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Ali DH, Gaji RY. TKL family kinases in human apicomplexan pathogens. Mol Biochem Parasitol 2024; 259:111628. [PMID: 38719028 PMCID: PMC11182715 DOI: 10.1016/j.molbiopara.2024.111628] [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: 01/18/2024] [Revised: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024]
Abstract
Apicomplexan parasites are the primary causative agents of many human diseases, including malaria, toxoplasmosis, and cryptosporidiosis. These opportunistic pathogens undergo complex life cycles with multiple developmental stages, wherein many key steps are regulated by phosphorylation mechanisms. The genomes of apicomplexan pathogens contain protein kinases from different groups including tyrosine kinase-like (TKL) family proteins. Although information on the role of TKL kinases in apicomplexans is quite limited, recent studies have revealed the important role of this family of proteins in apicomplexan biology. TKL kinases in these protozoan pathogens show unique organization with many novel domains thus making them attractive candidates for drug development. In this mini review, we summarize the current understanding of the role of TKL kinases in human apicomplexan pathogens' (Toxoplasma gondii, Plasmodium falciparum and Cryptosporidium parvum) biology and pathogenesis.
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Affiliation(s)
- Dima Hajj Ali
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Rajshekhar Y Gaji
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA.
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2
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Waldron-Young E, Wijitrmektong W, Choi R, Whitman GR, Hulverson MA, Charania R, Keelaghan A, Li L, Srinual S, Nikhar S, McNamara CW, Love MS, Huerta L, Bakowski MA, Hu M, Van Voorhis WC, Mead JR, Cuny GD. Pyridopyrimidinones as a new chemotype of calcium dependent protein kinase 1 (CDPK1) inhibitors for Cryptosporidium. Mol Biochem Parasitol 2024; 260:111637. [PMID: 38901801 DOI: 10.1016/j.molbiopara.2024.111637] [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: 03/31/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
The protozoan protein kinase calcium-dependent protein kinase 1 (CDPK1) has emerged as a potential therapeutic target for the treatment of cryptosporidiosis. A focused screen of known kinase inhibitors identified a pyridopyrimidinone as a new chemotype of Cryptosporidium parvum (Cp) CDPK1 inhibitors. Structural comparison of CpCDPK1 to two representative human kinases, RIPK2 and Src, revealed differences in the positioning of the αC-helix that was used in the design of a potent pyridopyrimidinone-based CpCDPK1 inhibitor 7 (a.k.a. UH15-16, IC50 = 10 nM), which blocked the growth of three C. parvum strains (EC50 = 12-40 nM) as well as C. hominis (EC50 = 85 nM) in HCT-8 host cells. Pharmacokinetic and tissue distribution analyses indicated that 7 had low systemic exposure after oral administration, but high gastrointestinal concentration, as well as good Caco-2 cell permeability. Finally, 7 demonstrated partial efficacy in an IL-12 knock-out mouse model of acute cryptosporidiosis.
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Affiliation(s)
- Elise Waldron-Young
- Department of Pharmaceutical and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, United States
| | - Wissarut Wijitrmektong
- Department of Pharmaceutical and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, United States
| | - Ryan Choi
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98109, United States
| | - Grant R Whitman
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98109, United States
| | - Matthew A Hulverson
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98109, United States
| | - Raheela Charania
- Department of Pediatrics, Emory University and Children's Healthcare Organization of Atlanta, Atlanta, GA 30322, United States; Atlanta VA Medical Center, Decatur, GA 30033, United States
| | - Aidan Keelaghan
- Department of Pediatrics, Emory University and Children's Healthcare Organization of Atlanta, Atlanta, GA 30322, United States; Atlanta VA Medical Center, Decatur, GA 30033, United States
| | - Li Li
- Department of Pharmaceutical and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, United States
| | - Songpol Srinual
- Department of Pharmaceutical and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, United States
| | - Sameer Nikhar
- Department of Pharmaceutical and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, United States
| | - Case W McNamara
- Calibr-Skaggs Institute for Innovative Medicines, A division of The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Melissa S Love
- Calibr-Skaggs Institute for Innovative Medicines, A division of The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Lauren Huerta
- Calibr-Skaggs Institute for Innovative Medicines, A division of The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Malina A Bakowski
- Calibr-Skaggs Institute for Innovative Medicines, A division of The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Ming Hu
- Department of Pharmaceutical and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, United States
| | - Wesley C Van Voorhis
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98109, United States
| | - Jan R Mead
- Department of Pediatrics, Emory University and Children's Healthcare Organization of Atlanta, Atlanta, GA 30322, United States; Atlanta VA Medical Center, Decatur, GA 30033, United States
| | - Gregory D Cuny
- Department of Pharmaceutical and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, United States.
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Tyrosine Kinase Inhibitors Display Potent Activity against Cryptosporidium parvum. Microbiol Spectr 2023; 11:e0387422. [PMID: 36533912 PMCID: PMC9927415 DOI: 10.1128/spectrum.03874-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The protozoan parasite Cryptosporidium is a leading cause of diarrheal disease (cryptosporidiosis) and death in young children. Cryptosporidiosis can be life-threatening in individuals with weak immunity such as HIV/AIDS patients and organ transplant recipients. There is currently no effective drug to treat cryptosporidiosis in the pediatric and immunocompromised population. Therefore, there is an urgent need to expedite the drug discovery process in order to develop new and effective therapies to reduce the global disease burden of cryptosporidiosis. In this study, we employed a drug repurposing strategy to screen a library of 473 human kinase inhibitors to determine their activity against Cryptosporidium parvum. We have identified 67 new anti-cryptosporidial compounds using phenotypic screening based on a transgenic C. parvum strain expressing a luciferase reporter. Further, dose-response assays led to the identification of 11 hit compounds that showed potent inhibition of C. parvum at nanomolar concentration. Kinome profiling of these 11 prioritized hits identified compounds that displayed selectivity in targeting specific families of kinases, particularly tyrosine kinases. Overall, this study identified tyrosine kinase inhibitors that hold potential for future development as new drug candidates against cryptosporidiosis. IMPORTANCE The intestinal parasite Cryptosporidium parvum is a major cause of diarrhea-associated morbidity and mortality in children, immunocompromised people, and young ruminant animals. With no effective drug available to treat cryptosporidiosis in humans and animals, there is an urgent need to identify anti-parasitic compounds and new targets for drug development. To address this unmet need, we screened a GSK library of kinase inhibitors and identified several potent compounds, including tyrosine kinase inhibitors, that were highly effective in killing C. parvum. Overall, our study revealed several novel compounds and a new family of kinases that can be targeted for anti-cryptosporidial drug development.
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Kar PP, Araveti PB, Srivastava A. Deciphering the kinome of Theileria annulata for identification of drug targets and anti-theilerial drug. Ticks Tick Borne Dis 2022; 13:102049. [PMID: 36215767 DOI: 10.1016/j.ttbdis.2022.102049] [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: 06/18/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/20/2022]
Abstract
Tropical theileriosis is one of the major parasitic diseases of ruminants. It is a tick-borne disease caused by an apicomplexan parasite, Theileria annulata. In the infected cells, these parasites induce phenotypes similar to cancerous cells. Among the most critical changes induced by the parasite are immortalization, hyperproliferation, and dissemination. The proliferative signal in the T. annulata transformed cells are provided by different kinases such as mitogen-activated protein kinases, SRC family kinases, casein kinase-2, and phosphatidylinositide 3-kinase. Deregulation of protein kinases in cancer is also well known. Targeting protein kinases in a cancerous cell is one of the most common methods in cancer therapy. Here, we revisited the kinome of T. annulata and studied its evolutionary relationship with other piroplasms. This analysis revealed that T. annulata kinome encodes 54 protein kinases. Based on our analysis, 12 of these 54 kinases were identified for the first time in the T. annulata proteome. Three protein kinases, TA16570, TA09820, and TA07000, had <40% identity with Bos taurus and >40% identity with the previously identified potential drug targets present in the Therapeutic Target Database (TTD). These 3 proteins were predicted to be essential for the survival of T. annulata and were selected as drug targets. Screening these drug targets in the Protein Kinase Inhibitor Database (PKID) led to shortlisting of 5 drugs. Only Dabrafenib, out of these 5 drugs, could bind to the ATP binding site (in silico) of the Calcium Dependent Protein Kinase 3 of both T. annulata and Theileria parva. Further, dabrafenib could inhibit the proliferation of T. annulata infected bovine leucocytes in 6 days proliferation assay with the IC50 value of 0.66 µM. Also, this drug did not have a cytotoxic effect on bovine peripheral blood mononuclear cells. In summary, the analysis of T. annulata kinome led to the identification of dabrafenib as a potential drug for treating theileriosis.
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Affiliation(s)
- Prajna Parimita Kar
- National Institute of Animal Biotechnology (NIAB), Hyderabad, India; Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Prasanna Babu Araveti
- National Institute of Animal Biotechnology (NIAB), Hyderabad, India; Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Anand Srivastava
- National Institute of Animal Biotechnology (NIAB), Hyderabad, India; Adjunct Assistant Professor, Regional Centre for Biotechnology (RCB), Faridabad, India.
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Fibrillarin RNA methylase is an interacting protein of Cryptosporidium parvum calmodulin-like protein (CpCML). Microb Pathog 2022; 170:105679. [PMID: 35843442 DOI: 10.1016/j.micpath.2022.105679] [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: 03/02/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022]
Abstract
Cryptosporidium parvum is an obligate protozoan parasite invading epithelial cells of small intestine of human and animals, and causing diarrheal disease. In apicomplexan parasites, calcium signaling can regulate many essential biological processes such as invasion and migration. As the main intracellular receptor for calcium ions, calmodulins control the activities of hundreds of enzymes and proteins. Calmodulin-like protein (CML) is an important member of the calmodulin family and may play a key role in C. parvum, however, the actual situation is still not clear. The present study aimed to identify the parasite interaction partner proteins of C. parvum calmodulin-like protein (CpCML). By constructing the cpcml bait plasmid, 5 potential CpCML - interacting proteins in C. parvum oocyst were screened by yeast-two-hybrid system (Y2H). Bimolecular fluorescence complementation (BiFC) and Co-immunoprecipitation (Co-IP) were performed as subsequent validations. Fibrillarin RNA methylase (FBL) was identified via this screening method as CpCML interacting protein in C. parvum. The identification of this interaction made it possible to get a further understanding of the function of CpCML and its contribution to the pathogenicity of C. parvum.
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Gupta Y, Goicoechea S, Pearce CM, Mathur R, Romero JG, Kwofie SK, Weyenberg MC, Daravath B, Sharma N, Poonam, Akala HM, Kanzok SM, Durvasula R, Rathi B, Kempaiah P. The emerging paradigm of calcium homeostasis as a new therapeutic target for protozoan parasites. Med Res Rev 2021; 42:56-82. [PMID: 33851452 DOI: 10.1002/med.21804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/10/2020] [Accepted: 03/31/2021] [Indexed: 12/13/2022]
Abstract
Calcium channels (CCs), a group of ubiquitously expressed membrane proteins, are involved in many pathophysiological processes of protozoan parasites. Our understanding of CCs in cell signaling, organelle function, cellular homeostasis, and cell cycle control has led to improved insights into their structure and functions. In this article, we discuss CCs characteristics of five major protozoan parasites Plasmodium, Leishmania, Toxoplasma, Trypanosoma, and Cryptosporidium. We provide a comprehensive review of current antiparasitic drugs and the potential of using CCs as new therapeutic targets. Interestingly, previous studies have demonstrated that human CC modulators can kill or sensitize parasites to antiparasitic drugs. Still, none of the parasite CCs, pumps, or transporters has been validated as drug targets. Information for this review draws from extensive data mining of genome sequences, chemical library screenings, and drug design studies. Parasitic resistance to currently approved therapeutics is a serious and emerging threat to both disease control and management efforts. In this article, we suggest that the disruption of calcium homeostasis may be an effective approach to develop new anti-parasite drug candidates and reduce parasite resistance.
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Affiliation(s)
- Yash Gupta
- Infectious Diseases, Mayo Clinic, Jacksonville, Florida, 32224, USA
| | - Steven Goicoechea
- Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
| | - Catherine M Pearce
- Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
| | - Raman Mathur
- Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
| | - Jesus G Romero
- Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
| | - Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana
| | - Matthew C Weyenberg
- Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
| | - Bharathi Daravath
- Stritch School of Medicine, Loyola University Chicago, Chicago, Illinois, USA
| | - Neha Sharma
- Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi, India
| | - Poonam
- Department of Chemistry, Miranda House University Enclave, University of Delhi, Delhi, India
| | | | - Stefan M Kanzok
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Ravi Durvasula
- Infectious Diseases, Mayo Clinic, Jacksonville, Florida, 32224, USA
| | - Brijesh Rathi
- Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi, India
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Jaskiewicz JJ, Tremblay JM, Tzipori S, Shoemaker CB. Identification and characterization of a new 34 kDa MORN motif-containing sporozoite surface-exposed protein, Cp-P34, unique to Cryptosporidium. Int J Parasitol 2021; 51:761-775. [PMID: 33774040 DOI: 10.1016/j.ijpara.2021.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 01/28/2021] [Indexed: 10/21/2022]
Abstract
Despite the public health impact of childhood diarrhea caused by Cryptosporidium, effective drugs and vaccines against this parasite are unavailable. Efforts to identify vaccine targets have focused on critical externally exposed virulence factors expressed in the parasite s invasive stages. However, no single surface antigen has yet been found that can elicit a significant protective immune response and it is likely that pooling multiple immune targets will be necessary. Discovery of surface proteins on Cryptosporidium sporozoites is therefore vital to this effort to develop a multi-antigenic vaccine. In this study we applied a novel single-domain camelid antibody (VHH) selection method to identify immunogenic proteins expressed on the surface of Cryptosporidium parvum sporozoites. By this approach, VHHs were identified that recognize two sporozoite surface-exposed antigens, the previously identified gp900 and an unrecognized immunogenic protein, Cp-P34. This Cp-P34 antigen, which contains multiple Membrane Occupation and Recognition Nexus (MORN) repeats, is found in excysted sporozoites as well as in the parasite s intracellular stages. Cp-P34 appears to accumulate inside the parasite and transiently appears on the surface of sporozoites to be shed in trails. Identical or nearly identical orthologs of Cp-P34 are found in the Cryptosporidium hominis and Cryptosporidium tyzzeri genomes. Except for the conserved MORN motifs, the Cp-P34 gene shares no significant homology with genes of other protozoans and thus appears to be unique to Cryptosporidium spp. Cp-P34 elicits immune responses in naturally exposed alpacas and warrants further investigation as a potential vaccine candidate.
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Affiliation(s)
- Justyna J Jaskiewicz
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Jacqueline M Tremblay
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Charles B Shoemaker
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA.
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Zhang Q, Shao Q, Guo Y, Li N, Li Y, Su J, Xu R, Zhang Z, Xiao L, Feng Y. Characterization of Three Calcium-Dependent Protein Kinases of Cryptosporidium parvum. Front Microbiol 2021; 11:622203. [PMID: 33510735 PMCID: PMC7835281 DOI: 10.3389/fmicb.2020.622203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/14/2020] [Indexed: 12/02/2022] Open
Abstract
In Cryptosporidium spp., calcium-dependent protein kinases (CDPKs) are considered promising targets for the development of pharmaceutical interventions. Whole-genome sequencing has revealed the presence of 11 CDPKs in Cryptosporidium parvum (CpCDPKs). In this study, we expressed recombinant CpCDPK4, CpCDPK5, and CpCDPK6 in Escherichia coli. The biological characteristics and functions of these CpCDPKs were examined by using quantitative reverse transcription PCR (qRT-PCR), immunofluorescence microscopy, and an in vitro neutralization assay. The expression of the CpCDPK4 gene peaked at 12 h post-infection, the CpCDPK5 gene peaked at 12 and 48 h, and the CpCDPK6 gene peaked at 2–6 h. CpCDPK4 protein was located in the anterior and mid-anterior regions of sporozoites, and CpCDPK5 protein was located over the entire sporozoites, while CpCDPK6 protein was expressed in a spotty pattern. Immune sera of CpCDPK4 and CpCDPK6 exhibited significant inhibitory effects on host cell invasion, while the immune sera of CpCDPK5 had no effects. These differences in protein localization, gene expressions, and neutralizing capacities indicated that the CpCDPK proteins may have different roles during the lifecycle of Cryptosporidium spp.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China
| | - Qian Shao
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yu Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiayuan Su
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China
| | - Rui Xu
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yaoyu Feng
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China.,Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Cellular Identification and In Silico Characterization of Protein Phosphatase 2C (PP2C) of Cryptosporidium parvum. Acta Parasitol 2020; 65:704-715. [PMID: 32347536 DOI: 10.2478/s11686-020-00209-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/25/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE Cryptosporidium parvum is an Apicomplexa parasite that causes watery diarrhea (cryptosporidiosis), especially in children and immunocompromised adults (the latter in a very severe form). No effective treatment exists against infection by this parasite. Phosphatases participate in the regulation of various cellular functions and are thus considered potential therapeutic targets in many diseases. The aim of the present study was to indirectly identify and in silico characterize a protein phosphatase 2C of C. parvum. METHODS Western blot and indirect immunofluorescence microscopy were performed with a polyclonal antibody against Leishmania major PP2C. Possible cross-reactivity with LmPP2C was assessed by in silico sequence homology to analyze phylogenetic relationships between distinct C. parvum PP2Cs. In addition, another bioinformatics approach was used to predict the possible relationship and function of C. parvum PP2C in the regulation of several cellular processes. RESULTS Western blotting showed a protein of approximately 72 kDa. With immunofluorescence, PP2C was localized in the nucleus of oocysts (with some additional labeling in the cytoplasm) and at the apical region of sporozoites. By aligning C. parvum PP2C with known ortholog sequences and carrying out PPI analysis, a determination could be made of the degree of conservation of these enzymes, their possible relationship, and their function in the regulation of several cellular processes associated with a likely nuclear location. CONCLUSION Microscopic localization by immunofluorescence identified CpPP2C at the nucleus in oocysts and at the apical end of the sporozoite body. Hence, this enzyme could be associated with proteins that have an important role in the regulation of transcription and other processes orchestrated by MAPK kinases, according to in silico analysis.
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Dhal AK, Pani A, Yun SI, Mahapatra RK. In-silico analysis of Calcium Dependent Protein Kinase 6 of Cr yptosporidium parvum through molecular modeling, docking, and dynamics simulation study. J Biomol Struct Dyn 2020; 39:5461-5470. [PMID: 32633680 DOI: 10.1080/07391102.2020.1790036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egress process during the infection of the host cells. The previous study reported that after the Calcium Dependent Protein Kinase 1 gene, Calcium Dependent Protein Kinase 6 of Cryptosporidium parvum is expressed in all stages of the parasite (merozoites/schizonts as well as sexual stages) at a comparable level and makes it as a valid drug target. In this study, an attempt is made to address the similarity in sequences and phylogenetic study of Calcium Dependent Protein Kinase 6 (CDPK6) among Calcium Dependent Protein Kinases of Apicomplexans. Further, the three-dimensional structure determination of CDPK6 of C. parvum was performed through a molecular modeling approach followed by virtual screening of small-molecule inhibitors from different datasets. The best inhibitor from Tres Cantos Antimalarial Set with ID 11730 reported a binding affinity of -8.2 kcal/mol against CDPK6 of C. parvum. Furthermore, the reliability of the binding mode of the inhibitor is validated through a complex molecular dynamics simulation study for a time interval of 100 ns. The simulation study advocates that the inhibitor Tres Cantos Antimalarial Set_11730 formed a stable interaction with the predicted active site residues and can be considered for industrial pharmaceutical research in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, India
| | - Alok Pani
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, South Korea
| | - Soon-Il Yun
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, South Korea
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11
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Zhang Q, Guo Y, Li N, Li Y, Su J, Xu R, Zhang Z, Feng Y, Xiao L. Characterization of Calcium-Dependent Protein Kinases 3, a Protein Involved in Growth of Cryptosporidium parvum. Front Microbiol 2020; 11:907. [PMID: 32457733 PMCID: PMC7225609 DOI: 10.3389/fmicb.2020.00907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Calcium-dependent protein kinases (CDPKs) are considered promising targets for pharmaceutical intervention of cryptosporidiosis. Whole-genome sequencing has revealed the presence of several CDPKs (CpCDPKs) in Cryptosporidium parvum. In this study, we expressed recombinant CpCDPK3 encoded by the cgd5_820 gene in Escherichia coli. The biologic characteristics and functions of CpCDPK3 were examined using qRT-PCR, immunofluorescence microscopy, and in vitro neutralization assay. The expression of the cgd5_820 gene peaked in merozoites during in vitro culture while the CpCDPK3 protein was expressed in both sporozoites and merozoites. Polyclonal antibodies against CpCDPK3 showed no significant inhibitory effects on host invasion by the parasites. We assessed the inhibitory effects of 46 candidate compounds from molecular docking of CpCDPK3 on both C. parvum development and CpCDPK3 enzyme activities. One compound was identified to be effective. Results of these analyses suggest that CpCDPK3 might play an important role in the growth of C. parvum.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China
| | - Yaqiong Guo
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Na Li
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yu Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiayuan Su
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China
| | - Rui Xu
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yaoyu Feng
- State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental, East China University of Science and Technology, Shanghai, China.,Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lihua Xiao
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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12
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Shahiduzzaman M, Ras R, Widmer G. Effect of Ginsenoside-Rh2 and Curcurbitacin-B on Cryptosporidium parvum in vitro. Exp Parasitol 2020; 212:107873. [PMID: 32165146 DOI: 10.1016/j.exppara.2020.107873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/27/2020] [Accepted: 03/07/2020] [Indexed: 12/09/2022]
Abstract
Ginsenoside-Rh2 and cucurbitacin-B (CuB) are secondary metabolites of Ginseng (Panax ginseng) and Cucurbitaceae plants respectively. We assessed the anticryptosporidial activity of these two functional compounds in a cell culture model of cryptosporidiosis. The highest concentration of each compound that was not toxic to the host cells was used to assess the activity against C. parvum during infection/invasion and growth in HCT-8 cell monolayers. Monolayers were infected with pre-excysted C. parvum oocysts. Infected monolayers were incubated at 37 °C for 24 h and 48 h in the presence of different concentrations of each test compound. A growth resumption assay was performed by incubating infected monolayers in the presence of compounds for 24 h followed by a second 24-h incubation in the absence of compound. To screen for invasion inhibiting activity, freshly excysted C. parvum sporozoites were pre-treated with different concentrations of compounds prior to adding them to the cell monolayers. Paromomycin, a known inhibitor of C. parvum, and DMSO were used as positive and negative control, respectively. The level of infection was initially assessed using an immunofluorescent assay and quantified by real-time PCR. Both compounds were found to strongly inhibit C. parvum intracellular development in a dose-dependent manner. IC50 values of 25 μM for a 24 h development period and 5.52 μM after 48 h development were measured for Rh2, whereas for CuB an IC50 value of 0.169 μg/ml and 0.118 μg/ml were obtained for the same incubation periods. CuB also effectively inhibited resumption of growth, an activity that was not observed with Rh2. CuB was more effective at inhibiting excystation and/or host cell invasion, indicating that this compound also targets extracellular stages of the parasite.
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Affiliation(s)
- Md Shahiduzzaman
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, 01536, USA; Department of Parasitology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
| | - Refaat Ras
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, 01536, USA; Department of Parasitology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Giovanni Widmer
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA, 01536, USA
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Öktem EK, Yazar M, Gulfidan G, Arga KY. Cancer Drug Repositioning by Comparison of Gene Expression in Humans and Axolotl (Ambystoma mexicanum) During Wound Healing. ACTA ACUST UNITED AC 2019; 23:389-405. [DOI: 10.1089/omi.2019.0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Elif Kubat Öktem
- Department of Genetics and Bioengineering, Istanbul Okan University, Istanbul, Turkey
| | - Metin Yazar
- Department of Genetics and Bioengineering, Istanbul Okan University, Istanbul, Turkey
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Marmara University, Istanbul, Turkey
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Jiang YY, Maier W, Baumeister R, Minevich G, Joachimiak E, Wloga D, Ruan Z, Kannan N, Bocarro S, Bahraini A, Vasudevan KK, Lechtreck K, Orias E, Gaertig J. LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena. PLoS Genet 2019; 15:e1008099. [PMID: 31339880 PMCID: PMC6682161 DOI: 10.1371/journal.pgen.1008099] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/05/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022] Open
Abstract
The length of cilia is controlled by a poorly understood mechanism that involves members of the conserved RCK kinase group, and among them, the LF4/MOK kinases. The multiciliated protist model, Tetrahymena, carries two types of cilia (oral and locomotory) and the length of the locomotory cilia is dependent on their position with the cell. In Tetrahymena, loss of an LF4/MOK ortholog, LF4A, lengthened the locomotory cilia, but also reduced their number. Without LF4A, cilia assembled faster and showed signs of increased intraflagellar transport (IFT). Consistently, overproduced LF4A shortened cilia and downregulated IFT. GFP-tagged LF4A, expressed in the native locus and imaged by total internal reflection microscopy, was enriched at the basal bodies and distributed along the shafts of cilia. Within cilia, most LF4A-GFP particles were immobile and a few either diffused or moved by IFT. We suggest that the distribution of LF4/MOK along the cilium delivers a uniform dose of inhibition to IFT trains that travel from the base to the tip. In a longer cilium, the IFT machinery may experience a higher cumulative dose of inhibition by LF4/MOK. Thus, LF4/MOK activity could be a readout of cilium length that helps to balance the rate of IFT-driven assembly with the rate of disassembly at steady state. We used a forward genetic screen to identify a CDK-related kinase, CDKR1, whose loss-of-function suppressed the shortening of cilia caused by overexpression of LF4A, by reducing its kinase activity. Loss of CDKR1 alone lengthened both the locomotory and oral cilia. CDKR1 resembles other known ciliary CDK-related kinases: LF2 of Chlamydomonas, mammalian CCRK and DYF-18 of C. elegans, in lacking the cyclin-binding motif and acting upstream of RCKs. The new genetic tools we developed here for Tetrahymena have potential for further dissection of the principles of cilia length regulation in multiciliated cells.
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Affiliation(s)
- Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Wolfgang Maier
- Bio 3/Bioinformatics and Molecular Genetics, Faculty of Biology and ZBMZ, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Ralf Baumeister
- Bio 3/Bioinformatics and Molecular Genetics, Faculty of Biology and ZBMZ, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Gregory Minevich
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York, United States of America
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Stephen Bocarro
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Anoosh Bahraini
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Krishna Kumar Vasudevan
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Eduardo Orias
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
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15
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Lippuner C, Ramakrishnan C, Basso WU, Schmid MW, Okoniewski M, Smith NC, Hässig M, Deplazes P, Hehl AB. RNA-Seq analysis during the life cycle of Cryptosporidium parvum reveals significant differential gene expression between proliferating stages in the intestine and infectious sporozoites. Int J Parasitol 2018; 48:413-422. [DOI: 10.1016/j.ijpara.2017.10.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 10/21/2017] [Indexed: 10/18/2022]
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16
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Kannan S, Pradhan MR, Cherian J, Joseph TL, Poh ZY, Hai Yan Y, Melvyn H, Boping L, Jeffrey H, Nacro K, Verma CS. Small Molecules Targeting the Inactive Form of the Mnk1/2 Kinases. ACS OMEGA 2017; 2:7881-7891. [PMID: 30023565 PMCID: PMC6045392 DOI: 10.1021/acsomega.7b01403] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/31/2017] [Indexed: 05/14/2023]
Abstract
Overexpression of the eukaryotic initiation factor 4E (eIF4E) is linked to a variety of cancers. Both mitogen-activated protein kinases-interacting kinases 1 and 2 (Mnk1/2) activate the oncogene eIF4E through posttranslational modification (phosphorylating it at the conserved Ser209). Inhibition of Mnk prevents eIF4E phosphorylation, making the Mnk-eIF4E axis a potential therapeutic target for oncology. Recently, the design and synthesis of a series of novel potent compounds inhibiting the Mnk1/2 kinases were carried out in-house. Here, we describe computational models of the interactions between Mnk1/2 kinases and these inhibitors. Molecular modeling combined with free energy calculations show that these compounds bind to the inactive forms of the kinases. All compounds adopt similar conformations in the catalytic sites of both kinases, stabilized by hydrogen bonds with the hinge regions and with the catalytic Lys78 (Mnk1) and Lys113 (Mnk2). These hydrogen bond interactions clearly play a critical role in determining the conformational stability and potency of the compounds. We also find that van der Waals interactions with an allosteric pocket are key to their binding and potency. Two distinct hydration sites that appear to further stabilize the ligand binding/interactions were observed. Critically, the inclusion of explicit water molecules in the calculations results in improving the agreement between calculated and experimental binding free energies.
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Affiliation(s)
- Srinivasaraghavan Kannan
- Bioinformatics
Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- E-mail: . Phone: +65 6478 8353. Fax: +65 6478 9048 (S.K.)
| | - Mohan R. Pradhan
- Bioinformatics
Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Joseph Cherian
- Experimental
Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Nanos, 138669, Singapore
| | - Thomas L. Joseph
- Bioinformatics
Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Zhi Ying Poh
- Experimental
Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Nanos, 138669, Singapore
| | - Yang Hai Yan
- Experimental
Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Nanos, 138669, Singapore
| | - Ho Melvyn
- Experimental
Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Nanos, 138669, Singapore
| | - Liu Boping
- Experimental
Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Nanos, 138669, Singapore
| | - Hill Jeffrey
- Experimental
Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Nanos, 138669, Singapore
| | - Kassoum Nacro
- Experimental
Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Nanos, 138669, Singapore
| | - Chandra S. Verma
- Bioinformatics
Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang
Drive, 637551, Singapore
- Department
of Biological Sciences, National University
of Singapore, 14 Science
Drive 4, 117543, Singapore
- E-mail: . Phone: +65 6478 8273. Fax: +65 6478 9048 (C.S.V.)
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17
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Murungi EK, Kariithi HM. Genome-Wide Identification and Evolutionary Analysis of Sarcocystis neurona Protein Kinases. Pathogens 2017; 6:pathogens6010012. [PMID: 28335576 PMCID: PMC5371900 DOI: 10.3390/pathogens6010012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/10/2017] [Accepted: 03/17/2017] [Indexed: 02/07/2023] Open
Abstract
The apicomplexan parasite Sarcocystis neurona causes equine protozoal myeloencephalitis (EPM), a degenerative neurological disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions, such as host cell invasion, cell cycle progression and host immune response evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. We identified 97 putative PKs clustering within the various eukaryotic kinase groups. Although containing the universally-conserved PKA (AGC group), S. neurona kinome was devoid of PKB and PKC. Moreover, the kinome contains the six-conserved apicomplexan CDPKs (CAMK group). Several OPK atypical kinases, including ROPKs 19A, 27, 30, 33, 35 and 37 were identified. Notably, S. neurona is devoid of the virulence-associated ROPKs 5, 6, 18 and 38, as well as the Alpha and RIO kinases. Two out of the three S. neurona CK1 enzymes had high sequence similarities to Toxoplasma gondii TgCK1-α and TgCK1-β and the Plasmodium PfCK1. Further experimental studies on the S. neurona putative PKs identified in this study are required to validate the functional roles of the PKs and to understand their involvement in mechanisms that regulate various cellular processes and host-parasite interactions. Given the essentiality of apicomplexan PKs in the survival of apicomplexans, the current study offers a platform for future development of novel therapeutics for EPM, for instance via application of PK inhibitors to block parasite invasion and development in their host.
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Affiliation(s)
- Edwin K Murungi
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, 20115 Njoro, Kenya.
| | - Henry M Kariithi
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Kaptagat Rd, Loresho, 00200 Nairobi, Kenya.
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18
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Osman KT, Ye J, Shi Z, Toker C, Lovato D, Jumani RS, Zuercher W, Huston CD, Edwards AM, Lautens M, Santhakumar V, Hui R. Discovery and structure activity relationship of the first potent cryptosporidium FIKK kinase inhibitor. Bioorg Med Chem 2017; 25:1672-1680. [DOI: 10.1016/j.bmc.2017.01.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 12/29/2022]
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19
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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: 1.6] [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.
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Affiliation(s)
- Brad A Haubrich
- Institute for Rare and Neglected Diseases Drug Discovery, 897 Independence Ave, Suite 2C, Mountain View, CA 94043, USA.
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20
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Mesquita I, Moreira D, Sampaio-Marques B, Laforge M, Cordeiro-da-Silva A, Ludovico P, Estaquier J, Silvestre R. AMPK in Pathogens. EXPERIENTIA SUPPLEMENTUM (2012) 2016; 107:287-323. [PMID: 27812985 DOI: 10.1007/978-3-319-43589-3_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
During host-pathogen interactions, a complex web of events is crucial for the outcome of infection. Pathogen recognition triggers powerful cellular signaling events that is translated into the induction and maintenance of innate and adaptive host immunity against infection. In opposition, pathogens employ active mechanisms to manipulate host cell regulatory pathways toward their proliferation and survival. Among these, subversion of host cell energy metabolism by pathogens is currently recognized to play an important role in microbial growth and persistence. Extensive studies have documented the role of AMP-activated protein kinase (AMPK) signaling, a central cellular hub involved in the regulation of energy homeostasis, in host-pathogen interactions. Here, we highlight the most recent advances detailing how pathogens hijack cellular metabolism by suppressing or increasing the activity of the host energy sensor AMPK. We also address the role of lower eukaryote AMPK orthologues in the adaptive process to the host microenvironment and their contribution for pathogen survival, differentiation, and growth. Finally, we review the effects of pharmacological or genetic AMPK modulation on pathogen growth and persistence.
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Affiliation(s)
- Inês Mesquita
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Guimarães, Braga, Portugal
| | - Diana Moreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Guimarães, Braga, Portugal
| | | | - Anabela Cordeiro-da-Silva
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Guimarães, Braga, Portugal
| | - Jérôme Estaquier
- CNRS FR 3636, Université Paris Descartes, Paris, France.,Centre de Recherche du CHU de Québec, Université Laval, Québec, QC, Canada
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal. .,ICVS/3Bs-PT Government Associate Laboratory, Guimarães, Braga, Portugal.
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21
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Inhibition of Calcium-Dependent Protein Kinase 1 (CDPK1) In Vitro by Pyrazolopyrimidine Derivatives Does Not Correlate with Sensitivity of Cryptosporidium parvum Growth in Cell Culture. Antimicrob Agents Chemother 2015; 60:570-9. [PMID: 26552986 DOI: 10.1128/aac.01915-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 11/06/2015] [Indexed: 11/20/2022] Open
Abstract
Cryptosporidiosis is a serious diarrheal disease in immunocompromised patients and malnourished children, and treatment is complicated by a lack of adequate drugs. Recent studies suggest that the natural occurrence of a small gatekeeper residue in serine threonine calcium-dependent protein kinase 1 (CDPK1) of Cryptosporidium parvum might be exploited to target this enzyme and block parasite growth. Here were explored the potency with which a series of pyrazolopyrimidine analogs, which are selective for small gatekeeper kinases, inhibit C. parvum CDPK1 and block C. parvum growth in tissue culture in vitro. Although these compounds potently inhibited kinase activity in vitro, most had no effect on parasite growth. Moreover, among those that were active against parasite growth, there was a very poor correlation with their 50% inhibitory concentrations against the enzyme. Active compounds also had no effect on cell invasion, unlike the situation in Toxoplasma gondii, where these compounds block CDPK1, prevent microneme secretion, and disrupt cell invasion. These findings suggest that CPDK1 is not essential for C. parvum host cell invasion or growth and therefore that it is not the optimal target for therapeutic intervention. Nonetheless, several inhibitors with low micromolar 50% effective concentrations were identified, and these may affect other essential targets in C. parvum that are worthy of further exploration.
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22
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Hui R, El Bakkouri M, Sibley LD. Designing selective inhibitors for calcium-dependent protein kinases in apicomplexans. Trends Pharmacol Sci 2015; 36:452-60. [PMID: 26002073 DOI: 10.1016/j.tips.2015.04.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 12/21/2022]
Abstract
Apicomplexan parasites cause some of the most severe human diseases, including malaria (caused by Plasmodium), toxoplasmosis, and cryptosporidiosis. Treatments are limited by the lack of effective drugs and development of resistance to available agents. By exploiting novel features of protein kinases in these parasites, it may be possible to develop new treatments. We summarize here recent advances in identifying small molecule inhibitors against a novel family of plant-like, calcium-dependent kinases that are uniquely expanded in apicomplexan parasites. Analysis of the 3D structure, activation mechanism, and sensitivity to small molecules had identified several attractive chemical scaffolds that are potent and selective inhibitors of these parasite kinases. Further optimization of these leads may yield promising new drugs for treatment of these parasitic infections.
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Affiliation(s)
- Raymond Hui
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, 101 College St, Toronto, ON, M5G 1L7, Canada; Toronto General Hospital Research Institute, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Majida El Bakkouri
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, 101 College St, Toronto, ON, M5G 1L7, Canada
| | - L David Sibley
- Department of Molecular Microbiology, 660 S. Euclid Ave., Washington University School of Medicine, St Louis, MO 63130, USA.
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23
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Abstract
PURPOSE OF REVIEW To highlight new findings on the relevance of gastrointestinal protozoan infections to global public health in low-income and middle-income countries and suggest new large-scale interventions. RECENT FINDINGS New disease burden assessments and epidemiological studies highlight the role of the major intestinal protozoa as important etiologic disease agents in low-income and middle-income countries. Despite their prevalence and adverse health impact, such information has not yet translated to the implementation of large-scale interventions as exist for helminth infections and other neglected tropical diseases. There are also several key research and development questions that must be addressed for intestinal protozoan infections and the potential need for new tools, for example, drugs, diagnostics, and vaccines. Additional studies have identified new and emerging species of intestinal protozoa relevant to global public health such as Dientamoeba fragilis and Blastocystis hominis and how they too might emerge as important gastrointestinal pathogens in the coming years. SUMMARY New and emerging information on intestinal protozoa are reviewed with emphasis on aspects considered relevant to global health policymakers including prospects for scaling up interventions against intestinal protozoan infections in resource-poor countries.
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Abstract
SUMMARYCryptosporidiumhost cell interaction remains fairly obscure compared with other apicomplexans such asPlasmodiumorToxoplasma. The reason for this is probably the inability of this parasite to complete its life cyclein vitroand the lack of a system to genetically modifyCryptosporidium. However, there is a substantial set of data about the molecules involved in attachment and invasion and about the host cell pathways involved in actin arrangement that are altered by the parasite. Here we summarize the recent advances in research on host cell infection regarding the excystation process, attachment and invasion, survival in the cell, egress and the available data on omics.
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25
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Goldberg JM, Griggs AD, Smith JL, Haas BJ, Wortman JR, Zeng Q. Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily. ACTA ACUST UNITED AC 2013; 29:2387-94. [PMID: 23904509 PMCID: PMC3777111 DOI: 10.1093/bioinformatics/btt419] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Motivation: Kinases of the eukaryotic protein kinase superfamily are key regulators of most aspects eukaryotic cellular behavior and have provided several drug targets including kinases dysregulated in cancers. The rapid increase in the number of genomic sequences has created an acute need to identify and classify members of this important class of enzymes efficiently and accurately. Results: Kinannote produces a draft kinome and comparative analyses for a predicted proteome using a single line command, and it is currently the only tool that automatically classifies protein kinases using the controlled vocabulary of Hanks and Hunter [Hanks and Hunter (1995)]. A hidden Markov model in combination with a position-specific scoring matrix is used by Kinannote to identify kinases, which are subsequently classified using a BLAST comparison with a local version of KinBase, the curated protein kinase dataset from www.kinase.com. Kinannote was tested on the predicted proteomes from four divergent species. The average sensitivity and precision for kinome retrieval from the test species are 94.4 and 96.8%. The ability of Kinannote to classify identified kinases was also evaluated, and the average sensitivity and precision for full classification of conserved kinases are 71.5 and 82.5%, respectively. Kinannote has had a significant impact on eukaryotic genome annotation, providing protein kinase annotations for 36 genomes made public by the Broad Institute in the period spanning 2009 to the present. Availability: Kinannote is freely available at http://sourceforge.net/projects/kinannote. Contact:jmgold@broadinstitute.org Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jonathan M Goldberg
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA and Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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26
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Abstract
Cryptosporidium is a protozoan parasite of medical and veterinary importance that causes gastroenteritis in a variety of vertebrate hosts. Several studies have reported different degrees of pathogenicity and virulence among Cryptosporidium species and isolates of the same species as well as evidence of variation in host susceptibility to infection. The identification and validation of Cryptosporidium virulence factors have been hindered by the renowned difficulties pertaining to the in vitro culture and genetic manipulation of this parasite. Nevertheless, substantial progress has been made in identifying putative virulence factors for Cryptosporidium. This progress has been accelerated since the publication of the Cryptosporidium parvum and C. hominis genomes, with the characterization of over 25 putative virulence factors identified by using a variety of immunological and molecular techniques and which are proposed to be involved in aspects of host-pathogen interactions from adhesion and locomotion to invasion and proliferation. Progress has also been made in the contribution of host factors that are associated with variations in both the severity and risk of infection. Here we provide a review comprised of the current state of knowledge on Cryptosporidium infectivity, pathogenesis, and transmissibility in light of our contemporary understanding of microbial virulence.
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Talevich E, Tobin AB, Kannan N, Doerig C. An evolutionary perspective on the kinome of malaria parasites. Philos Trans R Soc Lond B Biol Sci 2012; 367:2607-18. [PMID: 22889911 DOI: 10.1098/rstb.2012.0014] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Malaria parasites belong to an ancient lineage that diverged very early from the main branch of eukaryotes. The approximately 90-member plasmodial kinome includes a majority of eukaryotic protein kinases that clearly cluster within the AGC, CMGC, TKL, CaMK and CK1 groups found in yeast, plants and mammals, testifying to the ancient ancestry of these families. However, several hundred millions years of independent evolution, and the specific pressures brought about by first a photosynthetic and then a parasitic lifestyle, led to the emergence of unique features in the plasmodial kinome. These include taxon-restricted kinase families, and unique peculiarities of individual enzymes even when they have homologues in other eukaryotes. Here, we merge essential aspects of all three malaria-related communications that were presented at the Evolution of Protein Phosphorylation meeting, and propose an integrated discussion of the specific features of the parasite's kinome and phosphoproteome.
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Affiliation(s)
- Eric Talevich
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, 120 Green Street, Athens, GA 30602-7229, USA
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The kinomes of apicomplexan parasites. Microbes Infect 2012; 14:796-810. [DOI: 10.1016/j.micinf.2012.04.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 04/11/2012] [Accepted: 04/11/2012] [Indexed: 11/21/2022]
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Bista M, Smithson D, Pecak A, Salinas G, Pustelny K, Min J, Pirog A, Finch K, Zdzalik M, Waddell B, Wladyka B, Kedracka-Krok S, Dyer MA, Dubin G, Guy RK. On the mechanism of action of SJ-172550 in inhibiting the interaction of MDM4 and p53. PLoS One 2012; 7:e37518. [PMID: 22675482 PMCID: PMC3366986 DOI: 10.1371/journal.pone.0037518] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 04/20/2012] [Indexed: 12/22/2022] Open
Abstract
SJ-172550 (1) was previously discovered in a biochemical high throughput screen for inhibitors of the interaction of MDMX and p53 and characterized as a reversible inhibitor (J. Biol. Chem. 2010; 285∶10786). Further study of the biochemical mode of action of 1 has shown that it acts through a complicated mechanism in which the compound forms a covalent but reversible complex with MDMX and locks MDMX into a conformation that is unable to bind p53. The relative stability of this complex is influenced by many factors including the reducing potential of the media, the presence of aggregates, and other factors that influence the conformational stability of the protein. This complex mechanism of action hinders the further development of compound 1 as a selective MDMX inhibitor.
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Affiliation(s)
- Michal Bista
- Max-Planck Institute for Biochemistry, Martinsried, Germany
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - David Smithson
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Aleksandra Pecak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Gabriella Salinas
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Katarzyna Pustelny
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Artur Pirog
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kristin Finch
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Michal Zdzalik
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Brett Waddell
- Hartwell Center for Biotechnology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
| | - Michael A. Dyer
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
| | - R. Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
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Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa. BMC Evol Biol 2011; 11:321. [PMID: 22047078 PMCID: PMC3239843 DOI: 10.1186/1471-2148-11-321] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 11/02/2011] [Indexed: 12/04/2022] Open
Abstract
Background The Apicomplexa constitute an evolutionarily divergent phylum of protozoan pathogens responsible for widespread parasitic diseases such as malaria and toxoplasmosis. Many cellular functions in these medically important organisms are controlled by protein kinases, which have emerged as promising drug targets for parasitic diseases. However, an incomplete understanding of how apicomplexan kinases structurally and mechanistically differ from their host counterparts has hindered drug development efforts to target parasite kinases. Results We used the wealth of sequence data recently made available for 15 apicomplexan species to identify the kinome of each species and quantify the evolutionary constraints imposed on each family of apicomplexan kinases. Our analysis revealed lineage-specific adaptations in selected families, namely cyclin-dependent kinase (CDK), calcium-dependent protein kinase (CDPK) and CLK/LAMMER, which have been identified as important in the pathogenesis of these organisms. Bayesian analysis of selective constraints imposed on these families identified the sequence and structural features that most distinguish apicomplexan protein kinases from their homologs in model organisms and other eukaryotes. In particular, in a subfamily of CDKs orthologous to Plasmodium falciparum crk-5, the activation loop contains a novel PTxC motif which is absent from all CDKs outside Apicomplexa. Our analysis also suggests a convergent mode of regulation in a subset of apicomplexan CDPKs and mammalian MAPKs involving a commonly conserved arginine in the αC helix. In all recognized apicomplexan CLKs, we find a set of co-conserved residues involved in substrate recognition and docking that are distinct from metazoan CLKs. Conclusions We pinpoint key conserved residues that can be predicted to mediate functional differences from eukaryotic homologs in three identified kinase families. We discuss the structural, functional and evolutionary implications of these lineage-specific variations and propose specific hypotheses for experimental investigation. The apicomplexan-specific kinase features reported in this study can be used in the design of selective kinase inhibitors.
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