1
|
Zhao H, Li H, Liu Q, Dong G, Hou C, Li Y, Zhao Y. Using TransR to enhance drug repurposing knowledge graph for COVID-19 and its complications. Methods 2024; 221:82-90. [PMID: 38104883 DOI: 10.1016/j.ymeth.2023.12.001] [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: 09/21/2023] [Revised: 11/14/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
MOTIVATION The COVID-19 pandemic has been spreading globally for four years, yet specific drugs that effectively suppress the virus remain elusive. Furthermore, the emergence of complications associated with COVID-19 presents significant challenges, making the development of therapeutics for COVID-19 and its complications an urgent task. However, traditional drug development processes are time-consuming. Drug repurposing, which involves identifying new therapeutic applications for existing drugs, presents a viable alternative. RESULT In this study, we construct a knowledge graph by retrieving information on genes, drugs, and diseases from databases such as DRUGBANK and GNBR. Next, we employ the TransR knowledge representation learning approach to embed entities and relationships into the knowledge graph. Subsequently, we train the knowledge graph using a graph neural network model based on TransR scoring. This trained knowledge graph is then utilized to predict drugs for the treatment of COVID-19 and its complications. Based on experimental results, we have identified 15 drugs out of the top 30 with the highest success rates associated with treating COVID-19 and its complications. Notably, out of these 15 drugs, 10 specifically aimed at treating COVID-19, such as Torcetrapib and Tocopherol, has not been previously identified in the knowledge graph. This finding highlights the potential of our model in aiding healthcare professionals in drug development and research related to this disease.
Collapse
Affiliation(s)
- Hongxi Zhao
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Hongfei Li
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China; College of Life Science, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Qiaoming Liu
- School of Medicine and Health, Harbin Institute of Technology, 150001, Harbin, HeiLongJiang, China; Zhengzhou Research Institute, Harbin Institute of Technology, 450000, Zhengzhou, Henan, China
| | - Guanghui Dong
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Chang Hou
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Yang Li
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China.
| | - Yuming Zhao
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China; College of Life Science, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China.
| |
Collapse
|
2
|
Nag S, Mandal S, Mukherjee O, Mukherjee S, Kundu R. DPP-4 Inhibitors as a savior for COVID-19 patients with diabetes. Future Virol 2023:10.2217/fvl-2022-0112. [PMID: 37064327 PMCID: PMC10096336 DOI: 10.2217/fvl-2022-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 03/01/2023] [Indexed: 04/18/2023]
Abstract
Diabetic patients are at particular risk of severe COVID-19. Human dipeptidyl peptidase-4 (DPP-4) is a membrane-bound aminopeptidase that regulates insulin release by inactivating incretin. DPP-4 inhibitors (DPP-4is) are therefore used as oral anti-diabetic drugs to restore normal insulin levels. These molecules also have anti-inflammatory and anti-hypertension effects. Recent studies on the interactions of SARS-CoV-2 spike glycoprotein and DPP-4 predict a possible entry route for SARS-CoV-2. Therefore, DPP-4is could be effective at reducing the virus-induced 'cytokine storm', thereby ceasing inflammatory injury to vital organs. Moreover, DPP-4is may interfere with viral entry into host cells. Herein, we have reviewed the efficacy of DPP-4is as potential repurposed drugs to reduce the severity of SARS-CoV-2 infection in patients with diabetes.
Collapse
Affiliation(s)
- Snehasish Nag
- Department of Zoology, Cell Signaling Laboratory, Visva-Bharati University, Santiniketan, West Bengal, 731 235, India
| | - Samanwita Mandal
- Department of Zoology, Cell Signaling Laboratory, Visva-Bharati University, Santiniketan, West Bengal, 731 235, India
| | - Oindrila Mukherjee
- Department of Zoology, Cell Signaling Laboratory, Visva-Bharati University, Santiniketan, West Bengal, 731 235, India
| | - Suprabhat Mukherjee
- Department of Animal Science, Integrative Biochemistry & Immunology Laboratory, Kazi Nazrul University, Asansol, West Bengal, 713 340, India
- Author for correspondence:
| | - Rakesh Kundu
- Department of Zoology, Cell Signaling Laboratory, Visva-Bharati University, Santiniketan, West Bengal, 731 235, India
- Author for correspondence:
| |
Collapse
|
3
|
Maleksabet H, Rezaee E, Tabatabai SA. Host-Cell Surface Binding Targets in SARS-CoV-2 for Drug Design. Curr Pharm Des 2022; 28:3583-3591. [PMID: 36420875 DOI: 10.2174/1381612829666221123111849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/20/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022]
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a major public health threat to all countries worldwide. SARS-CoV-2 interactions with its receptor are the first step in the invasion of the host cell. The coronavirus spike protein (S) is crucial in binding to receptors on host cells. Additionally, targeting the SARS-CoV-2 viral receptors is considered a therapeutic option in this regard. In this review of literature, we summarized five potential host cell receptors, as host-cell surface bindings, including angiotensin-converting enzyme 2 (ACE2), neuropilin 1 (NRP-1), dipeptidyl peptidase 4 (DPP4), glucose regulated protein-78 (GRP78), and cluster of differentiation 147 (CD147) related to the SARS-CoV-2 infection. Among these targets, ACE2 was recognized as the main SARS-CoV-2 receptor, expressed at a low/moderate level in the human respiratory system, which is also involved in SARS-CoV-2 entrance, so the virus may utilize other secondary receptors. Besides ACE2, CD147 was discovered as a novel SARS-CoV-2 receptor, CD147 appears to be an alternate receptor for SARSCoV- 2 infection. NRP-1, as a single-transmembrane glycoprotein, has been recently found to operate as an entrance factor and enhance SARS Coronavirus 2 (SARS-CoV-2) infection under in-vitro. DPP4, which was discovered as the first gene clustered with ACE2, may serve as a potential SARS-CoV-2 spike protein binding target. GRP78 could be recognized as a secondary receptor for SARS-CoV-2 because it is widely expressed at substantially greater levels, rather than ACE2, in bronchial epithelial cells and the respiratory mucosa. This review highlights recent literature on this topic.
Collapse
Affiliation(s)
- Hanieh Maleksabet
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elham Rezaee
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sayyed Abbas Tabatabai
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
4
|
Singh AK, Khunti K. COVID-19 and Diabetes. Annu Rev Med 2022. [DOI: https:/doi.org/10.1146/annurev-med-042220-011857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The prevalence of diabetes in people with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has varied worldwide. Most of the available evidence suggests a significant increase in severity and mortality of COVID-19 in people with either type 1 (T1DM) or type 2 diabetes mellitus (T2DM), especially in association with poor glycemic control. While new-onset hyperglycemia and new-onset diabetes (both T1DM and T2DM) have been increasingly recognized in the context of COVID-19 and have been associated with worse outcome, no conclusive evidence yet suggests direct tropism of SARS-CoV-2 on the β cells of pancreatic islets. While all approved oral antidiabetic agents appear to be safe in people with T2DM having COVID-19, no conclusive data are yet available to indicate a mortality benefit with any class of these drugs, in the absence of large randomized controlled trials.
Collapse
Affiliation(s)
- Awadhesh Kumar Singh
- Department of Diabetes and Endocrinology, G.D. Hospital and Diabetes Institute, Kolkata 700014, India
| | - Kamlesh Khunti
- Department of Primary Care Diabetes and Vascular Medicine, Leicester Diabetes Research Centre, Leicester LE5 4PW, United Kingdom
| |
Collapse
|
5
|
Abstract
The prevalence of diabetes in people with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has varied worldwide. Most of the available evidence suggests a significant increase in severity and mortality of COVID-19 in people with either type 1 (T1DM) or type 2 diabetes mellitus (T2DM), especially in association with poor glycemic control. While new-onset hyperglycemia and new-onset diabetes (both T1DM and T2DM) have been increasingly recognized in the context of COVID-19 and have been associated with worse outcome, no conclusive evidence yet suggests direct tropism of SARS-CoV-2 on the β cells of pancreatic islets. While all approved oral antidiabetic agents appear to be safe in people with T2DM having COVID-19, no conclusive data are yet available to indicate a mortality benefit with any class of these drugs, in the absence of large randomized controlled trials. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Awadhesh Kumar Singh
- Department of Diabetes and Endocrinology, G.D. Hospital and Diabetes Institute, Kolkata 700014, India;
| | - Kamlesh Khunti
- Department of Primary Care Diabetes and Vascular Medicine, Leicester Diabetes Research Centre, Leicester LE5 4PW, United Kingdom
| |
Collapse
|
6
|
Pathan F, Selim S, Fariduddin M, Rahman MH, Ashrafuzzaman SM, Afsana F, Qureshi NK, Hossain T, Saifuddin M, Kamrul-Hasan AB, Mir AS. Bangladesh Endocrine Society (BES) Position Statement for Management of Diabetes and Other Endocrine Diseases in Patients with COVID-19. Diabetes Metab Syndr Obes 2021; 14:2217-2228. [PMID: 34040407 PMCID: PMC8140905 DOI: 10.2147/dmso.s293688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/26/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The year 2020 witnessed a largely unprecedented pandemic of coronavirus disease (COVID-19), caused by SARS COV-2. Many people with COVID-19 have comorbidities, including diabetes, hypertension and cardiovascular diseases, which are significantly associated with worse outcomes. Moreover, COVID-19 itself is allied with deteriorating hyperglycemia. Therefore, Bangladesh Endocrine Society has formulated some practical recommendations for management of diabetes and other endocrine diseases in patients with COVID-19 for use in both primary and specialist care settings. OBJECTIVE The objective of the article is to develop a guideline to protect the vulnerable group with utmost preference - the elderly and those with comorbid conditions. Therefore, to ensure the adequate protective measures and timely treatment for COVID-19 patients with diabetes, other endocrine diseases or any other comorbidities. CONSIDERING AND MONITORING ISSUES The risk of a fatal outcome from COVID-19 may be up to 50% higher in patients with diabetes than in non-diabetics.Patients with diabetes and COVID had CFR 7.3-9.2%, compared with 0.9-1.4% in patients without comorbidities.Diabetic ketoacidosis may be one of the causes of mortality in COVID-19.There is wide fluctuation of blood glucose in these patients, probably due to irregular diet, reduced exercise, increased glucocorticoids secretion, and use of glucocorticoids. HbA1c should be <7.0% for the majority of the patients, this target may be relaxed in appropriate clinical settings.More emphasis should be given on day-to-day blood glucose levels. Hypoglycemia (<3.9 mmol/l) must be avoided.Frequent monitoring of blood glucose is needed in critically ill patients. CONCLUSION The fight against COVID-19 has been proven to be a challenging one. Therefore, all healthcare personnel should make the best use of updated knowledge and skills to ensure adequate protective measures and timely treatment for COVID-19 patients with diabetes, other endocrine diseases or any other comorbidities.
Collapse
Affiliation(s)
- Faruque Pathan
- Department of Endocrinology, BIRDEM General Hospital, Dhaka, Bangladesh
| | - Shahjada Selim
- Department of Endocrinology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md Fariduddin
- Department of Endocrinology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | | | - S M Ashrafuzzaman
- Department of Endocrinology, BIRDEM General Hospital, Dhaka, Bangladesh
| | - Faria Afsana
- Department of Endocrinology, BIRDEM General Hospital, Dhaka, Bangladesh
| | | | - Tanjina Hossain
- Department of Endocrinology, Green Life Medical College Hospital, Dhaka, Bangladesh
| | - M Saifuddin
- Department of Endocrinology, Dhaka Medical College Hospital, Dhaka, Bangladesh
| | | | - Ahmed Salam Mir
- Department of Endocrinology, BIHS General Hospital, Dhaka, Bangladesh
| | - On behalf of the BES Diabetes and COVID Task Force
- Department of Endocrinology, BIRDEM General Hospital, Dhaka, Bangladesh
- Department of Endocrinology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
- Bangladesh Endocrine Society, Dhaka, Bangladesh
- National Healthcare Network (NHN) Uttara EC, Dhaka, Bangladesh
- Department of Endocrinology, Green Life Medical College Hospital, Dhaka, Bangladesh
- Department of Endocrinology, Dhaka Medical College Hospital, Dhaka, Bangladesh
- Mymensingh Medical College Hospital, Dhaka, Bangladesh
- Department of Endocrinology, BIHS General Hospital, Dhaka, Bangladesh
| |
Collapse
|
7
|
Scheen AJ. DPP-4 inhibition and COVID-19: From initial concerns to recent expectations. DIABETES & METABOLISM 2021; 47:101213. [PMID: 33249199 PMCID: PMC7690941 DOI: 10.1016/j.diabet.2020.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/15/2020] [Indexed: 12/18/2022]
Abstract
Dipeptidyl peptidase-4 inhibitors (DPP-4is) have gained a key place in the management of type 2 diabetes mellitus (T2DM) essentially because of their good safety profile even in the frail population. DPP-4, originally known as 'T-cell antigen CD26', is expressed in many immune cells and regulates their functions, so the initial concern over the use of DPP-4is was the possible increased susceptibility to infections. Furthermore, because of the high affinity between human DPP-4 and the spike (S) receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it was suspected that this virus, responsible for coronavirus disease 2019 (COVID-19), might be able to use the DPP-4 enzyme as a functional receptor to gain entry into the host. However, DPP-4is also exert anti-inflammatory effects, which could be beneficial in patients exposed to cytokine storms due to COVID-19. Yet, when observational (mostly retrospective) studies compared clinical outcomes in DPP-4i users vs non-users among diabetes patients with COVID-19, the overall results regarding the risk of progression towards more severe forms of the disease and mortality were heterogeneous, thereby precluding any definite conclusions. Nevertheless, new expectations have arisen following recent reports of significant reductions in admissions to intensive care units and mortality in DPP-4i users. However, given the limitations inherent in such observational studies, any available results should be considered, at best, as hypothetical and only suggestive of potentially substantial benefits with DPP-4is in diabetes patients with COVID-19. While the safe use of DPP-4is in COVID-19 patients appears to be an acceptable hypothesis, all such positive findings still need to be confirmed in randomized controlled trials (a few of which are currently ongoing) before any recommendations can be made for clinical practice.
Collapse
Affiliation(s)
- André J Scheen
- Division of Diabetes, Nutrition and Metabolic Disorders, CHU Liège, Liège, Belgium; Division of Clinical Pharmacology, Centre for Interdisciplinary Research on Medicines (CIRM), Liège University, Liège, Belgium.
| |
Collapse
|
8
|
Singh AK, Singh R, Saboo B, Misra A. Non-insulin anti-diabetic agents in patients with type 2 diabetes and COVID-19: A Critical Appraisal of Literature. Diabetes Metab Syndr 2021; 15:159-167. [PMID: 33352455 PMCID: PMC7832723 DOI: 10.1016/j.dsx.2020.12.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND & AIMS Several observational studies have recently reported the outcomes of non-insulin anti-diabetic agents (ADA) in patients with T2DM and coronavirus disease 2019 (COVID-19). We sought to review the literature to appraise the clinicians on these outcomes. METHODS A literature search using the specific keywords was carried out in the database of PubMed, MedRxiv and Google Scholar up till December 11, 2020 applying Boolean method. Full text of all the relevant articles that reported the outcomes of ADA in patients with T2DM and COVID-19 were retrieved. Subsequently, an appraisal of literature report was narratively presented. RESULTS Available studies that reported the outcomes of ADA are either case series or retrospective cohorts or prospective observational studies, in absence of the randomized controlled trials (RCTs). Results from these observational studies suggest that amongst all the non-insulin ADA, metformin users prior to the hospitalization had improved outcomes compared to the non-users. Data for dipeptidyl-peptidase-4 inhibitors (DPP-4i) are encouraging although inconsistent. No documentation of any harm or benefit has been observed for sulfonylureas (SUs), sodium glucose co-transporter-2 inhibitors (SGLT-2i) and glucagon-like peptide receptor agonists (GLP-1RAs). No data is yet available for pioglitazone. CONCLUSION Metformin and DPP-4i should be continued in patients with T2DM until hospitalization or unless contraindicated. No evidence of harm suggests that SUs, SGLT-2i or GLP-1RAs may not be stopped unless very sick, hospitalized or contraindicated. The results from RCTs are needed to claim any meaningful benefit with either metformin or DPP-4i in patients with T2DM and COVID-19.
Collapse
Affiliation(s)
| | - Ritu Singh
- G.D Hospital & Diabetes Institute, Kolkata, India
| | | | - Anoop Misra
- Fortis CDOC Hospital for Diabetes and Allied Science, Chirag Enclave, New Delhi, India; National Diabetes, Obesity and Cholesterol Foundation, New Delhi, India; Diabetes Foundation (India), New Delhi, India
| |
Collapse
|
9
|
Bodhini D, Mohan V. Management of coronavirus disease-2019 (COVID-19) in patients with diabetes. JOURNAL OF DIABETOLOGY 2020. [DOI: 10.4103/jod.jod_67_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|