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Stryiński R, Mateos J, Carrera M, Jastrzębski JP, Bogacka I, Łopieńska-Biernat E. Tandem Mass Tagging (TMT) Reveals Tissue-Specific Proteome of L4 Larvae of Anisakis simplex s. s.: Enzymes of Energy and/or Carbohydrate Metabolism as Potential Drug Targets in Anisakiasis. Int J Mol Sci 2022; 23:ijms23084336. [PMID: 35457153 PMCID: PMC9027741 DOI: 10.3390/ijms23084336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Anisakis simplex s. s. is a parasitic nematode of marine mammals and causative agent of anisakiasis in humans. The cuticle and intestine of the larvae are the tissues most responsible for direct and indirect contact, respectively, of the parasite with the host. At the L4 larval stage, tissues, such as the cuticle and intestine, are fully developed and functional, in contrast to the L3 stage. As such, this work provides for the first time the tissue-specific proteome of A. simplex s. s. larvae in the L4 stage. Statistical analysis (FC ≥ 2; p-value ≤ 0.01) showed that 107 proteins were differentially regulated (DRPs) between the cuticle and the rest of the larval body. In the comparison between the intestine and the rest of the larval body at the L4 stage, 123 proteins were identified as DRPs. Comparison of the individual tissues examined revealed a total of 272 DRPs, with 133 proteins more abundant in the cuticle and 139 proteins more abundant in the intestine. Detailed functional analysis of the identified proteins was performed using bioinformatics tools. Glycolysis and the tricarboxylic acid cycle were the most enriched metabolic pathways by cuticular and intestinal proteins, respectively, in the L4 stage of A. simplex s. s. The presence of two proteins, folliculin (FLCN) and oxoglutarate dehydrogenase (OGDH), was confirmed by Western blot, and their tertiary structure was predicted and compared with other species. In addition, host–pathogen interactions were identified, and potential new allergens were predicted. The result of this manuscript shows the largest number of protein identifications to our knowledge using proteomics tools for different tissues of L4 larvae of A. simplex s. s. The identified tissue-specific proteins could serve as targets for new drugs against anisakiasis.
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Affiliation(s)
- Robert Stryiński
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
- Correspondence: (R.S.); (M.C.); (E.Ł.-B.)
| | - Jesús Mateos
- Clinical Pharmacology Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, 15-706 A Coruña, Spain;
| | - Mónica Carrera
- Department of Food Technology, Marine Research Institute (IIM), Spanish National Research Council (CSIC), 36-208 Vigo, Spain
- Correspondence: (R.S.); (M.C.); (E.Ł.-B.)
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Iwona Bogacka
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Elżbieta Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
- Correspondence: (R.S.); (M.C.); (E.Ł.-B.)
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Correcting a widespread error: Neuroprotectant N-acetyl-L-tryptophan does not bind to the neurokinin-1 receptor. Mol Cell Neurosci 2022; 120:103728. [DOI: 10.1016/j.mcn.2022.103728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
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Structural characterization, biochemical, inhibition and computational studies of Entamoeba histolytica phosphoglycerate mutase: finding hits for a new antiamoebic drug. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2184-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Sharma OP, Kumar MS. Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase--a comprehensive drug target database for Lymphatic filariasis. Sci Rep 2016; 6:19842. [PMID: 26806463 PMCID: PMC4726333 DOI: 10.1038/srep19842] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 10/27/2015] [Indexed: 11/26/2022] Open
Abstract
Lymphatic filariasis (Lf) is one of the oldest and most debilitating tropical diseases. Millions of people are suffering from this prevalent disease. It is estimated to infect over 120 million people in at least 80 nations of the world through the tropical and subtropical regions. More than one billion people are in danger of getting affected with this life-threatening disease. Several studies were suggested its emerging limitations and resistance towards the available drugs and therapeutic targets for Lf. Therefore, better medicine and drug targets are in demand. We took an initiative to identify the essential proteins of Wolbachia endosymbiont of Brugia malayi, which are indispensable for their survival and non-homologous to human host proteins. In this current study, we have used proteome subtractive approach to screen the possible therapeutic targets for wBm. In addition, numerous literatures were mined in the hunt for potential drug targets, drugs, epitopes, crystal structures, and expressed sequence tag (EST) sequences for filarial causing nematodes. Data obtained from our study were presented in a user friendly database named FiloBase. We hope that information stored in this database may be used for further research and drug development process against filariasis. URL: http://filobase.bicpu.edu.in.
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Affiliation(s)
- Om Prakash Sharma
- Centre for Bioinformatics, School of Life Science, Pondicherry University, Pondicherry-605014, India
| | - Muthuvel Suresh Kumar
- Centre for Bioinformatics, School of Life Science, Pondicherry University, Pondicherry-605014, India
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Sharma OP, Hari Krishna K, Suresh Kumar M. Probing the Structural and Conformational Stability of the Wb-iPGM Enzyme and Role of Mn2+ Ions in Their Catalytic Site. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Banavath HN, Sharma OP, Kumar MS, Baskaran R. Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study. Sci Rep 2014; 4:6948. [PMID: 25382104 PMCID: PMC4225644 DOI: 10.1038/srep06948] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/20/2014] [Indexed: 11/09/2022] Open
Abstract
BCR-ABL tyrosine kinase plays a major role in the pathogenesis of chronic myeloid leukemia (CML) and is a proven target for drug development. Currently available drugs in the market are effective against CML; however, side-effects and drug-resistant mutations in BCR-ABL limit their full potential. Using high throughput virtual screening approach, we have screened several small molecule databases and docked against wild-type and drug resistant T315I mutant BCR-ABL. Drugs that are currently available, such as imatinib and ponatinib, were also docked against BCR-ABL protein to set a cutoff value for our screening. Selected lead compounds were further evaluated for chemical reactivity employing density functional theory approach, all selected ligands shows HLG value > 0.09900 and the binding free energy between protein-ligand complex interactions obtained was rescored using MM-GBSA. The selected compounds showed least ΔG score -71.53 KJ/mol to maximum -126.71 KJ/mol in both wild type and drug resistant T315I mutant BCR-ABL. Following which, the stability of the docking complexes were evaluated by molecular dynamics simulation (MD) using GROMACS4.5.5. Results uncovered seven lead molecules, designated with Drug-Bank and PubChem ids as DB07107, DB06977, ST013616, DB04200, ST007180 ST019342, and DB01172, which shows docking scores higher than imatinib and ponatinib.
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Affiliation(s)
- Hemanth Naick Banavath
- Department of Biochemistry &Molecular biology, School of Life Sciences, Pondicherry University-India
| | - Om Prakash Sharma
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University-India
| | | | - R Baskaran
- Department of Biochemistry &Molecular biology, School of Life Sciences, Pondicherry University-India
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Physicochemical properties of the modeled structure of astacin metalloprotease moulting enzyme NAS-36 and mapping the druggable allosteric space of Heamonchus contortus, Brugia malayi and Ceanorhabditis elegans via molecular dynamics simulation. Interdiscip Sci 2014; 5:312-23. [PMID: 24402824 DOI: 10.1007/s12539-013-0182-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 12/06/2012] [Accepted: 04/22/2013] [Indexed: 10/25/2022]
Abstract
Nematodes represent the second largest phylum in the animal kingdom. It is the most abundant species (500,000) in the planet. It causes chronic, debilitating infections worldwide such as ascariasis, trichuriasis, hookworm, enterobiasis, strongyloidiasis, filariasis and trichinosis, among others. Molecular modeling tools can play an important role in the identification and structural investigation of molecular targets that can act as a vital candidate against filariasis. In this study, sequence analysis of NAS-36 from H. contortus (Heamonchus contortus), B. malayi (Brugia malayi) and C. elegans (Ceanorhabditis elegans) has been performed, in order to identify the conserved residues. Tertiary structure was developed for an insight into the molecular structure of the enzyme. Molecular Dynamics Simulation (MDS) studies have been carried out to analyze the stability and the physical properties of the proposed enzyme models in the H. contortus, B. malayi and C. elegans. Moreover, the drug binding sites have been mapped for inhibiting the function of NAS-36 enzyme. The molecular identity of this protease could eventually demonstrate how ex-sheathment is regulated, as well as provide a potential target of anthelmintics for the prevention of nematode infections.
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Crowther GJ, Booker ML, He M, Li T, Raverdy S, Novelli JF, He P, Dale NRG, Fife AM, Barker RH, Kramer ML, Van Voorhis WC, Carlow CKS, Wang MW. Cofactor-independent phosphoglycerate mutase from nematodes has limited druggability, as revealed by two high-throughput screens. PLoS Negl Trop Dis 2014; 8:e2628. [PMID: 24416464 PMCID: PMC3886921 DOI: 10.1371/journal.pntd.0002628] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 11/21/2013] [Indexed: 11/19/2022] Open
Abstract
Cofactor-independent phosphoglycerate mutase (iPGAM) is essential for the growth of C. elegans but is absent from humans, suggesting its potential as a drug target in parasitic nematodes such as Brugia malayi, a cause of lymphatic filariasis (LF). iPGAM's active site is small and hydrophilic, implying that it may not be druggable, but another binding site might permit allosteric inhibition. As a comprehensive assessment of iPGAM's druggability, high-throughput screening (HTS) was conducted at two different locations: ∼220,000 compounds were tested against the C. elegans iPGAM by Genzyme Corporation, and ∼160,000 compounds were screened against the B. malayi iPGAM at the National Center for Drug Screening in Shanghai. iPGAM's catalytic activity was coupled to downstream glycolytic enzymes, resulting in NADH consumption, as monitored by a decline in visible-light absorbance at 340 nm. This assay performed well in both screens (Z′-factor >0.50) and identified two novel inhibitors that may be useful as chemical probes. However, these compounds have very modest potency against the B. malayi iPGAM (IC50 >10 µM) and represent isolated singleton hits rather than members of a common scaffold. Thus, despite the other appealing properties of the nematode iPGAMs, their low druggability makes them challenging to pursue as drug targets. This study illustrates a “druggability paradox” of target-based drug discovery: proteins are generally unsuitable for resource-intensive HTS unless they are considered druggable, yet druggability is often difficult to predict in the absence of HTS data. Parasitic worms like Brugia malayi cause widespread lymphatic filariasis (LF) in southeast Asia and sub-Saharan Africa. The adult worms causing most of the symptoms of LF are difficult to treat with existing drugs. As a possible step toward new LF drugs, we searched for inhibitors of the B. malayi cofactor-independent phosphoglycerate mutase (iPGAM), an enzyme thought to be critical to survival and development of this parasite. Despite testing over 100,000 compounds at each of two screening centers, we found only two compounds that consistently inhibited the B. malayi enzyme more strongly than the cofactor-dependent enzyme found in humans. These compounds have limited potency and are not especially great starting points for drug development. The 3-dimensional structure of iPGAM suggests that the active site is difficult to access from the surrounding solvent, which may partly explain our very low yield of inhibitors. We conclude that iPGAM may not be an ideal drug target in B. malayi or related organisms because it is difficult to inhibit with druglike compounds.
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Affiliation(s)
- Gregory J. Crowther
- Division of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Michael L. Booker
- Genzyme Corporation, Waltham, Massachusetts, United States of America
| | - Min He
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ting Li
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Sylvine Raverdy
- Division of Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jacopo F. Novelli
- Division of Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Panqing He
- Division of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Natalie R. G. Dale
- Division of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Amy M. Fife
- Genzyme Corporation, Waltham, Massachusetts, United States of America
| | - Robert H. Barker
- Genzyme Corporation, Waltham, Massachusetts, United States of America
| | - Martin L. Kramer
- Genzyme Corporation, Waltham, Massachusetts, United States of America
| | - Wesley C. Van Voorhis
- Division of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Clotilde K. S. Carlow
- Division of Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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Masilamani R, Sharma OP, Muthuvel SK, Natarajan S. Cloning, expression of b-1,3-1,4 glucanase from Bacillus subtilis SU40 and the effect of calcium ion on the stability of recombinant enzyme: in vitro and in silico analysis. Bioinformation 2013; 9:958-62. [PMID: 24391357 PMCID: PMC3867647 DOI: 10.6026/97320630009958] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 11/05/2013] [Accepted: 11/06/2013] [Indexed: 11/24/2022] Open
Abstract
A new glucanolytic bacterial strain, SU40 was isolated, and identified as Bacillus subtilis on the basis of 16S rRNA sequence
homology and phylogenetic tree analysis. The gene encoding β-1,3-1,4-glucanase was delineated, cloned into pET 28a+ vector and
heterologously overexpressed in Escherichia coli BL21(DE3). The purified recombinant enzyme was about 24 kDa. The enzyme
exhibited maximum activity (36.84 U/ml) at 60°C, pH 8.0 and maintained 54% activity at 80°C after incubation for 60 min. The
enzyme showed activity against β-glucan, lichenan, and xylan. Amino acid sequence shared a conserved motif EIDIEF. The
predicted three-dimensional homology model of the enzyme showed the presence of catalytic residues Glu105, Glu109 and
Asp107, single disulphide bridge between Cys32 and Cys61 and three calcium binding site residues Pro9, Gly45 and Asp207.
Presence of calcium ion improves the thermal stability of SU40 β-1,3-1,4-glucanase. Molecular dynamics simulation studies
revealed that the absence of calcium ion fluctuate the active site residues which are responsible for thermostability. The high
catalytic activity and its stability to temperature, pH and metal ions indicated that the enzyme β-1,3-1,4-glucanase by B. subtilis
SU40 is a good candidate for biotechnological applications.
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Affiliation(s)
- Revathi Masilamani
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Om Prakash Sharma
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Suresh Kumar Muthuvel
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Sakthivel Natarajan
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
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