1
|
Adelusi TI, Ojo TO, Bolaji OQ, Oyewole MP, Olaoba OT, Oladipo EK. Predicting Plasmodium falciparum kinase inhibitors from antimalarial medicinal herbs using computational modeling approach. In Silico Pharmacol 2023; 12:4. [PMID: 38130691 PMCID: PMC10730500 DOI: 10.1007/s40203-023-00175-z] [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: 08/23/2023] [Accepted: 11/03/2023] [Indexed: 12/23/2023] Open
Abstract
Malaria remains a significant public health challenge, with resistance to available drugs necessitating the development of novel therapies targeting invasion-dependent proteins. Plasmodium falciparum calcium-dependent protein kinase 1 (PfCDPK-1) is essential for host erythrocyte invasion and parasite asexual development. This study screened a library of 490 compounds using computational methods to identify potential PfCDPK-1 inhibitors. Three compounds; 17-hydroxyazadiradione, Picracin, and Epicatechin-gallate derived from known antimalarial botanicals, showed potent inhibitory effects on PfCDPK-1. These compounds exhibited better binding affinities (-8.8, -9.1, -9.3 kCal/mol respectively), pharmacokinetics, and physicochemical properties than the purported inhibitory standard of PfCDPK-1, Purfalcamine. Molecular dynamics simulations (50 ns) and molecular mechanics analyses confirmed the stability and binding rigidity of these compounds at the active pocket of PfCDPK-1. The results suggest that these compounds are promising pharmacological targets with potential therapeutic effects for malaria treatment/management without undesirable side effects. Therefore, this study provides new insights into the development of effective antimalarial agents targeting invasion-dependent proteins, which could help combat the global malaria burden. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00175-z.
Collapse
Affiliation(s)
- Temitope Isaac Adelusi
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B 210214, Ogbomoso, Oyo State Nigeria
| | - Taiwo Ooreoluwa Ojo
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B 210214, Ogbomoso, Oyo State Nigeria
- Genomics unit, Helix Biogen Institute, P.M.B 212102, Ogbomoso, Oyo State Nigeria
| | - Olawale Quadri Bolaji
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B 210214, Ogbomoso, Oyo State Nigeria
| | - Moyosoluwa Precious Oyewole
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B 210214, Ogbomoso, Oyo State Nigeria
| | - Olamide Tosin Olaoba
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211 USA
| | - Elijah Kolawole Oladipo
- Genomics unit, Helix Biogen Institute, P.M.B 212102, Ogbomoso, Oyo State Nigeria
- Laboratory of Molecular Biology, Bioinformatics and Immunology, Department of Microbiology, Adeleke University, Ede, Osun State Nigeria
| |
Collapse
|
2
|
Bredow M, Monaghan J. Cross-kingdom regulation of calcium- and/or calmodulin-dependent protein kinases by phospho-switches that relieve autoinhibition. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102251. [PMID: 35767936 DOI: 10.1016/j.pbi.2022.102251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/04/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Mechanisms to sense and respond to calcium have evolved in all organisms. Calmodulin is a universal calcium sensor across eukaryotes that directly binds calcium and associates with many downstream signal transducers including protein kinases. All eukaryotes encode calcium-dependent and/or calmodulin-dependent kinases, however there are distinct protein families across kingdoms. Here, we compare the activation mechanisms of calmodulin-dependent protein kinases (CaMKs), calcium- and calmodulin-dependent protein kinases (CCaMKs) and calcium-dependent protein kinases (CDPKs), noting striking similarities regarding phosphorylation in a regulatory segment known as the autoinhibitory junction. We thus propose that conserved regulation by phosphorylation underlies the activation of calcium-responsive proteins from different kingdoms.
Collapse
Affiliation(s)
- Melissa Bredow
- Department of Plant Pathology and Microbiology, Iowa State University, Ames IA, USA.
| | | |
Collapse
|
3
|
Gupta P, Mohanty D. Allosteric regulation of the inactive to active state conformational transition in CDPK1 protein of Plasmodium falciparum. Int J Biol Macromol 2022; 215:489-500. [PMID: 35709874 DOI: 10.1016/j.ijbiomac.2022.06.065] [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: 03/15/2022] [Revised: 06/05/2022] [Accepted: 06/10/2022] [Indexed: 11/05/2022]
Abstract
The aim of the current study is to investigate the role of the CAD domain in the activation mechanism of calcium dependent protein kinase-1 of Plasmodium falciparum (PfCDPK1) and explore the possibility of allosteric inhibition of this kinase. PfCDPK1 belongs to CDPK family of apicomplexan kinases which have a C-terminal CAD domain. Microsecond scale MD simulations were performed on modeled structures of complete PfCDPK1 and its kinase domain alone. The simulations revealed that in absence of CAD the salt bridge between Glu116 in αC-helix and Lys85 in β3-sheet of kinase breaks after 200 ns resulting in inactive conformation of the kinase, but the salt bridge stays intact in the complete protein stabilizing it in active conformation. These results highlight the novel CAD mediated allosteric stabilization of the crucial salt bridge which is a hallmark of active conformation of kinase domains. The mechanistic details of the allosteric activation revealed by our study, opens up the possibility for design of allosteric inhibitors of PfCDPK1 kinase by disrupting the kinase:CAD interactions. Using a combination of machine learning and structure-based in silico screening, we have identified novel PPI modulators for allosteric inactivation of PfCDPK1 kinase.
Collapse
Affiliation(s)
- Priya Gupta
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
| |
Collapse
|
4
|
Baindara P, Agrawal S, Franco OL. Host-directed therapies for malaria and tuberculosis: common infection strategies and repurposed drugs. Expert Rev Anti Infect Ther 2022; 20:849-869. [DOI: 10.1080/14787210.2022.2044794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Piyush Baindara
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Missouri, Columbia, MO, USA
| | - Sonali Agrawal
- Immunology Division, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - O. L. Franco
- Proteomics Analysis and Biochemical Center, Catholic University of Brasilia, Brasilia, Brazil; S-Inova Biotech, Catholic University Dom Bosco, Campo Grande, MS, Brazil
| |
Collapse
|
5
|
Maurya R, Tripathi A, Kumar M, Antil N, Yamaryo‐Botté Y, Kumar P, Bansal P, Doerig C, Botté CY, Prasad TSK, Sharma P. PI4-kinase and PfCDPK7 signaling regulate phospholipid biosynthesis in Plasmodium falciparum. EMBO Rep 2022; 23:e54022. [PMID: 34866326 PMCID: PMC8811644 DOI: 10.15252/embr.202154022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/30/2021] [Accepted: 11/11/2021] [Indexed: 02/05/2023] Open
Abstract
PfCDPK7 is an atypical member of the calcium-dependent protein kinase (CDPK) family and is crucial for the development of Plasmodium falciparum. However, the mechanisms whereby PfCDPK7 regulates parasite development remain unknown. Here, we perform quantitative phosphoproteomics and phospholipid analysis and find that PfCDPK7 promotes phosphatidylcholine (PC) synthesis by regulating two key enzymes involved in PC synthesis, phosphoethanolamine-N-methyltransferase (PMT) and ethanolamine kinase (EK). In the absence of PfCDPK7, both enzymes are hypophosphorylated and PMT is degraded. We further find that PfCDPK7 interacts with 4'-phosphorylated phosphoinositides (PIPs) generated by PI4-kinase. Inhibition of PI4K activity disrupts the vesicular localization PfCDPK7. P. falciparum PI4-kinase, PfPI4K is a prominent drug target and one of its inhibitors, MMV39048, has reached Phase I clinical trials. Using this inhibitor, we demonstrate that PfPI4K controls phospholipid biosynthesis and may act in part by regulating PfCDPK7 localization and activity. These studies not only unravel a signaling pathway involving PfPI4K/4'-PIPs and PfCDPK7 but also provide novel insights into the mechanism of action of a promising series of candidate anti-malarial drugs.
Collapse
Affiliation(s)
- Ranjana Maurya
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Anuj Tripathi
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Manish Kumar
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
- Institute of BioinformaticsInternational Tech ParkBangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Neelam Antil
- Institute of BioinformaticsInternational Tech ParkBangaloreIndia
- ApicoLipid TeamInstitute of Advanced BiosciencesCNRS UMR5309Université Grenoble AlpesINSERM U1209GrenobleFrance
- Amrita School of BiotechnologyAmrita Vishwa VidyapeethamKollamIndia
| | - Yoshiki Yamaryo‐Botté
- Center for Systems Biology and Molecular MedicineYenepoya Research CentreYenepoya (Deemed to be University)MangaloreIndia
| | - Praveen Kumar
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Priyanka Bansal
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| | - Christian Doerig
- NIMHANS IOB Proteomics and Bioinformatics LaboratoryNeurobiology Research CentreNational Institute of Mental Health and Neuro SciencesBangaloreIndia
| | - Cyrille Y Botté
- Center for Systems Biology and Molecular MedicineYenepoya Research CentreYenepoya (Deemed to be University)MangaloreIndia
| | - T S Keshava Prasad
- Institute of BioinformaticsInternational Tech ParkBangaloreIndia
- Amrita School of BiotechnologyAmrita Vishwa VidyapeethamKollamIndia
- School of Health and Biomedical SciencesRMIT UniversityBundooraVic.Australia
| | - Pushkar Sharma
- Eukaryotic Gene Expression laboratoryNational Institute of ImmunologyNew DelhiIndia
| |
Collapse
|
6
|
Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector. mBio 2021; 12:e0257521. [PMID: 34724830 PMCID: PMC8561384 DOI: 10.1128/mbio.02575-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gametocytes of the malaria parasite Plasmodium are taken up by the mosquito vector with an infectious blood meal, representing a critical stage for parasite transmission. Calcium-independent protein kinases (CDPKs) play key roles in calcium-mediated signaling across the complex life cycle of the parasite. We sought to understand their role in human parasite transmission from the host to the mosquito vector and thus investigated the role of the human-infective parasite Plasmodium falciparum CDPK4 in the parasite life cycle. P. falciparumcdpk4− parasites created by targeted gene deletion showed no effect in blood stage development or gametocyte development. However, cdpk4− parasites showed a severe defect in male gametogenesis and the emergence of flagellated male gametes. To understand the molecular underpinnings of this defect, we performed mass spectrometry-based phosphoproteomic analyses of wild-type and Plasmodium falciparumcdpk4− late gametocyte stages to identify key CDPK4-mediated phosphorylation events that may be important for the regulation of male gametogenesis. We further employed in vitro assays to identify these putative substrates of Plasmodium falciparum CDPK4. This indicated that CDPK4 regulates male gametogenesis by directly or indirectly controlling key essential events, such as DNA replication, mRNA translation, and cell motility. Taken together, our work demonstrates that PfCDPK4 is a central kinase that regulates exflagellation and thereby is critical for parasite transmission to the mosquito vector.
Collapse
|
7
|
Bansal P, Antil N, Kumar M, Yamaryo-Botté Y, Rawat RS, Pinto S, Datta KK, Katris NJ, Botté CY, Prasad TSK, Sharma P. Protein kinase TgCDPK7 regulates vesicular trafficking and phospholipid synthesis in Toxoplasma gondii. PLoS Pathog 2021; 17:e1009325. [PMID: 33635921 PMCID: PMC7909640 DOI: 10.1371/journal.ppat.1009325] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/20/2021] [Indexed: 02/06/2023] Open
Abstract
Apicomplexan parasites are causative agents of major human diseases. Calcium Dependent Protein Kinases (CDPKs) are crucial components for the intracellular development of apicomplexan parasites and are thus considered attractive drug targets. CDPK7 is an atypical member of this family, which initial characterization suggested to be critical for intracellular development of both Apicomplexa Plasmodium falciparum and Toxoplasma gondii. However, the mechanisms via which it regulates parasite replication have remained unknown. We performed quantitative phosphoproteomics of T. gondii lacking TgCDPK7 to identify its parasitic targets. Our analysis lead to the identification of several putative TgCDPK7 substrates implicated in critical processes like phospholipid (PL) synthesis and vesicular trafficking. Strikingly, phosphorylation of TgRab11a via TgCDPK7 was critical for parasite intracellular development and protein trafficking. Lipidomic analysis combined with biochemical and cellular studies confirmed that TgCDPK7 regulates phosphatidylethanolamine (PE) levels in T. gondii. These studies provide novel insights into the regulation of these processes that are critical for parasite development by TgCDPK7. In this study, we demonstrate that protein kinase TgCDPK7 regulates cellular processes like vesicular trafficking and the synthesis of phospholipids, which are critical for the development of the parasite Toxoplasma gondii. It regulates the localization of a small GTPase TgRab11a by phosphorylating it at a specific site, which is critical for trafficking of important parasite proteins and is important for parasite division. TgCDPK7 may regulate key enzymes involved biogenesis of phosphatidylethanolamine, which may contribute to the synthesis of this important phospholipid. These and other studies shed light on a novel signaling pathway in apicomplexan parasite Toxoplasma gondii.
Collapse
Affiliation(s)
- Priyanka Bansal
- Eukaryotic Gene Expression laboratory, National Institute of Immunology, New Delhi, India
| | - Neelam Antil
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Manish Kumar
- Eukaryotic Gene Expression laboratory, National Institute of Immunology, New Delhi, India
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Yoshiki Yamaryo-Botté
- ApicoLipid Team, Institute of Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Rahul Singh Rawat
- Eukaryotic Gene Expression laboratory, National Institute of Immunology, New Delhi, India
| | - Sneha Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Keshava K. Datta
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Nicholas J. Katris
- ApicoLipid Team, Institute of Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Cyrille Y. Botté
- ApicoLipid Team, Institute of Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- NIMHANS IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka, India
| | - Pushkar Sharma
- Eukaryotic Gene Expression laboratory, National Institute of Immunology, New Delhi, India
- * E-mail:
| |
Collapse
|
8
|
Molecular dynamics simulations and biochemical characterization of Pf14-3-3 and PfCDPK1 interaction towards its role in growth of human malaria parasite. Biochem J 2020; 477:2153-2177. [PMID: 32484216 DOI: 10.1042/bcj20200145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/17/2022]
Abstract
Scaffold proteins play pivotal role as modulators of cellular processes by operating as multipurpose conformation clamps. 14-3-3 proteins are gold-standard scaffold modules that recognize phosphoSer/Thr (pS/pT) containing conserved motifs, and confer conformational changes leading to modulation of functional parameters of their target proteins. Modulation in functional activity of kinases has been attributed to their interaction with 14-3-3 proteins. Herein, we have annotated and characterized PF3D7_0818200 as 14-3-3 isoform I in Plasmodium falciparum 3D7, and its interaction with one of the key kinases of the parasite, Calcium-Dependent Protein Kinase 1 (CDPK1) by performing various analytical biochemistry and biophysical assays. Molecular dynamics simulation studies indicated that CDPK1 polypeptide sequence (61KLGpS64) behaves as canonical Mode I-type (RXXpS/pT) consensus 14-3-3 binding motif, mediating the interaction. The 14-3-3I/CDPK1 interaction was validated in vitro with ELISA and SPR, which confirmed that the interaction is phosphorylation dependent, with binding affinity constant of 670 ± 3.6 nM. The interaction of 14-3-3I with CDPK1 was validated with well characterized optimal 14-3-3 recognition motifs: Mode I-type ARSHpSYPA and Mode II-type RLYHpSLPA, by simulation studies and ITC. This interaction was found to marginally enhance CDPK1 functional activity. Furthermore, interaction antagonizing peptidomimetics showed growth inhibitory impact on the parasite indicating crucial physiological role of 14-3-3/CDPK1 interaction. Overall, this study characterizes 14-3-3I as a scaffold protein in the malaria parasite and unveils CDPK1 as its previously unidentified target. This sets a precedent for the rational design of 14-3-3 based PPI inhibitors by utilizing 14-3-3 recognition motif peptides, as a potential antimalarial strategy.
Collapse
|
9
|
Sharma GP, Gurung SK, Inam A, Nigam L, Bist A, Mohapatra D, Senapati S, Subbarao N, Azam A, Mondal N. CID-6033590 inhibits p38MAPK pathway and induces S-phase cell cycle arrest and apoptosis in DU145 and PC-3 cells. Toxicol In Vitro 2019; 60:420-436. [PMID: 31175925 DOI: 10.1016/j.tiv.2019.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 06/04/2019] [Indexed: 01/08/2023]
Abstract
Metastatic prostate cancer, with no effective treatment, is among the leading causes of cancer-associated deaths in men. Overexpression of p38αMAPK has been observed in neuroendocrine prostate cancer patients and in both DU145 and PC-3 cell lines and represents a good drug target. Sulfonamide derivatives have shown biological activities against many human diseases, including cancer. CID-6033590, a sulfonylhydrazide compound, screened from PubChem database by molecular docking with p38αMAPK, was evaluated for anti-cancerous activities. CID-6033590 induced toxicity in both DU145 and PC-3 cells in a concentration and time-dependent manner with an IC50 value of 60 μM and 66 μM, respectively. Sub-cytotoxic concentrations of the compound significantly induced S-phase cell cycle arrest, inhibited cyclinA/CDK2 complex and blocked cell proliferation. Further, CID-6033590 downregulated phosphorylation of p38MAPK (P-p38) as well as its downstream targets, Activating transcription factor 2 (ATF-2) and Heat shock protein 27 (Hsp27). The compound increased ROS and decreased mitochondrial membrane potential (Δψm), downregulated Bcl-2 and survivin and cleaved poly ADP ribose polymerase (PARP) and caspase-3, indicating the induction of apoptosis. The evaluaion of the compound on noncancerous, human prostatic epithelial cell line RWPE-1, and healthy murine tissues yielded no significant toxicity. Taken together, we suggest CID-6033590 as a potential candidate for prostate cancer therapy.
Collapse
Affiliation(s)
| | | | - Afreen Inam
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India
| | - Lokesh Nigam
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Archana Bist
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Amir Azam
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India.
| | - Neelima Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
10
|
Choudhary HH, Gupta R, Mishra S. PKAc is not required for the preerythrocytic stages of Plasmodium berghei. Life Sci Alliance 2019; 2:2/3/e201900352. [PMID: 31142638 PMCID: PMC6545604 DOI: 10.26508/lsa.201900352] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 12/12/2022] Open
Abstract
The mutant salivary gland sporozoites lacking PKAc are able to glide, invade hepatocytes, and mature into hepatic merozoites, which release successfully from the merosome, however, fail to initiate blood stage infection when inoculated into mice. Plasmodium sporozoites invade hepatocytes to initiate infection in the mammalian host. In the infected hepatocytes, sporozoites undergo rapid expansion and differentiation, resulting in the formation and release of thousands of invasive merozoites into the bloodstream. Both sporozoites and merozoites invade their host cells by activation of a signaling cascade followed by discharge of micronemal content. cAMP-dependent protein kinase catalytic subunit (PKAc)–mediated signaling plays an important role in merozoite invasion of erythrocytes, but its role during other stages of the parasite remains unknown. Becaused of the essentiality of PKAc in blood stages, we generated conditional mutants of PKAc by disrupting the gene in Plasmodium berghei sporozoites. The mutant salivary gland sporozoites were able to glide, invaded hepatocytes, and matured into hepatic merozoites which were released successfully from merosome, however failed to initiate blood stage infection when inoculated into mice. Our results demonstrate that malaria parasite complete preerythrocytic stages development without PKAc, raising the possibility that the PKAc independent signaling operates in preerythrocytic stages of P. berghei.
Collapse
Affiliation(s)
| | - Roshni Gupta
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Satish Mishra
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India .,Academy of Scientific and Innovative Research, Ghaziabad, India
| |
Collapse
|
11
|
Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P, Billker O. Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation. Cell Rep 2018; 21:2017-2029. [PMID: 29141230 PMCID: PMC5700370 DOI: 10.1016/j.celrep.2017.10.071] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/02/2017] [Accepted: 10/18/2017] [Indexed: 12/31/2022] Open
Abstract
The transmission of malaria parasites to mosquitoes relies on the rapid induction of sexual reproduction upon their ingestion into a blood meal. Haploid female and male gametocytes become activated and emerge from their host cells, and the males enter the cell cycle to produce eight microgametes. The synchronized nature of gametogenesis allowed us to investigate phosphorylation signaling during its first minute in Plasmodium berghei via a high-resolution time course of the phosphoproteome. This revealed an unexpectedly broad response, with proteins related to distinct cell cycle events undergoing simultaneous phosphoregulation. We implicate several protein kinases in the process, and we validate our analyses on the plant-like calcium-dependent protein kinase 4 (CDPK4) and a homolog of serine/arginine-rich protein kinases (SRPK1). Mutants in these kinases displayed distinct phosphoproteomic disruptions, consistent with differences in their phenotypes. The results reveal the central role of protein phosphorylation in the atypical cell cycle regulation of a divergent eukaryote.
Collapse
Affiliation(s)
- Brandon M Invergo
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mathieu Brochet
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Microbiology & Molecular Medicine, CMU, University of Geneva, 1211 Geneva 4, Geneva, Switzerland
| | - Lu Yu
- Proteomics Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; The Institute of Cancer Research, Chester Betty Laboratory, London, Greater London SW7 3RP, UK
| | - Jyoti Choudhary
- Proteomics Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; The Institute of Cancer Research, Chester Betty Laboratory, London, Greater London SW7 3RP, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK.
| | - Oliver Billker
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
| |
Collapse
|
12
|
PfCDPK1 mediated signaling in erythrocytic stages of Plasmodium falciparum. Nat Commun 2017; 8:63. [PMID: 28680058 PMCID: PMC5498596 DOI: 10.1038/s41467-017-00053-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/26/2017] [Indexed: 01/11/2023] Open
Abstract
Calcium Dependent Protein Kinases are key effectors of calcium signaling in malaria parasite. PfCDPK1 is critical for asexual development of Plasmodium falciparum, but its precise function and substrates remain largely unknown. Using a conditional knockdown strategy, we here establish that this kinase is critical for the invasion of host erythrocytes. Furthermore, using a multidisciplinary approach involving comparative phosphoproteomics we gain insights into the underlying molecular mechanisms. We identify substrates of PfCDPK1, which includes proteins of Inner Membrane Complex and glideosome-actomyosin motor assembly. Interestingly, PfCDPK1 phosphorylates PfPKA regulatory subunit (PfPKA-R) and regulates PfPKA activity in the parasite, which may be relevant for the process of invasion. This study delineates the signaling network of PfCDPK1 and sheds light on mechanisms via which it regulates invasion.Calcium dependent protein kinase 1 (CDPK1) plays an important role in asexual development of Plasmodium falciparum. Using phosphoproteomics and conditional knockdown of CDPK1, the authors here identify CDPK1 substrates and a cross-talk between CDPK1 and PKA, and show the role of CDPK1 in parasite invasion.
Collapse
|
13
|
Haubrich BA, Swinney DC. Enzyme Activity Assays for Protein Kinases: Strategies to Identify Active Substrates. Curr Drug Discov Technol 2016; 13:2-15. [PMID: 26768716 DOI: 10.2174/1570163813666160115125930] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 11/22/2022]
Abstract
Protein kinases are an important class of enzymes and drug targets. New opportunities to discover medicines for neglected diseases can be leveraged by the extensive kinase tools and knowledge created in targeting human kinases. A valuable tool for kinase drug discovery is an enzyme assay that measures catalytic function. The functional assay can be used to identify inhibitors, estimate affinity, characterize molecular mechanisms of action (MMOAs) and evaluate selectivity. However, establishing an enzyme assay for a new kinases requires identification of a suitable substrate. Identification of a new kinase's endogenous physiologic substrate and function can be extremely costly and time consuming. Fortunately, most kinases are promiscuous and will catalyze the phosphotransfer from ATP to alternative substrates with differing degrees of catalytic efficiency. In this manuscript we review strategies and successes in the identification of alternative substrates for kinases from organisms responsible for many of the neglected tropical diseases (NTDs) towards the goal of informing strategies to identify substrates for new kinases. Approaches for establishing a functional kinase assay include measuring auto-activation and use of generic substrates and peptides. The most commonly used generic substrates are casein, myelin basic protein, and histone. Sequence homology modeling can provide insights into the potential substrates and the requirement for activation. Empirical approaches that can identify substrates include screening of lysates (which may also help identify native substrates) and use of peptide arrays. All of these approaches have been used with a varying degree of success to identify alternative substrates.
Collapse
Affiliation(s)
- Brad A Haubrich
- Institute for Rare and Neglected Diseases Drug Discovery, 897 Independence Ave, Suite 2C, Mountain View, CA 94043, USA.
| | | |
Collapse
|
14
|
Aswathy L, Jisha RS, Masand VH, Gajbhiye JM, Shibi IG. Computational strategies to explore antimalarial thiazine alkaloid lead compounds based on an Australian marine sponge Plakortis Lita. J Biomol Struct Dyn 2016; 35:2407-2429. [PMID: 27494993 DOI: 10.1080/07391102.2016.1220870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In this work, an attempt was made to propose new leads based on the natural scaffold Thiaplakortone-A active against malaria. The 2D QSAR studies suggested that three descriptors correlate with the anti-malarial activity with an R2 value of 0.814. Robustness, reliability, and predictive power of the model were tested by internal validation, external validation, Y-scrambling, and applicability domain analysis. HQSAR studies were carried out as an additional tool to find the sub-structural fingerprints. The CoMFA and CoMSIA models gave Q2 values of 0.813 and 0.647, and [Formula: see text] values of 0.994 and 0.984, respectively. Using the 2D-QSAR equation, the activity values of the seven modified compounds were calculated and it was found that three molecules showed good anti-malarial activity. Molecular docking of the 42 Thiaplakortone-A derivatives with Plasmodium falciparum calcium-dependent protein kinase 1 (PfCDPK1) was carried out to find out protein-ligand interactions. Data mining of the bioassay data-set AID: 504850 using the classifier based on Random Forest of Weka suggested that all of the eight molecules selected and three out of the seven virtual molecules were anti-malarial active. Both the virtual molecules and drug molecules were docked with CYP3A4, indicating that the virtual molecules could metabolize easily. Toxicity studies using Osiris shows that three molecules showed no toxic characters.
Collapse
Affiliation(s)
- Lilly Aswathy
- a Department of Chemistry , Sree Narayana College , Thiruvananthapuram , Kerala , India
| | - Radhakrishnan S Jisha
- a Department of Chemistry , Sree Narayana College , Thiruvananthapuram , Kerala , India
| | - Vijay H Masand
- b Department of Chemistry , Vidya Bharati College , Camp, Amravati , Maharashtra , India
| | - Jayant M Gajbhiye
- c Division of Organic Chemistry , CSIR-National Chemical Laboratory , Pune , India
| | - Indira G Shibi
- a Department of Chemistry , Sree Narayana College , Thiruvananthapuram , Kerala , India
| |
Collapse
|
15
|
Abstract
Calcium-dependent protein kinases (CDPKs) comprise the major group of Ca2+-regulated kinases in plants and protists. It has long been assumed that CDPKs are activated, like other Ca2+-regulated kinases, by derepression of the kinase domain (KD). However, we found that removal of the autoinhibitory domain from Toxoplasma gondii CDPK1 is not sufficient for kinase activation. From a library of heavy chain-only antibody fragments (VHHs), we isolated an antibody (1B7) that binds TgCDPK1 in a conformation-dependent manner and potently inhibits it. We uncovered the molecular basis for this inhibition by solving the crystal structure of the complex and simulating, through molecular dynamics, the effects of 1B7-kinase interactions. In contrast to other Ca2+-regulated kinases, the regulatory domain of TgCDPK1 plays a dual role, inhibiting or activating the kinase in response to changes in Ca2+ concentrations. We propose that the regulatory domain of TgCDPK1 acts as a molecular splint to stabilize the otherwise inactive KD. This dependence on allosteric stabilization reveals a novel susceptibility in this important class of parasite enzymes.
Collapse
|
16
|
Ramamoorthi R, Graef KM, Krattiger A, Dent JC. WIPO Re:Search: Catalyzing Collaborations to Accelerate Product Development for Diseases of Poverty. Chem Rev 2014; 114:11272-9. [DOI: 10.1021/cr5000656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roopa Ramamoorthi
- BIO Ventures for Global Health, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Katy M. Graef
- BIO Ventures for Global Health, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Anatole Krattiger
- World Intellectual Property Organization, 34, Chemin des Colombettes, CH-1211 Geneva 20, Switzerland
| | - Jennifer C. Dent
- BIO Ventures for Global Health, 401 Terry Avenue North, Seattle, Washington 98109, United States
| |
Collapse
|
17
|
Biochemical and antiparasitic properties of inhibitors of the Plasmodium falciparum calcium-dependent protein kinase PfCDPK1. Antimicrob Agents Chemother 2014; 58:6032-43. [PMID: 25070106 PMCID: PMC4187893 DOI: 10.1128/aac.02959-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PfCDPK1 is a Plasmodium falciparum calcium-dependent protein kinase, which has been identified as a potential target for novel antimalarial chemotherapeutics. In order to further investigate the role of PfCDPK1, we established a high-throughput in vitro biochemical assay and used it to screen a library of over 35,000 small molecules. Five chemical series of inhibitors were initially identified from the screen, from which series 1 and 2 were selected for chemical optimization. Indicative of their mechanism of action, enzyme inhibition by these compounds was found to be sensitive to both the ATP concentration and substitution of the amino acid residue present at the “gatekeeper” position at the ATP-binding site of the enzyme. Medicinal chemistry efforts led to a series of PfCDPK1 inhibitors with 50% inhibitory concentrations (IC50s) below 10 nM against PfCDPK1 in a biochemical assay and 50% effective concentrations (EC50s) less than 100 nM for inhibition of parasite growth in vitro. Potent inhibition was combined with acceptable absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties and equipotent inhibition of Plasmodium vivax CDPK1. However, we were unable to correlate biochemical inhibition with parasite growth inhibition for this series overall. Inhibition of Plasmodium berghei CDPK1 correlated well with PfCDPK1 inhibition, enabling progression of a set of compounds to in vivo evaluation in the P. berghei rodent model for malaria. These chemical series have potential for further development as inhibitors of CDPK1.
Collapse
|
18
|
Treeck M, Sanders JL, Gaji RY, LaFavers KA, Child MA, Arrizabalaga G, Elias JE, Boothroyd JC. The calcium-dependent protein kinase 3 of toxoplasma influences basal calcium levels and functions beyond egress as revealed by quantitative phosphoproteome analysis. PLoS Pathog 2014; 10:e1004197. [PMID: 24945436 PMCID: PMC4063958 DOI: 10.1371/journal.ppat.1004197] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 05/05/2014] [Indexed: 12/19/2022] Open
Abstract
Calcium-dependent protein kinases (CDPKs) are conserved in plants and apicomplexan parasites. In Toxoplasma gondii, TgCDPK3 regulates parasite egress from the host cell in the presence of a calcium-ionophore. The targets and the pathways that the kinase controls, however, are not known. To identify pathways regulated by TgCDPK3, we measured relative phosphorylation site usage in wild type and TgCDPK3 mutant and knock-out parasites by quantitative mass-spectrometry using stable isotope-labeling with amino acids in cell culture (SILAC). This revealed known and novel phosphorylation events on proteins predicted to play a role in host-cell egress, but also a novel function of TgCDPK3 as an upstream regulator of other calcium-dependent signaling pathways, as we also identified proteins that are differentially phosphorylated prior to egress, including proteins important for ion-homeostasis and metabolism. This observation is supported by the observation that basal calcium levels are increased in parasites where TgCDPK3 has been inactivated. Most of the differential phosphorylation observed in CDPK3 mutants is rescued by complementation of the mutants with a wild type copy of TgCDPK3. Lastly, the TgCDPK3 mutants showed hyperphosphorylation of two targets of a related calcium-dependent kinase (TgCDPK1), as well as TgCDPK1 itself, indicating that this latter kinase appears to play a role downstream of TgCDPK3 function. Overexpression of TgCDPK1 partially rescues the egress phenotype of the TgCDPK3 mutants, reinforcing this conclusion. These results show that TgCDPK3 plays a pivotal role in regulating tachyzoite functions including, but not limited to, egress.
Collapse
Affiliation(s)
- Moritz Treeck
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - John L. Sanders
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rajshekhar Y. Gaji
- Department of Pharmacology and Toxicology, School of Medicine, University of Indianapolis, Indianapolis, Indiana, United States of America
| | - Kacie A. LaFavers
- Department of Pharmacology and Toxicology, School of Medicine, University of Indianapolis, Indianapolis, Indiana, United States of America
| | - Matthew A. Child
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gustavo Arrizabalaga
- Department of Pharmacology and Toxicology, School of Medicine, University of Indianapolis, Indianapolis, Indiana, United States of America
| | - Joshua E. Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - John C. Boothroyd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| |
Collapse
|
19
|
Expression of the essential Kinase PfCDPK1 from Plasmodium falciparum in Toxoplasma gondii facilitates the discovery of novel antimalarial drugs. Antimicrob Agents Chemother 2014; 58:2598-607. [PMID: 24550330 DOI: 10.1128/aac.02261-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We have previously shown that genetic disruption of Toxoplasma gondii calcium-dependent protein kinase 3 (TgCDPK3) affects calcium ionophore-induced egress. We examined whether Plasmodium falciparum CDPK1 (PfCDPK1), the closest homolog of TgCDPK3 in the malaria parasite P. falciparum, could complement a TgCDPK3 mutant strain. PfCDPK1 is essential and plays critical roles in merozoite development, motility, and secretion. We show that expression of PfCDPK1 in the TgCDPK3 mutant strain rescues the egress defect. This phenotypic complementation requires the localization of PfCDPK1 to the plasma membrane and kinase activity. Interestingly, PfCDPK1-expressing Toxoplasma becomes more sensitive to egress inhibition by purfalcamine, a potent inhibitor of PfCDPK1 with low activity against TgCDPK3. Based on this result, we tested eight small molecules previously determined to inhibit the kinase activity of recombinant PfCDPK1 for their abilities to inhibit ionophore-induced egress in the PfCDPK1-expressing strain. While two of these chemicals did not inhibit egress, we found that six drugs affected this process selectively in PfCDPK1-expressing Toxoplasma. Using mutant versions of PfCDPK1 and TgCDPK3, we show that the selectivities of dasatinib and PLX-4720 are regulated by the gatekeeper residue in the ATP binding site. Importantly, we have confirmed that the three most potent inhibitors of egress in the PfCDPK1-expressing strain effectively kill P. falciparum. Thus, we have established and validated a recombinant strain of Toxoplasma that can be used as a surrogate for the discovery and analysis of PfCDPK1-specific inhibitors that can be developed as antimalarials.
Collapse
|
20
|
Morlon-Guyot J, Berry L, Chen CT, Gubbels MJ, Lebrun M, Daher W. The Toxoplasma gondii calcium-dependent protein kinase 7 is involved in early steps of parasite division and is crucial for parasite survival. Cell Microbiol 2013; 16:95-114. [PMID: 24011186 DOI: 10.1111/cmi.12186] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 12/22/2022]
Abstract
Apicomplexan parasites express various calcium-dependent protein kinases (CDPKs), and some of them play essential roles in invasion and egress. Five of the six CDPKs conserved in most Apicomplexa have been studied at the molecular and cellular levels in Plasmodium species and/or in Toxoplasma gondii parasites, but the function of CDPK7 was so far uncharacterized. In T. gondii, during intracellular replication, two parasites are formed within a mother cell through a unique process called endodyogeny. Here we demonstrate that the knock-down of CDPK7 protein in T. gondii results in pronounced defects in parasite division and a major growth deficiency, while it is dispensable for motility, egress and microneme exocytosis. In cdpk7-depleted parasites, the overall DNA content was not impaired, but the polarity of daughter cells budding and the fate of several subcellular structures or proteins involved in cell division were affected, such as the centrosomes and the kinetochore. Overall, our data suggest that CDPK7 is crucial for proper maintenance of centrosome integrity required for the initiation of endodyogeny. Our findings provide a first insight into the probable role of calcium-dependent signalling in parasite multiplication, in addition to its more widely explored role in invasion and egress.
Collapse
Affiliation(s)
- Juliette Morlon-Guyot
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR5235 CNRS, Université de Montpellier I et II, Montpellier, France
| | | | | | | | | | | |
Collapse
|
21
|
Sharma P, Chitnis CE. Key molecular events during host cell invasion by Apicomplexan pathogens. Curr Opin Microbiol 2013; 16:432-7. [PMID: 23895827 DOI: 10.1016/j.mib.2013.07.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/03/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
Abstract
The ability of Apicomplexan parasites to invade host cells is key to their survival and pathogenesis. Plasmodium and Toxoplasma parasites share common mechanisms for invasion of host cells. Secretion of microneme and rhoptry proteins, tight junction formation and assembly of an acto-myosin motor are key steps for successful invasion by both parasites. Here, we review our understanding of the molecular basis for these steps.
Collapse
|