1
|
Ali A, Mir GJ, Ayaz A, Maqbool I, Ahmad SB, Mushtaq S, Khan A, Mir TM, Rehman MU. In silico analysis and molecular docking studies of natural compounds of Withania somnifera against bovine NLRP9. J Mol Model 2023; 29:171. [PMID: 37155030 PMCID: PMC10165590 DOI: 10.1007/s00894-023-05570-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
CONTEXT NLRP9 is a member of nucleotide-binding domain leucine-rich repeat-containing receptors and is found to be associated with many inflammatory diseases. In the current scenario, the identification of promising anti-inflammatory compounds from natural sources by repurposing approach is still relevant for the early prevention and effective management of the disease. METHODS In the present study, we docked bioactives of Ashwagandha (Withanoside IV, Withanoside V, Withanolide A, Withanolide B, and Sitoindoside IX) and two control drugs against bovine NLRP9 protein. ADME/T analysis was used to determine the physiochemical properties of compounds and standard drugs. Molecular modeling was used to evaluate the correctness and quality of protein structures. In silico docking analysis revealed Withanolide B had the highest binding affinity score of -10.5 kcal/mol, whereas, among control drugs, doxycycline hydrochloride was most effective (-10.3 kcal/mol). The results of this study revealed that bioactives of Withania somnifera could be promising inhibitors against bovine NLRP9. In the present study, molecular simulation was used to measure protein conformational changes over time. The Rg value was found to be 34.77A°. RMSD and B-factor were also estimated to provide insights into the flexibility and mobile regions of protein structure. A functional protein network interaction was constructed from information collected from non-curative sources as protein-protein interactions (PPI) that play an important role in determining the function of the target protein and the ability of the drug molecule. Thus, in the present situation, it is important to identify bioactives with the potential to combat inflammatory diseases and provide strength and immunity to the host. However, there is still a need to study in vitro and in vivo to further support these findings.
Collapse
Affiliation(s)
- Aarif Ali
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, 190006, J&K, India
| | - Gh Jeelani Mir
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, 190006, J&K, India
| | - Aadil Ayaz
- Department of Microbiology, SKIMS Medical College Bemina, Srinagar, 190018, J&K, India
| | - Illiyas Maqbool
- Department of Microbiology, Government Medical College, Baramulla, 193101, J&K, India
| | - Sheikh Bilal Ahmad
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir (SKUAST-K), Shuhama, Srinagar, 190006, J&K, India
| | - Saima Mushtaq
- Veterinary Microbiology Department, Indian Veterinary Research Institute (IVRI), Bareilly, Uttar Pradesh, 243122, India
| | - Altaf Khan
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Tahir Maqbool Mir
- National Centre for Natural Products Research, University of Mississippi, Oxford, MS, 38677, USA
| | - Muneeb U Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.
| |
Collapse
|
2
|
Liu Z, Fu S, He X, Liu X, Shi C, Dai L, Wang B, Chai Y, Liu Y, Zhang W. Estimates of Genomic Heritability and the Marker-Derived Gene for Re(Production) Traits in Xinggao Sheep. Genes (Basel) 2023; 14:genes14030579. [PMID: 36980850 PMCID: PMC10048694 DOI: 10.3390/genes14030579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Xinggao sheep are a breed of Chinese domestic sheep that are adapted to the extremely cold climatic features of the Hinggan League in China. The economically vital reproductive trait of ewes (litter size, LS) and productive traits of lambs (birth weight, BWT; weaning weight, WWT; and average daily gain, ADG) are expressed in females and later in life after most of the selection decisions have been made. This study estimated the genetic parameters for four traits to explore the genetic mechanisms underlying the variation, and we performed genome-wide association study (GWAS) tests on a small sample size to identify novel marker trait associations (MTAs) associated with prolificacy and growth. We detected two suggestive significant single-nucleotide polymorphisms (SNPs) associated with LS and eight significant SNPs for BWT, WWT, and ADG. These candidate loci and genes also provide valuable information for further fine-mapping of QTLs and improvement of reproductive and productive traits in sheep.
Collapse
Affiliation(s)
- Zaixia Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
| | - Shaoyin Fu
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xiaolong He
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xuewen Liu
- College of Agronomy, Animal Husbandry and Bioengineering, Xing’an Vocational and Technical College, Ulanhot 137400, China
| | - Caixia Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lingli Dai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- Veterinary Research Institute, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Biao Wang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Yuan Chai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yongbin Liu
- School of Life Science, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (Y.L.); (W.Z.)
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
- Correspondence: (Y.L.); (W.Z.)
| |
Collapse
|
3
|
Mullins B, Chen J. NLRP9 in innate immunity and inflammation. Immunology 2020; 162:262-267. [PMID: 33283292 DOI: 10.1111/imm.13290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 12/30/2022] Open
Abstract
The nucleotide-binding domain leucine-rich repeat containing receptors (NLRs) are a family of evolutionarily conserved proteins. Several members of NLRs, notably NLRP1, NLRP3 and NLRC4, are able to form cytosolic oligomeric signalling platforms termed inflammasomes to mediate immune response towards pathogens, damage and stress. However, the functions of many NLRs still remain elusive. In the past few years, a couple of less-characterized NLR members are emerging as important signalling molecules with fundamental functions in host defence and inflammation. Among them, NLRP9 is an NLR originally proposed to be expressed and function solely in the reproductive system. Recent evidence has suggested that NLRP9 is also capable of initiating inflammasome formation in the intestine to restrict replication and damage brought by rotavirus infection. Here, we highlight the latest progress in characterization of the role of NLRP9 in infectious and inflammatory diseases, as well as the newest crystallographic and biochemical studies on NLRP9. Finally, we discuss some important questions remained to be answered regarding the molecular and cellular mechanisms governing NLRP9's function in innate immunity and inflammation.
Collapse
Affiliation(s)
- Breanne Mullins
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Jueqi Chen
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| |
Collapse
|
4
|
Amoushahi M, Steffensen LL, Galieva A, Agger J, Heuck A, Siupka P, Ernst E, Nielsen MS, Sunde L, Lykke-Hartmann K. Maternally contributed Nlrp9b expressed in human and mouse ovarian follicles contributes to early murine preimplantation development. J Assist Reprod Genet 2020; 37:1355-1365. [PMID: 32399794 PMCID: PMC7311623 DOI: 10.1007/s10815-020-01767-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/27/2020] [Indexed: 02/03/2023] Open
Abstract
PURPOSE The aim of the study is to investigate presence and role of the gene encoding the maternally contributed nucleotide-binding oligomerization domain (NOD)-like receptors with a pyrin domain (PYD)-containing protein 9 (NLRP9) in human and mouse ovaries, respectively, and in preimplantation mouse embryo development by knocking down Nlrp9b. METHODS Expression levels of NLRP9 mRNA in human follicles were extracted from RNA sequencing data from previous studies. In this study, we performed a qPCR analysis of Nlpr9b mRNA in mouse oocytes and found it present. Intracellular ovarian distribution of NLRP9B protein was accomplished using immunohistochemistry. The distribution of NLRP9B was explored using a reporter gene approach, fusing NLRP9B to green fluorescent protein and microinjection of in vitro-generated mRNA. Nlrp9b mRNA function was knocked down by microinjection of short interference (si) RNA targeting Nlrp9b, into mouse pronuclear zygotes. Knockdown of the Nlrp9b mRNA transcript was confirmed by qPCR. RESULT We found that the human NLRP9 gene and its corresponding protein are highly expressed in human primordial and primary follicles. The NLRP9B protein is localized to the cytoplasm in the blastomeres of a 2-cell embryo in mice. SiRNA-mediated knockdown of Nlrp9b caused rapid elimination of endogenous Nlrp9b mRNA and premature embryo arrest at the 2- to 4-cell stages compared with that of the siRNA-scrambled control group. CONCLUSIONS These results suggest that mouse Nlrp9b, as a maternal effect gene, could contribute to mouse preimplantation embryo development. It remains to investigate whether NLRP9 have a crucial role in human preimplantation embryo and infertility.
Collapse
Affiliation(s)
| | | | - Adelya Galieva
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jens Agger
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Anders Heuck
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Piotr Siupka
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Erik Ernst
- The Fertility Clinic, Horsens Hospital, Horsens, Denmark.,The Fertility Clinic, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Morten S Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Lundbeck Foundation Research Initiative on Brain Barriers and Drug Delivery, Aarhus, Denmark
| | - Lone Sunde
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Karin Lykke-Hartmann
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark. .,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
5
|
NLRs as Helpline in the Brain: Mechanisms and Therapeutic Implications. Mol Neurobiol 2018; 55:8154-8178. [DOI: 10.1007/s12035-018-0957-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/12/2018] [Indexed: 12/13/2022]
|
6
|
Peng H, Lin X, Liu F, Wang C, Zhang W. NLRP9B protein is dispensable for oocyte maturation and early embryonic development in the mouse. J Reprod Dev 2015; 61:559-64. [PMID: 26411641 PMCID: PMC4685222 DOI: 10.1262/jrd.2015-050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nlrp9a, Nlrp9b and Nlrp9c are preferentially expressed in
oocytes and early embryos in the mouse. Simultaneous genetic ablation of Nlrp9a and
Nlrp9c does not affect early embryonic development, but the function of
Nlrp9b in the process of oocyte maturation and embryonic development has not been
elucidated. Here we show that both Nlrp9b mRNA and its protein are expressed in ovaries and
the small intestine. Moreover, the NLRP9B protein was restricted to oocytes in the ovary and declined with
oocyte aging. After ovulation and fertilization, NLRP9B protein was found in preimplantation embryos. Confocal
microscopy demonstrated that it was mainly localized in the cytoplasm in the oocytes and blastomeres. Thus,
this protein might play a role in oocyte maturation and early embryonic development. However, knockdown of
Nlrp9b expression in GV-stage oocytes using RNA interference did not affect oocyte
maturation or subsequent parthenogenetic development after Nlrp9b-deficient oocytes were
activated. Furthermore, Nlrp9b knockdown zygotes could reach the blastocyst stage after being
cultured for 3.5 days in vitro. These results provide the first evidence that the NLRP9B
protein is dispensable for oocyte maturation and early embryonic development in the mouse.
Collapse
Affiliation(s)
- Hui Peng
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian 350002, P. R. China
| | | | | | | | | |
Collapse
|
7
|
Abstract
The Nlrp gene family contains 20 members and plays a pivotal role in the innate immune and reproductive systems in the mouse. During evolution, seven Nlrp4 gene copies (named from Nlrp4a to Nlrp4g). Nlrp4a-Nlrp4g have arisen that display specific or preferential ovarian expression patterns. However, the expression pattern and localization of Nlrp4g in mouse preimplantation embryo development are unknown. Here we report that Nlrp4g was highly expressed in mature oocytes and zygotes, then downregulated and not detected after the 2-cell embryo stage. NLRP4G protein remained present through the blastocyst stage and was mainly localized in the cytoplasm. Furthermore, overexpression of Nlrp4g in zygotes did not affect normal development in terms of the rate of blastocyst formation. These results provide the first evidence that NLRP4G is a maternal factor that may play essential role during zygotic genome activation in the mouse.
Collapse
|
8
|
Van Gorp H, Kuchmiy A, Van Hauwermeiren F, Lamkanfi M. NOD-like receptors interfacing the immune and reproductive systems. FEBS J 2014; 281:4568-82. [PMID: 25154302 DOI: 10.1111/febs.13014] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/13/2014] [Accepted: 08/19/2014] [Indexed: 12/13/2022]
Abstract
Nucleotide-binding oligomerization domain receptors (NOD-like receptors, NLRs) are intracellular proteins that are chiefly known for their critical functions in inflammatory responses and host defense against microbial pathogens. Several NLRs have been demonstrated to assemble inflammasomes or to engage transcriptional signaling cascades that result in the production of pro-inflammatory cytokines and bactericidal factors. In recent years, NLRs have also emerged as key regulators of early mammalian embryogenesis and reproduction. A subset of phylogenetically related NLRs represents a new class of maternal effect genes that are highly expressed in maturing oocytes and pre-implantation embryos. Mutations in several of these NLRs have been linked to hereditary reproductive defects and imprinting diseases. In this review, we discuss the expression profiles, the emerging functions and molecular mode of action of these NLRs with newly recognized roles at the interfaces of the immune and reproductive systems. In addition, we provide an overview of coding mutations in NLRs that have been associated with human reproductive diseases, and outline crucial outstanding questions in this emerging research field.
Collapse
Affiliation(s)
- Hanne Van Gorp
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
| | | | | | | |
Collapse
|