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de Oliveira D, Luiz GP, Scussel R, Fagundes MI, Galvani NC, Abel JDS, Zaccaron RP, de Bem Silveira G, de Andrade TAM, Lock Silveira PC, Andrez Machado-de-Ávila R. The combined treatment of gold nanoparticles associated with photobiomodulation accelerate the healing of dermonecrotic lesion. J Drug Target 2024; 32:172-185. [PMID: 38155427 DOI: 10.1080/1061186x.2023.2298848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/10/2023] [Indexed: 12/30/2023]
Abstract
Introduction: The search for fast and efficient treatment for dermonecrotic lesions caused by the venom of the spider from the Loxosceles simillis, is a demand in health. Prednisolone is one of the most used drugs, however it has side effects. In this context, addictionally gold nanoparticles (GNPs) have anti-inflammatory, antioxidant, and antibacterial properties. The use of photobiomodulation has show to be efficient in the process of tissue repair. Therefore, the purpose of this study was to investigate the anti-inflammatory effect of photobiomodulation and GNPs associated or not with a low concentration of prednisolone in animal models of dermonecrotic lesion.Methodology: For this, rabbits with venon-induced dermonecrotic lesion were subjected to topical treatment with prednisolone + laser or GNPs + laser or Pred-GNPs + laser. The area of edema, necrosis and erythema were measured. On the last day of treatment, the animals were euthanized to remove the organs for histopathological and biochemical analysis.Results: All treatments combinations were effective in promoting the reduction of necrotic tissue and erythema.Conclusion: With this results, we suggest that the use of laser and nanoparticles, associated or not with prednisolone, should be considered for the treatment of dermonecrotic injury.
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Affiliation(s)
- Daysiane de Oliveira
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Gabriel Paulino Luiz
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Rahisa Scussel
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Mirian Ivens Fagundes
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Nathália Coral Galvani
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Jessica da Silva Abel
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Rubya Pereira Zaccaron
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Gustavo de Bem Silveira
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Thiago Antônio Moretti de Andrade
- Postgraduate in Biomedical Sciences, University Center of Herminio Ometto Foundation, Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
| | - Paulo Cesar Lock Silveira
- Postgraduate in Health Sciences, Universidade do Extremo Sul de Catarinense, Criciúma, Santa Catarina, Brazil
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Tasleem M, Pelletier J, Sévigny J, Hussain Z, Khan A, Al-Harrasi A, El-Kott AF, Taslimi P, Negm S, Shafiq Z, Iqbal J. Synthesis, in vitro, and in silico studies of morpholine-based thiosemicarbazones as ectonucleotide pyrophosphatase/phosphodiesterase-1 and -3 inhibitors. Int J Biol Macromol 2024; 266:131068. [PMID: 38531526 DOI: 10.1016/j.ijbiomac.2024.131068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/06/2024] [Accepted: 03/20/2024] [Indexed: 03/28/2024]
Abstract
An extensive range of new biologically active morpholine based thiosemicarbazones derivatives 3a-r were synthesized, characterized by spectral techniques and evaluated as inhibitors of ENPP isozymes. Most of the novel thiosemicarbazones exhibit potent inhibition towards NPP1 and NPP3 isozymes. Compound 3 h was potent inhibitor of NPP1 with IC50 value of 0.55 ± 0.02. However, the most powerful inhibitor of NPP3 was 3e with an IC50 value of 0.24 ± 0.02. Furthermore, Lineweaver-Burk plot for compound 3 h against NPP1 and for compound 3e against NPP3 was devised through enzymes kinetics studies. Molecular docking and in silico studies was also done for analysis of interaction pattern of all newly synthesized compounds. The results were further validated by molecular dynamic (MD) simulation where the stability of conformational transformation of the best protein-ligand complex (3e) were justified on the basis of RMSD and RMSF analysis.
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Affiliation(s)
- Mussarat Tasleem
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Julie Pelletier
- Centre de Recherche du CHU de Québec-Université Laval, Québec G1V 4G2, Canada
| | - Jean Sévigny
- Centre de Recherche du CHU de Québec-Université Laval, Québec G1V 4G2, Canada; Département de Microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec G1V 0A6, Canada
| | - Zahid Hussain
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Centre, University of Nizwa, P.O. Box 33, PC 616, Birkat Al Mauz, Nizwa, Sultanate of Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, P.O. Box 33, PC 616, Birkat Al Mauz, Nizwa, Sultanate of Oman.
| | - Attalla F El-Kott
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia; Department of Zoology, College of Science, Damanhour University, Egypt
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, 74100 Bartin, Türkiye
| | - Sally Negm
- Department of Life Sciences, College of Science and Art Mahyel Aseer, King Khalid University, Abha 62529, Saudi Arabia
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan; Department of Pharmaceutical & Medicinal Chemistry, An der Immenburg 4, D-53121 Bonn, Germany.
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan.
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3
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Hejazian SM, Pirmoradi S, Zununi Vahed S, Kumar Roy R, Hosseiniyan Khatibi SM. An update on Glycerophosphodiester Phosphodiesterases; From Bacteria to Human. Protein J 2024; 43:187-199. [PMID: 38491249 DOI: 10.1007/s10930-024-10190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2024] [Indexed: 03/18/2024]
Abstract
The hydrolysis of deacylated glycerophospholipids into sn-glycerol 3-phosphate and alcohol is facilitated by evolutionarily conserved proteins known as glycerophosphodiester phosphodiesterases (GDPDs). These proteins are crucial for the pathogenicity of bacteria and for bioremediation processes aimed at degrading organophosphorus esters that pose a hazard to both humans and the environment. Additionally, GDPDs are enzymes that respond to multiple nutrients and could potentially serve as candidate genes for addressing deficiencies in zinc, iron, potassium, and especially phosphate in important plants like rice. In mammals, glycerophosphodiesterases (GDEs) play a role in regulating osmolytes, facilitating the biosynthesis of anandamine, contributing to the development of skeletal muscle, promoting the differentiation of neurons and osteoblasts, and influencing pathological states. Due to their capacity to enhance a plant's ability to tolerate various nutrient deficiencies and their potential as pharmaceutical targets in humans, GDPDs have received increased attention in recent times. This review provides an overview of the functions of GDPD families as vital and resilient enzymes that regulate various pathways in bacteria, plants, and humans.
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Affiliation(s)
| | - Saeed Pirmoradi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Electrical Engineering, K.N. Toosi University of Technology, Tehran, Iran
| | | | | | - Seyed Mahdi Hosseiniyan Khatibi
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.
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4
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Andrilli LHS, Sebinelli HG, Cominal JG, Bolean M, Hayann L, Millán JL, Ramos AP, Ciancaglini P. Differential effects of the lipidic and ionic microenvironment on NPP1's phosphohydrolase and phosphodiesterase activities. Biochim Biophys Acta Biomembr 2024; 1866:184292. [PMID: 38342362 DOI: 10.1016/j.bbamem.2024.184292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/30/2023] [Accepted: 01/31/2024] [Indexed: 02/13/2024]
Abstract
Ecto-nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) is an enzyme present in matrix vesicles (MV). NPP1 participates on the regulation of bone formation by producing pyrophosphate (PPi) from adenosine triphosphate (ATP). Here, we have used liposomes bearing dipalmitoylphosphatidylcholine (DPPC), sphingomyelin (SM), and cholesterol (Chol) harboring NPP1 to mimic the composition of MV lipid rafts to investigate ionic and lipidic influence on NPP1 activity and mineral propagation. Atomic force microscopy (AFM) revealed that DPPC-liposomes had spherical and smooth surface. The presence of SM and Chol elicited rough and smooth surface, respectively. NPP1 insertion produced protrusions in all the liposome surface. Maximum phosphodiesterase activity emerged at 0.082 M ionic strength, whereas maximum phosphomonohydrolase activity arose at low ionic strength. Phosphoserine-Calcium Phosphate Complex (PS-CPLX) and amorphous calcium-phosphate (ACP) induced mineral propagation in DPPC- and DPPC:SM-liposomes and in DPPC:Chol-liposomes, respectively. Mineral characterization revealed the presence of bands assigned to HAp in the mineral propagated by NPP1 harbored in DPPC-liposomes without nucleators or in DPPC:Chol-liposomes with ACP nucleators. These data show that studying how the ionic and lipidic environment affects NPP1 properties is important, especially for HAp obtained under controlled conditions in vitro.
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Affiliation(s)
- Luiz H S Andrilli
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil; Sanford Children's Health Research Center, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Heitor G Sebinelli
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Juçara G Cominal
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Maytê Bolean
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Larwsk Hayann
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - José Luís Millán
- Sanford Children's Health Research Center, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Ana P Ramos
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil.
| | - Pietro Ciancaglini
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil.
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5
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Du B, Ru J, Zhan Z, Lin C, Liu Y, Mao W, Zhang J. Insight into small-molecule inhibitors targeting extracellular nucleotide pyrophosphatase/phosphodiesterase1 for potential multiple human diseases. Eur J Med Chem 2024; 268:116286. [PMID: 38432057 DOI: 10.1016/j.ejmech.2024.116286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/06/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Extracellular nucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) has been identified as a type II transmembrane glycoprotein. It plays a crucial role in various biological processes, such as bone mineralization, cancer cell proliferation, and immune regulation. Consequently, ENPP1 has garnered attention as a promising target for pharmacological interventions. Despite its potential, the development of clinical-stage ENPP1 inhibitors for solid tumors, diabetes, and silent rickets remains limited. However, there are encouraging findings from preclinical trials involving small molecules exhibiting favorable therapeutic effects and safety profiles. This perspective aims to shed light on the structural properties, biological functions and the relationship between ENPP1 and diseases. Additionally, it focuses on the structure-activity relationship of ENPP1 inhibitors, with the intention of guiding the future development of new and effective ENPP1 inhibitors.
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Affiliation(s)
- Baochan Du
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinxiao Ru
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zixuan Zhan
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Congcong Lin
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Yang Liu
- Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, China
| | - Wuyu Mao
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Neurology, Neuro-system and Multimorbidity Laboratory and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Lachmayr H, Merrill AH. A Brief Overview of the Toxic Sphingomyelinase Ds of Brown Recluse Spider Venom and Other Organisms and Simple Methods To Detect Production of Its Signature Cyclic Ceramide Phosphate. Mol Pharmacol 2024; 105:144-154. [PMID: 37739813 PMCID: PMC10877732 DOI: 10.1124/molpharm.123.000709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/05/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023] Open
Abstract
A special category of phospholipase D (PLD) in the venom of the brown recluse spider (Loxosceles reclusa) and several other sicariid spiders accounts for the dermonecrosis and many of the other clinical symptoms of envenomation. Related proteins are produced by other organisms, including fungi and bacteria. These PLDs are often referred to as sphingomyelinase Ds (SMase Ds) because they cleave sphingomyelin (SM) to choline and "ceramide phosphate." The lipid product has actually been found to be a novel sphingolipid: ceramide 1,3-cyclic phosphate (Cer1,3P). Since there are no effective treatments for the injury induced by the bites of these spiders, SMase D/PLDs are attractive targets for therapeutic intervention, and some of their features will be described in this minireview. In addition, two simple methods are described for detecting the characteristic SMase D activity using a fluorescent SM analog, (N-[12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]dodecanoyl]-SM (C12-NBD-SM), that is cleaved to C12-NBD-Cer1,3P, which is easily separated from other potential metabolites by thin-layer chromatography and visualized under UV light. Besides confirming that C12-NBD-Cer1,3P is the only product detected upon incubation of C12-NBD-SM with brown recluse spider venom, the method was also able to detect for the first time very low levels of activity in venom from another spider, Kukulcania hibernalis The simplicity of the methods makes it relatively easy to determine this signature activity of SMase D/PLD. SIGNIFICANCE STATEMENT: The sphingomyelinase D/phospholipase D that are present in the venom of the brown recluse spider and other sources cause considerable human injury, but detection of the novel sphingolipid product, ceramide 1,3-cyclic phosphate, is not easy by previously published methods. This minireview describes simple methods for detection of this activity that will be useful for studies of its occurrence in spider venoms and other biological samples, perhaps including lesions from suspected spider bites and infections.
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Affiliation(s)
- Hannah Lachmayr
- School of Biological Sciences and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Alfred H Merrill
- School of Biological Sciences and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
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7
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Jin Z, Song D, Wang W, Feng L, Li Z, Chen H, Xiao X, Liu X. Synthesis and degradation of the cyclic dinucleotide messenger c-di-AMP in the hyperthermophilic archaeon Pyrococcus yayanosii. Protein Sci 2023; 32:e4829. [PMID: 37921047 PMCID: PMC10680344 DOI: 10.1002/pro.4829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a newly identified prokaryotic cyclic dinucleotide second messenger well elucidated in bacteria, while less studied in archaea. Here, we describe the enzymes involved in c-di-AMP metabolism in the hyperthermophilic archaeon Pyrococcus yayanosii. Our results demonstrate that c-di-AMP is synthesized from two molecules of ATP by diadenylate cyclase (DAC) and degraded into pApA and then to AMP by a DHH family phosphodiesterase (PDE). DAC can be activated by a wider variety of ions, using two conserved residues, D188 and E244, to coordinate divalent metal ions, which is different from bacterial CdaA and DisA. PDE possesses a broad substrate spectrum like bacterial DHH family PDEs but shows a stricter base selection between A and G in cyclic dinucleotides hydrolysis. PDE shows differences in substrate binding patches from bacterial counterparts. C-di-AMP was confirmed to exist in Thermococcus kodakarensis cells, and the deletion of the dac or pde gene supports that the synthesis and degradation of c-di-AMP are catalyzed by DAC and PDE, respectively. Our results provide a further understanding of the metabolism of c-di-AMP in archaea.
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Affiliation(s)
- Zheng Jin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Instrumental analysis centerShanghai Jiao Tong UniversityShanghaiChina
| | - Dong Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Wei‐Wei Wang
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghaiChina
| | - Lei Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zheng‐Xin Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hai‐Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiChina
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil EngineeringShanghai Jiao Tong UniversityShanghaiChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)ZhuhaiGuangdongChina
| | - Xi‐Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiChina
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Chaves-Moreira D, Gremski LH, de Moraes FR, Vuitika L, Wille ACM, Hernández González JE, Chaim OM, Senff-Ribeiro A, Arni RK, Veiga SS. Brown Spider Venom Phospholipase-D Activity upon Different Lipid Substrates. Toxins (Basel) 2023; 15:toxins15020109. [PMID: 36828423 PMCID: PMC9965952 DOI: 10.3390/toxins15020109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Brown spider envenomation results in dermonecrosis, characterized by an intense inflammatory reaction. The principal toxins of brown spider venoms are phospholipase-D isoforms, which interact with different cellular membrane components, degrade phospholipids, and generate bioactive mediators leading to harmful effects. The Loxosceles intermedia phospholipase D, LiRecDT1, possesses a loop that modulates the accessibility to the active site and plays a crucial role in substrate. In vitro and in silico analyses were performed to determine aspects of this enzyme's substrate preference. Sphingomyelin d18:1/6:0 was the preferred substrate of LiRecDT1 compared to other Sphingomyelins. Lysophosphatidylcholine 16:0/0:0 was preferred among other lysophosphatidylcholines, but much less than Sphingomyelin d18:1/6:0. In contrast, phosphatidylcholine d18:1/16:0 was not cleaved. Thus, the number of carbon atoms in the substrate plays a vital role in determining the optimal activity of this phospholipase-D. The presence of an amide group at C2 plays a key role in recognition and activity. In silico analyses indicated that a subsite containing the aromatic residues Y228 and W230 appears essential for choline recognition by cation-π interactions. These findings may help to explain why different cells, with different phospholipid fatty acid compositions exhibit distinct susceptibilities to brown spider venoms.
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Affiliation(s)
- Daniele Chaves-Moreira
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Luiza Helena Gremski
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Fábio Rogério de Moraes
- Department of Physics, Multi-User Center for Biomolecular Innovation, State University of São Paulo (UNESP), São Paulo 05315-970, Brazil
| | - Larissa Vuitika
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Ana Carolina Martins Wille
- Department of Structural and Molecular Biology, State University of Ponta Grossa (UEPG), Ponta Grossa 84030-900, Brazil
| | - Jorge Enrique Hernández González
- Department of Physics, Multi-User Center for Biomolecular Innovation, State University of São Paulo (UNESP), São Paulo 05315-970, Brazil
| | - Olga Meiri Chaim
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea Senff-Ribeiro
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Raghuvir Krishnaswamy Arni
- Department of Physics, Multi-User Center for Biomolecular Innovation, State University of São Paulo (UNESP), São Paulo 05315-970, Brazil
| | - Silvio Sanches Veiga
- Department of Cell Biology, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
- Correspondence: ; Tel.: +55-41-3361-1776
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Vít O, Petrák J. Autotaxin and Lysophosphatidic Acid Signalling: the Pleiotropic Regulatory Network in Cancer. Folia Biol (Praha) 2023; 69:149-162. [PMID: 38583176 DOI: 10.14712/fb2023069050149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Autotaxin, also known as ecto-nucleotide pyrophosphatase/phosphodiesterase family member 2, is a secreted glycoprotein that plays multiple roles in human physiology and cancer pathology. This protein, by converting lysophosphatidylcholine into lysophosphatidic acid, initiates a complex signalling cascade with significant biological implications. The article outlines the autotaxin gene and protein structure, expression regulation and physiological functions, but focuses mainly on the role of autotaxin in cancer development and progression. Autotaxin and lysophosphatidic acid signalling influence several aspects of cancer, including cell proliferation, migration, metastasis, therapy resistance, and interactions with the immune system. The potential of autotaxin as a diagnostic biomarker and promising drug target is also examined.
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Affiliation(s)
- Ondřej Vít
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.
| | - Jiří Petrák
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
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10
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Kwiatkowski M, Wong A, Bi C, Gehring C, Jaworski K. Twin cyclic mononucleotide cyclase and phosphodiesterase domain architecture as a common feature in complex plant proteins. Plant Sci 2022; 325:111493. [PMID: 36216295 DOI: 10.1016/j.plantsci.2022.111493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The majority of proteins in both prokaryote and eukaryote proteomes consist of two or more functional centers, which allows for intramolecular tuning of protein functions. Such architecture, as opposed to animal orthologs, applies to the plant cyclases (CNC) and phosphodiesterases (PDEs), the vast majority of which are part of larger multifunctional proteins. In plants, until recently, only two cases of combinations of CNC-PDE in one protein were reported. Here we propose that in plants, multifunctional proteins in which the PDE motif has been identified, the presence of the additional CNC center is common. Searching the Arabidopsis thaliana proteome with a combined PDE-CNC motif allowed the creation of a database of proteins with both activities. One such example is methylenetetrahydrofolate dehydrogenase, in which we determined the activities of adenylate cyclase (AC) and PDE. Based on biochemical and mutagenesis analyses we assessed the impact of the AC and PDE catalytic centers on the dehydrogenase activity. This allowed us to propose additional regulatory mechanism that govern folate metabolism by cAMP. It is therefore conceivable that the combined CNC-PDE architecture is a common regulatory configuration, where control of the level of cyclic nucleotides (cNMP) influences other catalytic activities of the protein.
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Affiliation(s)
- Mateusz Kwiatkowski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100 Toruń, Poland.
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou 325060, Zhejiang Province, China.
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou 325060, Zhejiang Province, China
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy.
| | - Krzysztof Jaworski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100 Toruń, Poland
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11
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Moutoussamy EE, Waheed Q, Binford GJ, Khan HM, Moran SM, Eitel AR, Cordes MHJ, Reuter N. Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage. PLoS Comput Biol 2022; 18:e1009871. [PMID: 35180220 PMCID: PMC8893692 DOI: 10.1371/journal.pcbi.1009871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/03/2022] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lipids with choline head groups such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (Sicarius terrosus, St_βIB1). A structural comparison of available structures of phospholipases D (PLDs) reveals a conserved aromatic cage in the α clade. To test the potential influence of the aromatic cage on membrane-lipid specificity we performed molecular dynamics (MD) simulations of the binding of several PLDs onto lipid bilayers containing choline headgroups; two SicTox from the α clade, Loxosceles intermedia αIA1 (Li_αIA) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the β clade, St_βIB1. The simulation results reveal that the aromatic cage captures a choline-headgroup and suggest that the cage plays a major role in lipid specificity. We also simulated an engineered St_βIB1, where we introduced the aromatic cage, and this led to binding with choline-containing lipids. Moreover, a multiple sequence alignment revealed the conservation of the aromatic cage among the α clade PLDs. Here, we confirmed that the i-face of α and β clade PLDs is involved in their binding to choline and ethanolamine-containing bilayers, respectively. Furthermore, our results suggest a major role in choline lipid recognition of the aromatic cage of the α clade PLDs. The MD simulation results are supported by in vitro liposome binding assay experiments. Envenomation following bites from recluse spiders (Loxosceles) causes loxoscelism, a necrotic tissue breakdown in mammals, and leads to skin degeneration and systemic reactions in the worst case. Recluse spiders belong to the Sicariidae family which also includes six-eyed sand spiders in the genera Sicarius and Hexopthalma. While sicariid spiders are found natively on all continents except Australia, treatments of loxoscelism are typically antibody based and available in some regions of the Americas. Sphingomyelinase D/phospholipase D enzymes are one of the major toxins in venom of sicariid spiders, and have been divided in two clades called α and β. The activity of α and β clades toxins differs; most α clade toxins present high activity against lipids with choline headgroups (-N (CH3)3+) such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (-NH3+). When comparing the structures of two α clade toxins and one β clade toxin, we noticed the presence in the α clade toxins only of a cage consisting of three aromatic amino acids. In this work we used numerical molecular simulations to probe the role of this cage in the preference of α clade toxins for choline head groups over ethanolamine head groups.
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Affiliation(s)
- Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Qaiser Waheed
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Greta J. Binford
- Department of Biology, Lewis and Clark College, Portland, Oregon, United States
| | - Hanif M. Khan
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Shane M. Moran
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Anna R. Eitel
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Matthew H. J. Cordes
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Chemistry, University of Bergen, Bergen, Norway
- * E-mail:
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12
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Salomatina OV, Dyrkheeva NS, Popadyuk II, Zakharenko AL, Ilina ES, Komarova NI, Reynisson J, Salakhutdinov NF, Lavrik OI, Volcho KP. New Deoxycholic Acid Derived Tyrosyl-DNA Phosphodiesterase 1 Inhibitors Also Inhibit Tyrosyl-DNA Phosphodiesterase 2. Molecules 2021; 27:molecules27010072. [PMID: 35011303 PMCID: PMC8746696 DOI: 10.3390/molecules27010072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/04/2022] Open
Abstract
A series of deoxycholic acid (DCA) amides containing benzyl ether groups on the steroid core were tested against the tyrosyl-DNA phosphodiesterase 1 (TDP1) and 2 (TDP2) enzymes. In addition, 1,2,4- and 1,3,4-oxadiazole derivatives were synthesized to study the linker influence between a para-bromophenyl moiety and the steroid scaffold. The DCA derivatives demonstrated promising inhibitory activity against TDP1 with IC50 in the submicromolar range. Furthermore, the amides and the 1,3,4-oxadiazole derivatives inhibited the TDP2 enzyme but at substantially higher concentration. Tryptamide 5 and para-bromoanilide 8 derivatives containing benzyloxy substituent at the C-3 position and non-substituted hydroxy group at C-12 on the DCA scaffold inhibited both TDP1 and TDP2 as well as enhanced the cytotoxicity of topotecan in non-toxic concentration in vitro. According to molecular modeling, ligand 5 is anchored into the catalytic pocket of TDP1 by one hydrogen bond to the backbone of Gly458 as well as by π–π stacking between the indolyl rings of the ligand and Tyr590, resulting in excellent activity. It can therefore be concluded that these derivatives contribute to the development of specific TDP1 and TDP2 inhibitors for adjuvant therapy against cancer in combination with topoisomerase poisons.
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Affiliation(s)
- Oksana V. Salomatina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (N.S.D.); (A.L.Z.); (E.S.I.); (O.I.L.)
| | - Irina I. Popadyuk
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
| | - Alexandra L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (N.S.D.); (A.L.Z.); (E.S.I.); (O.I.L.)
| | - Ekaterina S. Ilina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (N.S.D.); (A.L.Z.); (E.S.I.); (O.I.L.)
| | - Nina I. Komarova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Staffordshire ST5 5BG, UK;
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (N.S.D.); (A.L.Z.); (E.S.I.); (O.I.L.)
| | - Konstantin P. Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
- Correspondence:
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13
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Kwiatkowski M, Wong A, Kozakiewicz-Piekarz A, Gehring C, Jaworski K. In Search of Monocot Phosphodiesterases: Identification of a Calmodulin Stimulated Phosphodiesterase from Brachypodium distachyon. Int J Mol Sci 2021; 22:ijms22179654. [PMID: 34502563 PMCID: PMC8431786 DOI: 10.3390/ijms22179654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022] Open
Abstract
In plants, rapid and reversible biological responses to environmental cues may require complex cellular reprograming. This is enabled by signaling molecules such as the cyclic nucleotide monophosphates (cNMPs) cAMP and cGMP, as well as Ca2+. While the roles and synthesis of cAMP and cGMP in plants are increasingly well-characterized, the “off signal” afforded by cNMP-degrading enzymes, the phosphodiesterases (PDEs), is, however, poorly understood, particularly so in monocots. Here, we identified a candidate PDE from the monocot Brachypodium distachyon (BDPDE1) and showed that it can hydrolyze cNMPs to 5′NMPs but with a preference for cAMP over cGMP in vitro. Notably, the PDE activity was significantly enhanced by Ca2+ only in the presence of calmodulin (CaM), which interacts with BDPDE1, most likely at a predicted CaM-binding site. Finally, based on our biochemical, mutagenesis and structural analyses, we constructed a comprehensive amino acid consensus sequence extracted from the catalytic centers of annotated and/or experimentally validated PDEs across species to enable a broad application of this search motif for the identification of similar active sites in eukaryotes and prokaryotes.
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Affiliation(s)
- Mateusz Kwiatkowski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska St. 1, 87-100 Torun, Poland;
- Correspondence: ; Tel.: +48-56-611-44-56; Fax: +48-56-61-14-772
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, China;
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou 325060, China
| | - Anna Kozakiewicz-Piekarz
- Department of Biomedical and Polymer Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina St. 7, 87-100 Torun, Poland;
| | - Christoph Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX giugno, 74, 06121 Perugia, Italy;
| | - Krzysztof Jaworski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska St. 1, 87-100 Torun, Poland;
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14
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Zhang X, Li M, Yin N, Zhang J. The Expression Regulation and Biological Function of Autotaxin. Cells 2021; 10:cells10040939. [PMID: 33921676 PMCID: PMC8073485 DOI: 10.3390/cells10040939] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
Autotaxin (ATX) is a secreted glycoprotein and functions as a key enzyme to produce extracellular lysophosphatidic acid (LPA). LPA interacts with at least six G protein-coupled receptors, LPAR1-6, on the cell membrane to activate various signal transduction pathways through distinct G proteins, such as Gi/0, G12/13, Gq/11, and Gs. The ATX-LPA axis plays an important role in physiological and pathological processes, including embryogenesis, obesity, and inflammation. ATX is one of the top 40 most unregulated genes in metastatic cancer, and the ATX-LPA axis is involved in the development of different types of cancers, such as colorectal cancer, ovarian cancer, breast cancer, and glioblastoma. ATX expression is under multifaceted controls at the transcription, post-transcription, and secretion levels. ATX and LPA in the tumor microenvironment not only promote cell proliferation, migration, and survival, but also increase the expression of inflammation-related circuits, which results in poor outcomes for patients with cancer. Currently, ATX is regarded as a potential cancer therapeutic target, and an increasing number of ATX inhibitors have been developed. In this review, we focus on the mechanism of ATX expression regulation and the functions of ATX in cancer development.
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Affiliation(s)
| | | | | | - Junjie Zhang
- Correspondence: ; Tel.: +86-10-58802137; Fax: +86-10-58807720
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15
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Gladkova ED, Chepanova AA, Ilina ES, Zakharenko AL, Reynisson J, Luzina OA, Volcho KP, Lavrik OI, Salakhutdinov NF. Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors. Molecules 2021; 26:molecules26071945. [PMID: 33808389 PMCID: PMC8037669 DOI: 10.3390/molecules26071945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
A new type of berberine derivatives was obtained by the reaction of berberrubine with aliphatic sulfonyl chlorides. The new polycyclic compounds have a sultone ring condensed to C and D rings of a protoberberine core. The reaction conditions were developed to facilitate the formation of sultones with high yields without by-product formation. Thus, it was shown that the order of addition of reagents affects the composition of the reaction products: when sulfochlorides are added to berberrubine, their corresponding 9-O-sulfonates are predominantly formed; when berberrubine is added to pre-generated sulfenes, sultones are the only products. The reaction was shown to proceed stereo-selectively and the cycle configuration was confirmed by 2D NMR spectroscopy. The inhibitory activity of the synthesized sultones and their 12-brominated analogs against the DNA-repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1), an important target for a potential antitumor therapy, was studied. All derivatives were active in the micromolar and submicromolar range, in contrast to the acyclic analogs and 9-O-sulfonates, which were inactive. The significance of the sultone cycle and bromine substituent in binding with the enzyme was confirmed using molecular modeling. The active inhibitors are mostly non-toxic to the HeLa cancer cell line, and several ligands show synergy with topotecan, a topoisomerase 1 poison in clinical use. Thus, novel berberine derivatives can be considered as candidates for adjuvant therapy against cancer.
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Affiliation(s)
- Elizaveta D. Gladkova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Ekaterina S. Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK;
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Correspondence: (O.A.L.); (N.F.S.)
| | - Konstantin P. Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
| | - Olga I. Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Correspondence: (O.A.L.); (N.F.S.)
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16
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Lambert MR, Spinazzola JM, Widrick JJ, Pakula A, Conner JR, Chin JE, Owens JM, Kunkel LM. PDE10A Inhibition Reduces the Manifestation of Pathology in DMD Zebrafish and Represses the Genetic Modifier PITPNA. Mol Ther 2020; 29:1086-1101. [PMID: 33221436 PMCID: PMC7934586 DOI: 10.1016/j.ymthe.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/04/2020] [Accepted: 11/15/2020] [Indexed: 12/25/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe genetic disorder caused by mutations in the DMD gene. Absence of dystrophin protein leads to progressive degradation of skeletal and cardiac function and leads to premature death. Over the years, zebrafish have been increasingly used for studying DMD and are a powerful tool for drug discovery and therapeutic development. In our study, a birefringence screening assay led to identification of phosphodiesterase 10A (PDE10A) inhibitors that reduced the manifestation of dystrophic muscle phenotype in dystrophin-deficient sapje-like zebrafish larvae. PDE10A has been validated as a therapeutic target by pde10a morpholino-mediated reduction in muscle pathology and improvement in locomotion, muscle, and vascular function as well as long-term survival in sapje-like larvae. PDE10A inhibition in zebrafish and DMD patient-derived myoblasts were also associated with reduction of PITPNA expression that has been previously identified as a protective genetic modifier in two exceptional dystrophin-deficient golden retriever muscular dystrophy (GRMD) dogs that escaped the dystrophic phenotype. The combination of a phenotypic assay and relevant functional assessments in the sapje-like zebrafish enhances the potential for the prospective discovery of DMD therapeutics. Indeed, our results suggest a new application for a PDE10A inhibitor as a potential DMD therapeutic to be investigated in a mouse model of DMD.
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Affiliation(s)
- Matthias R Lambert
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Janelle M Spinazzola
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey J Widrick
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Pakula
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - James R Conner
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Janice E Chin
- Rare Disease Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Jane M Owens
- Rare Disease Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Louis M Kunkel
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; The Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; The Manton Center for Orphan Disease Research at Boston Children's Hospital, Boston, MA 02115, USA.
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17
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Ikuta T, Shihoya W, Sugiura M, Yoshida K, Watari M, Tokano T, Yamashita K, Katayama K, Tsunoda SP, Uchihashi T, Kandori H, Nureki O. Structural insights into the mechanism of rhodopsin phosphodiesterase. Nat Commun 2020; 11:5605. [PMID: 33154353 PMCID: PMC7644710 DOI: 10.1038/s41467-020-19376-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase and photosensitive adenylyl cyclase. Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The crystal structure of the rhodopsin domain at 2.6 Å resolution revealed a new topology of rhodopsins, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the rhodopsin domain (3.5 Å) and PDE domain (2.1 Å) with their connecting linkers, which showed a rough sketch of the full-length Rh-PDE. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.
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Affiliation(s)
- Tatsuya Ikuta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Kazuho Yoshida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Masahito Watari
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Takaya Tokano
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya, 466-8555, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
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18
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Tian Y, Yang S, Gao S. Advances, Perspectives and Potential Engineering Strategies of Light-Gated Phosphodiesterases for Optogenetic Applications. Int J Mol Sci 2020; 21:E7544. [PMID: 33066112 PMCID: PMC7590022 DOI: 10.3390/ijms21207544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
The second messengers, cyclic adenosine 3'-5'-monophosphate (cAMP) and cyclic guanosine 3'-5'-monophosphate (cGMP), play important roles in many animal cells by regulating intracellular signaling pathways and modulating cell physiology. Environmental cues like temperature, light, and chemical compounds can stimulate cell surface receptors and trigger the generation of second messengers and the following regulations. The spread of cAMP and cGMP is further shaped by cyclic nucleotide phosphodiesterases (PDEs) for orchestration of intracellular microdomain signaling. However, localized intracellular cAMP and cGMP signaling requires further investigation. Optogenetic manipulation of cAMP and cGMP offers new opportunities for spatio-temporally precise study of their signaling mechanism. Light-gated nucleotide cyclases are well developed and applied for cAMP/cGMP manipulation. Recently discovered rhodopsin phosphodiesterase genes from protists established a new and direct biological connection between light and PDEs. Light-regulated PDEs are under development, and of demand to complete the toolkit for cAMP/cGMP manipulation. In this review, we summarize the state of the art, pros and cons of artificial and natural light-regulated PDEs, and discuss potential new strategies of developing light-gated PDEs for optogenetic manipulation.
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Affiliation(s)
| | | | - Shiqiang Gao
- Department of Neurophysiology, Physiological Institute, University of Wuerzburg, 97070 Wuerzburg, Germany; (Y.T.); (S.Y.)
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Dennis ML, Newman J, Dolezal O, Hattarki M, Surjadi RN, Nuttall SD, Pham T, Nebl T, Camerino M, Khoo PS, Monahan BJ, Peat TS. Crystal structures of human ENPP1 in apo and bound forms. Acta Crystallogr D Struct Biol 2020; 76:889-898. [PMID: 32876064 PMCID: PMC7466750 DOI: 10.1107/s2059798320010505] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/31/2020] [Indexed: 11/26/2022] Open
Abstract
Cancer is one of the leading causes of mortality in humans, and recent work has focused on the area of immuno-oncology, in which the immune system is used to specifically target cancerous cells. Ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) is an emerging therapeutic target in human cancers owing to its role in degrading cyclic GMP-AMP (cGAMP), an agonist of the stimulator of interferon genes (STING). The available structures of ENPP1 are of the mouse enzyme, and no structures are available with anything other than native nucleotides. Here, the first X-ray crystal structures of the human ENPP1 enzyme in an apo form, with bound nucleotides and with two known inhibitors are presented. The availability of these structures and a robust crystallization system will allow the development of structure-based drug-design campaigns against this attractive cancer therapeutic target.
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Affiliation(s)
- Matthew L. Dennis
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
- Cancer Therapeutics CRC, Parkville, VIC 3052, Australia
| | - Janet Newman
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Olan Dolezal
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Meghan Hattarki
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Regina N. Surjadi
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Stewart D. Nuttall
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Tam Pham
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Tom Nebl
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Michelle Camerino
- Cancer Therapeutics CRC, Parkville, VIC 3052, Australia
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Poh Sim Khoo
- Cancer Therapeutics CRC, Parkville, VIC 3052, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
| | - Brendon J. Monahan
- Cancer Therapeutics CRC, Parkville, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas S. Peat
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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Czopek A, Partyka A, Bucki A, Pawłowski M, Kołaczkowski M, Siwek A, Głuch-Lutwin M, Koczurkiewicz P, Pękala E, Jaromin A, Tyliszczak B, Wesołowska A, Zagórska A. Impact of N-Alkylamino Substituents on Serotonin Receptor (5-HTR) Affinity and Phosphodiesterase 10A (PDE10A) Inhibition of Isoindole-1,3-dione Derivatives. Molecules 2020; 25:molecules25173868. [PMID: 32854402 PMCID: PMC7504677 DOI: 10.3390/molecules25173868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 11/16/2022] Open
Abstract
In this study, a series of compounds derived from 4-methoxy-1H-isoindole-1,3(2H)-dione, potential ligands of phosphodiesterase 10A and serotonin receptors, were investigated as potential antipsychotics. A library of 4-methoxy-1H-isoindole-1,3(2H)-dione derivatives with various amine moieties was synthesized and examined for their phosphodiesterase 10A (PDE10A)-inhibiting properties and their 5-HT1A and 5-HT7 receptor affinities. Based on in vitro studies, the most potent compound, 18 (2-[4-(1H-benzimidazol-2-yl)butyl]-4-methoxy-1H-isoindole-1,3(2H)-dione), was selected and its safety in vitro was evaluated. In order to explain the binding mode of compound 18 in the active site of the PDE10A enzyme and describe the molecular interactions responsible for its inhibition, computer-aided docking studies were performed. The potential antipsychotic properties of compound 18 in a behavioral model of schizophrenia were also investigated.
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Affiliation(s)
- Anna Czopek
- Department of Medicinal Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Krakow, Poland; (A.B.); (M.P.); (M.K.); (A.Z.)
- Correspondence: ; Tel.: +48-12-620-5450
| | - Anna Partyka
- Department of Clinical Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Krakow, Poland; (A.P.); (A.W.)
| | - Adam Bucki
- Department of Medicinal Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Krakow, Poland; (A.B.); (M.P.); (M.K.); (A.Z.)
| | - Maciej Pawłowski
- Department of Medicinal Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Krakow, Poland; (A.B.); (M.P.); (M.K.); (A.Z.)
| | - Marcin Kołaczkowski
- Department of Medicinal Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Krakow, Poland; (A.B.); (M.P.); (M.K.); (A.Z.)
| | - Agata Siwek
- Department of Pharmacobiology, Jagiellonian University Collegium Medicum, 9 Medyczna Street, 30-688 Krakow, Poland; (A.S.); (M.G.-L.)
| | - Monika Głuch-Lutwin
- Department of Pharmacobiology, Jagiellonian University Collegium Medicum, 9 Medyczna Street, 30-688 Krakow, Poland; (A.S.); (M.G.-L.)
| | - Paulina Koczurkiewicz
- Department of Pharmaceutical Biochemistry, Jagiellonian University Collegium Medicum, 9 Medyczna Street, 30-688 Krakow, Poland; (P.K.); (E.P.)
| | - Elżbieta Pękala
- Department of Pharmaceutical Biochemistry, Jagiellonian University Collegium Medicum, 9 Medyczna Street, 30-688 Krakow, Poland; (P.K.); (E.P.)
| | - Anna Jaromin
- Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, 14a Joliot-Curie, 50-383 Wroclaw, Poland;
| | - Bożena Tyliszczak
- Faculty of Materials Engineering and Physics, Cracow University of Technology, Institute of Materials Science, 24 Warszawska Street, 31-155 Krakow, Poland;
| | - Anna Wesołowska
- Department of Clinical Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Krakow, Poland; (A.P.); (A.W.)
| | - Agnieszka Zagórska
- Department of Medicinal Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Krakow, Poland; (A.B.); (M.P.); (M.K.); (A.Z.)
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21
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Fu Y, Ding X, Zhang X, Shao X, Zhao J, Xu Y, Luo X, Zhao W. Diterpenoids from the Root Bark of Pinus massoniana and Evaluation of Their Phosphodiesterase Type 4D Inhibitory Activity. J Nat Prod 2020; 83:1229-1237. [PMID: 32100544 DOI: 10.1021/acs.jnatprod.9b01269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thirty-two diterpenoids were obtained from the root bark of Pinus massoniana, and, among them, five compounds (pinmassins A-E) were identified as undescribed analogues. Spectroscopic methods, X-ray single-crystal diffraction analysis, and ECD calculations were applied to establish the structure of the new isolates. Pinmassin D (4) and abieta-8,11,13,15-tetraen-18-oic acid (23) showed moderate phosphodiesterase type 4D (PDE4D) inhibitory effects with IC50 values of 2.8 ± 0.18 and 3.3 ± 0.50 μM, respectively, and their binding modes were investigated by a molecular docking study.
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Affiliation(s)
- Yifan Fu
- Department of Natural Products Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiaoyu Ding
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Xianglei Zhang
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Xingcheng Shao
- Department of Natural Products Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jihui Zhao
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Yechun Xu
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Xiaomin Luo
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Weimin Zhao
- Department of Natural Products Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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22
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Gremski LH, da Justa HC, da Silva TP, Polli NLC, Antunes BC, Minozzo JC, Wille ACM, Senff-Ribeiro A, Arni RK, Veiga SS. Forty Years of the Description of Brown Spider Venom Phospholipases-D. Toxins (Basel) 2020; 12:toxins12030164. [PMID: 32155765 PMCID: PMC7150852 DOI: 10.3390/toxins12030164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 01/24/2023] Open
Abstract
Spiders of the genus Loxosceles, popularly known as Brown spiders, are considered a serious public health issue, especially in regions of hot or temperate climates, such as parts of North and South America. Although the venoms of these arachnids are complex in molecular composition, often containing proteins with distinct biochemical characteristics, the literature has primarily described a family of toxins, the Phospholipases-D (PLDs), which are highly conserved in all Loxosceles species. PLDs trigger most of the major clinical symptoms of loxoscelism i.e., dermonecrosis, thrombocytopenia, hemolysis, and acute renal failure. The key role played by PLDs in the symptomatology of loxoscelism was first described 40 years ago, when researches purified a hemolytic toxin that cleaved sphingomyelin and generated choline, and was referred to as a Sphingomyelinase-D, which was subsequently changed to Phospholipase-D when it was demonstrated that the enzyme also cleaved other cellular phospholipids. In this review, we present the information gleaned over the last 40 years about PLDs from Loxosceles venoms especially with regard to the production and characterization of recombinant isoforms. The history of obtaining these toxins is discussed, as well as their molecular organization and mechanisms of interaction with their substrates. We will address cellular biology aspects of these toxins and how they can be used in the development of drugs to address inflammatory processes and loxoscelism. Present and future aspects of loxoscelism diagnosis will be discussed, as well as their biotechnological applications and actions expected for the future in this field.
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Affiliation(s)
- Luiza Helena Gremski
- Departamento de Biologia Celular, Universidade Federal do Paraná (UFPR), Curitiba 81531-980, PR, Brazil; (L.H.G.); (H.C.d.J.); (T.P.d.S.); (N.L.C.P.); (B.C.A.); (A.S.-R.)
| | - Hanna Câmara da Justa
- Departamento de Biologia Celular, Universidade Federal do Paraná (UFPR), Curitiba 81531-980, PR, Brazil; (L.H.G.); (H.C.d.J.); (T.P.d.S.); (N.L.C.P.); (B.C.A.); (A.S.-R.)
| | - Thaís Pereira da Silva
- Departamento de Biologia Celular, Universidade Federal do Paraná (UFPR), Curitiba 81531-980, PR, Brazil; (L.H.G.); (H.C.d.J.); (T.P.d.S.); (N.L.C.P.); (B.C.A.); (A.S.-R.)
| | - Nayanne Louise Costacurta Polli
- Departamento de Biologia Celular, Universidade Federal do Paraná (UFPR), Curitiba 81531-980, PR, Brazil; (L.H.G.); (H.C.d.J.); (T.P.d.S.); (N.L.C.P.); (B.C.A.); (A.S.-R.)
| | - Bruno César Antunes
- Departamento de Biologia Celular, Universidade Federal do Paraná (UFPR), Curitiba 81531-980, PR, Brazil; (L.H.G.); (H.C.d.J.); (T.P.d.S.); (N.L.C.P.); (B.C.A.); (A.S.-R.)
- Centro de Produção e Pesquisa de Imunobiológicos (CPPI), Piraquara 83302-200, PR, Brazil;
| | - João Carlos Minozzo
- Centro de Produção e Pesquisa de Imunobiológicos (CPPI), Piraquara 83302-200, PR, Brazil;
| | - Ana Carolina Martins Wille
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil;
| | - Andrea Senff-Ribeiro
- Departamento de Biologia Celular, Universidade Federal do Paraná (UFPR), Curitiba 81531-980, PR, Brazil; (L.H.G.); (H.C.d.J.); (T.P.d.S.); (N.L.C.P.); (B.C.A.); (A.S.-R.)
| | - Raghuvir Krishnaswamy Arni
- Centro Multiusuário de Inovação Biomolecular, Departamento de Física, Universidade Estadual Paulista (UNESP), São José do Rio Preto 15054-000, SP, Brazil;
| | - Silvio Sanches Veiga
- Departamento de Biologia Celular, Universidade Federal do Paraná (UFPR), Curitiba 81531-980, PR, Brazil; (L.H.G.); (H.C.d.J.); (T.P.d.S.); (N.L.C.P.); (B.C.A.); (A.S.-R.)
- Correspondence: ; Tel.: +55-(41)-3361-1776
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23
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Nie H, Xiao Y, He J, Liu H, Nie L, Chen W, Huang Q. Phenotypic-genotypic analysis of GGDEF/EAL/HD-GYP domain-encoding genes in Pseudomonas putida. Environ Microbiol Rep 2020; 12:38-48. [PMID: 31691501 DOI: 10.1111/1758-2229.12808] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
Cyclic diguanylate (c-di-GMP) is a broadly conserved bacterial signalling molecule that modulates diverse cellular processes, such as biofilm formation, colony morphology and swimming motility. The intracellular level of c-di-GMP is controlled by diguanylate cyclases (DGCs) with GGDEF domain and phosphodiesterases (PDEs) with either EAL or HD-GYP domain. Pseudomonas putida KT2440 has a large group of genes on its genome encoding proteins with GGDEF/EAL/HD-GYP domains. However, phenotypic-genotypic correlation and c-di-GMP metabolism of these genes were largely unknown. Herein, by systematically constructing deletion mutants/overexpression strains of the 42 predicted c-di-GMP metabolism-related genes and analysing the phenotypes, we preliminarily revealed the role of each gene in biofilm formation, colony morphology and swimming motility. Subsequent results from protein sequence alignments and cellular c-di-GMP assessment indicated that 25 out of the 42 genes were likely to encode DGCs, nine genes were predicted to encode PDEs, four genes encoded bifunctional enzymes and the other four genes encoded enzymatically inactive proteins. This study offers a basic understanding of the roles of these 42 genes and can serve as a toolkit for investigators to further elucidate the functions of these GGDEF and EAL/HD-GYP domain-containing proteins.
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Affiliation(s)
- Hailing Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yujie Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinzhi He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huizhong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
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24
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Gerokonstantis DT, Nikolaou A, Magkrioti C, Afantitis A, Aidinis V, Kokotos G, Moutevelis-Minakakis P. Synthesis of novel 2-pyrrolidinone and pyrrolidine derivatives and study of their inhibitory activity against autotaxin enzyme. Bioorg Med Chem 2019; 28:115216. [PMID: 31864778 DOI: 10.1016/j.bmc.2019.115216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022]
Abstract
Autotaxin (ATX), a glycoprotein (~125 kDa) isolated as an autocrine motility factor from melanoma cells, belongs to a seven-membered family of ectonucleotide pyrophosphatase/phosphodiesterase (ENPP), and exhibits lysophospholipase D activity. ATX is responsible for the hydrolysis of lysophosphatidylcholine (LPC) to produce the bioactive lipid lysophosphatidic acid (LPA), which is upregulated in a variety of pathological inflammatory conditions, including fibrosis, cancer, liver toxicity and thrombosis. Given its role in human disease, the ATX-LPA axis is an interesting target for therapy, and the development of novel potent ATX inhibitors is of great importance. In the present work a novel class of ATX inhibitors, optically active derivatives of 2-pyrrolidinone and pyrrolidine heterocycles were synthesized. Some of them exhibited interesting in vitro activity, namely the hydroxamic acid 16 (IC50 700 nM) and the carboxylic acid 40b (IC50 800 nM), while the boronic acid derivatives 3k (IC50 50 nM), 3l (IC50 120 nM), 3 m (IC50 180 nM) and 21 (IC50 35 nM) were found to be potent inhibitors of ATX.
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Affiliation(s)
| | - Aikaterini Nikolaou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Christiana Magkrioti
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Athens 16672, Greece
| | | | - Vassilis Aidinis
- Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Athens 16672, Greece
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Panagiota Moutevelis-Minakakis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
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25
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Boia-Ferreira M, Moreno KG, Basílio ABC, da Silva LP, Vuitika L, Soley B, Wille ACM, Donatti L, Barbaro KC, Chaim OM, Gremski LH, Veiga SS, Senff-Ribeiro A. TCTP from Loxosceles Intermedia (Brown Spider) Venom Contributes to the Allergic and Inflammatory Response of Cutaneous Loxoscelism. Cells 2019; 8:E1489. [PMID: 31766608 PMCID: PMC6953063 DOI: 10.3390/cells8121489] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/07/2019] [Accepted: 11/10/2019] [Indexed: 12/24/2022] Open
Abstract
LiTCTP is a toxin from the Translationally Controlled Tumor Protein (TCTP) family identified in Loxosceles brown spider venoms. These proteins are known as histamine-releasing factors (HRF). TCTPs participate in allergic and anaphylactic reactions, which suggest their potential role as therapeutic targets. The histaminergic effect of TCTP is related to its pro-inflammatory functions. An initial characterization of LiTCTP in animal models showed that this toxin can increase the microvascular permeability of skin vessels and induce paw edema in a dose-dependent manner. We evaluated the role of LiTCTP in vitro and in vivo in the inflammatory and allergic aspects that undergo the biological responses observed in Loxoscelism, the clinical condition after an accident with Loxosceles spiders. Our results showed LiTCTP recombinant toxin (LiRecTCTP) as an essential synergistic factor for the dermonecrotic toxin actions (LiRecDT1, known as the main toxin in the pathophysiology of Loxoscelism), revealing its contribution to the exacerbated inflammatory response clinically observed in envenomated patients.
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Affiliation(s)
- Marianna Boia-Ferreira
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
| | - Kamila G. Moreno
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
| | - Alana B. C. Basílio
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
| | - Lucas P. da Silva
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
| | - Larissa Vuitika
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
| | - Bruna Soley
- Department of Pharmacology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil;
| | - Ana Carolina M. Wille
- Department of Structural and Molecular Biology, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil;
| | - Lucélia Donatti
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
| | - Katia C. Barbaro
- Laboratory of Immunopathology, Butantan Institute, São Paulo 05503-900, SP, Brazil;
| | - Olga M. Chaim
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Luiza Helena Gremski
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
| | - Silvio S. Veiga
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
| | - Andrea Senff-Ribeiro
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil; (M.B.-F.); (K.G.M.); (A.B.C.B.); (L.P.d.S.); (L.V.); (L.D.); or (L.H.G.); (S.S.V.)
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Onyedibe KI, Wang M, Sintim HO. ENPP1, an Old Enzyme with New Functions, and Small Molecule Inhibitors-A STING in the Tale of ENPP1. Molecules 2019; 24:molecules24224192. [PMID: 31752288 PMCID: PMC6891441 DOI: 10.3390/molecules24224192] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 11/16/2022] Open
Abstract
Ectonucleotide pyrophosphatase/phosphodiesterase I (ENPP1) was identified several decades ago as a type II transmembrane glycoprotein with nucleotide pyrophosphatase and phosphodiesterase enzymatic activities, critical for purinergic signaling. Recently, ENPP1 has emerged as a critical phosphodiesterase that degrades the stimulator of interferon genes (STING) ligand, cyclic GMP-AMP (cGAMP). cGAMP or analogs thereof have emerged as potent immunostimulatory agents, which have potential applications in immunotherapy. This emerging role of ENPP1 has placed this "old" enzyme at the frontier of immunotherapy. This review highlights the roles played by ENPP1, the mechanism of cGAMP hydrolysis by ENPP1, and small molecule inhibitors of ENPP1 with potential applications in diverse disease states, including cancer.
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Affiliation(s)
- Kenneth I. Onyedibe
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA; (K.I.O.); (M.W.)
- Purdue Institute for Inflammation, Immunology, and Infectious Diseases, West Lafayette, IN 47907, USA
| | - Modi Wang
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA; (K.I.O.); (M.W.)
| | - Herman O. Sintim
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA; (K.I.O.); (M.W.)
- Purdue Institute for Inflammation, Immunology, and Infectious Diseases, West Lafayette, IN 47907, USA
- Purdue University Center for Cancer Research, West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +1-(765)-496-6078; Fax: +1-(765)-494-0239
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27
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Lee MH, Lee DY, Balupuri A, Jeong JW, Kang NS. Pharmacophoric Site Identification and Inhibitor Design for Autotaxin. Molecules 2019; 24:molecules24152808. [PMID: 31374894 PMCID: PMC6696049 DOI: 10.3390/molecules24152808] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 02/06/2023] Open
Abstract
Autotaxin (ATX) is a potential drug target that is associated with inflammatory diseases and various cancers. In our previous studies, we have designed several inhibitors targeting ATX using computational and experimental approaches. Here, we have analyzed topological water networks (TWNs) in the binding pocket of ATX. TWN analysis revealed a pharmacophoric site inside the pocket. We designed and synthesized compounds considering the identified pharmacophoric site. Furthermore, we performed biological experiments to determine their ATX inhibitory activities. High potency of the designed compounds supports the predictions of the TWN analysis.
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Affiliation(s)
- Myeong Hwi Lee
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Dae-Yon Lee
- LegoChem Biosciences, Inc., 8-26 Munoyeongseo-ro, Daedeok-gu, Daejeon 34302, Korea
| | - Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Jong-Woo Jeong
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
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28
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Abstract
Molecular mechanisms of dark-to-light state transitions in flavoprotein photoreceptors have been the subject of intense investigation. Blue-light sensing flavoproteins fall into three general classes that share aspects of their activation processes: LOV domains, BLUF proteins, and cryptochromes. In all cases, light-induced changes in flavin redox, protonation, and bonding states result in hydrogen-bond and conformational rearrangements important for regulation of downstream targets. Physical characterization of these flavoprotein states can provide valuable insights into biological function, but clear conclusions are often challenging to draw owing to complexities of data collection and interpretation. In this chapter, we briefly review the three classes of flavoprotein photoreceptors and provide methods for their recombinant production, reconstitution with flavin cofactor, and characterization. We then relate best practices and special considerations for the application of several types of spectroscopies, redox potential measurements, and X-ray scattering experiments to photosensitive flavoproteins. The methods presented are generally accessible to most laboratories.
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Affiliation(s)
- Estella F Yee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | | | - Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States.
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29
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Nomura Y, Roston D, Montemayor EJ, Cui Q, Butcher SE. Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1. Nucleic Acids Res 2018; 46:11488-11501. [PMID: 30215753 PMCID: PMC6265477 DOI: 10.1093/nar/gky812] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 01/08/2023] Open
Abstract
Post-transcriptional modification of snRNA is central to spliceosome function. Usb1 is an exoribonuclease that shortens the oligo-uridine tail of U6 snRNA, resulting in a terminal 2',3' cyclic phosphate group in most eukaryotes, including humans. Loss of function mutations in human Usb1 cause the rare disorder poikiloderma with neutropenia (PN), and result in U6 snRNAs with elongated 3' ends that are aberrantly adenylated. Here, we show that human Usb1 removes 3' adenosines with 20-fold greater efficiency than uridines, which explains the presence of adenylated U6 snRNAs in cells lacking Usb1. We determined three high-resolution co-crystal structures of Usb1: wild-type Usb1 bound to the substrate analog adenosine 5'-monophosphate, and an inactive mutant bound to RNAs with a 3' terminal adenosine and uridine. These structures, along with QM/MM MD simulations of the catalytic mechanism, illuminate the molecular basis for preferential deadenylation of U6 snRNA. The extent of Usb1 processing is influenced by the secondary structure of U6 snRNA.
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Affiliation(s)
- Yuichiro Nomura
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Daniel Roston
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric J Montemayor
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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30
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Döhler C, Zebisch M, Krinke D, Robitzki A, Sträter N. Crystallization of ectonucleotide phosphodiesterase/pyrophosphatase-3 and orientation of the SMB domains in the full-length ectodomain. Acta Crystallogr F Struct Biol Commun 2018; 74:696-703. [PMID: 30387774 PMCID: PMC6213977 DOI: 10.1107/s2053230x18011111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 08/03/2018] [Indexed: 11/11/2022] Open
Abstract
Ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3, ENPP3) is an ATP-hydrolyzing glycoprotein that is located in the extracellular space. The full-length ectodomain of rat NPP3 was expressed in HEK293S GntI- cells, purified using two chromatographic steps and crystallized. Its structure at 2.77 Å resolution reveals that the active-site zinc ions are missing and a large part of the active site and the surrounding residues are flexible. The SMB-like domains have the same orientation in all four molecules in the asymmetric unit. The SMB2 domain is oriented as in NPP2, but the SMB1 domain does not interact with the PDE domain but extends further away from the PDE domain. Deletion of the SMB domains resulted in crystals that diffracted to 2.4 Å resolution and are suitable for substrate-binding studies.
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Affiliation(s)
- Christoph Döhler
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Matthias Zebisch
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
- Division of Structural Biology, Evotec, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, England
| | - Dana Krinke
- Division of Molecular Biological–Biochemical Processing Technology, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Andrea Robitzki
- Division of Molecular Biological–Biochemical Processing Technology, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
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31
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Li-Zhulanov NS, Zakharenko AL, Chepanova AA, Patel J, Zafar A, Volcho KP, Salakhutdinov NF, Reynisson J, Leung IKH, Lavrik OI. A Novel Class of Tyrosyl-DNA Phosphodiesterase 1 Inhibitors That Contains the Octahydro-2 H-chromen-4-ol Scaffold. Molecules 2018; 23:E2468. [PMID: 30261631 PMCID: PMC6222798 DOI: 10.3390/molecules23102468] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/25/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that mends topoisomerase 1-mediated DNA damage. Tdp1 is a current inhibition target for the development of improved anticancer treatments, as its inhibition may enhance the therapeutic effect of topoisomerase 1 poisons. Here, we report a study on the development of a novel class of Tdp1 inhibitors that is based on the octahydro-2H-chromene scaffold. Inhibition and binding assays revealed that these compounds are potent inhibitors of Tdp1, with IC50 and KD values in the low micromolar concentration range. Molecular modelling predicted plausible conformations of the active ligands, blocking access to the enzymatic machinery of Tdp1. Our results thus help establish a structural-activity relationship for octahydro-2H-chromene-based Tdp1 inhibitors, which will be useful for future Tdp1 inhibitor development work.
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Affiliation(s)
- Nikolai S Li-Zhulanov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
| | - Arina A Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Ayesha Zafar
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Konstantin P Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Nariman F Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Olga I Lavrik
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
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32
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Damm M, Hempel BF, Nalbantsoy A, Süssmuth RD. Comprehensive Snake Venomics of the Okinawa Habu Pit Viper, Protobothrops flavoviridis, by Complementary Mass Spectrometry-Guided Approaches. Molecules 2018; 23:molecules23081893. [PMID: 30060607 PMCID: PMC6222445 DOI: 10.3390/molecules23081893] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 11/16/2022] Open
Abstract
The Asian world is home to a multitude of venomous and dangerous snakes, which are used to induce various medical effects in the preparation of traditional snake tinctures and alcoholics, like the Japanese snake wine, named Habushu. The aim of this work was to perform the first quantitative proteomic analysis of the Protobothrops flavoviridis pit viper venom. Accordingly, the venom was analyzed by complimentary bottom-up and top-down mass spectrometry techniques. The mass spectrometry-based snake venomics approach revealed that more than half of the venom is composed of different phospholipases A2 (PLA₂). The combination of this approach and an intact mass profiling led to the identification of the three main Habu PLA₂s. Furthermore, nearly one-third of the total venom consists of snake venom metalloproteinases and disintegrins, and several minor represented toxin families were detected: C-type lectin-like proteins (CTL), cysteine-rich secretory proteins (CRISP), snake venom serine proteases (svSP), l-amino acid oxidases (LAAO), phosphodiesterase (PDE) and 5'-nucleotidase. Finally, the venom of P. flavoviridis contains certain bradykinin-potentiating peptides and related peptides, like the svMP inhibitors, pEKW, pEQW, pEEW and pENW. In preliminary MTT cytotoxicity assays, the highest cancerous-cytotoxicity of crude venom was measured against human neuroblastoma SH-SY5Y cells and shows disintegrin-like effects in some fractions.
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Affiliation(s)
- Maik Damm
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany.
| | | | - Ayse Nalbantsoy
- Department of Bioengineering, Ege University, 35100 Izmir, Turkey.
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33
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Rehman I, Basu SM, Das SK, Bhattacharjee S, Ghosh A, Pommier Y, Das BB. PRMT5-mediated arginine methylation of TDP1 for the repair of topoisomerase I covalent complexes. Nucleic Acids Res 2018; 46:5601-5617. [PMID: 29718323 PMCID: PMC6009676 DOI: 10.1093/nar/gky291] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 03/18/2018] [Accepted: 04/13/2018] [Indexed: 01/01/2023] Open
Abstract
Human tyrosyl-DNA phosphodiesterases (TDP) hydrolyze the phosphodiester bond between DNA and the catalytic tyrosine of Top1 to excise topoisomerase I cleavage complexes (Top1cc) that are trapped by camptothecin (CPT) and by genotoxic DNA alterations. Here we show that the protein arginine methyltransferase PRMT5 enhances the repair of Top1cc by direct binding to TDP1 and arginine dimethylation of TDP1 at residues R361 and R586. Top1-induced replication-mediated DNA damage induces TDP1 arginine methylation, enhancing its 3'- phosphodiesterase activity. TDP1 arginine methylation also increases XRCC1 association with TDP1 in response to CPT, and the recruitment of XRCC1 to Top1cc DNA damage foci. PRMT5 knockdown cells exhibit defective TDP1 activity with marked elevation in replication-coupled CPT-induced DNA damage and lethality. Finally, methylation of R361 and R586 stimulate TDP1 repair function and promote cell survival in response to CPT. Together, our findings provide evidence for the importance of PRMT5 for the post-translational regulation of TDP1 and repair of Top1cc.
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Affiliation(s)
- Ishita Rehman
- Laboratory of Molecular Biology, Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Suparna M Basu
- Laboratory of Molecular Biology, Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Subhendu K Das
- Laboratory of Molecular Biology, Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sangheeta Bhattacharjee
- Laboratory of Molecular Biology, Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Arijit Ghosh
- Laboratory of Molecular Biology, Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - Benu Brata Das
- Laboratory of Molecular Biology, Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
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Yang L, Yin Z, Zhang X, Feng W, Xiao Y, Zhang H, Zheng X, Zhang Z. New findings on phosphodiesterases, MoPdeH and MoPdeL, in Magnaporthe oryzae revealed by structural analysis. Mol Plant Pathol 2018; 19:1061-1074. [PMID: 28752677 PMCID: PMC6638029 DOI: 10.1111/mpp.12586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/27/2017] [Accepted: 07/22/2017] [Indexed: 05/29/2023]
Abstract
The cyclic adenosine monophosphate (cAMP) signalling pathway mediates signal communication and sensing during infection-related morphogenesis in eukaryotes. Many studies have implicated cAMP as a critical mediator of appressorium development in the rice blast fungus, Magnaporthe oryzae. The cAMP phosphodiesterases, MoPdeH and MoPdeL, as key regulators of intracellular cAMP levels, play pleiotropic roles in cell wall integrity, cellular morphology, appressorium formation and infectious growth in M. oryzae. Here, we analysed the roles of domains of MoPdeH and MoPdeL separately or in chimeras. The results indicated that the HD and EAL domains of MoPdeH are indispensable for its phosphodiesterase activity and function. Replacement of the MoPdeH HD domain with the L1 and L2 domains of MoPdeL, either singly or together, resulted in decreased cAMP hydrolysis activity of MoPdeH. All of the transformants exhibited phenotypes similar to that of the ΔMopdeH mutant, but also revealed that EAL and L1 play additional roles in conidiation, and that L1 is involved in infectious growth. We further found that the intracellular cAMP level is important for surface signal recognition and hyphal autolysis. The intracellular cAMP level negatively regulates Mps1-MAPK and positively regulates Pmk1-MAPK in the rice blast fungus. Our results provide new information to better understand the cAMP signalling pathway in the development, differentiation and plant infection of the fungus.
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Affiliation(s)
- Li‐Na Yang
- Department of Plant PathologyKey Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural UniversityNanjing 210095China
| | - Ziyi Yin
- Department of Plant PathologyKey Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural UniversityNanjing 210095China
| | - Xi Zhang
- Department of Plant PathologyKey Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural UniversityNanjing 210095China
| | - Wanzhen Feng
- Department of Plant PathologyKey Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural UniversityNanjing 210095China
| | - Yuhan Xiao
- Department of Plant PathologyKey Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural UniversityNanjing 210095China
| | - Haifeng Zhang
- Department of Plant PathologyKey Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural UniversityNanjing 210095China
| | - Xiaobo Zheng
- Department of Plant PathologyKey Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural UniversityNanjing 210095China
| | - Zhengguang Zhang
- Department of Plant PathologyKey Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural UniversityNanjing 210095China
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Abstract
Posttranslational modifications are covalent changes made to proteins that typically alter the function or location of the protein. AMPylation is an emerging posttranslational modification that involves the addition of adenosine monophosphate (AMP) to a protein. Like other, more well-studied posttranslational modifications, AMPylation is predicted to regulate the activity of the modified target proteins. However, the scope of this modification both in bacteria and in eukaryotes remains to be fully determined. In this review, we provide an up to date overview of the known AMPylating enzymes, the regulation of these enzymes, and the effect of this modification on target proteins.
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Affiliation(s)
- Amanda K. Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
- Howard Hughes Medical Institute, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
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36
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She S, Yang M, Hu H, Hu P, Yang Y, Ren H. Proteomics Based Identification of Autotaxin As An Anti-Hepatitis B Virus Factor and a Promoter of Hepatoma Cell Invasion and Migration. Cell Physiol Biochem 2018; 45:744-760. [PMID: 29414802 DOI: 10.1159/000487166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/14/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Hepatitis B virus (HBV) infection is a major cause of cirrhosis and hepatocellular carcinoma. Therefore, we aimed to obtain further information on HBV pathogenesis, and to search for novel putative molecules for anti-HBV therapy. METHODS We utilized Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) to identify the secretory proteins that are differentially expressed in the HBV DNA-transfected HepG2.2.15 cell line and its parental HepG2 cell line. Immunohistochemistry (IHC) was employed to assess the clinical relevance of the observations. Small interfering (si)RNA-based silencing transfection methods were carried out to study the function of ENPP2. RESULTS Totally, 133 unique proteins were identified as differentially expressed in HepG2.2.15 cell line compared with HepG2 cell line. Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 precursor (ENPP2) is one of the most significantly up-regulated secretory proteins associated with HBV replication. This differential expression of ENPP2 was further validated by real-time quantitative RT-PCR, Western Blot and immunohistochemical analysis. To study the function of ENPP2, we knockdown ENPP2 expression in HepG2.2.15 cell line by RNA interference. ENPP2 silencing increased HBV replication approximately 2.3-fold by enhancing, via the type I IFN signaling pathway, HBV cccDNA (covalently closed circular DNA) translation into viral RNA. Moreover, attenuation of ENPP2 expression inhibited both the invasion and migration ability of hepatoma cells in vitro via interacting with the molecules in the tumor microenvironment. CONCLUSION Our study demonstrates that ENPP2 may be a novel anti-HBV target and indicate that suppression of its expression may inhibit the invasion and migration ability of hepatoma cells.
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Flett FJ, Ruksenaite E, Armstrong LA, Bharati S, Carloni R, Morris ER, Mackay CL, Interthal H, Richardson JM. Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1. Nat Commun 2018; 9:24. [PMID: 29295983 PMCID: PMC5750209 DOI: 10.1038/s41467-017-02530-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/06/2017] [Indexed: 11/15/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA 3'-end processing enzyme that repairs topoisomerase 1B-induced DNA damage. We use a new tool combining site-specific DNA-protein cross-linking with mass spectrometry to identify Tdp1 interactions with DNA. A conserved phenylalanine (F259) of Tdp1, required for efficient DNA processing in biochemical assays, cross-links to defined positions in DNA substrates. Crystal structures of Tdp1-DNA complexes capture the DNA repair machinery after 3'-end cleavage; these reveal how Tdp1 coordinates the 3'-phosphorylated product of nucleosidase activity and accommodates duplex DNA. A hydrophobic wedge splits the DNA ends, directing the scissile strand through a channel towards the active site. The F259 side-chain stacks against the -3 base pair, delimiting the junction of duplexed and melted DNA, and fixes the scissile strand in the channel. Our results explain why Tdp1 cleavage is non-processive and provide a molecular basis for DNA 3'-end processing by Tdp1.
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Affiliation(s)
- Fiona J Flett
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Emilija Ruksenaite
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Lee A Armstrong
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Shipra Bharati
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Roberta Carloni
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Elizabeth R Morris
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Heidrun Interthal
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK.
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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García AM, Brea J, González-García A, Pérez C, Cadavid MI, Loza MI, Martinez A, Gil C. Targeting PDE10A GAF Domain with Small Molecules: A Way for Allosteric Modulation with Anti-Inflammatory Effects. Molecules 2017; 22:molecules22091472. [PMID: 28869560 PMCID: PMC6151459 DOI: 10.3390/molecules22091472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/01/2017] [Accepted: 09/01/2017] [Indexed: 11/16/2022] Open
Abstract
Phosphodiesterase (PDE) enzymes regulate the levels of cyclic nucleotides, cAMP, and/or cGMP, being attractive therapeutic targets. In order to modulate PDE activity in a selective way, we focused our efforts on the search of allosteric modulators. Based on the crystal structure of the PDE10A GAF-B domain, a virtual screening study allowed the discovery of new hits that were also tested experimentally, showing inhibitory activities in the micromolar range. Moreover, these new PDE10A inhibitors were able to decrease the nitrite production in LPS-stimulated cells, thus demonstrating their potential as anti-inflammatory agents.
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Affiliation(s)
- Ana M García
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - José Brea
- Instituto de Farmacia Industrial, Facultad de Farmacia, Universidad de Santiago de Compostela, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain.
| | - Alejandro González-García
- Instituto de Farmacia Industrial, Facultad de Farmacia, Universidad de Santiago de Compostela, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain.
| | - Concepción Pérez
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain.
| | - María Isabel Cadavid
- Instituto de Farmacia Industrial, Facultad de Farmacia, Universidad de Santiago de Compostela, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain.
| | - María Isabel Loza
- Instituto de Farmacia Industrial, Facultad de Farmacia, Universidad de Santiago de Compostela, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain.
| | - Ana Martinez
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Carmen Gil
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
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Tulsian NK, Krishnamurthy S, Anand GS. Channeling of cAMP in PDE-PKA Complexes Promotes Signal Adaptation. Biophys J 2017; 112:2552-2566. [PMID: 28636912 PMCID: PMC5479052 DOI: 10.1016/j.bpj.2017.04.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/29/2017] [Accepted: 04/06/2017] [Indexed: 01/21/2023] Open
Abstract
Spatiotemporal control of the cAMP signaling pathway is governed by both hormonal stimulation of cAMP generation by adenylyl cyclases (activation phase) and cAMP hydrolysis by phosphodiesterases (PDEs) (termination phase). The termination phase is initiated by PDEs actively targeting the protein kinase A (PKA) R-subunit through formation of a PDE-PKAR-cyclic adenosine monophosphate (cAMP) complex (the termination complex). Our results using PDE8 as a model PDE, reveal that PDEs mediate active hydrolysis of cAMP bound to its receptor RIα by enhancing the enzymatic activity. This accelerated cAMP turnover occurs via formation of a stable PDE8-RIα complex, where the protein-protein interface forms peripheral contacts and the central ligand cements this ternary interaction. The basis for enhanced catalysis is active translocation of cAMP from its binding site on RIα to the hydrolysis site on PDE8 through direct "channeling." Our results reveal cAMP channeling in the PDE8-RIα complex and a molecular description of how this channel facilitates processive hydrolysis of unbound cAMP. Thus, unbound cAMP maintains the PDE8-RIα complex while being hydrolyzed, revealing an undiscovered mode for amplification of PKA activity by cAMP-mediated sequestration of the R-subunit by PDEs. This novel regulatory mode explains the paradox of cAMP signal amplification by accelerated PDE-mediated cAMP turnover. This highlights how target effector proteins of small-molecule ligands can promote enzyme-mediated ligand hydrolysis by scaffolding effects. Enhanced activity of the PDE8-RIα complex facilitates robust desensitization, allowing the cell to respond to dynamic levels of cAMP rather than steady-state levels. The PDE8-RIα complex represents a new class of PDE-based complexes for specific drug discovery targeting the cAMP signaling pathway.
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Affiliation(s)
- Nikhil Kumar Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Srinath Krishnamurthy
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Röhrig T, Liesenfeld D, Richling E. Identification of a Phosphodiesterase-Inhibiting Fraction from Roasted Coffee (Coffea arabica) through Activity-Guided Fractionation. J Agric Food Chem 2017; 65:3792-3800. [PMID: 28443667 DOI: 10.1021/acs.jafc.6b05613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent reports that coffee can significantly inhibit cAMP phosphodiesterases (PDEs) in vitro, as well as in vivo, have described another beneficial effect of coffee consumption. However, the PDE-inhibiting substances remain mostly unknown. We chose activity-guided fractionation and an in vitro test system to identify the coffee components that are responsible for PDE inhibition. This approach indicated that a fraction of melanoidins reveals strong PDE-inhibiting potential (IC50 = 130 ± 42 μg/mL). These melanoidins were characterized as water-soluble, low-molecular weight melanoidins (<3 kDa) with a nitrogen content of 4.2% and a carbohydrate content lower than those of other melanoidins. Fractions containing known PDE inhibitors such as chlorogenic acids, alkylpyrazines, or trigonelline as well as N-caffeoyl-tryptophan and N-p-coumaroyl-tryptophan did not exert PDE-inhibiting activity. We also observed that the known PDE inhibitor caffeine does not contribute to the PDE-inhibiting effects of coffee.
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Affiliation(s)
- Teresa Röhrig
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schroedinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - David Liesenfeld
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schroedinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Elke Richling
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schroedinger-Straße 52, D-67663 Kaiserslautern, Germany
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41
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Shimizu T. [Structure and function relationships of a heme sensor, HRI, and heme-based oxygen sensors, EcDOS, YddV and AfGcHK, and related heme sensors]. Seikagaku 2017; 89:176-188. [PMID: 29624980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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Knott EP, Assi M, Rao SNR, Ghosh M, Pearse DD. Phosphodiesterase Inhibitors as a Therapeutic Approach to Neuroprotection and Repair. Int J Mol Sci 2017; 18:E696. [PMID: 28338622 PMCID: PMC5412282 DOI: 10.3390/ijms18040696] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/10/2017] [Accepted: 03/15/2017] [Indexed: 12/21/2022] Open
Abstract
A wide diversity of perturbations of the central nervous system (CNS) result in structural damage to the neuroarchitecture and cellular defects, which in turn are accompanied by neurological dysfunction and abortive endogenous neurorepair. Altering intracellular signaling pathways involved in inflammation and immune regulation, neural cell death, axon plasticity and remyelination has shown therapeutic benefit in experimental models of neurological disease and trauma. The second messengers, cyclic adenosine monophosphate (cyclic AMP) and cyclic guanosine monophosphate (cyclic GMP), are two such intracellular signaling targets, the elevation of which has produced beneficial cellular effects within a range of CNS pathologies. The only known negative regulators of cyclic nucleotides are a family of enzymes called phosphodiesterases (PDEs) that hydrolyze cyclic nucleotides into adenosine monophosphate (AMP) or guanylate monophosphate (GMP). Herein, we discuss the structure and physiological function as well as the roles PDEs play in pathological processes of the diseased or injured CNS. Further we review the approaches that have been employed therapeutically in experimental paradigms to block PDE expression or activity and in turn elevate cyclic nucleotide levels to mediate neuroprotection or neurorepair as well as discuss both the translational pathway and current limitations in moving new PDE-targeted therapies to the clinic.
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Affiliation(s)
- Eric P Knott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA.
| | - Mazen Assi
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Sudheendra N R Rao
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Mousumi Ghosh
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Department of Neurological Surgery, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Damien D Pearse
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Department of Neurological Surgery, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Neuroscience Program, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Interdisciplinary Stem Cell Institute, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- Bruce Wayne Carter Department of Veterans Affairs Medical Center, Miami, FL 33136, USA.
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Halder AK, Amin SA, Jha T, Gayen S. Insight into the structural requirements of pyrimidine-based phosphodiesterase 10A (PDE10A) inhibitors by multiple validated 3D QSAR approaches. SAR QSAR Environ Res 2017; 28:253-273. [PMID: 28322591 DOI: 10.1080/1062936x.2017.1302991] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/02/2017] [Indexed: 06/06/2023]
Abstract
Schizophrenia is a complex disorder of thinking and behaviour (0.3-0.7% of the population is affected). The over-expression of phosphodiesterase 10A (PDE10A) enzyme may be a potential target for schizophrenia and Huntington's disease. Because 3D QSAR analysis is one of the most frequently used modelling techniques, in the present study, five different 3D QSAR tools, namely CoMFA, CoMSIA, kNN-MFA, Open3DQSAR and topomer CoMFA methods, were used on a dataset of pyrimidine-based PDE10A inhibitors. All developed models were validated internally and externally. The non-commercial Open3DQSAR produced the best statistical results amongst 3D QSAR tools. The structural interpretations obtained from different methods were thoroughly analysed and were justified on the basis of information obtained from the crystal structure. Information from one method was mostly validated by the results of other methods and vice versa. In the current work, the use of multiple tools in the same analysis revealed more complete information about the structural requirements of these compounds. On the basis of the observations of the 3D QSAR studies, 12 new compounds were designed for better PDE10A inhibitory activity. The current investigation may help in further designing new PDE10A inhibitors with promising activity.
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Affiliation(s)
- A K Halder
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
| | - S A Amin
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
- b Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University (A Central University) , Sagar , India
| | - T Jha
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
| | - S Gayen
- b Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University (A Central University) , Sagar , India
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Matsubara FH, Meissner GO, Herzig V, Justa HC, Dias BCL, Trevisan-Silva D, Gremski LH, Gremski W, Senff-Ribeiro A, Chaim OM, King GF, Veiga SS. Insecticidal activity of a recombinant knottin peptide from Loxosceles intermedia venom and recognition of these peptides as a conserved family in the genus. Insect Mol Biol 2017; 26:25-34. [PMID: 27743460 DOI: 10.1111/imb.12268] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Loxosceles intermedia venom comprises a complex mixture of proteins, glycoproteins and low molecular mass peptides that act synergistically to immobilize envenomed prey. Analysis of a venom-gland transcriptome from L. intermedia revealed that knottins, also known as inhibitor cystine knot peptides, are the most abundant class of toxins expressed in this species. Knottin peptides contain a particular arrangement of intramolecular disulphide bonds, and these peptides typically act upon ion channels or receptors in the insect nervous system, triggering paralysis or other lethal effects. Herein, we focused on a knottin peptide with 53 amino acid residues from L. intermedia venom. The recombinant peptide, named U2 -sicaritoxin-Li1b (Li1b), was obtained by expression in the periplasm of Escherichia coli. The recombinant peptide induced irreversible flaccid paralysis in sheep blowflies. We screened for knottin-encoding sequences in total RNA extracts from two other Loxosceles species, Loxosceles gaucho and Loxosceles laeta, which revealed that knottin peptides constitute a conserved family of toxins in the Loxosceles genus. The insecticidal activity of U2 -SCTX-Li1b, together with the large number of knottin peptides encoded in Loxosceles venom glands, suggests that studies of these venoms might facilitate future biotechnological applications of these toxins.
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Affiliation(s)
- F H Matsubara
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
| | - G O Meissner
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - V Herzig
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - H C Justa
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
| | - B C L Dias
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
| | - D Trevisan-Silva
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
| | - L H Gremski
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
| | - W Gremski
- Health and Biological Science Institute, Catholic University of Parana, Prado Velho, Curitiba, Paraná, Brazil
| | - A Senff-Ribeiro
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
| | - O M Chaim
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
| | - G F King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - S S Veiga
- Department of Cell Biology, Federal University of Parana, Jardim das Américas, Curitiba, Paraná, Brazil
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Abstract
The 2H phosphoesterase family contains enzymes with two His-X-Ser/Thr motifs in the active site. 2H enzymes are found in all kingdoms of life, sharing little sequence identity despite the conserved overall fold and active site. For many 2H enzymes, the physiological function is unknown. Here, we studied the structure of the 2H family member LigT from Escherichia coli both in the apo form and complexed with different active-site ligands, including ATP, 2′-AMP, 3′-AMP, phosphate, and NADP+. Comparisons to the well-characterized vertebrate myelin enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase) highlight specific features of the catalytic cycle and substrate recognition in both enzymes. The role played by the helix α7, unique to CNPases within the 2H family, is apparently taken over by Arg130 in the bacterial enzyme. Other residues and loops lining the active site groove are likely to be important for RNA substrate binding. We visualized conformational changes related to ligand binding, as well as the position of the nucleophilic water molecule. We also present a low-resolution model of E. coli LigT bound to tRNA in solution, and provide a model for RNA binding by LigT, involving flexible loops lining the active site cavity. Taken together, our results both aid in understanding the common features of 2H family enzymes and help highlight the distinct features in the 2H family members, which must result in different reaction mechanisms. Unique aspects in different 2H family members can be observed in ligand recognition and binding, and in the coordination of the nucleophilic water molecule and the reactive phosphate moiety.
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Affiliation(s)
- Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
- * E-mail:
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Kasahara M, Suetsugu N, Urano Y, Yamamoto C, Ohmori M, Takada Y, Okuda S, Nishiyama T, Sakayama H, Kohchi T, Takahashi F. An adenylyl cyclase with a phosphodiesterase domain in basal plants with a motile sperm system. Sci Rep 2016; 6:39232. [PMID: 27982074 PMCID: PMC5159850 DOI: 10.1038/srep39232] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/18/2016] [Indexed: 01/03/2023] Open
Abstract
Adenylyl cyclase (AC), which produces the signalling molecule cAMP, has numerous important cellular functions in diverse organisms from prokaryotes to eukaryotes. Here we report the identification and characterization of an AC gene from the liverwort Marchantia polymorpha. The encoded protein has both a C-terminal AC catalytic domain similar to those of class III ACs and an N-terminal cyclic nucleotide phosphodiesterase (PDE) domain that degrades cyclic nucleotides, thus we designated the gene MpCAPE (COMBINED AC with PDE). Biochemical analyses of recombinant proteins showed that MpCAPE has both AC and PDE activities. In MpCAPE-promoter-GUS lines, GUS activity was specifically detected in the male sexual organ, the antheridium, suggesting MpCAPE and thus cAMP signalling may be involved in the male reproductive process. CAPE orthologues are distributed only in basal land plants and charophytes that use motile sperm as the male gamete. CAPE is a subclass of class III AC and may be important in male organ and cell development in basal plants.
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Affiliation(s)
- Masahiro Kasahara
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Urano
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Chiaki Yamamoto
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Mikiya Ohmori
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Yuki Takada
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Ishikawa 920-0934, Japan
| | - Hidetoshi Sakayama
- Department of Biology, Graduate School of Science, Kobe University, Hyogo 657-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Fumio Takahashi
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
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Myers CL, Li FKK, Koo BM, El-Halfawy OM, French S, Gross CA, Strynadka NCJ, Brown ED. Identification of Two Phosphate Starvation-induced Wall Teichoic Acid Hydrolases Provides First Insights into the Degradative Pathway of a Key Bacterial Cell Wall Component. J Biol Chem 2016; 291:26066-26082. [PMID: 27780866 PMCID: PMC5207077 DOI: 10.1074/jbc.m116.760447] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/22/2016] [Indexed: 11/06/2022] Open
Abstract
The cell wall of most Gram-positive bacteria contains equal amounts of peptidoglycan and the phosphate-rich glycopolymer wall teichoic acid (WTA). During phosphate-limited growth of the Gram-positive model organism Bacillus subtilis 168, WTA is lost from the cell wall in a response mediated by the PhoPR two-component system, which regulates genes involved in phosphate conservation and acquisition. It has been thought that WTA provides a phosphate source to sustain growth during starvation conditions; however, WTA degradative pathways have not been described for this or any condition of bacterial growth. Here, we uncover roles for the Bacillus subtilis PhoP regulon genes glpQ and phoD as encoding secreted phosphodiesterases that function in WTA metabolism during phosphate starvation. Unlike the parent 168 strain, ΔglpQ or ΔphoD mutants retained WTA and ceased growth upon phosphate limitation. Characterization of GlpQ and PhoD enzymatic activities, in addition to X-ray crystal structures of GlpQ, revealed distinct mechanisms of WTA depolymerization for the two enzymes; GlpQ catalyzes exolytic cleavage of individual monomer units, and PhoD catalyzes endo-hydrolysis at nonspecific sites throughout the polymer. The combination of these activities appears requisite for the utilization of WTA as a phosphate reserve. Phenotypic characterization of the ΔglpQ and ΔphoD mutants revealed altered cell morphologies and effects on autolytic activity and antibiotic susceptibilities that, unexpectedly, also occurred in phosphate-replete conditions. Our findings offer novel insight into the B. subtilis phosphate starvation response and implicate WTA hydrolase activity as a determinant of functional properties of the Gram-positive cell envelope.
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Affiliation(s)
- Cullen L Myers
- From the Department of Biochemistry and Biomedical Sciences and
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Franco K K Li
- the Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Byoung-Mo Koo
- the Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158
| | - Omar M El-Halfawy
- From the Department of Biochemistry and Biomedical Sciences and
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Shawn French
- From the Department of Biochemistry and Biomedical Sciences and
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Carol A Gross
- the Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158
| | - Natalie C J Strynadka
- the Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Eric D Brown
- From the Department of Biochemistry and Biomedical Sciences and
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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Brescia M, Zaccolo M. Modulation of Compartmentalised Cyclic Nucleotide Signalling via Local Inhibition of Phosphodiesterase Activity. Int J Mol Sci 2016; 17:E1672. [PMID: 27706091 PMCID: PMC5085705 DOI: 10.3390/ijms17101672] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/20/2016] [Accepted: 09/23/2016] [Indexed: 12/20/2022] Open
Abstract
Cyclic nucleotide phosphodiesterases (PDEs) are the only enzymes that degrade the cyclic nucleotides cAMP and cGMP, and play a key role in modulating the amplitude and duration of the signal delivered by these two key intracellular second messengers. Defects in cyclic nucleotide signalling are known to be involved in several pathologies. As a consequence, PDEs have long been recognized as potential drug targets, and they have been the focus of intense research for the development of therapeutic agents. A number of PDE inhibitors are currently available for the treatment of disease, including obstructive pulmonary disease, erectile dysfunction, and heart failure. However, the performance of these drugs is not always satisfactory, due to a lack of PDE-isoform specificity and their consequent adverse side effects. Recent advances in our understanding of compartmentalised cyclic nucleotide signalling and the role of PDEs in local regulation of cAMP and cGMP signals offers the opportunity for the development of novel strategies for therapeutic intervention that may overcome the current limitation of conventional PDE inhibitors.
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Affiliation(s)
- Marcella Brescia
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3TP, UK.
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3TP, UK.
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Katsamakas S, Papadopoulos AG, Hadjipavlou-Litina D. Boronic Acid Group: A Cumbersome False Negative Case in the Process of Drug Design. Molecules 2016; 21:molecules21091185. [PMID: 27617984 PMCID: PMC6273881 DOI: 10.3390/molecules21091185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 11/26/2022] Open
Abstract
Herein we present, an exhaustive docking analysis considering the case of autotaxin (ATX). HA155, a small molecule inhibitor of ATX, is co-crystallized. In order to further extract conclusions on the nature of the bond formed between the ligands and the amino acid residues of the active site, density functional theory (DFT) calculations were undertaken. However, docking does not provide reproducible results when screening boronic acid derivatives and their binding orientations to protein drug targets. Based on natural bond orbital (NBO) calculations, the formed bond between Ser/Thr residues is characterized more accurately as a polar covalent bond instead of a simple nonpolar covalent one. The presented results are acceptable and could be used in screening as an active negative filter for boron compounds. The hydroxyl groups of amino acids are bonded with the inhibitor’s boron atom, converting its hybridization to sp3.
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Affiliation(s)
- Sotirios Katsamakas
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece.
| | - Anastasios G Papadopoulos
- Laboratory of Applied Quantum Chemistry, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece.
| | - Dimitra Hadjipavlou-Litina
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece.
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Mehra P, Giri J. Rice and chickpea GDPDs are preferentially influenced by low phosphate and CaGDPD1 encodes an active glycerophosphodiester phosphodiesterase enzyme. Plant Cell Rep 2016; 35:1699-1717. [PMID: 27108120 DOI: 10.1007/s00299-016-1984-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/13/2016] [Indexed: 06/05/2023]
Abstract
Rice and chickpea GDPD s are transcriptionally influenced by mineral deficiencies; especially, by phosphate starvation and CaGDP1 encodes an active glycerophosphodiester phosphodiesterase enzyme. Glycerophosphodiester phosphodiesterases (GDPDs) are enzymes involved in the degradation of glycerophosphodiesters into sn-glycerol-3-phosphate and corresponding alcohols. These phospholipid remodeling genes have been suggested to play important roles in phosphate homeostasis. However, comprehensive information about the role of GDPDs under low phosphate (P) and other nutrient deficiencies (N, K, Fe, Zn) in rice and chickpea is missing. Here, we identified 13 OsGDPDs and 6 CaGDPDs in rice and chickpea, respectively, and partly characterized their roles in multiple nutrient stresses. Expression profiling after 7 and 15 days of deficiency treatments revealed unique and overlapping differential expression patterns of OsGDPDs and CaGDPDs under different nutrient stresses. Principal component analysis on the expression patterns of OsGDPDs and CaGDPDs revealed their preferential role in P starvation. Some of the GDPDs were also induced by N, K, Fe and Zn deficiency in temporal manner in both crops suggesting their roles in multiple nutrient stresses. Biochemical characterization of highly responsive chickpea GDPD, CaGDPD1, confirmed its in vitro GDPD activity and revealed its optimal temperature, pH and cofactor requirements. Further, CaGDPD1 showed its accumulation in ER and endomembranes. We hereby propose CaGDPD1 and various OsGDPDs as low P responsive marker genes in chickpea and rice, respectively. Our data uphold role of GDPDs in multinutrient responses and suggest them as candidates for rice and chickpea improvement for tolerance to various nutrient deficiencies.
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Affiliation(s)
- P Mehra
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - J Giri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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