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Hassan M, Shahzadi S, Yasir M, Chun W, Kloczkowski A. Computational prognostic evaluation of Alzheimer's drugs from FDA-approved database through structural conformational dynamics and drug repositioning approaches. Sci Rep 2023; 13:18022. [PMID: 37865690 PMCID: PMC10590448 DOI: 10.1038/s41598-023-45347-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
Drug designing is high-priced and time taking process with low success rate. To overcome this obligation, computational drug repositioning technique is being promptly used to predict the possible therapeutic effects of FDA approved drugs against multiple diseases. In this computational study, protein modeling, shape-based screening, molecular docking, pharmacogenomics, and molecular dynamic simulation approaches have been utilized to retrieve the FDA approved drugs against AD. The predicted MADD protein structure was designed by homology modeling and characterized through different computational resources. Donepezil and galantamine were implanted as standard drugs and drugs were screened out based on structural similarities. Furthermore, these drugs were evaluated and based on binding energy (Kcal/mol) profiles against MADD through PyRx tool. Moreover, pharmacogenomics analysis showed good possible associations with AD mediated genes and confirmed through detail literature survey. The best 6 drug (darifenacin, astemizole, tubocurarine, elacridar, sertindole and tariquidar) further docked and analyzed their interaction behavior through hydrogen binding. Finally, MD simulation study were carried out on these drugs and evaluated their stability behavior by generating root mean square deviation and fluctuations (RMSD/F), radius of gyration (Rg) and soluble accessible surface area (SASA) graphs. Taken together, darifenacin, astemizole, tubocurarine, elacridar, sertindole and tariquidar displayed good lead like profile as compared with standard and can be used as possible therapeutic agent in the treatment of AD after in-vitro and in-vivo assessment.
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Affiliation(s)
- Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA.
| | - Saba Shahzadi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Muhammad Yasir
- Department of Pharmacology, College of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Wanjoo Chun
- Department of Pharmacology, College of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA.
- Department of Pediatrics, The Ohio State University, Columbus, OH, 43205, USA.
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Roos D, van Leeuwen K, Madkaikar M, Kambli PM, Gupta M, Mathews V, Rawat A, Kuhns DB, Holland SM, de Boer M, Kanegane H, Parvaneh N, Lorenz M, Schwarz K, Klein C, Sherkat R, Jafari M, Wolach B, den Dunnen JT, Kuijpers TW, Köker MY. Hematologically important mutations: Leukocyte adhesion deficiency (second update). Blood Cells Mol Dis 2023; 99:102726. [PMID: 36696755 DOI: 10.1016/j.bcmd.2023.102726] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Leukocyte adhesion deficiency (LAD) is an immunodeficiency caused by defects in the adhesion of leukocytes (especially neutrophils) to the blood vessel wall. As a result, patients with LAD suffer from severe bacterial infections and impaired wound healing, accompanied by neutrophilia. In LAD-I, characterized directly after birth by delayed separation of the umbilical cord, mutations are found in ITGB2, the gene that encodes the β subunit (CD18) of the β2 integrins. In the rare LAD-II disease, the fucosylation of selectin ligands is disturbed, caused by mutations in SLC35C1, the gene that encodes a GDP-fucose transporter of the Golgi system. LAD-II patients lack the H and Lewis Lea and Leb blood group antigens. Finally, in LAD-III, the conformational activation of the hematopoietically expressed β integrins is disturbed, leading to leukocyte and platelet dysfunction. This last syndrome is caused by mutations in FERMT3, encoding the kindlin-3 protein in all blood cells, involved in the regulation of β integrin conformation. This article contains an update of the mutations that we consider to be relevant for the various forms of LAD.
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Affiliation(s)
- Dirk Roos
- Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Karin van Leeuwen
- Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Manisha Madkaikar
- Pediatric Immunology and Leukocyte Biology Lab CMR, National Institute of Immunohaematology, K E M Hospital, Parel, Mumbai, India
| | - Priyanka M Kambli
- Pediatric Immunology and Leukocyte Biology Lab CMR, National Institute of Immunohaematology, K E M Hospital, Parel, Mumbai, India
| | - Maya Gupta
- Pediatric Immunology and Leukocyte Biology Lab CMR, National Institute of Immunohaematology, K E M Hospital, Parel, Mumbai, India
| | - Vikram Mathews
- Dept of Hematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Amit Rawat
- Paediatric Allergy Immunology Unit, Department of Paediatrics, Advanced Paediatrics Centre, Chandigarh, India
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Martin de Boer
- Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Nima Parvaneh
- Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Myriam Lorenz
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany; Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg - Hessen, Ulm, Germany
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Roya Sherkat
- Immunodeficiency Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahbube Jafari
- Immunodeficiency Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Baruch Wolach
- Pediatric Immunology Service, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Johan T den Dunnen
- Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Taco W Kuijpers
- Sanquin Research, and Landsteiner Laboratory, Amsterdam University Medical Center, location AMC, University of Amsterdam, Amsterdam, the Netherlands; Emma Children's Hospital, Amsterdam University Medical Centre, location AMC, Amsterdam, the Netherlands
| | - M Yavuz Köker
- Department of Immunology, Erciyes Medical School, University of Erciyes, Kayseri, Türkiye
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Novel ITGB2 Mutation Is Responsible for a Severe Form of Leucocyte Adhesion Deficiency Type 1. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1141280. [PMID: 35281597 PMCID: PMC8913115 DOI: 10.1155/2022/1141280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/10/2022] [Indexed: 11/18/2022]
Abstract
Leukocyte adhesion deficiency type 1 (LAD1) is a rare autosomal recessive hereditary disorder characterized by recurrent infections, impaired pus formation, delayed wound healing, omphalitis, and delayed separation of the umbilical cord as hallmark features of the disease. It results from mutations in the integrin β2 subunit gene ITGB2, which encodes the integrin beta chain-2 protein CD18. In this study, we aimed to investigate the case of a five-month-old boy who presented with a clinical phenotype and flow cytometry results suggesting LAD1 disease. Sanger sequencing of all exons and intron boundaries of ITGB2 identified a novel in-frame deletion in exon 7 (ITGB2 c.844_846delAAC, p.Asn282del) in the patient. The p.Asn282del mutation was heterozygous in the child's parents, whereas it was absent in the 96 control individuals from North Africa. This variant was evaluated by two in silico mutation analysis tools, PROVEAN and MutationTaster, which predicted that the mutation was likely to be pathogenic. In addition, molecular modeling with the YASARA View software suggested that this novel mutation may affect the structure of integrin beta-2 and, subsequently, its interaction with integrin alpha-X. In summary, we report a novel pathogenic mutation p.Asn282del associated with LAD1 that expands the mutation diversity of ITGB2 and suggest the combination of flow cytometry and ITGB2 sequencing as a first-line diagnostic approach for LAD disease.
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Chen G, Zhou L, Chen Q, Wang J, Jiang P, Shen R, Long M, Zhou H. Case Report: A Deletion Variant in the DCAF17 Gene Underlying Woodhouse-Sakati Syndrome in a Chinese Consanguineous Family. Front Genet 2021; 12:741323. [PMID: 34630532 PMCID: PMC8498701 DOI: 10.3389/fgene.2021.741323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022] Open
Abstract
Woodhouse-Sakati syndrome (WSS, MIM 241080) is a rare neuroendocrine disease characterized by hair loss, hypogonadism, diabetes, hearing loss, and extrapyramidal syndrome, and is usually caused by mutations in the DCAF17 gene as an inherited disease. DCAF17 plays an important role in mammalian gonadal development and infertility. So far, there have been no WSS reports in China. The patient introduced in this case is from a consanguineous family. The main symptoms of the patient were alopecia and gonadal agenesis. Other symptoms such as hearing loss, intellectual disability, and hyperglycemia were remarkable, and these symptoms are often observed in WSS patients. We found a nonsense mutation in the 11th exon of the gene DCAF17 (Refseq: NM_025000) in the patient and her younger brother, which confirmed the diagnosis of WSS. The genetic results also showed that the mutation was inherited from their healthy first-cousin parents.
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Affiliation(s)
- Guangmin Chen
- Department of Endocrinology, University-Town Hospital of Chongqing Medical University, Chongqing, China
| | - Ling Zhou
- Department of Endocrinology, Translational Research Key Laboratory for Diabetes, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qimou Chen
- Department of Endocrinology, University-Town Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Wang
- Department of Endocrinology, University-Town Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Jiang
- Department of Endocrinology, University-Town Hospital of Chongqing Medical University, Chongqing, China
| | - Rufei Shen
- Department of Endocrinology, Translational Research Key Laboratory for Diabetes, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Min Long
- Department of Endocrinology, Translational Research Key Laboratory for Diabetes, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Houdi Zhou
- Department of Endocrinology, University-Town Hospital of Chongqing Medical University, Chongqing, China
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Qin R, Peng W, Wang X, Li C, Xi Y, Zhong Z, Sun C. Identification of Genes Related to Immune Infiltration in the Tumor Microenvironment of Cutaneous Melanoma. Front Oncol 2021; 11:615963. [PMID: 34136377 PMCID: PMC8202075 DOI: 10.3389/fonc.2021.615963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/28/2021] [Indexed: 01/02/2023] Open
Abstract
Cutaneous melanoma (CM) is the leading cause of skin cancer deaths and is typically diagnosed at an advanced stage, resulting in a poor prognosis. The tumor microenvironment (TME) plays a significant role in tumorigenesis and CM progression, but the dynamic regulation of immune and stromal components is not yet fully understood. In the present study, we quantified the ratio between immune and stromal components and the proportion of tumor-infiltrating immune cells (TICs), based on the ESTIMATE and CIBERSORT computational methods, in 471 cases of skin CM (SKCM) obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) were analyzed by univariate Cox regression analysis, least absolute shrinkage, and selection operator (LASSO) regression analysis, and multivariate Cox regression analysis to identify prognosis-related genes. The developed prognosis model contains ten genes, which are all vital for patient prognosis. The areas under the curve (AUC) values for the developed prognostic model at 1, 3, 5, and 10 years were 0.832, 0.831, 0.880, and 0.857 in the training dataset, respectively. The GSE54467 dataset was used as a validation set to determine the predictive ability of the prognostic signature. Protein–protein interaction (PPI) analysis and weighted gene co-expression network analysis (WGCNA) were used to verify “real” hub genes closely related to the TME. These hub genes were verified for differential expression by immunohistochemistry (IHC) analyses. In conclusion, this study might provide potential diagnostic and prognostic biomarkers for CM.
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Affiliation(s)
- Rujia Qin
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Wen Peng
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Xuemin Wang
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Chunyan Li
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Yan Xi
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Zhaoming Zhong
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China.,Department of Medical Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chuanzheng Sun
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
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Qian X, Wang P, Wang H, Jiang W, Sun J, Wang X, Zhai X. Successful umbilical cord blood transplantation in children with leukocyte adhesion deficiency type I. Transl Pediatr 2020; 9:34-42. [PMID: 32154133 PMCID: PMC7036647 DOI: 10.21037/tp.2020.01.06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND This study aims to investigate the efficacy and safety of umbilical cord blood transplantation (UCBT) without serotherapy for treating children with leukocyte adhesion deficiency type I (LAD-I). METHODS Clinical characteristics and data of five children with LAD-I who underwent UCBT at our hospital between September 2016 and September 2018 were retrospectively analyzed. RESULTS Five (two boys and three girls) patients with LAD-I were included. The median age at UCBT was 9 months (range, 8 to 32 months). The same myeloablative conditioning regimen was administered for each patient and included busulfan, fludarabine, and cyclophosphamide. HLA matching of patients and umbilical cord blood was 8/10 to 10/10. The median dose of total nucleated cells (TNC) infused was 10.2×107/kg (range, 4.5×107 to 20.6×107/kg) and the median dose of CD34+ cells was 3.2×105/kg (range, 1.9×105 to 5.7×105/kg). The median time of neutrophil engraftment was 20 days (range, 13 to 28 days). The median time of platelet engraftment was 36 days (range, 32 to 56 days). All patients received complete donor chimerism (CDC). Four of the five patients developed grade II-IV acute graft-versus-host disease (GvHD). The median follow-up time after transplantation was 19 months (range, 8 to 38 months). Four of the patients survived and achieved complete clinical remission. The other patient died of bronchiolitis obliterans 8 months after UCBT. CONCLUSIONS UCBT is an effective treatment method for LAD-I patients. Also, severe LAD-I patients should undergo stem cell transplantation as early as possible.
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Affiliation(s)
- Xiaowen Qian
- Department of Hematology/Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Ping Wang
- Department of Hematology/Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Hongsheng Wang
- Department of Hematology/Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Wenjin Jiang
- Department of Hematology/Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jinqiao Sun
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaochuan Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaowen Zhai
- Department of Hematology/Oncology, Children's Hospital of Fudan University, Shanghai 201102, China
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