1
|
Mishra S, Rout M, Singh MK, Dehury B, Pati S. Illuminating the structural basis of human neurokinin 1 receptor (NK1R) antagonism through classical all-atoms molecular dynamics simulations. J Cell Biochem 2023; 124:1848-1869. [PMID: 37942587 DOI: 10.1002/jcb.30493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
Advances in structural biology have bestowed insights into the pleiotropic effects of neurokinin 1 receptors (NK1R) in diverse patho-physiological processes, thereby highlighting the potential therapeutic value of antagonists directed against NK1R. Herein, we investigate the mode of antagonist recognition to discern the obscure atomic facets germane for the function and molecular determinants of NK1R. To commence discernment of potent antagonists and the conformational changes in NK1R, induced upon antagonist binding, state-of-the-art classical all-atoms molecular dynamics (MD) simulations in lipid mimetic bilayers have been utilized. MD simulations of structural ensembles reveals the involvement of TM5 and TM6 in tight anchoring of antagonists through a network of interhelical hydrogen-bonds, while, the extracellular loop 2 (ECL2) governs the overall size and nature of the pocket, thereby modulating NK1R. Consistent comparison between experiments and MD simulation results discerns the predominant role of TM3, TM4, and TM6 in lipid-NK1R interaction. Correlation between hydrophobic index and helicity of TM domains elucidates their importance in maintaining the structural stability in addition to regulating NK1R antagonism. Taken together, we anticipate that our computational study marks a comprehensive structural basis of NK1R antagonism in lipid bilayers, which may facilitate designing of new therapeutics against associated diseases targeting human neurokinin receptors.
Collapse
Affiliation(s)
- Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| |
Collapse
|
2
|
Bahaaeldine MA, El Garhy M, Fahmy SR, Mohamed AS. In vitro anti-Toxocara vitulorum effect of silver nanoparticles. J Parasit Dis 2022; 46:409-420. [DOI: 10.1007/s12639-021-01464-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
|
3
|
Kapur A, Beres T, Rathi K, Nayak AP, Czarnecki A, Felder M, Gillette A, Ericksen SS, Sampene E, Skala MC, Barroilhet L, Patankar MS. Oxidative stress via inhibition of the mitochondrial electron transport and Nrf-2-mediated anti-oxidative response regulate the cytotoxic activity of plumbagin. Sci Rep 2018; 8:1073. [PMID: 29348410 PMCID: PMC5773707 DOI: 10.1038/s41598-018-19261-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/19/2017] [Indexed: 11/15/2022] Open
Abstract
Plumbagin, an anti-cancer agent, is toxic to cells of multiple species. We investigated if plumbagin targets conserved biochemical processes. Plumbagin induced DNA damage and apoptosis in cells of diverse mutational background with comparable potency. A 3-5 fold increase in intracellular oxygen radicals occurred in response to plumbagin. Neutralization of the reactive oxygen species by N-acetylcysteine blocked apoptosis, indicating a central role for oxidative stress in plumbagin-mediated cell death. Plumbagin docks in the ubiquinone binding sites (Q0 and Qi) of mitochondrial complexes I-III, the major sites for oxygen radicals. Plumbagin decreased oxygen consumption rate, ATP production and optical redox ratio (NAD(P)H/FAD) indicating interference with electron transport downstream of mitochondrial Complex II. Oxidative stress induced by plumbagin triggered an anti-oxidative response via activation of Nrf2. Plumbagin and the Nrf2 inhibitor, brusatol, synergized to inhibit cell proliferation. These data indicate that while inhibition of electron transport is the conserved mechanism responsible for plumbagin's chemotoxicity, activation of Nrf2 is the resulting anti-oxidative response that allows plumbagin to serve as a chemopreventive agent. This study provides the basis for designing potent and selective plumbagin analogs that can be coupled with suitable Nrf2 inhibitors for chemotherapy or administered as single agents to induce Nrf2-mediated chemoprevention.
Collapse
Affiliation(s)
- Arvinder Kapur
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792-6188, USA.
| | - Thomas Beres
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792-6188, USA
| | - Kavya Rathi
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792-6188, USA
| | - Amruta P Nayak
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792-6188, USA
- Indian Institute for Science Education and Research, Pune, India
| | - Austin Czarnecki
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792-6188, USA
| | - Mildred Felder
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792-6188, USA
| | - Amani Gillette
- Morgridge Institute for Research and the Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Spencer S Ericksen
- Small Molecule Screening Facility, University of Wisconsin Paul P. Carbone Comprehensive Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Emmanuel Sampene
- Department of Biostatistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Melissa C Skala
- Morgridge Institute for Research and the Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Lisa Barroilhet
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792-6188, USA
| | - Manish S Patankar
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53792-6188, USA.
| |
Collapse
|
4
|
Brantley SJ, Cotten SW, Lamson DR, Smith GR, Liu R, Williams KP. Discovery of small molecule inhibitors for the C. elegans caspase CED-3 by high-throughput screening. Biochem Biophys Res Commun 2017; 491:773-779. [PMID: 28733033 DOI: 10.1016/j.bbrc.2017.07.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/17/2017] [Indexed: 11/24/2022]
Abstract
C. elegans has been widely used as a model organism for programmed cell death and apoptosis. Although the CED-3 caspase is the primary effector of cell death in C. elegans, no selective inhibitors have been identified. Utilizing high-throughput screening with recombinant C. elegans CED-3 protein, we have discovered and confirmed 21 novel small molecule inhibitors. Six compounds had IC50 values < 10 μM. From these, four distinct chemotypes were identified. The inhibitor scaffolds described here could lead to the development of selective molecular probes to facilitate our understanding of programmed cell death in this model organism.
Collapse
Affiliation(s)
- Scott J Brantley
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven W Cotten
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David R Lamson
- Biomanufacturing Research Institute and Technology Enterprise, Durham, NC 27707, USA
| | - Ginger R Smith
- Biomanufacturing Research Institute and Technology Enterprise, Durham, NC 27707, USA
| | - Rihe Liu
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Kevin P Williams
- Biomanufacturing Research Institute and Technology Enterprise, Durham, NC 27707, USA; Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA.
| |
Collapse
|
5
|
de Paula Aguiar D, Brunetto Moreira Moscardini M, Rezende Morais E, Graciano de Paula R, Ferreira PM, Afonso A, Belo S, Tomie Ouchida A, Curti C, Cunha WR, Rodrigues V, Magalhães LG. Curcumin Generates Oxidative Stress and Induces Apoptosis in Adult Schistosoma mansoni Worms. PLoS One 2016; 11:e0167135. [PMID: 27875592 PMCID: PMC5119855 DOI: 10.1371/journal.pone.0167135] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/09/2016] [Indexed: 12/20/2022] Open
Abstract
Inducing apoptosis is an interesting therapeutic approach to develop drugs that act against helminthic parasites. Researchers have investigated how curcumin (CUR), a biologically active compound extracted from rhizomes of Curcuma longa, affects Schistosoma mansoni and several cancer cell lines. This study evaluates how CUR influences the induction of apoptosis and oxidative stress in couples of adult S. mansoni worms. CUR decreased the viability of adult worms and killed them. The tegument of the parasite suffered morphological changes, the mitochondria underwent alterations, and chromatin condensed. Different apoptotic parameters were determined in an attempt to understand how CUR affected adult S. mansoni worms. CUR induced DNA damage and fragmentation and increased the expression of SmCASP3/7 transcripts and the activity of Caspase 3 in female and male worms. However, CUR did not intensify the activity of Caspase 8 in female or male worms. Evaluation of the superoxide anion and different antioxidant enzymes helped to explore the mechanism of parasite death further. The level of superoxide anion and the activity of Superoxide Dismutase (SOD) increased, whereas the activity of Glutathione-S-Transferase (GST), Glutathione reductase (GR), and Glutathione peroxidase (GPX) decreased, which culminated in the oxidation of proteins in adult female and male worms incubated with CUR. In conclusion, CUR generated oxidative stress followed by apoptotic-like-events in both adult female and male S. mansoni worms, ultimately killing them.
Collapse
Affiliation(s)
- Daniela de Paula Aguiar
- Núcleo de Pesquisa em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, Brazil
| | | | - Enyara Rezende Morais
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Patos de Minas, Brazil
| | | | - Pedro Manuel Ferreira
- Global Health and Tropical Medicine, GHTM, UEI Medical Parasitology, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Ana Afonso
- Global Health and Tropical Medicine, GHTM, UEI Medical Parasitology, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Departamento de Morfologia e Patologia, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Silvana Belo
- Global Health and Tropical Medicine, GHTM, UEI Medical Parasitology, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Amanda Tomie Ouchida
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Carlos Curti
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Wilson Roberto Cunha
- Núcleo de Pesquisa em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, Brazil
| | - Vanderlei Rodrigues
- Departamento de Bioquímica e Imunologia, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Lizandra Guidi Magalhães
- Núcleo de Pesquisa em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, Brazil
- * E-mail:
| |
Collapse
|
6
|
Abdel Moneim AE, Ortiz F, Leonardo-Mendonça RC, Vergano-Villodres R, Guerrero-Martínez JA, López LC, Acuña-Castroviejo D, Escames G. Protective effects of melatonin against oxidative damage induced by Egyptian cobra (Naja haje) crude venom in rats. Acta Trop 2015; 143:58-65. [PMID: 25542296 DOI: 10.1016/j.actatropica.2014.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 10/21/2014] [Accepted: 12/14/2014] [Indexed: 01/20/2023]
Abstract
Naja haje envenomation is one of the leading causes of death due to snakebite. Antiserum therapy sometimes fails to provide enough protection against venom toxicity. In this study, we investigated the protective effects of melatonin against N. haje venom in rats. The animals were injected with venom (0.25mg/kg) and/or melatonin (10mg/kg) and compared with vehicle-treated rats. There was oxidative/nitrosative damage and apoptosis in the liver, heart, and kidneys of venom-injected rats. Melatonin counteracted the increased lipoperoxidation and nitric oxide, prevented decreased glutathione peroxidase and reductase activity, reduced the glutathione disulfide/glutathione (GSSG/GSH) ratio, and maintained the GSH pool. Furthermore, melatonin administration was associated with a reduction of apoptosis, which was increased in venom-injected rats. Overall, these results suggest that melatonin mitigates oxidative/nitrosative stress in venom-induced cardio-hepato-renal injury in rats. Our results suggest that melatonin treatment may ameliorate some of the effects of N. haje envenomation.
Collapse
|
7
|
Yan HB, Lou ZZ, Li L, Brindley PJ, Zheng Y, Luo X, Hou J, Guo A, Jia WZ, Cai X. Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium. BMC Genomics 2014; 15:428. [PMID: 24899069 PMCID: PMC4070553 DOI: 10.1186/1471-2164-15-428] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 05/19/2014] [Indexed: 12/20/2022] Open
Abstract
Background Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere. Owing to the emerging drug resistance and the inability of current drugs to prevent re-infection, identification of novel vaccines and chemotherapeutic agents against Taenia solium and related helminth pathogens is a public health priority. The T. solium genome and the predicted proteome were reported recently, providing a wealth of information from which new interventional targets might be identified. In order to characterize and classify the entire repertoire of protease-encoding genes of T. solium, which act fundamental biological roles in all life processes, we analyzed the predicted proteins of this cestode through a combination of bioinformatics tools. Functional annotation was performed to yield insights into the signaling processes relevant to the complex developmental cycle of this tapeworm and to highlight a suite of the proteases as potential intervention targets. Results Within the genome of this helminth parasite, we identified 200 open reading frames encoding proteases from five clans, which correspond to 1.68% of the 11,902 protein-encoding genes predicted to be present in its genome. These proteases include calpains, cytosolic, mitochondrial signal peptidases, ubiquitylation related proteins, and others. Many not only show significant similarity to proteases in the Conserved Domain Database but have conserved active sites and catalytic domains. KEGG Automatic Annotation Server (KAAS) analysis indicated that ~60% of these proteases share strong sequence identities with proteins of the KEGG database, which are involved in human disease, metabolic pathways, genetic information processes, cellular processes, environmental information processes and organismal systems. Also, we identified signal peptides and transmembrane helices through comparative analysis with classes of important regulatory proteases. Phylogenetic analysis using Bayes approach provided support for inferring functional divergence among regulatory cysteine and serine proteases. Conclusion Numerous putative proteases were identified for the first time in T. solium, and important regulatory proteases have been predicted. This comprehensive analysis not only complements the growing knowledge base of proteolytic enzymes, but also provides a platform from which to expand knowledge of cestode proteases and to explore their biochemistry and potential as intervention targets. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-428) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hong-Bin Yan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu Province, PR China.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Kumar S, Biswal DK, Tandon V. In-silico analysis of caspase-3 and -7 proteases from blood-parasitic Schistosoma species (Trematoda) and their human host. Bioinformation 2013; 9:456-63. [PMID: 23847399 PMCID: PMC3705615 DOI: 10.6026/97320630009456] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/21/2012] [Accepted: 04/17/2013] [Indexed: 12/24/2022] Open
Abstract
Proteolytic enzymes of the caspase family, which reside as latent precursors in most nucleated metazoan cells, are core effectors of apoptosis. Of them, the executioner caspases- 3 and -7 exist within the cytosol as inactive dimers and are activated by a process called dimerization. Caspase inhibition is looked upon as a promising approach for treating multiple diseases. Though caspases have been extensively studied in the human system, their role in eukaryotic pathogens and parasites of human hosts has not drawn enough attention. In protein sequence analysis, caspases of blood flukes (Schistosoma spp) were revealed to have a low sequence identity with their counterparts in human and other mammalian hosts, which encouraged us to analyse interacting domains that participate in dimerization of caspases in the parasite and to reveal differences, if any, between the host-parasite systems. Significant differences in the molecular surface arrangement of the dimer interfaces reveal that in schistosomal caspases only eight out of forty dimer conformations are similar to human caspase structures. Thus, the parasite-specific dimer conformations (that are different from caspases of the host) may emerge as potential drug targets of therapeutic value against schistosomal infections. Three important factors namely, the size of amino acids, secondary structures and geometrical arrangement of interacting domains influence the pattern of caspase dimer formation, which, in turn, is manifested in varied structural conformations of caspases in the parasite and its human hosts.
Collapse
Affiliation(s)
- Shakti Kumar
- Bioinformatics Centre, North-Eastern Hill University, Shillong 793022, Meghalaya, India
- Department of Zoology, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| | - Devendra Kumar Biswal
- Bioinformatics Centre, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| | - Veena Tandon
- Bioinformatics Centre, North-Eastern Hill University, Shillong 793022, Meghalaya, India
- Department of Zoology, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| |
Collapse
|
9
|
Ruano AL, López-Abán J, Gajate C, Mollinedo F, De Melo AL, Muro A. Apoptotic mechanisms are involved in the death of Strongyloides venezuelensis after triggering of nitric oxide. Parasite Immunol 2013; 34:570-80. [PMID: 22897441 DOI: 10.1111/pim.12004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 07/27/2012] [Indexed: 12/01/2022]
Abstract
Despite progress in understanding the role of nitric oxide (NO) in the pathogenesis of helminth infections, the role in strongyloidosis is unknown. Firstly, we studied the production of NO in mice infected with Strongyloides venezuelensis as well as in macrophage cultures stimulated with parasite antigens. Somatic larvae 3 (L3) and excretory-secretory female antigens stimulate specific NO production measured by Griess reaction and expression of inducible NO synthase by RT-PCR and quantitative PCR. Moreover, mice infected with S. venezuelensis produce NO in migration stages. Secondly, we analysed the effect of NO production on L3 and females of S. venezuelensis using NO donors such as diethylenetriamine and 3,3-bis(aminoethyl)-1-hydroxy-2-oxo-1-triazene. Parasites died after NO donor treatment in a dose-dependent manner. Finally, apoptotic mechanisms are involved in the death of S. venezuelensis larvae.
Collapse
Affiliation(s)
- A L Ruano
- Laboratorio de Inmunología y Parasitología Molecular, IBSAL-CIETUS, Universidad de Salamanca, Salamanca, Spain
| | | | | | | | | | | |
Collapse
|
10
|
Ravindran B. Deworming conundrum - are we missing an undesirable dimension? Indian J Med Res 2013; 138:178-81. [PMID: 24056592 PMCID: PMC3788201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- B. Ravindran
- Institute of Life Sciences (An autonomous Institute under Department of Biotechnology), Bhubaneswar 751 023, India
| |
Collapse
|