing impacts in chemotaxis, host inflammatory responses and infectivity at the early stages of infection.
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Affiliation(s)
- Frederico Crepaldi
- Clinical and Toxicological Analysis Department, School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Centro de Metabolómica y Bioanálisis, Unidad Metabolómica, Interacciones y Bioanálisis (UMIB), Universidad CEU San Pablo, Boadilla del Monte, Spain
| | - Juliano Simões de Toledo
- Clinical and Toxicological Analysis Department, School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Centro de Metabolómica y Bioanálisis, Unidad Metabolómica, Interacciones y Bioanálisis (UMIB), Universidad CEU San Pablo, Boadilla del Monte, Spain
| | - Anderson Oliveira do Carmo
- Laboratory of Biotechnology and Molecular Markers, General Biology Department, Institute of Biological Science, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Daniela Diniz Viana de Brito
- Clinical and Toxicological Analysis Department, School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Angela Vieira Serufo
- Clinical and Toxicological Analysis Department, School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Ana Paula Martins Almeida
- Clinical and Toxicological Analysis Department, School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Leandro Gonzaga de Oliveira
- Clinical and Toxicological Analysis Department, School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Tiago Queiroga Nery Ricotta
- Clinical and Toxicological Analysis Department, School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Ariane Barros Diniz
- Morphology Department, Institute of Biological Science, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Gustavo Batista Menezes
- Morphology Department, Institute of Biological Science, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Ángeles López-Gonzálvez
- Centro de Metabolómica y Bioanálisis, Unidad Metabolómica, Interacciones y Bioanálisis (UMIB), Universidad CEU San Pablo, Boadilla del Monte, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis, Unidad Metabolómica, Interacciones y Bioanálisis (UMIB), Universidad CEU San Pablo, Boadilla del Monte, Spain
| | - Ana Paula Fernandes
- Clinical and Toxicological Analysis Department, School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
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30
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Harupa A, De Las Heras L, Colmenarejo G, Lyons-Abbott S, Reers A, Caballero Hernandez I, Chung CW, Charter D, Myler PJ, Fernández-Menéndez RM, Calderón F, Palomo S, Rodríguez B, Berlanga M, Herreros-Avilés E, Staker BL, Fernández Álvaro E, Kaushansky A. Identification of Selective Inhibitors of Plasmodium N-Myristoyltransferase by High-Throughput Screening. J Med Chem 2019; 63:591-600. [DOI: 10.1021/acs.jmedchem.9b01343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anke Harupa
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
- Novartis Institute for Biomedical Research, Emeryville, California 94608, United States
| | | | | | - Sally Lyons-Abbott
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
| | - Alexandra Reers
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | | | | | - Peter J. Myler
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | | | - Sara Palomo
- GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
| | | | | | | | - Bart L. Staker
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | - Alexis Kaushansky
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department of Global Health, University of Washington, Seattle, Washington 98195, United States
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31
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Khalil R, Ashraf S, Khalid A, Ul-Haq Z. Exploring Novel N-Myristoyltransferase Inhibitors: A Molecular Dynamics Simulation Approach. ACS OMEGA 2019; 4:13658-13670. [PMID: 31497683 PMCID: PMC6714517 DOI: 10.1021/acsomega.9b00843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/25/2019] [Indexed: 05/06/2023]
Abstract
N-Myristoyltransferase (NMT) is a cytosolic monomeric enzyme involved in the allocation of the myristoyl group to the aminoterminal of glycine in several viral and eukaryotic cellular proteins. NMT has been validated as a potential drug target against kinetoplastid for parasitic protozoa. A multistep virtual screening protocol based on the pharmacophore modeling, molecular docking, and molecular dynamics simulation was carried out. Initially, Maybridge database was virtually screened via a validated pharmacophore model. The effective pharmacophore models were accompanied with exclusion volumes to improve their receiver operating characteristic curve to identify potential NMT inhibitors. The hits identified as actives based on the 3D-pharmacophore model were evaluated by molecular docking studies. In stepwise screening, six compounds were shortlisted for the dynamic simulation to get insights into their binding mode. In conclusion, this study provides fundamental information about the architecture of the binding site and some crucial residues that may provide insights into the development of new antiparasitic agents.
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Affiliation(s)
- Ruqaiya Khalil
- Dr.
Panjwani Center for Molecular Medicine and Drug Research, International
Center for Chemical and Biological Sciences, and HEJ Research Institute of Chemistry,
International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sajda Ashraf
- Dr.
Panjwani Center for Molecular Medicine and Drug Research, International
Center for Chemical and Biological Sciences, and HEJ Research Institute of Chemistry,
International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box
2424, Khartoum 11111, Sudan
| | - Zaheer Ul-Haq
- Dr.
Panjwani Center for Molecular Medicine and Drug Research, International
Center for Chemical and Biological Sciences, and HEJ Research Institute of Chemistry,
International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- E-mail:
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32
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Negrão F, Giorgio S, Eberlin MN, Yates JR. Comparative Proteomic Analysis of Murine Cutaneous Lesions Induced by Leishmania amazonensis or Leishmania major. ACS Infect Dis 2019; 5:1295-1305. [PMID: 31094195 DOI: 10.1021/acsinfecdis.8b00370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cutaneous leishmaniasisis is the most common clinical form of leishmaniasis and one of the most relevant neglected diseases. It is known that the progress of the disease is species specific and the host's immune response plays an important role in its outcome. However, the pathways that lead to parasite clearance or survival remain unknown. In this work, skin tissue from mice experimentally infected with L. amazonensis, one of the causative agents of cutaneous leishmaniasis in the Amazon region, L. major, another causative agent of cutaneous leishmaniasis in Africa, the Middle East, China, and India, or lipopolysaccharides from Escherichia coli as an inflammation model were investigated using label-free proteomics to unveil Leishmania-specific protein alterations. Proteomics is a powerful tool to investigate host-pathogen relationships to address biological questions. In this work, proteins from mice skin biopsies were identified and quantified using nano-LC coupled with tandem mass spectrometry analyses. Integrated Proteomics Pipeline was used for peptide/protein identification and quantification. Western blot was used for validation of protein quantification by mass spectrometry, and protein pathways were predicted using Ingenuity Pathway Analysis. In this proteomics study, several proteins were pointed out as hypothetical targets to guide future studies on Leishmania-specific modulation of proteins in the host. We identified hundreds of exclusively modulated proteins after Leishmania spp. infection and 17 proteins that were differentially modulated in the host after L. amazonensis or L. major infection.
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Affiliation(s)
- Fernanda Negrão
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR302, La Jolla, California 92037, United States
- Department of Animal Biology, Institute of Biology, Rua Monteiro Lobato, 255, Campinas, Sao Paulo 13083-862, Brazil
- Department of Organic Chemistry, Institute of Chemistry, UNICAMP, Rua Josué de Castro SN, Room A111, Campinas, Sao Paulo 13083-862, Brazil
| | - Selma Giorgio
- Department of Animal Biology, Institute of Biology, Rua Monteiro Lobato, 255, Campinas, Sao Paulo 13083-862, Brazil
| | - Marcos Nogueira Eberlin
- Department of Organic Chemistry, Institute of Chemistry, UNICAMP, Rua Josué de Castro SN, Room A111, Campinas, Sao Paulo 13083-862, Brazil
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR302, La Jolla, California 92037, United States
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Schlott AC, Mayclin S, Reers AR, Coburn-Flynn O, Bell AS, Green J, Knuepfer E, Charter D, Bonnert R, Campo B, Burrows J, Lyons-Abbott S, Staker BL, Chung CW, Myler PJ, Fidock DA, Tate EW, Holder AA. Structure-Guided Identification of Resistance Breaking Antimalarial N‑Myristoyltransferase Inhibitors. Cell Chem Biol 2019; 26:991-1000.e7. [PMID: 31080074 PMCID: PMC6658617 DOI: 10.1016/j.chembiol.2019.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/25/2019] [Accepted: 03/25/2019] [Indexed: 01/26/2023]
Abstract
The attachment of myristate to the N-terminal glycine of certain proteins is largely a co-translational modification catalyzed by N-myristoyltransferase (NMT), and involved in protein membrane-localization. Pathogen NMT is a validated therapeutic target in numerous infectious diseases including malaria. In Plasmodium falciparum, NMT substrates are important in essential processes including parasite gliding motility and host cell invasion. Here, we generated parasites resistant to a particular NMT inhibitor series and show that resistance in an in vitro parasite growth assay is mediated by a single amino acid substitution in the NMT substrate-binding pocket. The basis of resistance was validated and analyzed with a structure-guided approach using crystallography, in combination with enzyme activity, stability, and surface plasmon resonance assays, allowing identification of another inhibitor series unaffected by this substitution. We suggest that resistance studies incorporated early in the drug development process help selection of drug combinations to impede rapid evolution of parasite resistance.
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Affiliation(s)
- Anja C Schlott
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.
| | - Stephen Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Alexandra R Reers
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Andrew S Bell
- Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK
| | - Judith Green
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ellen Knuepfer
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Charter
- Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Roger Bonnert
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Jeremy Burrows
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Chun-Wa Chung
- Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK; Crick-GSK Biomedical LinkLabs, GSK Medicines Research Centre, Stevenage, UK
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA; Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, USA; Department of Global Health, University of Washington, Seattle, USA
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Edward W Tate
- Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.
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Negrão F, Fernandez-Costa C, Zorgi N, Giorgio S, Nogueira Eberlin M, Yates JR. Label-Free Proteomic Analysis Reveals Parasite-Specific Protein Alterations in Macrophages Following Leishmania amazonensis, Leishmania major, or Leishmania infantum Infection. ACS Infect Dis 2019; 5:851-862. [PMID: 30978002 DOI: 10.1021/acsinfecdis.8b00338] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Leishmania is an obligate intracellular parasite known to modulate the host cell to survive and proliferate. However, the complexity of host-parasite interactions remains unclear. Also, the outcome of the disease has been recognized to be species-specific and dependent on the host's immune responses. Proteomics has emerged as a powerful tool to investigate the host-pathogen interface, allowing us to deepen our knowledge about infectious diseases. Quantification of the relative amount of proteins in a sample can be achieved using label-free proteomics, and for the first time, we have used it to quantify Leishmania-specific protein alterations in macrophages. Protein extracts were obtained and digested, and peptides were identified and quantified using nano-LC coupled with tandem mass spectrometry analyses. Protein expression was validated by Western blot analysis. Integrated Proteomics Pipeline was used for peptide/protein identification and for quantification and data processing. Ingenuity Pathway Analysis was used for network analysis. In this work, we investigated how this intracellular parasite modulates protein expression on a host macrophage by comparing three different Leishmania species- L. amazonensis, one of the causative agents of cutaneous disease in the Amazon region; L. major, another causative agent of cutaneous leishmaniasis in Africa, the Middle East, China, and India; L. infantum, the causative agent of visceral leishmaniasis affecting humans and dogs in Latin America-and lipopolysaccharide stimulated macrophages as an in vitro inflammation model. Our results revealed that Leishmania infection downregulates apoptosis pathways while upregulating the activation of phagocytes/leukocytes and lipid accumulation.
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Affiliation(s)
- Fernanda Negrão
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR302, La Jolla, California 92037, United States
- Department of Animal Biology, Institute of Biology, Rua Monteiro Lobato, 255, Campinas, Sao Paulo 13083-862, Brazil
- Department of Organic Chemistry, Institute of Chemistry, UNICAMP, Rua Josué de Castro SN, Room A111, Campinas, Sao Paulo 13083-862, Brazil
| | - Carolina Fernandez-Costa
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR302, La Jolla, California 92037, United States
| | - Nahiara Zorgi
- Department of Animal Biology, Institute of Biology, Rua Monteiro Lobato, 255, Campinas, Sao Paulo 13083-862, Brazil
| | - Selma Giorgio
- Department of Animal Biology, Institute of Biology, Rua Monteiro Lobato, 255, Campinas, Sao Paulo 13083-862, Brazil
| | - Marcos Nogueira Eberlin
- Department of Organic Chemistry, Institute of Chemistry, UNICAMP, Rua Josué de Castro SN, Room A111, Campinas, Sao Paulo 13083-862, Brazil
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR302, La Jolla, California 92037, United States
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35
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Storck EM, Morales-Sanfrutos J, Serwa RA, Panyain N, Lanyon-Hogg T, Tolmachova T, Ventimiglia LN, Martin-Serrano J, Seabra MC, Wojciak-Stothard B, Tate EW. Dual chemical probes enable quantitative system-wide analysis of protein prenylation and prenylation dynamics. Nat Chem 2019; 11:552-561. [PMID: 30936521 PMCID: PMC6544531 DOI: 10.1038/s41557-019-0237-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 02/27/2019] [Indexed: 12/14/2022]
Abstract
Post-translational farnesylation or geranylgeranylation at a C-terminal cysteine residue regulates the localization and function of over 100 proteins, including the Ras isoforms, and is a therapeutic target in diseases including cancer and infection. Here, we report global and selective profiling of prenylated proteins in living cells enabled by the development of isoprenoid analogues YnF and YnGG in combination with quantitative chemical proteomics. Eighty prenylated proteins were identified in a single human cell line, 64 for the first time at endogenous abundance without metabolic perturbation. We further demonstrate that YnF and YnGG enable direct identification of post-translationally processed prenylated peptides, proteome-wide quantitative analysis of prenylation dynamics and alternative prenylation in response to four different prenyltransferase inhibitors, and quantification of defective Rab prenylation in a model of the retinal degenerative disease choroideremia.
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Affiliation(s)
- Elisabeth M Storck
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Julia Morales-Sanfrutos
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Remigiusz A Serwa
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Nattawadee Panyain
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Tanya Tolmachova
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Leandro N Ventimiglia
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Juan Martin-Serrano
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Miguel C Seabra
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, UK
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Beata Wojciak-Stothard
- Centre for Pharmacology and Therapeutics, Department of Medicine, Imperial College London, London, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK.
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Alonso AM, Turowski VR, Ruiz DM, Orelo BD, Moresco JJ, Yates JR, Corvi MM. Exploring protein myristoylation in Toxoplasma gondii. Exp Parasitol 2019; 203:8-18. [PMID: 31150653 DOI: 10.1016/j.exppara.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/15/2019] [Accepted: 05/27/2019] [Indexed: 10/26/2022]
Abstract
Toxoplasma gondii is an important human and veterinary pathogen and the causative agent of toxoplasmosis, a potentially severe disease especially in immunocompromised or congenitally infected humans. Current therapeutic compounds are not well-tolerated, present increasing resistance, limited efficacy and require long periods of treatment. On this context, searching for new therapeutic targets is crucial to drug discovery. In this sense, recent works suggest that N-myristoyltransferase (NMT), the enzyme responsible for protein myristoylation that is essential in some parasites, could be the target of new anti-parasitic compounds. However, up to date there is no information on NMT and the extent of this modification in T. gondii. In this work, we decided to explore T. gondii genome in search of elements related with the N-myristoylation process. By a bioinformatics approach it was possible to identify a putative T. gondii NMT (TgNMT). This enzyme that is homologous to other parasitic NMTs, presents activity in vitro, is expressed in both intra- and extracellular parasites and interacts with predicted TgNMT substrates. Additionally, NMT activity seems to be important for the lytic cycle of Toxoplasma gondii. In parallel, an in silico myristoylome predicts 157 proteins to be affected by this modification. Myristoylated proteins would be affecting several metabolic functions with some of them being critical for the life cycle of this parasite. Together, these data indicate that TgNMT could be an interesting target of intervention for the treatment of toxoplasmosis.
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Affiliation(s)
- Andrés M Alonso
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (INTECH), CONICET, Universidad Nacional de San Martín. Intendente Marino Km 8.2, B7130, Chascomús, Buenos Aires, Argentina
| | - Valeria R Turowski
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (INTECH), CONICET, Universidad Nacional de San Martín. Intendente Marino Km 8.2, B7130, Chascomús, Buenos Aires, Argentina
| | - Diego M Ruiz
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (INTECH), CONICET, Universidad Nacional de San Martín. Intendente Marino Km 8.2, B7130, Chascomús, Buenos Aires, Argentina
| | - Barbara D Orelo
- Department of Chemical Physiology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - James J Moresco
- Department of Chemical Physiology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - John R Yates
- Department of Chemical Physiology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - María M Corvi
- Laboratorio de Bioquímica y Biología Celular de Parásitos, Instituto Tecnológico de Chascomús (INTECH), CONICET, Universidad Nacional de San Martín. Intendente Marino Km 8.2, B7130, Chascomús, Buenos Aires, Argentina.
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37
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Corpas-Lopez V, Moniz S, Thomas M, Wall RJ, Torrie LS, Zander-Dinse D, Tinti M, Brand S, Stojanovski L, Manthri S, Hallyburton I, Zuccotto F, Wyatt PG, De Rycker M, Horn D, Ferguson MAJ, Clos J, Read KD, Fairlamb AH, Gilbert IH, Wyllie S. Pharmacological Validation of N-Myristoyltransferase as a Drug Target in Leishmania donovani. ACS Infect Dis 2019; 5:111-122. [PMID: 30380837 PMCID: PMC6332449 DOI: 10.1021/acsinfecdis.8b00226] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Indexed: 01/23/2023]
Abstract
Visceral leishmaniasis (VL), caused by the protozoan parasites Leishmania donovani and L. infantum, is responsible for ∼30 000 deaths annually. Available treatments are inadequate, and there is a pressing need for new therapeutics. N-Myristoyltransferase (NMT) remains one of the few genetically validated drug targets in these parasites. Here, we sought to pharmacologically validate this enzyme in Leishmania. A focused set of 1600 pyrazolyl sulfonamide compounds was screened against L. major NMT in a robust high-throughput biochemical assay. Several potent inhibitors were identified with marginal selectivity over the human enzyme. There was little correlation between the enzyme potency of these inhibitors and their cellular activity against L. donovani axenic amastigotes, and this discrepancy could be due to poor cellular uptake due to the basicity of these compounds. Thus, a series of analogues were synthesized with less basic centers. Although most of these compounds continued to suffer from relatively poor antileishmanial activity, our most potent inhibitor of LmNMT (DDD100097, K i of 0.34 nM) showed modest activity against L. donovani intracellular amastigotes (EC50 of 2.4 μM) and maintained a modest therapeutic window over the human enzyme. Two unbiased approaches, namely, screening against our cosmid-based overexpression library and thermal proteome profiling (TPP), confirm that DDD100097 (compound 2) acts on-target within parasites. Oral dosing with compound 2 resulted in a 52% reduction in parasite burden in our mouse model of VL. Thus, NMT is now a pharmacologically validated target in Leishmania. The challenge in finding drug candidates remains to identify alternative strategies to address the drop-off in activity between enzyme inhibition and in vitro activity while maintaining sufficient selectivity over the human enzyme, both issues that continue to plague studies in this area.
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Affiliation(s)
- Victoriano Corpas-Lopez
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Sonia Moniz
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Michael Thomas
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Richard J. Wall
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Leah S. Torrie
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Dorothea Zander-Dinse
- Leishmaniasis Group, Bernhard Nocht Institute
for Tropical Medicine, Hamburg D-20359, Germany
| | - Michele Tinti
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Stephen Brand
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Laste Stojanovski
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Sujatha Manthri
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Irene Hallyburton
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Fabio Zuccotto
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Paul G. Wyatt
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Manu De Rycker
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - David Horn
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Michael A. J. Ferguson
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Joachim Clos
- Leishmaniasis Group, Bernhard Nocht Institute
for Tropical Medicine, Hamburg D-20359, Germany
| | - Kevin D. Read
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Alan H. Fairlamb
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Ian H. Gilbert
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Susan Wyllie
- The Wellcome Trust
Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
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Yadav P, Ayana R, Garg S, Jain R, Sah R, Joshi N, Pati S, Singh S. Plasmodium palmitoylation machinery engineered in E. coli for high-throughput screening of palmitoyl acyl-transferase inhibitors. FEBS Open Bio 2019; 9:248-264. [PMID: 30761251 PMCID: PMC6356172 DOI: 10.1002/2211-5463.12564] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/21/2018] [Accepted: 11/19/2018] [Indexed: 12/23/2022] Open
Abstract
Lipid‐based palmitoylation is a post‐translation modification (PTM) which acts as a biological rheostat in life cycle progression of a deadly human malaria parasite, Plasmodium falciparum. P. falciparum palmitoylation is catalyzed by 12 putative palmitoyl acyl‐transferase enzymes containing the conserved DHHC‐CRD (DHHC motif within a cysteine‐rich domain) which can serve as a druggable target. However, the paucity of high‐throughput assays has impeded the design of drugs targeting palmitoylation. We have developed a novel strategy which involves engineering of Escherichia coli, a PTM‐null system, to enforce ectopic expression of palmitoyl acyl‐transferase in order to study Plasmodium‐specific palmitoylation and screening of inhibitors. In this study, we have developed three synthetic E. coli strains expressing Plasmodium‐specific DHHC proteins (PfDHHC7/8/9). These cells were used for validating acyl‐transferase activity via acyl‐biotin exchange (ABE) and clickable chemistry methods. E. coli proteome was found to be palmitoylated in PfDHHC‐expressing clones, suggesting that plasmodium DHHC can catalyze palmitoylation of E. coli proteins. Upon treatment with generic inhibitor 2‐bromopalmitate (2‐BMP), a predominant reduction in palmitic acid incorporation is detected. Overall, these findings suggest that synthetic E. coli strains expressing PfDHHCs can enforce global palmitoylation in the E. coli proteome. Interestingly, this finding was corroborated by our in silico palmitoylome profiling, which revealed that out of the total E. coli proteome, 108 proteins were predicted to be palmitoylated as represented by the presence of three cysteine consensus motifs (cluster type I, II, III). In summary, our study reports a proof of concept for screening of chemotherapeutics targeting the palmitoylation machinery using a high‐throughput screening platform.
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Affiliation(s)
- Preeti Yadav
- Special Centre for Molecular Medicine Jawaharlal Nehru University New Delhi India
| | - R Ayana
- Department of Life Sciences School of Natural Sciences Shiv Nadar University Greater Noida, Uttar Pradesh India
| | - Swati Garg
- Department of Life Sciences School of Natural Sciences Shiv Nadar University Greater Noida, Uttar Pradesh India
| | - Ravi Jain
- Department of Life Sciences School of Natural Sciences Shiv Nadar University Greater Noida, Uttar Pradesh India
| | - Raj Sah
- Special Centre for Molecular Medicine Jawaharlal Nehru University New Delhi India
| | - Nishant Joshi
- Department of Life Sciences School of Natural Sciences Shiv Nadar University Greater Noida, Uttar Pradesh India
| | - Soumya Pati
- Department of Life Sciences School of Natural Sciences Shiv Nadar University Greater Noida, Uttar Pradesh India
| | - Shailja Singh
- Special Centre for Molecular Medicine Jawaharlal Nehru University New Delhi India
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Goya Grocin A, Serwa RA, Morales Sanfrutos J, Ritzefeld M, Tate EW. Whole Proteome Profiling of N-Myristoyltransferase Activity and Inhibition Using Sortase A. Mol Cell Proteomics 2019; 18:115-126. [PMID: 30341083 PMCID: PMC6317481 DOI: 10.1074/mcp.ra118.001043] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/24/2018] [Indexed: 11/30/2022] Open
Abstract
N-myristoylation is the covalent addition of a 14-carbon saturated fatty acid (myristate) to the N-terminal glycine of specific protein substrates by N-myristoyltransferase (NMT) and plays an important role in protein regulation by controlling localization, stability, and interactions. We developed a novel method for whole-proteome profiling of free N-terminal glycines through labeling with S. Aureus sortase A (SrtA) and used it for assessment of target engagement by an NMT inhibitor. Analysis of the SrtA-labeling pattern with an engineered biotinylated depsipeptide SrtA substrate (Biotin-ALPET-Haa, Haa = 2-hydroxyacetamide) enabled whole proteome identification and quantification of de novo generated N-terminal Gly proteins in response to NMT inhibition by nanoLC-MS/MS proteomics, and was confirmed for specific substrates across multiple cell lines by gel-based analyses and ELISA. To achieve optimal signal over background noise we introduce a novel and generally applicable improvement to the biotin/avidin affinity enrichment step by chemically dimethylating commercial NeutrAvidin resin and combining this with two-step LysC on-bead/trypsin off-bead digestion, effectively eliminating avidin-derived tryptic peptides and enhancing identification of enriched peptides. We also report SrtA substrate specificity in whole-cell lysates for the first time, confirming SrtA promiscuity beyond its recognized preference for N-terminal glycine, and its usefulness as a tool for unbiased labeling of N-terminal glycine-containing proteins. Our new methodology is complementary to metabolic tagging strategies, providing the first approach for whole proteome gain-of signal readout for NMT inhibition in complex samples which are not amenable to metabolic tagging.
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Affiliation(s)
- Andrea Goya Grocin
- From the ‡Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, UK
| | - Remigiusz A Serwa
- From the ‡Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, UK
| | - Julia Morales Sanfrutos
- From the ‡Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, UK
| | - Markus Ritzefeld
- From the ‡Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, UK
| | - Edward W Tate
- From the ‡Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, UK..
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40
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Zhao Y, Dang Z, Wei R, Gui W, Zhang Y, Chong S. The effects of CCR7 and related signaling pathways on Leishmania major -infected human dendritic cells. J Cell Physiol 2018; 234:13145-13156. [PMID: 30584667 DOI: 10.1002/jcp.27985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023]
Abstract
OBJECTIVES In our research, we aimed to investigate the roles of CC-chemokine receptor 7 (CCR7) and relevant signaling pathways in Leishmania major-infected human dendritic cells (DCs). METHODS Differentially expressed genes (DEGs) in L. major-infected human DCs were selected out and visualized using R program. Kyoto Encyclopedia of Genes and Genomes pathway analysis was conducted for investigation of significantly enriched signaling pathways and Gene Ontology enrichment analysis was carried out for the unveiling of enriched Molecular Functions and Biological Processes in L. major-infected human DCs. Besides, Hub gene was screened out using weighted gene coexpression network analysis and Cytoscape. In addition, enzyme-linked immunosorbent assay and real-time quantitative polymerase chain reaction were used for detection of relative expression of CCR7, interleukin-12 (IL-12), and interferon-γ (IFN-γ) in L. major-infected human DCs and western blot analysis was used for detection of relative expression of CCR7 and other proteins in JAK-STAT signaling pathway in L. major-infected human DCs. RESULTS CCR7 was upregulated and both chemokine and JAK-STAT signaling pathway were activated in L. major-infected human DCs. During the L. major infection, total number of L. major-infected human DCs were increased, as well as the relative expression levels of CCR7, IL-12, and IFN-γ and proteins in the JAK-STAT signaling pathway. Overexpression of CCR7 not only increased expression levels of IL-12 and IFN-γ but also activated the JAK-STAT signaling pathway to affect the leishmaniasis progression. CONCLUSION L. major infection-induced activation of CCR7, as well as JAK2 and STAT1, might well upregulate the expression of BAX yet suppress the expression of both Bcl2 and c-Jun to affect leishmaniasis progression.
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Affiliation(s)
- Yumin Zhao
- Department of Parasitology, Guilin Medical University, Guilin, China
| | - Zhisheng Dang
- Key Laboratory on Biology of Parasite and Vector, Parasitic Disease Control Center of China Center for Disease Control and Prevention, Ministry of Health, Shanghai, China
| | - Riming Wei
- Collge of Biotechnology, Guilin Medical University, Guilin, China
| | - Weifeng Gui
- Department of Parasitology, Guilin Medical University, Guilin, China
| | - Yishu Zhang
- Department of Parasitology, Guilin Medical University, Guilin, China
| | - Shigui Chong
- School of Nursing, Guilin Medical University, Guilin, China
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41
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The Cellular Senescence-Inhibited Gene Is Essential for PPM1A Myristoylation To Modulate Transforming Growth Factor β Signaling. Mol Cell Biol 2018; 38:MCB.00414-18. [PMID: 30201805 DOI: 10.1128/mcb.00414-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/05/2018] [Indexed: 12/16/2022] Open
Abstract
The cellular senescence-inhibited gene (CSIG) is implicated in important biological processes, including cellular senescence and apoptosis. Our work showed that CSIG is involved in the myristoylation of the serine/threonine protein phosphatase PPM1A. Previous research has shown that myristoylation is necessary for PPM1A to dephosphorylate Smad2 and Smad3. However, the control and the biological significance of the myristoylation remain poorly understood. In this study, we found that CSIG knockdown disturbs PPM1A myristoylation and reduces the dephosphorylation by PPM1A of its substrate Smad2. By regulating PPM1A myristoylation, CSIG is involved in modulating the signaling of transforming growth factor β (TGF-β). Further study of the mechanism indicated that CSIG facilitates the interaction between N-myristoyltransferase 1 (NMT1) and PPM1A. Taking the data together, we found that CSIG is a regulator of PPM1A myristoylation and TGF-β signaling. By promoting the myristoylation of PPM1A, CSIG enhanced the phosphatase activity of PPM1A and further inhibited TGF-β signaling. This work not only extends the biological significance of CSIG but also provides new ideas and a reference for the study of the regulatory mechanism of myristoylation.
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42
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Kaiser N, Mejuch T, Fedoryshchak R, Janning P, Tate EW, Waldmann H. Photoactivatable Myristic Acid Probes for UNC119-Cargo Interactions. Chembiochem 2018; 20:134-139. [DOI: 10.1002/cbic.201800406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Nadine Kaiser
- Department of Chemical Biology; Max-Planck-Institute of, Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Tom Mejuch
- Department of Chemical Biology; Max-Planck-Institute of, Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Roman Fedoryshchak
- Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Petra Janning
- Department of Chemical Biology; Max-Planck-Institute of, Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Edward W. Tate
- Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Herbert Waldmann
- Department of Chemical Biology; Max-Planck-Institute of, Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
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43
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Opportunities for Lipid-Based Probes in the Field of Immunology. Curr Top Microbiol Immunol 2018; 420:283-319. [PMID: 30242513 DOI: 10.1007/82_2018_127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Lipids perform a wide range of functions inside the cell, ranging from structural building block of membranes and energy storage to cell signaling. The mode of action of many signaling lipids has remained elusive due to their low abundance, high lipophilicity, and inherent instability. Various chemical biology approaches, such as photoaffinity or activity-based protein profiling methods, have been employed to shed light on the biological role of lipids and the lipid-protein interaction profile. In this review, we will summarize the recent developments in the field of chemical probes to study lipid biology, especially in immunology, and indicate potential avenues for future research.
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44
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Ayana R, Yadav P, Kumari R, Ramu D, Garg S, Pati S, Singh S. Identification and Characterization of a Novel Palmitoyl Acyltransferase as a Druggable Rheostat of Dynamic Palmitoylome in L. donovani. Front Cell Infect Microbiol 2018; 8:186. [PMID: 29977865 PMCID: PMC6022219 DOI: 10.3389/fcimb.2018.00186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/14/2018] [Indexed: 01/08/2023] Open
Abstract
Palmitoylation has been recently identified as an important post-translational rheostat for controlling protein function in eukaryotes. However, the molecular machinery underlying palmitoylation remains unclear in the neglected tropical parasite, Leishmania donovani. Herein, we have identified a catalog of 20 novel palmitoyl acyltransferases (PATs) and characterized the promastigote-specific PAT (LdPAT4) containing the canonical Asp-His-His-Cys (DHHC) domain. Immunofluorescence analysis using in-house generated LdPAT4-specific antibody demonstrated distinct expression of LdPAT4 in the flagellar pocket of promastigotes. Using metabolic labeling-coupled click chemistry method, the functionality of this recombinant enzyme could be authenticated in E. coli strain expressing LdPAT4-DHHC domain. This was evident by the cellular uptake of palmitic acid analogs, which could be successfully inhibited by 2-BMP, a PAT-specific inhibitor. Using CSS-Palm based in-silico proteomic analysis, we could predict up to 23 palmitoylated sites per protein in the promastigotes, and further identify distinctive palmitoylated protein clusters involved in microtubule assembly, flagella motility and vesicular trafficking. To highlight, proteins such as Flagellar Member proteins (FLAM1, FLAM5), Intraflagellar Transport proteins (IFT88), and flagellar motor assembly proteins including the Dynein family were found to be enriched. Furthermore, analysis of global palmitoylation in promastigotes using Acyl-biotin exchange purification identified a set of S-palmitoylated proteins overlapping with the in-silico proteomics data. The attenuation of palmitoylation using 2-BMP demonstrated several phenotypic alterations in the promastigotes including distorted morphology, reduced motility (flagellar loss or slow flagellar beating), and inefficient invasion of promastigotes to host macrophages. These analyses confirm the essential role of palmitoylation in promastigotes. In summary, the findings suggest that LdPAT4 acts as a functional acyltransferase that can regulate palmitoylation of proteins involved in parasite motility and invasion, thus, can serve as a potential target for designing chemotherapeutics in Visceral Leishmaniasis.
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Affiliation(s)
- R Ayana
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Preeti Yadav
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rajesh Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Dandugudumula Ramu
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Swati Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Soumya Pati
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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45
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Aldrich CC, Calderón F. 2 nd SCI/RSC Symposium on Medicinal Chemistry for Global Health: A Unique Opportunity for the Field. ACS Infect Dis 2018; 4:424-428. [PMID: 29649878 DOI: 10.1021/acsinfecdis.8b00022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Courtney C. Aldrich
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 8-174 Weaver-Densford Hall, 308 Harvard Street S.E., Minneapolis, Minneosta 55455, United States
| | - Félix Calderón
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
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46
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Schlott AC, Holder AA, Tate EW. N-Myristoylation as a Drug Target in Malaria: Exploring the Role of N-Myristoyltransferase Substrates in the Inhibitor Mode of Action. ACS Infect Dis 2018; 4:449-457. [PMID: 29363940 DOI: 10.1021/acsinfecdis.7b00203] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Malaria continues to be a significant cause of death and morbidity worldwide, and there is a need for new antimalarial drugs with novel targets. We have focused as a potential target for drug development on N-myristoyl transferase (NMT), an enzyme that acylates a wide range of substrate proteins. The NMT substrates in Plasmodium falciparum include some proteins that are common to processes in eukaryotes such as secretory transport and others that are unique to apicomplexan parasites. Myristoylation facilitates a protein interaction with membranes that may be strengthened by further lipidation, and the inhibition of NMT results in incorrect protein localization and the consequent disruption of function. The diverse roles of NMT substrates mean that NMT inhibition has a pleiotropic and severe impact on parasite development, growth, and multiplication. To study the mode of action underlying NMT inhibition, it is important to consider the function of proteins upstream and downstream of NMT. In this work, we therefore present our current perspective on the different functions of known NMT substrates as well as compare the inhibition of cotranslational myristoylation to the inhibition of known targets upstream of NMT.
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Affiliation(s)
- Anja C. Schlott
- Malaria Parasitology, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, Imperial College Road, SW7 2AZ London, United Kingdom
| | - Anthony A. Holder
- Malaria Parasitology, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, Imperial College Road, SW7 2AZ London, United Kingdom
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47
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Sobocińska J, Roszczenko-Jasińska P, Ciesielska A, Kwiatkowska K. Protein Palmitoylation and Its Role in Bacterial and Viral Infections. Front Immunol 2018; 8:2003. [PMID: 29403483 PMCID: PMC5780409 DOI: 10.3389/fimmu.2017.02003] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022] Open
Abstract
S-palmitoylation is a reversible, enzymatic posttranslational modification of proteins in which palmitoyl chain is attached to a cysteine residue via a thioester linkage. S-palmitoylation determines the functioning of proteins by affecting their association with membranes, compartmentalization in membrane domains, trafficking, and stability. In this review, we focus on S-palmitoylation of proteins, which are crucial for the interactions of pathogenic bacteria and viruses with the host. We discuss the role of palmitoylated proteins in the invasion of host cells by bacteria and viruses, and those involved in the host responses to the infection. We highlight recent data on protein S-palmitoylation in pathogens and their hosts obtained owing to the development of methods based on click chemistry and acyl-biotin exchange allowing proteomic analysis of protein lipidation. The role of the palmitoyl moiety present in bacterial lipopolysaccharide and lipoproteins, contributing to infectivity and affecting recognition of bacteria by innate immune receptors, is also discussed.
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Affiliation(s)
- Justyna Sobocińska
- Laboratory of Molecular Membrane Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Paula Roszczenko-Jasińska
- Laboratory of Molecular Membrane Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Anna Ciesielska
- Laboratory of Molecular Membrane Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Kwiatkowska
- Laboratory of Molecular Membrane Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
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48
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Oliveira MP, Martins VT, Santos TTO, Lage DP, Ramos FF, Salles BCS, Costa LE, Dias DS, Ribeiro PAF, Schneider MS, Machado-de-Ávila RA, Teixeira AL, Coelho EAF, Chávez-Fumagalli MA. Small Myristoylated Protein-3, Identified as a Potential Virulence Factor in Leishmania amazonensis, Proves to be a Protective Antigen against Visceral Leishmaniasis. Int J Mol Sci 2018; 19:E129. [PMID: 29301342 PMCID: PMC5796078 DOI: 10.3390/ijms19010129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/14/2017] [Accepted: 12/25/2017] [Indexed: 11/23/2022] Open
Abstract
In a proteomics approach conducted with Leishmania amazonensis, parasite proteins showed either an increase or a decrease in their expression content during extensive in vitro cultivation, and were related to the survival and the infectivity of the parasites, respectively. In the current study, a computational screening was performed to predict virulence factors among these molecules. Three proteins were selected, one of which presented no homology to human proteins. This candidate, namely small myristoylated protein-3 (SMP-3), was cloned, and its recombinant version (rSMP-3) was used to stimulate peripheral blood mononuclear cells (PBMCs) from healthy subjects living in an endemic area of leishmaniasis and from visceral leishmaniasis patients. Results showed high interferon-γ (IFN-γ) production and low levels of interleukin 10 (IL-10) in the cell supernatants. An in vivo experiment was then conducted on BALB/c mice, which were immunized with rSMP-3/saponin and later challenged with Leishmania infantum promastigotes. The rSMP-3/saponin combination induced high production of protein-specific IFN-γ, IL-12, and granulocyte-macrophage colony-stimulating factor (GM-CSF) by the spleen cells of the immunized mice. This pattern was associated with protection, which was characterized by a significant reduction in the parasite load in distinct organs of the animals. Altogether, these results have revealed that this new virulence factor is immunogenic in both mice and humans, and have proven its protective efficacy against visceral leishmaniasis in a murine model.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Protozoan/chemistry
- Antigens, Protozoan/metabolism
- Computational Biology
- Cytokines/metabolism
- Epitopes, T-Lymphocyte/metabolism
- Humans
- Immunity, Cellular
- Immunity, Humoral
- Leishmania/pathogenicity
- Leishmania infantum
- Leishmaniasis, Visceral/immunology
- Leishmaniasis, Visceral/parasitology
- Leishmaniasis, Visceral/prevention & control
- Leukocytes, Mononuclear/metabolism
- Linear Models
- Mice, Inbred BALB C
- Molecular Sequence Annotation
- Protozoan Proteins/chemistry
- Protozoan Proteins/metabolism
- Reproducibility of Results
- Structural Homology, Protein
- Virulence Factors/metabolism
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Affiliation(s)
- Marcelo P Oliveira
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Vívian T Martins
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Thaís T O Santos
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Daniela P Lage
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Fernanda F Ramos
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Beatriz C S Salles
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Lourena E Costa
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Daniel S Dias
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Patrícia A F Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Mônica S Schneider
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
| | - Ricardo A Machado-de-Ávila
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma 88806-000, Santa Catarina, Brazil.
| | - Antônio L Teixeira
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
- Neuropsychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, 1941 East Road, Houston, TX 77041, USA.
| | - Eduardo A F Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
- Departamento de Patologia Clínica, do Colégio Técnico (COLTEC), Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Miguel A Chávez-Fumagalli
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil.
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49
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Jiang H, Zhang X, Chen X, Aramsangtienchai P, Tong Z, Lin H. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 2018; 118:919-988. [PMID: 29292991 DOI: 10.1021/acs.chemrev.6b00750] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein lipidation, including cysteine prenylation, N-terminal glycine myristoylation, cysteine palmitoylation, and serine and lysine fatty acylation, occurs in many proteins in eukaryotic cells and regulates numerous biological pathways, such as membrane trafficking, protein secretion, signal transduction, and apoptosis. We provide a comprehensive review of protein lipidation, including descriptions of proteins known to be modified and the functions of the modifications, the enzymes that control them, and the tools and technologies developed to study them. We also highlight key questions about protein lipidation that remain to be answered, the challenges associated with answering such questions, and possible solutions to overcome these challenges.
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Affiliation(s)
- Hong Jiang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiaoyu Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiao Chen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Pornpun Aramsangtienchai
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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50
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Peng T, Hang HC. Chemical Proteomic Profiling of Protein Fatty-Acylation in Microbial Pathogens. Curr Top Microbiol Immunol 2018; 420:93-110. [PMID: 30128826 DOI: 10.1007/82_2018_126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein fatty-acylation describes the covalent modification of protein with fatty acids during or after translation. Chemical proteomic profiling methods have provided new opportunities to explore protein fatty-acylation in microbial pathogens. Recent studies suggest that protein fatty-acylation is essential to survival and pathogenesis of eukaryotic pathogens such as parasites and fungi. Moreover, fatty-acylation in host cells can be exploited or manipulated by pathogenic bacteria. Herein, we first review the prevalent classes of fatty-acylation in microbial pathogens and the chemical proteomic profiling methods for their global analysis. We then summarize recent fatty-acylation profiling studies performed in eukaryotic pathogens and during bacterial infections, highlighting how they contribute to functional characterization of fatty-acylation under these contexts.
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Affiliation(s)
- Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, 10065, USA.
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