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King HR, Bycroft M, Nguyen TB, Kelly G, Vinogradov AA, Rowling PJE, Stott K, Ascher DB, Suga H, Itzhaki LS, Artavanis-Tsakonas K. Targeting the Plasmodium falciparum UCHL3 ubiquitin hydrolase using chemically constrained peptides. Proc Natl Acad Sci U S A 2024; 121:e2322923121. [PMID: 38739798 PMCID: PMC11126973 DOI: 10.1073/pnas.2322923121] [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: 01/11/2024] [Accepted: 03/18/2024] [Indexed: 05/16/2024] Open
Abstract
The ubiquitin-proteasome system is essential to all eukaryotes and has been shown to be critical to parasite survival as well, including Plasmodium falciparum, the causative agent of the deadliest form of malarial disease. Despite the central role of the ubiquitin-proteasome pathway to parasite viability across its entire life-cycle, specific inhibitors targeting the individual enzymes mediating ubiquitin attachment and removal do not currently exist. The ability to disrupt P. falciparum growth at multiple developmental stages is particularly attractive as this could potentially prevent both disease pathology, caused by asexually dividing parasites, as well as transmission which is mediated by sexually differentiated parasites. The deubiquitinating enzyme PfUCHL3 is an essential protein, transcribed across both human and mosquito developmental stages. PfUCHL3 is considered hard to drug by conventional methods given the high level of homology of its active site to human UCHL3 as well as to other UCH domain enzymes. Here, we apply the RaPID mRNA display technology and identify constrained peptides capable of binding to PfUCHL3 with nanomolar affinities. The two lead peptides were found to selectively inhibit the deubiquitinase activity of PfUCHL3 versus HsUCHL3. NMR spectroscopy revealed that the peptides do not act by binding to the active site but instead block binding of the ubiquitin substrate. We demonstrate that this approach can be used to target essential protein-protein interactions within the Plasmodium ubiquitin pathway, enabling the application of chemically constrained peptides as a novel class of antimalarial therapeutics.
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Affiliation(s)
- Harry R. King
- Department of Pathology, University of Cambridge, CambridgeCB2 1QP, United Kingdom
- Department of Pharmacology, University of Cambridge, CambridgeCB2 1PD, United Kingdom
| | - Mark Bycroft
- Department of Pharmacology, University of Cambridge, CambridgeCB2 1PD, United Kingdom
| | - Thanh-Binh Nguyen
- School of Chemistry and Molecular Biosciences, University of Queensland, BrisbaneQLD 4067, Australia
| | - Geoff Kelly
- NMR Centre, Francis Crick Institute, LondonNW1 1AT, United Kingdom
| | - Alexander A. Vinogradov
- Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo113-0033, Japan
| | - Pamela J. E. Rowling
- Department of Pharmacology, University of Cambridge, CambridgeCB2 1PD, United Kingdom
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, CambridgeCB2 1GA, United Kingdom
| | - David B. Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, BrisbaneQLD 4067, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo113-0033, Japan
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, CambridgeCB2 1PD, United Kingdom
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2
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Kudo G, Yanagisawa K, Yoshino R, Hirokawa T. AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics. J Chem Inf Model 2023; 63:7768-7777. [PMID: 38085669 PMCID: PMC10751795 DOI: 10.1021/acs.jcim.3c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/26/2023]
Abstract
Peptides have attracted much attention recently owing to their well-balanced properties as drugs against protein-protein interaction (PPI) surfaces. Molecular simulation-based predictions of binding sites and amino acid residues with high affinity to PPI surfaces are expected to accelerate the design of peptide drugs. Mixed-solvent molecular dynamics (MSMD), which adds probe molecules or fragments of functional groups as solutes to the hydration model, detects the binding hotspots and cryptic sites induced by small molecules. The detection results vary depending on the type of probe molecule; thus, they provide important information for drug design. For rational peptide drug design using MSMD, we proposed MSMD with amino acid residue probes, named amino acid probe-based MSMD (AAp-MSMD), to detect hotspots and identify favorable amino acid types on protein surfaces to which peptide drugs bind. We assessed our method in terms of hotspot detection at the amino acid probe level and binding free energy prediction with amino acid probes at the PPI site for the complex structure that formed the PPI. In hotspot detection, the max-spatial probability distribution map (max-PMAP) obtained from AAp-MSMD detected the PPI site, to which each type of amino acid can bind favorably. In the binding free energy prediction using amino acid probes, ΔGFE obtained from AAp-MSMD roughly estimated the experimental binding affinities from the structure-activity relationship. AAp-MSMD, with amino acid probes, provides estimated binding sites and favorable amino acid types at the PPI site of a target protein.
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Affiliation(s)
- Genki Kudo
- Physics
Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8571, Ibaraki Japan
| | - Keisuke Yanagisawa
- Department
of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro 152-8550, Tokyo Japan
- Middle
Molecule IT-based Drug Discovery Laboratory, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro 152-8550, Tokyo Japan
| | - Ryunosuke Yoshino
- Faculty
of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Ibaraki Japan
- Transborder
Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki Japan
| | - Takatsugu Hirokawa
- Faculty
of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Ibaraki Japan
- Transborder
Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki Japan
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3
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Cheng J, Zhou J, Kong L, Wang H, Zhang Y, Wang X, Liu G, Chu Q. Stabilized cyclic peptides as modulators of protein-protein interactions: promising strategies and biological evaluation. RSC Med Chem 2023; 14:2496-2508. [PMID: 38107173 PMCID: PMC10718590 DOI: 10.1039/d3md00487b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 12/19/2023] Open
Abstract
Protein-protein interactions (PPIs) control many essential biological pathways which are often misregulated in disease. As such, selective PPI modulators are desirable to unravel complex functions of PPIs and thus expand the repertoire of therapeutic targets. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets for conventional drug modalities, rendering most PPIs "undruggable". Therefore, there is a growing need to discover innovative molecules that are able to modulate crucial PPIs. Peptides are ideal candidates to deliver such therapeutics attributed to their ability to closely mimic structural features of protein interfaces. However, their inherently poor proteolysis resistance and cell permeability inevitably hamper their biomedical applications. The introduction of a constraint (i.e., peptide cyclization) to stabilize peptides' secondary structure is a promising strategy to address this problem as witnessed by the rapid development of cyclic peptide drugs in the past two decades. Here, we comprehensively review the recent progress on stabilized cyclic peptides in targeting challenging PPIs. Technological advancements and emerging chemical approaches for stabilizing active peptide conformations are categorized in terms of α-helix stapling, β-hairpin mimetics and macrocyclization. To discover potent and selective ligands, cyclic peptide library technologies were updated based on genetic, biochemical or synthetic methodologies. Moreover, several advances to improve the permeability and oral bioavailability of biologically active cyclic peptides enable the de novo development of cyclic peptide ligands with pharmacological properties. In summary, the development of cyclic peptide-based PPI modulators carries tremendous promise for the next generation of therapeutic agents to target historically "intractable" PPI systems.
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Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Junlong Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
| | - Lingyan Kong
- College of Food Science and Engineering, Nanjing University of Finance and Economics Nanjing 210023 China
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University Nanjing 210009 China
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4
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Mannuthodikayil J, Sinha S, Singh S, Biswas A, Ali I, Mashurabad PC, Tabassum W, Vydyam P, Bhattacharyya MK, Mandal K. A Chimeric Peptide Inhibits Red Blood Cell Invasion by Plasmodium falciparum with Hundredfold Increased Efficacy. Chembiochem 2022; 24:e202200533. [PMID: 36449557 DOI: 10.1002/cbic.202200533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Inhibiting the formation of a tight junction between two malaria parasite proteins, apical membrane antigen 1 and rhoptry neck protein 2, crucial for red blood cell invasion, prevents progression of the disease. In this work, we have used a unique approach to design a chimeric peptide, prepared by fusion of the best features of two peptide inhibitors, that has displayed parasite growth inhibition ex vivo with nanomolar IC50 , which is 100 times better than any of its parent peptides. Furthermore, to gain structural insights, we computationally modelled the hybrid peptide on its receptor.
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Affiliation(s)
- Jamsad Mannuthodikayil
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Suman Sinha
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Sameer Singh
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Anamika Biswas
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Irshad Ali
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Purna Chandra Mashurabad
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Wahida Tabassum
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Pratap Vydyam
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Mrinal Kanti Bhattacharyya
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Kalyaneswar Mandal
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
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5
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Rittipornlertrak A, Nambooppha B, Muenthaisong A, Apinda N, Koonyosying P, Srisawat W, Chomjit P, Sangkakam K, Punyapornwithaya V, Tiwananthagorn S, Yokoyama N, Sthitmatee N. Immunization of Cattle With Recombinant Structural Ectodomains I and II of Babesia bovis Apical Membrane Antigen 1 [BbAMA-1(I/II)] Induces Strong Th1 Immune Response. Front Vet Sci 2022; 9:917389. [PMID: 35812841 PMCID: PMC9260583 DOI: 10.3389/fvets.2022.917389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
Both strong innate and adaptive immune responses are an important component of protection against intraerythrocytic protozoan parasites. Resistance to bovine babesiosis is associated with interferon (IFN)-γ mediated responses. CD4+ T cells and macrophages have been identified as major effector cells mediating the clearance of pathogens. Previously, the apical membrane antigen 1 (AMA-1) was found to significantly induce the immune response inhibiting B. bovis merozoite growth and invasion. However, a detailed characterization of both humoral and cellular immune responses against the structure of B. bovis AMA-1 (BbAMA-1) has not yet been established. Herein, the present study aimed to express the recombinant BbAMA-1 domain I+II protein [rBbAMA-1(I/II)], which is the most predominant immune response region, and to characterize its immune response. As a result, cattle vaccinated with BbAMA-1(I/II) significantly developed high titters of total immunoglobulin (Ig) G antibodies and a high ratio of IgG2/IgG1 when compared to control groups. Interestingly, the BbAMA-1(I/II)-based formulations produced in our study could elicit CD4+ T cells and CD8+ T cells producing IFN-γ and tumor necrosis factor (TNF)-α. Collectively, the results indicate that immunization of cattle with BbAMA-1(I/II) could induce strong Th1 cell responses. In support of this, we observed the up-regulation of Th1 cytokine mRNA transcripts, including IFN-γ, TNF-α, Interleukin (IL)-2 and IL-12, in contrast to down regulation of IL-4, IL-6 and IL-10, which would be indicative of a Th2 cytokine response. Moreover, the up-regulation of inducible nitric oxide synthase (iNOS) was observed. In conclusion, this is the first report on the in-depth immunological characterization of the response to BbAMA-1. According to our results, BbAMA-1 is recognized as a potential candidate vaccine against B. bovis infection. As evidenced by the Th1 cell response, it could potentially provide protective immunity. However, further challenge-exposure with virulent B. bovis strain in immunized cattle would be needed to determine its protective efficacy.
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Affiliation(s)
- Amarin Rittipornlertrak
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Ruminant Clinic, Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Boondarika Nambooppha
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Department of Veterinary Bioscience and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Anucha Muenthaisong
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nisachon Apinda
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pongpisid Koonyosying
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Wanwisa Srisawat
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Paweena Chomjit
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kanokwan Sangkakam
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Veerasak Punyapornwithaya
- Ruminant Clinic, Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Saruda Tiwananthagorn
- Department of Veterinary Bioscience and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Naoaki Yokoyama
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Nattawooti Sthitmatee
- Laboratory of Veterinary Vaccine and Biological Products, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Department of Veterinary Bioscience and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Excellent Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- *Correspondence: Nattawooti Sthitmatee ;
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6
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Molina-Franky J, Patarroyo ME, Kalkum M, Patarroyo MA. The Cellular and Molecular Interaction Between Erythrocytes and Plasmodium falciparum Merozoites. Front Cell Infect Microbiol 2022; 12:816574. [PMID: 35433504 PMCID: PMC9008539 DOI: 10.3389/fcimb.2022.816574] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum is the most lethal human malaria parasite, partly due to its genetic variability and ability to use multiple invasion routes via its binding to host cell surface receptors. The parasite extensively modifies infected red blood cell architecture to promote its survival which leads to increased cell membrane rigidity, adhesiveness and permeability. Merozoites are initially released from infected hepatocytes and efficiently enter red blood cells in a well-orchestrated process that involves specific interactions between parasite ligands and erythrocyte receptors; symptoms of the disease occur during the life-cycle’s blood stage due to capillary blockage and massive erythrocyte lysis. Several studies have focused on elucidating molecular merozoite/erythrocyte interactions and host cell modifications; however, further in-depth analysis is required for understanding the parasite’s biology and thus provide the fundamental tools for developing prophylactic or therapeutic alternatives to mitigate or eliminate Plasmodium falciparum-related malaria. This review focuses on the cellular and molecular events during Plasmodium falciparum merozoite invasion of red blood cells and the alterations that occur in an erythrocyte once it has become infected.
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Affiliation(s)
- Jessica Molina-Franky
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Department of Immunology and Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA, United States
- PhD Programme in Biotechnology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Manuel Elkin Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Health Sciences Division, Universidad Santo Tomás, Bogotá, Colombia
- Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Markus Kalkum
- Department of Immunology and Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA, United States
- *Correspondence: Markus Kalkum, ; Manuel Alfonso Patarroyo,
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Health Sciences Division, Universidad Santo Tomás, Bogotá, Colombia
- Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- *Correspondence: Markus Kalkum, ; Manuel Alfonso Patarroyo,
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7
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Biswas A, Raran-Kurussi S, Narayan A, Kar A, Chandra Mashurabad P, Bhattacharyya MK, Mandal K. Efficient refolding and functional characterization of PfAMA1(DI+DII) expressed in E. coli. Biochem Biophys Rep 2021; 26:100950. [PMID: 33665380 PMCID: PMC7907217 DOI: 10.1016/j.bbrep.2021.100950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/18/2021] [Accepted: 02/04/2021] [Indexed: 11/30/2022] Open
Abstract
Apical membrane antigen 1 (AMA1) is a surface protein of Plasmodium sp. that plays a crucial role in forming moving junction (MJ) during the invasion of human red blood cells. The obligatory presence of AMA1 in the parasite lifecycle designates this protein as a potential vaccine candidate and an essential target for the development of novel peptide or protein therapeutics. However, due to multiple cysteine residues in the protein sequence, attaining the native fold with correct disulfide linkages during the refolding process after expression in bacteria has remained challenging for years. Although several approaches to obtain the refolded protein from bacterial expression have been reported previously, achieving high yield during refolding and proper functional validation of the expressed protein was lacking. We report here an improved method of refolding to obtain higher quantity of refolded protein. We have also validated the refolded protein's functional activity by evaluating the expressed AMA1 protein binding with a known inhibitory peptide, rhoptry neck protein 2 (RON2), using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). A simple yet effective protocol for P. falciparum AMA1 protein expression from E. coli. Highly reproducible and scalable refolding protocol. The modified refolding method uses a step-wise dialysis technique. Functional validation of the refolded protein shown by binding with PfRON2 ectodomain using SPR and ITC.
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Affiliation(s)
- Anamika Biswas
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana 500046, India
| | - Sreejith Raran-Kurussi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana 500046, India
| | - Akash Narayan
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana 500046, India
| | - Abhisek Kar
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana 500046, India
| | - Purna Chandra Mashurabad
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana 500046, India
| | - Mrinal Kanti Bhattacharyya
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana 500046, India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana 500046, India
- Corresponding author.
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8
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Mishra M, Singh V, Tellis MB, Joshi RS, Pandey KC, Singh S. Cyclic peptide engineered from phytocystatin inhibitory hairpin loop as an effective modulator of falcipains and potent antimalarial. J Biomol Struct Dyn 2020; 40:3642-3654. [PMID: 33292080 DOI: 10.1080/07391102.2020.1848629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cystatins are classical competitive inhibitors of C1 family cysteine proteases (papain family). Phytocystatin superfamily shares high sequence homology and typical tertiary structure with conserved glutamine-valine-glycine (Q-X-V-X-G) loop blocking the active site of C1 proteases. Here, we develop a cysteine-bounded cyclic peptide (CYS-cIHL) and linear peptide (CYS-IHL), using the conserved inhibitory hairpin loop amino acid sequence. Using an in silico approach based on modeling, protein-peptide docking, molecular dynamics simulations and calculation of free energy of binding, we designed and validated inhibitory peptides against falcipain-2 (FP-2) and -3 (FP-3), cysteine proteases from the malarial parasite Plasmodium falciparum. Falcipains are critical hemoglobinases of P. falciparum that are validated targets for the development of antimalarial therapies. CYS-cIHL was able to bind with micromolar affinity to FP-2 and modulate its binding with its substrate, hemoglobin in in vitro and in vivo assays. CYS-cIHL could effectively block parasite growth and displayed antimalarial activity in culture assays with no cytotoxicity towards human cells. These results indicated that cyclization can substantially increase the peptide affinity to the target. Furthermore, this can be applied as an effective strategy for engineering peptide inhibitory potency against proteases.
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Affiliation(s)
- Manasi Mishra
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Uttar Pradesh, India
| | - Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Meenakshi B Tellis
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Rakesh S Joshi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kailash C Pandey
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, Dwarka, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Uttar Pradesh, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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9
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Míguez Amil S, Jiménez-Ortega E, Ramírez-Escudero M, Talens-Perales D, Marín-Navarro J, Polaina J, Sanz-Aparicio J, Fernandez-Leiro R. The cryo-EM Structure of Thermotoga maritima β-Galactosidase: Quaternary Structure Guides Protein Engineering. ACS Chem Biol 2020; 15:179-188. [PMID: 31874027 DOI: 10.1021/acschembio.9b00752] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Lactose intolerance is a common digestive disorder that affects a large proportion of the adult human population. The severity of the symptoms is highly variable, depending on the susceptibility to the sugar and the amount digested. For that reason, enzymes that can be used for the production of lactose-free milk and milk derivatives have acquired singular biotechnological importance. One such case is Thermotoga maritima β-galactosidase (TmLac). Here, we report the cryo-EM structure of TmLac at 2.0 Å resolution. The protein features a newly solved domain at its C-terminus, characteristic of the genus Thermotoga, which promotes a peculiar octameric arrangement. We have assessed the constraints imposed by the quaternary protein structure on the construction of hybrid versions of this GH2 enzyme. Carbohydrate binding modules (CBM) from the CBM2 and CBM9 families have been added at either the amino or carboxy terminus, and the structural and functional effects of such modifications have been analyzed. The results provide a basis for the rational design of hybrid enzymes that can be efficiently attached to different solid supports.
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Affiliation(s)
- Samuel Míguez Amil
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Elena Jiménez-Ortega
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Mercedes Ramírez-Escudero
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain
| | - David Talens-Perales
- Institute of Agrochemical and Food Technology, Spanish National Research Council (CSIC), 46980-Paterna, Valencia, Spain
| | - Julia Marín-Navarro
- Institute of Agrochemical and Food Technology, Spanish National Research Council (CSIC), 46980-Paterna, Valencia, Spain
| | - Julio Polaina
- Institute of Agrochemical and Food Technology, Spanish National Research Council (CSIC), 46980-Paterna, Valencia, Spain
| | - Julia Sanz-Aparicio
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Rafael Fernandez-Leiro
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
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10
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Salinas ND, Tang WK, Tolia NH. Blood-Stage Malaria Parasite Antigens: Structure, Function, and Vaccine Potential. J Mol Biol 2019; 431:4259-4280. [PMID: 31103771 DOI: 10.1016/j.jmb.2019.05.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/22/2019] [Accepted: 05/08/2019] [Indexed: 10/26/2022]
Abstract
Plasmodium parasites are the causative agent of malaria, a disease that kills approximately 450,000 individuals annually, with the majority of deaths occurring in children under the age of 5 years and the development of a malaria vaccine is a global health priority. Plasmodium parasites undergo a complex life cycle requiring numerous diverse protein families. The blood stage of parasite development results in the clinical manifestation of disease. A vaccine that disrupts the blood stage is highly desired and will aid in the control of malaria. The blood stage comprises multiple steps: invasion of, asexual growth within, and egress from red blood cells. This review focuses on blood-stage antigens with emphasis on antigen structure, antigen function, neutralizing antibodies, and vaccine potential.
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Affiliation(s)
- Nichole D Salinas
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD,, 20892, USA
| | - Wai Kwan Tang
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD,, 20892, USA
| | - Niraj H Tolia
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD,, 20892, USA.
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11
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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12
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Drew DR, Sanders PR, Weiss G, Gilson PR, Crabb BS, Beeson JG. Functional Conservation of the AMA1 Host-Cell Invasion Ligand Between P. falciparum and P. vivax: A Novel Platform to Accelerate Vaccine and Drug Development. J Infect Dis 2019; 217:498-507. [PMID: 29165651 DOI: 10.1093/infdis/jix583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/17/2017] [Indexed: 01/20/2023] Open
Abstract
Plasmodium vivax and P. falciparum malaria species have diverged significantly in receptor-ligand interactions and host-cell invasion. One protein common to both is the merozoite invasion ligand AMA1. While the general structure of AMA1 is similar between species, their sequences are divergent. Surprisingly, it was possible to genetically replace PfAMA1 with PvAMA1 in P. falciparum parasites. PvAMA1 complemented PfAMA1 function and supported invasion of erythrocytes by P. falciparum. Genetically modified P. falciparum expressing PvAMA1 evaded the invasion inhibitory effects of antibodies to PfAMA1, demonstrating species specificity of functional antibodies. We generated antibodies to recombinant PvAMA1 that effectively inhibited invasion, confirming the function of PvAMA1 in genetically modified parasites. Results indicate significant molecular flexibility in AMA1 enabling conserved function despite substantial sequence divergence across species. This provides powerful new tools to quantify the inhibitory activities of antibodies or drugs targeting PvAMA1, opening new opportunities for vaccine and therapeutic development against P. vivax.
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Affiliation(s)
| | | | | | | | - Brendan S Crabb
- Burnet Institute, Melbourne, Australia.,Department of Medicine, University of Melbourne, Victoria, Australia.,Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - James G Beeson
- Burnet Institute, Melbourne, Australia.,Department of Medicine, University of Melbourne, Victoria, Australia.,Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia.,Central Clinical School and Department of Microbiology, Monash University, Victoria, Australia
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13
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Akter M, Drinkwater N, Devine SM, Drew SC, Krishnarjuna B, Debono CO, Wang G, Scanlon MJ, Scammells PJ, McGowan S, MacRaild CA, Norton RS. Identification of the Binding Site of Apical Membrane Antigen 1 (AMA1) Inhibitors Using a Paramagnetic Probe. ChemMedChem 2019; 14:603-612. [PMID: 30653832 DOI: 10.1002/cmdc.201800802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/08/2022]
Abstract
Apical membrane antigen 1 (AMA1) is essential for the invasion of host cells by malaria parasites. Several small-molecule ligands have been shown to bind to a conserved hydrophobic cleft in Plasmodium falciparum AMA1. However, a lack of detailed structural information on the binding pose of these molecules has hindered their further optimisation as inhibitors. We have developed a spin-labelled peptide based on RON2, the native binding partner of AMA1, to probe the binding sites of compounds on PfAMA1. The crystal structure of this peptide bound to PfAMA1 shows that it binds at one end of the hydrophobic groove, leaving much of the binding site unoccupied and allowing fragment hits to bind without interference. In paramagnetic relaxation enhancement (PRE)-based NMR screening, the 1 H relaxation rates of compounds binding close to the probe were enhanced. Compounds experienced different degrees of PRE as a result of their different orientations relative to the spin label while bound to AMA1. Thus, PRE-derived distance constraints can be used to identify binding sites and guide further hit optimisation.
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Affiliation(s)
- Mansura Akter
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Nyssa Drinkwater
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Wellington Road, Clayton, Victoria, 3800, Australia
| | - Shane M Devine
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Simon C Drew
- Department of Medicine (Royal Melbourne Hospital), The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Cael O Debono
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Geqing Wang
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Wellington Road, Clayton, Victoria, 3800, Australia
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
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14
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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15
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Spiegel H, Boes A, Fendel R, Reimann A, Schillberg S, Fischer R. Immunization with the Malaria Diversity-Covering Blood-Stage Vaccine Candidate Plasmodium falciparum Apical Membrane Antigen 1 DiCo in Complex with Its Natural Ligand PfRon2 Does Not Improve the In Vitro Efficacy. Front Immunol 2017; 8:743. [PMID: 28702028 PMCID: PMC5484772 DOI: 10.3389/fimmu.2017.00743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/12/2017] [Indexed: 01/05/2023] Open
Abstract
The blood-stage malaria vaccine candidate Plasmodium falciparum apical membrane antigen 1 (PfAMA1) can induce strong parasite growth-inhibitory antibody responses in animals but has not achieved the anticipated efficacy in clinical trials. Possible explanations in humans are the insufficient potency of the elicited antibody responses, as well as the high degree of sequence polymorphisms found in the field. Several strategies have been developed to improve the cross-strain coverage of PfAMA1-based vaccines, whereas innovative concepts to increase the potency of PfAMA1-specific IgG responses have received little attention even though this may be an essential requirement for protective efficacy. A previous study has demonstrated that immunization with a complex of PyAMA1 and PyRON2, a ligand with an essential functional role in erythrocyte invasion, leads to protection from lethal Plasmodium yoelli challenge in an animal model and suggested to extend this strategy toward improved strain coverage by using multiple PfAMA1 alleles in combination with PfRon2L. As an alternative approach along this line, we decided to use PfRon2L in combination with three PfAMA1 diversity covering variants (DiCo) to investigate the potential of this complex to induce more potent parasite growth inhibitory immune response in combination with better cross-strain-specific efficacy. Within the limits of the study design, the ability of the PfAMA1 DiCo-Mix to induce cross-strain-specific antibodies was not affected in all immunization groups, but the DiCo-PfRon2L complexes did not improve the potency of PfAMA1-specific IgG responses.
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Affiliation(s)
- Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Alexander Boes
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Rolf Fendel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Andreas Reimann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.,Institute for Phytopathology and Applied Zoology, Justus-Liebig University Giessen, Giessen, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.,RWTH Aachen University, Institute for Molecular Biotechnology, Aachen, Germany.,Indiana Biosciences Research Institute (IBRI), Indianapolis, IN, United States
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16
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Devine SM, MacRaild CA, Norton RS, Scammells PJ. Antimalarial drug discovery targeting apical membrane antigen 1. MEDCHEMCOMM 2017; 8:13-20. [PMID: 30108688 PMCID: PMC6072474 DOI: 10.1039/c6md00495d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/27/2016] [Indexed: 01/06/2023]
Abstract
Malaria continues to frustrate humanity's attempts to eradicate this deadly disease. Although gains have been made over the last 15 years, drug resistance to malaria continues to be a major concern. The lack of new antimalarials with novel mechanisms of action continues to challenge the scientific community to find innovative targets to combat this persistent disease. One such target, apical membrane antigen 1 (AMA1), is an essential protein that helps the parasite invade host erythrocytes. Recently, a number of efforts have focused on the druggability of this target, aiming to block the interactions of AMA1 that mediate invasion of host cells. This review covers recent progress in drug discovery targeting this crucial protein-protein interaction in malaria.
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Affiliation(s)
- Shane M Devine
- Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
| | - Christopher A MacRaild
- Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
| | - Raymond S Norton
- Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
| | - Peter J Scammells
- Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , VIC 3052 , Australia . ;
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