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Gu Y, Xu Z, Yang C. Empowering Graph Neural Network-Based Computational Drug Repositioning with Large Language Model-Inferred Knowledge Representation. Interdiscip Sci 2024:10.1007/s12539-024-00654-7. [PMID: 39325266 DOI: 10.1007/s12539-024-00654-7] [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: 05/30/2024] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 09/27/2024]
Abstract
Computational drug repositioning, through predicting drug-disease associations (DDA), offers significant potential for discovering new drug indications. Current methods incorporate graph neural networks (GNN) on drug-disease heterogeneous networks to predict DDAs, achieving notable performances compared to traditional machine learning and matrix factorization approaches. However, these methods depend heavily on network topology, hampered by incomplete and noisy network data, and overlook the wealth of biomedical knowledge available. Correspondingly, large language models (LLMs) excel in graph search and relational reasoning, which can possibly enhance the integration of comprehensive biomedical knowledge into drug and disease profiles. In this study, we first investigate the contribution of LLM-inferred knowledge representation in drug repositioning and DDA prediction. A zero-shot prompting template was designed for LLM to extract high-quality knowledge descriptions for drug and disease entities, followed by embedding generation from language models to transform the discrete text to continual numerical representation. Then, we proposed LLM-DDA with three different model architectures (LLM-DDANode Feat, LLM-DDADual GNN, LLM-DDAGNN-AE) to investigate the best fusion mode for LLM-based embeddings. Extensive experiments on four DDA benchmarks show that, LLM-DDAGNN-AE achieved the optimal performance compared to 11 baselines with the overall relative improvement in AUPR of 23.22%, F1-Score of 17.20%, and precision of 25.35%. Meanwhile, selected case studies of involving Prednisone and Allergic Rhinitis highlighted the model's capability to identify reliable DDAs and knowledge descriptions, supported by existing literature. This study showcases the utility of LLMs in drug repositioning with its generality and applicability in other biomedical relation prediction tasks.
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Affiliation(s)
- Yaowen Gu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Zidu Xu
- School of Nursing, Columbia University, 560 W 168th Street, New York, NY, 10032, USA.
| | - Carl Yang
- Department of Computer Science, Emory College of Arts and Sciences, Emory University, Atlanta, GA, 30322, USA
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2
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Li G, Li S, Liang C, Xiao Q, Luo J. Drug repositioning based on residual attention network and free multiscale adversarial training. BMC Bioinformatics 2024; 25:261. [PMID: 39118000 PMCID: PMC11308596 DOI: 10.1186/s12859-024-05893-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/06/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Conducting traditional wet experiments to guide drug development is an expensive, time-consuming and risky process. Analyzing drug function and repositioning plays a key role in identifying new therapeutic potential of approved drugs and discovering therapeutic approaches for untreated diseases. Exploring drug-disease associations has far-reaching implications for identifying disease pathogenesis and treatment. However, reliable detection of drug-disease relationships via traditional methods is costly and slow. Therefore, investigations into computational methods for predicting drug-disease associations are currently needed. RESULTS This paper presents a novel drug-disease association prediction method, RAFGAE. First, RAFGAE integrates known associations between diseases and drugs into a bipartite network. Second, RAFGAE designs the Re_GAT framework, which includes multilayer graph attention networks (GATs) and two residual networks. The multilayer GATs are utilized for learning the node embeddings, which is achieved by aggregating information from multihop neighbors. The two residual networks are used to alleviate the deep network oversmoothing problem, and an attention mechanism is introduced to combine the node embeddings from different attention layers. Third, two graph autoencoders (GAEs) with collaborative training are constructed to simulate label propagation to predict potential associations. On this basis, free multiscale adversarial training (FMAT) is introduced. FMAT enhances node feature quality through small gradient adversarial perturbation iterations, improving the prediction performance. Finally, tenfold cross-validations on two benchmark datasets show that RAFGAE outperforms current methods. In addition, case studies have confirmed that RAFGAE can detect novel drug-disease associations. CONCLUSIONS The comprehensive experimental results validate the utility and accuracy of RAFGAE. We believe that this method may serve as an excellent predictor for identifying unobserved disease-drug associations.
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Affiliation(s)
- Guanghui Li
- School of Information Engineering, East China Jiaotong University, Nanchang, China.
| | - Shuwen Li
- School of Information Engineering, East China Jiaotong University, Nanchang, China
| | - Cheng Liang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Qiu Xiao
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
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3
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Borba JRBDM, de Araújo LP, Veloso MP, da Silveira NJF. Applying the bioisosterism strategy to obtain lead compounds against SARS-CoV-2 cysteine proteases: An in-silico approach. J Comput Chem 2024; 45:35-46. [PMID: 37641955 DOI: 10.1002/jcc.27217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/17/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
SARS-CoV-2 cysteine proteases are essential nonstructural proteins due to their role in the formation of the virus multiple enzyme replication-transcription complex. As a result, those functional proteins are extremely relevant targets in the development of a new drug candidate to fight COVID-19. Based on this fact and guided by the bioisosterism strategy, the present work has selected 126 out of 1050 ligands from DrugBank website. Subsequently, 831 chemical analogs containing bioisosteres, some of which became structurally simplified, were created using the MB-Isoster software, and molecular docking simulations were performed using AutoDock Vina. Finally, a study of physicochemical properties, along with pharmacokinetic profiles, was carried out through SwissADME and ADMETlab 2.0 platforms. The promising results obtained with the molecules encoded as DB00549_BI_005, DB04868_BI_003, DB11984_BI_002, DB12364_BI_006 and DB12805_BI_004 must be confirmed by molecular dynamics studies, followed by in vitro and in vivo empirical tests that ratify the advocated in-silico results.
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Affiliation(s)
- João Ricardo Bueno de Morais Borba
- João Ricardo Bueno de Morais Borba, Laboratory of Molecular Modeling and Computer Simulation - MolMod-CS, Institute of Chemistry, Federal University of Alfenas - UNIFAL-MG, Alfenas, Brazil
| | - Leonardo Pereira de Araújo
- Leonardo Pereira de Araújo, Laboratory of Molecular Modeling and Computer Simulation - MolMod-CS, Institute of Chemistry, Federal University of Alfenas - UNIFAL-MG, Alfenas, Brazil
| | - Marcia Paranho Veloso
- Marcia Paranho Veloso, Laboratory of Molecular Modeling and Computer Simulation - MolMod-CS, Institute of Chemistry, Federal University of Alfenas - UNIFAL-MG, Alfenas, Brazil
| | - Nelson José Freitas da Silveira
- Nelson José Freitas da Silveira, Laboratory of Molecular Modeling and Computer Simulation - MolMod-CS, Institute of Chemistry, Federal University of Alfenas - UNIFAL-MG, Alfenas, Brazil
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4
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Aleebrahim-Dehkordi E, Soveyzi F, Deravi N, Saghazadeh A, Rezaei N. Mental Healthcare in Pediatrics During the COVID-19 Pandemic: A Call for International Public Health Action. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1458:19-34. [PMID: 39102187 DOI: 10.1007/978-3-031-61943-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Public health measures associated with coronavirus disease 2019 (COVID-19), such as lockdowns and quarantine of suspected cases, can negatively affect children's mental health status. Although the current crisis provides personal growth and family cohesion opportunities, pitfalls appear to outweigh the benefits. The magnitude and quality of its impact on children depend on several factors, including anxiety, lack of social contact, and a reduced opportunity for stress regulation, along with an increased risk for parental mental health issues, child maltreatment, and domestic violence. Children with special needs and social disadvantages like trauma experiences, disabilities, pre-existing mental illness, e.g., autism spectrum disorders and hyperactivity, and low socioeconomic status, may be at higher risk in this context. Here, the potentials social support can provide for pediatrics, both healthy children and children with special needs, are reviewed after an overview of quarantine's adverse effects on this special population during a pandemic. The most common psychological issues associated with the COVID-19 pandemic are sleep disorders, mood swings, depression, anxiety, decreased attention, stress, irritability, anger, and fear. Moreover, the impact of COVID-19 on children's physical health includes weight gain, reduced physical activity, immune dysregulation, and cardiometabolic disorders. All support systems, involving parents, teachers/school counselors, pediatricians, mental healthcare workers, and Health and Art (HEART) groups, need to enter the scene and make their share of children's mental health care.
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Affiliation(s)
- Elahe Aleebrahim-Dehkordi
- Systematic Review and Meta-Analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Faezeh Soveyzi
- Systematic Review and Meta-Analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Radiology Resident at MUMS, Radiology Department Mashhad University of Medical Sciences, Mashhad, Iran
| | - Niloofar Deravi
- Systematic Review and Meta-Analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Student's Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amene Saghazadeh
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Dr. Qarib St, Keshavarz Blvd, 14194, Tehran, Iran
- MetaCognition Interest Group (MCIG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Dr. Qarib St, Keshavarz Blvd, 14194, Tehran, Iran.
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
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5
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Yazdanpanah N, Sedikides C, Ochs HD, Camargo CA, Darmstadt GL, Cerda A, Cauda V, Peters GJ, Sellke F, Wong ND, Comini E, Jimeno AR, Glover V, Hatziargyriou N, Vincenot CE, Bordas SPA, Rao IM, Abolhassani H, Gharehpetian GB, Weiskirchen R, Gupta M, Chandel SS, Olusanya BO, Cheson B, Pomponio A, Tanzer M, Myles PS, Ma WX, Bella F, Ghavami S, Moein Moghimi S, Pratico D, Hernandez AM, Martinez-Urbistondo M, Urbistondo DM, Fereshtehnejad SM, Ali I, Kimura S, Wallace Hayes A, Cai W, Ernest CKJ, Thomas S, Rahimi K, Sorooshian A, Schreiber M, Kato K, Luong JHT, Pluchino S, Lozano AM, Seymour JF, Kosik KS, Hofmann SG, McIntyre RS, Perc M, Leemans A, Klein RS, Ogino S, Wlezien C, Perry G, Nieto JJ, Levin L, Klionsky DJ, Mobasher B, Dorigo T, Rezaei N. Global Challenges After a Global Challenge: Lessons Learned from the COVID-19 Pandemic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1457:1-31. [PMID: 39283418 DOI: 10.1007/978-3-031-61939-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Coronavirus disease 2019 (COVID-19) has affected not only individual lives but also the world and global systems, both natural and human-made. Besides millions of deaths and environmental challenges, the rapid spread of the infection and its very high socioeconomic impact have affected healthcare, economic status and wealth, and mental health across the globe. To better appreciate the pandemic's influence, multidisciplinary and interdisciplinary approaches are needed. In this chapter, world-leading scientists from different backgrounds share collectively their views about the pandemic's footprint and discuss challenges that face the international community.
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Affiliation(s)
- Niloufar Yazdanpanah
- , Houston, USA
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hans D Ochs
- , Houston, USA
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA, USA
| | - Carlos A Camargo
- , Houston, USA
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Gary L Darmstadt
- , Houston, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Artemi Cerda
- , Houston, USA
- Soil Erosion and Degradation Research Group, Department of Geography, Valencia University, Blasco Ibàñez, Valencia, Spain
| | - Valentina Cauda
- , Houston, USA
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi, Turin, Italy
| | - Godefridus J Peters
- , Houston, USA
- Laboratory Medical Oncology, Amsterdam University Medical Centers, Location VUMC, Amsterdam, the Netherlands
- Department of Biochemistry, Medical University of Gdańsk, Gdańsk, Poland
| | - Frank Sellke
- , Houston, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
- Division of Cardiothoracic Surgery, Rhode Island Hospital, Providence, RI, USA
| | - Nathan D Wong
- , Houston, USA
- Heart Disease Prevention Program, Division of Cardiology, University of California Irvine, C-240 Medical Sciences, Irvine, CA, USA
| | - Elisabetta Comini
- , Houston, USA
- SENSOR Laboratory, University of Brescia, Brescia, Italy
| | - Alberto Ruiz Jimeno
- , Houston, USA
- Instituto de Física de Cantabria (IFCA), CSIC-Universidad de Cantabria, Santander, Spain
| | - Vivette Glover
- , Houston, USA
- Department of Metabolism, Digestion and Reproduction Hammersmith Hospital Campus, Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Nikos Hatziargyriou
- , Houston, USA
- School of Electrical and Computer Engineering, National Technical University of Athens (NTUA), Athens, Greece
| | - Christian E Vincenot
- , Houston, USA
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Stéphane P A Bordas
- , Houston, USA
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Idupulapati M Rao
- , Houston, USA
- Alliance of Bioversity International, International Center for Tropical Agriculture, Cali, Colombia
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Hassan Abolhassani
- , Houston, USA
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | | | - Ralf Weiskirchen
- , Houston, USA
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, Aachen, Germany
| | - Manoj Gupta
- , Houston, USA
- Department of Mechanical Engineering, National University of Singapore, Singapore, Singapore
| | - Shyam Singh Chandel
- , Houston, USA
- Photovoltaics Research Group, Centre of Excellence in Energy Science and Technology, Shoolini University, Solan, Himachal Pradesh, 173212, India
| | | | - Bruce Cheson
- , Houston, USA
- Center for Cancer and Blood Disorders, Bethesda, MD, USA
| | - Alessio Pomponio
- , Houston, USA
- Dipartimento di Meccanica, Matematica e Management, Politecnico di Bari, Bari, Italy
| | - Michael Tanzer
- , Houston, USA
- Division of Orthopedic Surgery, McGill University, Montreal, QC, Canada
| | - Paul S Myles
- , Houston, USA
- Alfred Hospital and Monash University, Melbourne, Australia
| | - Wen-Xiu Ma
- , Houston, USA
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, USA
- Department of Mathematics, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Material Science Innovation and Modelling, North-West University, Mafikeng Campus, Mmabatho, 2735, South Africa
| | - Federico Bella
- , Houston, USA
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi, Turin, Italy
| | - Saeid Ghavami
- , Houston, USA
- Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB, Canada
| | - S Moein Moghimi
- , Houston, USA
- School of Pharmacy, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Faculty of Health and Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Colorado Center for Nanomedicine and Nanosafety, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Domenico Pratico
- , Houston, USA
- Alzheimer's Center at Temple, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Alfredo M Hernandez
- , Houston, USA
- Medicine and Endocrinology Department, Universidad de Valladolid and IMDEA, Madrid, Spain
| | | | | | - Seyed-Mohammad Fereshtehnejad
- , Houston, USA
- Division of Neurology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Division of Clinical Geriatrics, NVS Department, Karolinska Institutet, Stockholm, Sweden
| | - Imran Ali
- , Houston, USA
- Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi, India
| | - Shinya Kimura
- , Houston, USA
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - A Wallace Hayes
- , Houston, USA
- Center for Environmental/Occupational Risk Analysis and Management, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
- Michigan State University, East Lansing, MI, USA
| | - Wenju Cai
- , Houston, USA
- CSIRO Environment, Hobart, TAS, Australia
| | - Chua K J Ernest
- , Houston, USA
- Department of Mechanical Engineering, National University of Singapore, Singapore, Singapore
| | - Sabu Thomas
- , Houston, USA
- School of Energy Materials, Mahatma Gandhi University, Kottayam, Kerala, India
| | - Kazem Rahimi
- , Houston, USA
- Deep Medicine, Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Armin Sorooshian
- , Houston, USA
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, AZ, USA
| | - Michael Schreiber
- , Houston, USA
- Institut für Physik, Technische Universität Chemnitz, 09107, Chemnitz, Germany
| | - Koichi Kato
- , Houston, USA
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - John H T Luong
- , Houston, USA
- School of Chemistry, University College Cork, Cork, T12 YN60, Ireland
| | - Stefano Pluchino
- , Houston, USA
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Andres M Lozano
- , Houston, USA
- Division of Neurosurgery, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, Toronto, ON, Canada
| | - John F Seymour
- , Houston, USA
- Clinical Haematology, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Kenneth S Kosik
- , Houston, USA
- Department of Molecular Cellular Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Stefan G Hofmann
- , Houston, USA
- Department of Psychology, Philipps-University Marburg, Marburg, Germany
| | - Roger S McIntyre
- , Houston, USA
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Matjaz Perc
- , Houston, USA
- Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, Maribor, Slovenia
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 404332, Taiwan
- Alma Mater Europaea, Slovenska ulica 17, 2000, Maribor, Slovenia
- Complexity Science Hub Vienna, Josefstädterstraße 39, 1080, Vienna, Austria
- Department of Physics, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea
| | - Alexander Leemans
- , Houston, USA
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Robyn S Klein
- , Houston, USA
- Center for Neuroimmunology and Neuroinfectious Diseases, St. Louis, MO, USA
- Departments of Medicine, Pathology and Immunology, and Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Shuji Ogino
- , Houston, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher Wlezien
- , Houston, USA
- Department of Government, University of Texas at Austin, Austin, TX, USA
| | - George Perry
- , Houston, USA
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Juan J Nieto
- , Houston, USA
- CITMAga, University of Santiago de Compostela, A Coruña, Spain
| | - Lisa Levin
- , Houston, USA
- Center for Marine Biodiversity and Conservation, Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, USA
| | - Daniel J Klionsky
- , Houston, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Bahram Mobasher
- , Houston, USA
- Department of Physics and Astronomy, University of California, Riverside, CA, USA
| | - Tommaso Dorigo
- , Houston, USA
- Lulea University of Technology, Laboratorievagen 14, Lulea, Sweden
- Istituto Nazionale di Fisica Nucleare (INFN), Via Francesco Marzolo, Sezione di Padova, Italy
| | - Nima Rezaei
- , Houston, USA.
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
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6
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Bogoyavlenskiy A, Zaitseva I, Alexyuk P, Alexyuk M, Omirtaeva E, Manakbayeva A, Moldakhanov Y, Anarkulova E, Imangazy A, Berezin V, Korulkin D, Hasan AH, Noamaan M, Jamalis J. Naturally Occurring Isorhamnetin Glycosides as Potential Agents Against Influenza Viruses: Antiviral and Molecular Docking Studies. ACS OMEGA 2023; 8:48499-48514. [PMID: 38144046 PMCID: PMC10734298 DOI: 10.1021/acsomega.3c08407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023]
Abstract
Influenza remains one of the most widespread infections, causing an annual illness in adults and children. Therefore, the search for new antiviral drugs is one of the priorities of practical health care. Eight isorhamnetin glycosides were purified from Persicaria species, characterized by nuclear magnetic resonance spectroscopy and mass spectrometry and then evaluated as potential agents against influenza virus. A comprehensive in vitro and in vivo assessment of the compounds revealed that compound 5 displayed the most potent inhibitory activity with an EC50 value of 1.2-1.3 μM, better than standard drugs (isorhamnetin 28.0-56.0 μM and oseltamivir 1.3-9.1 μM). Molecular docking results also revealed that compound 5 has the lowest binding energy (-10.7 kcal/mol) among the tested compounds and isorhamnetin (-8.1 kcal/mol). The ability of the isorhamnetin glycosides to suppress the reproduction of the influenza virus was studied on a model of a cell culture and chicken embryos. The ability of active compounds to influence the structure of the virion, as well as the activity of hemagglutinin and neuraminidase, has been demonstrated. Compound 1, 5, and 6 demonstrated the most effective inhibition of virus replication for all tested viruses. Molecular dynamics simulation techniques were run for 100 ns for compound 5 with two protein receptors Hem (1RUY) and Neu (3BEQ). These results revealed that the Hem-complex system acquired a relatively more stable conformation and even better descriptors than the other Neu-complex studied systems, suggesting that it can be an effective inhibiting drug toward hemagglutinin than neuraminidase inhibition. Based on the reported results, compound 5 can be a good candidate to be evaluated for effectiveness in preclinical testing.
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Affiliation(s)
- Andrey Bogoyavlenskiy
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Irina Zaitseva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Pavel Alexyuk
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Elmira Omirtaeva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Adolat Manakbayeva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Yergali Moldakhanov
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Elmira Anarkulova
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Anar Imangazy
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Vladimir Berezin
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Dmitry Korulkin
- Department
of Chemistry and Chemical Technology, al-Farabi
Kazakh National University, Almaty 050010, Kazakhstan
| | - Aso Hameed Hasan
- Department
of Chemistry, College of Science, University
of Garmian, Kalar, Kurdistan Region 46021, Iraq
| | - Mahmoud Noamaan
- Mathematics
Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Joazaizulfazli Jamalis
- Department
of Chemistry Faculty of Science, Universiti
Teknologi Malaysia, UTM Johor
Bahru, Johor 81310, Malaysia
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7
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Gattan HS, Mahmoud Alawi M, Bajrai LH, Alandijany TA, Alsaady IM, El-Daly MM, Dwivedi VD, Azhar EI. A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds' Interaction. Mar Drugs 2023; 21:626. [PMID: 38132947 PMCID: PMC10744363 DOI: 10.3390/md21120626] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Middle East Respiratory Syndrome (MERS) is a viral respiratory disease caused b a special type of coronavirus called MERS-CoV. In the search for effective substances against the MERS-CoV main protease, we looked into compounds from brown algae, known for their medicinal benefits. From a set of 1212 such compounds, our computer-based screening highlighted four-CMNPD27819, CMNPD1843, CMNPD4184, and CMNPD3156. These showed good potential in how they might attach to the MERS-CoV protease, comparable to a known inhibitor. We confirmed these results with multiple computer tests. Studies on the dynamics and steadiness of these compounds with the MERS-CoV protease were performed using molecular dynamics (MD) simulations. Metrics like RMSD and RMSF showed their stability. We also studied how these compounds and the protease interact in detail. An analysis technique, PCA, showed changes in atomic positions over time. Overall, our computer studies suggest brown algae compounds could be valuable in fighting MERS. However, experimental validation is needed to prove their real-world effectiveness.
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Affiliation(s)
- Hattan S. Gattan
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Maha Mahmoud Alawi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Infection Control & Environmental Health Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Leena H. Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Isra M. Alsaady
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Mai M. El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Chennai 605102, India
- Bioinformatics Research Division, Quanta Calculus, Greater Noida 201310, India
| | - Esam I. Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (H.S.G.); (M.M.A.); (L.H.B.); (T.A.A.); (M.M.E.-D.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
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8
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Tan H, Wang Z, Hu G. GAABind: a geometry-aware attention-based network for accurate protein-ligand binding pose and binding affinity prediction. Brief Bioinform 2023; 25:bbad462. [PMID: 38102069 PMCID: PMC10724026 DOI: 10.1093/bib/bbad462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Protein-ligand interactions are increasingly profiled at high-throughput, playing a vital role in lead compound discovery and drug optimization. Accurate prediction of binding pose and binding affinity constitutes a pivotal challenge in advancing our computational understanding of protein-ligand interactions. However, inherent limitations still exist, including high computational cost for conformational search sampling in traditional molecular docking tools, and the unsatisfactory molecular representation learning and intermolecular interaction modeling in deep learning-based methods. Here we propose a geometry-aware attention-based deep learning model, GAABind, which effectively predicts the pocket-ligand binding pose and binding affinity within a multi-task learning framework. Specifically, GAABind comprehensively captures the geometric and topological properties of both binding pockets and ligands, and employs expressive molecular representation learning to model intramolecular interactions. Moreover, GAABind proficiently learns the intermolecular many-body interactions and simulates the dynamic conformational adaptations of the ligand during its interaction with the protein through meticulously designed networks. We trained GAABind on the PDBbindv2020 and evaluated it on the CASF2016 dataset; the results indicate that GAABind achieves state-of-the-art performance in binding pose prediction and shows comparable binding affinity prediction performance. Notably, GAABind achieves a success rate of 82.8% in binding pose prediction, and the Pearson correlation between predicted and experimental binding affinities reaches up to 0.803. Additionally, we assessed GAABind's performance on the severe acute respiratory syndrome coronavirus 2 main protease cross-docking dataset. In this evaluation, GAABind demonstrates a notable success rate of 76.5% in binding pose prediction and achieves the highest Pearson correlation coefficient in binding affinity prediction compared with all baseline methods.
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Affiliation(s)
- Huishuang Tan
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhixin Wang
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Guang Hu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
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9
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Girgis AS, Panda SS, Kariuki BM, Bekheit MS, Barghash RF, Aboshouk DR. Indole-Based Compounds as Potential Drug Candidates for SARS-CoV-2. Molecules 2023; 28:6603. [PMID: 37764378 PMCID: PMC10537473 DOI: 10.3390/molecules28186603] [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: 08/05/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
The COVID-19 pandemic has posed a significant threat to society in recent times, endangering human health, life, and economic well-being. The disease quickly spreads due to the highly infectious SARS-CoV-2 virus, which has undergone numerous mutations. Despite intense research efforts by the scientific community since its emergence in 2019, no effective therapeutics have been discovered yet. While some repurposed drugs have been used to control the global outbreak and save lives, none have proven universally effective, particularly for severely infected patients. Although the spread of the disease is generally under control, anti-SARS-CoV-2 agents are still needed to combat current and future infections. This study reviews some of the most promising repurposed drugs containing indolyl heterocycle, which is an essential scaffold of many alkaloids with diverse bio-properties in various biological fields. The study also discusses natural and synthetic indole-containing compounds with anti-SARS-CoV-2 properties and computer-aided drug design (in silico studies) for optimizing anti-SARS-CoV-2 hits/leads.
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Affiliation(s)
- Adel S. Girgis
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt; (M.S.B.); (R.F.B.); (D.R.A.)
| | - Siva S. Panda
- Department of Chemistry and Biochemistry, Augusta University, Augusta, GA 30912, USA
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA
| | - Benson M. Kariuki
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK; (B.M.K.)
| | - Mohamed S. Bekheit
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt; (M.S.B.); (R.F.B.); (D.R.A.)
| | - Reham F. Barghash
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt; (M.S.B.); (R.F.B.); (D.R.A.)
| | - Dalia R. Aboshouk
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt; (M.S.B.); (R.F.B.); (D.R.A.)
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10
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Ruan Z, Tang J, Zeng M, Fan P. Virtual high-throughput screening: Potential inhibitors targeting aminopeptidase N (CD13) and PIKfyve for SARS-CoV-2. Open Life Sci 2023; 18:20220637. [PMID: 37426619 PMCID: PMC10329278 DOI: 10.1515/biol-2022-0637] [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: 03/14/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
Since the outbreak of the novel coronavirus nearly 3 years ago, the world's public health has been under constant threat. At the same time, people's travel and social interaction have also been greatly affected. The study focused on the potential host targets of SARS-CoV-2, CD13, and PIKfyve, which may be involved in viral infection and the viral/cell membrane fusion stage of SARS-CoV-2 in humans. In this study, electronic virtual high-throughput screening for CD13 and PIKfyve was conducted using Food and Drug Administration-approved compounds in ZINC database. The results showed that dihydroergotamine, Saquinavir, Olysio, Raltegravir, and Ecteinascidin had inhibitory effects on CD13. Dihydroergotamine, Sitagliptin, Olysio, Grazoprevir, and Saquinavir could inhibit PIKfyve. After 50 ns of molecular dynamics simulation, seven compounds showed stability at the active site of the target protein. Hydrogen bonds and van der Waals forces were formed with target proteins. At the same time, the seven compounds showed good binding free energy after binding to the target proteins, providing potential drug candidates for the treatment and prevention of SARS-CoV-2 and SARS-CoV-2 variants.
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Affiliation(s)
- Zijing Ruan
- Department of Clinical Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiaxi Tang
- Department of Clinical Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Mingtang Zeng
- Department of Clinical Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ping Fan
- Department of Clinical Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
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11
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Bogoyavlenskiy A, Alexyuk M, Alexyuk P, Berezin V, Almalki FA, Ben Hadda T, Alqahtani AM, Ahmed SA, Dall'Acqua S, Jamalis J. Computer Analysis of the Inhibition of ACE2 by Flavonoids and Identification of Their Potential Antiviral Pharmacophore Site. Molecules 2023; 28:molecules28093766. [PMID: 37175179 PMCID: PMC10179817 DOI: 10.3390/molecules28093766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In the present study, we investigated the antiviral activities of 17 flavonoids as natural products. These derivatives were evaluated for their in vitro antiviral activities against HIV and SARS-CoV-2. Their antiviral activity was evaluated for the first time based on POM (Petra/Osiris/Molispiration) theory and docking analysis. POM calculation was used to analyze the atomic charge and geometric characteristics. The side effects, drug similarities, and drug scores were also assumed for the stable structure of each compound. These results correlated with the experimental values. The bioinformatics POM analyses of the relative antiviral activities of these derivatives are reported for the first time.
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Affiliation(s)
- Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Pavel Alexyuk
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Vladimir Berezin
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Alaa M Alqahtani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Stefano Dall'Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35121 Padova, Italy
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM, Johor Bahru 81310, Johor, Malaysia
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12
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Zhang J, Jiang Y, Wu C, Zhou D, Gong J, Zhao T, Jin Z. Development of FRET and Stress Granule Dual-Based System to Screen for Viral 3C Protease Inhibitors. Molecules 2023; 28:molecules28073020. [PMID: 37049786 PMCID: PMC10096049 DOI: 10.3390/molecules28073020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
3C proteases (3Cpros) of picornaviruses and 3C-like proteases (3CLpros) of coronaviruses and caliciviruses represent a group of structurally and functionally related viral proteases that play pleiotropic roles in supporting the viral life cycle and subverting host antiviral responses. The design and screening for 3C/3CLpro inhibitors may contribute to the development broad-spectrum antiviral therapeutics against viral diseases related to these three families. However, current screening strategies cannot simultaneously assess a compound’s cytotoxicity and its impact on enzymatic activity and protease-mediated physiological processes. The viral induction of stress granules (SGs) in host cells acts as an important antiviral stress response by blocking viral translation and stimulating the host immune response. Most of these viruses have evolved 3C/3CLpro-mediated cleavage of SG core protein G3BP1 to counteract SG formation and disrupt the host defense. Yet, there are no SG-based strategies screening for 3C/3CLpro inhibitors. Here, we developed a fluorescence resonance energy transfer (FRET) and SG dual-based system to screen for 3C/3CLpro inhibitors in living cells. We took advantage of FRET to evaluate the protease activity of poliovirus (PV) 3Cpro and live-monitor cellular SG dynamics to cross-verify its effect on the host antiviral response. Our drug screen uncovered a novel role of Telaprevir and Trifluridine as inhibitors of PV 3Cpro. Moreover, Telaprevir and Trifluridine also modulated 3Cpro-mediated physiological processes, including the cleavage of host proteins, inhibition of the innate immune response, and consequent facilitation of viral replication. Taken together, the FRET and SG dual-based system exhibits a promising potential in the screening for inhibitors of viral proteases that cleave G3BP1.
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Yousafzai ADK, Bangash AH, Asghar SY, Abbas SMM, Khawaja HF, Zehra S, Khan AU, Kamil M, Ayesha N, Khan AK, Mohsin R, Ahmed O, Fatima A, Ali A, Badar AU, Abbasi MN, Ashraf M, Shah AH, Iqbal T. Clinical efficacy of Azithromycin for COVID-19 management: A systematic meta-analysis of meta-analyses. Heart Lung 2023; 60:127-132. [PMID: 36996755 PMCID: PMC10017380 DOI: 10.1016/j.hrtlng.2023.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023]
Abstract
Background Azithromycin has been adopted as a component of the COVID-19 management protocol throughout the global healthcare settings but with a questionable if not downright unsubstantiated evidence base. Objectives In order to amalgamate and critically appraise the conflicting evidence around the clinical efficacy of Azithromycin (AZO) vis a vis COVID-19 management outcomes, a meta-analysis of meta-analyses was carried out to establish an evidence-based holistic status of AZO vis a vis its efficacy as a component-in-use of the COVID-19 management protocol. Methods A comprehensive systematic search was carried out through PubMed/Medline, Cochrane and Epistemonikos with a subsequent appraisal of abstracts and full-texts, as required. The Quality of Reporting of Meta-analyses (QUOROM) checklist and the Assessment of Multiple Systematic Reviews (AMSTAR) methodology were adopted to assess the methodological quality of the included meta-analyses. Random-effects models were developed to calculate summarized pool Odds Ratios (with 95% confidence interval) for the afore determined primary and secondary outcomes. Results AZO, when compared with best available therapy (BAT) including or excluding Hydroxychloroquine, exhibited statistically insignificant reduction in mortality [(n= 27,204 patients) OR= 0.77 (95% CI: 0.51-1.16) (I2= 97%)], requirement of mechanical ventilation [(n= 14,908 patients) OR= 1.4 (95% CI: 0.58-3.35) (I2= 98%)], induction of arrhythmia [(n= 9,723 patients) OR= 1.21 (95% CI: 0.63-2.32) (I2= 92%)] and QTc prolongation (a surrogate for torsadogenic effect) [(n= 6,534 patients) OR= 0.62 (95% CI: 0.23-1.73) (I2= 96%)]. Conclusion The meta-analysis of meta-analyses portrays AZO as a pharmacological agent that does not appear to have a comparatively superior clinical efficacy than BAT when it comes to COVID-19 management. Secondary to a very real threat of anti-bacterial resistance, it is suggested that AZO be discontinued and removed from COVID-19 management protocols.
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Affiliation(s)
| | - Ali Haider Bangash
- Shifa International Hospital, Islamabad, Pakistan,Corresponding author: Dr Ali Haider Bangash, MBBS, Shifa International Hospital, Islamabad, Pakistan. Medical student member of the American College of Physicians (ACP), American Society of Clinical Oncology (ASCO), European Academy of Neurology (EAN), Congress of Neurological Surgeons (CNS), North American Spine Society (NASS), Society for Neuro-Oncology (SNO), Alzheimer's Association International Society to Advance Alzheimer's Research and Treatment (ISTAART), International Parkinson and Movement Disorder Society & Spine Intervention Society
| | | | | | | | - Saiqa Zehra
- Shifa International Hospital, Islamabad, Pakistan
| | | | - Musa Kamil
- Shifa International Hospital, Islamabad, Pakistan
| | - Noor Ayesha
- Shifa International Hospital, Islamabad, Pakistan
| | | | - Rabia Mohsin
- Shifa International Hospital, Islamabad, Pakistan
| | - Osama Ahmed
- Shifa International Hospital, Islamabad, Pakistan
| | | | - Aliya Ali
- Shifa International Hospital, Islamabad, Pakistan
| | - Ain ul Badar
- Shifa International Hospital, Islamabad, Pakistan
| | | | - Mohammad Ashraf
- Rawalpindi Medical College, Rawalpindi Medical University, Rawalpindi, Pakistan
| | | | - Tahir Iqbal
- Head of Department, Department of Medicine, Shifa College of Medicine, Islamabad, Pakistan
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14
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Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
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Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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15
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Cai Y, Golay MW. A dynamic Bayesian network-based emergency decision-making framework highlighting emergency propagations: Illustrated using the Fukushima nuclear accidents and the Covid-19 pandemic. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2023; 43:480-497. [PMID: 35474323 PMCID: PMC9115531 DOI: 10.1111/risa.13928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
When facing public emergencies, human societies need to make decisions rapidly in order to mitigate the problems. However, this process can be difficult due to complexity of the emergency scenarios and lack of systematic methods for analyzing them. In the work reported here, we develop a framework based upon dynamic Bayesian networks in order to simulate emergency scenarios and support corresponding decisions. In this framework, we highlight the importance of emergency propagation, which is a critical factor often ignored by decisionmakers. We illustrate that failure of considering emergency propagation can lead to suboptimal mitigation strategies. By incorporating this critical factor, our framework enables decisionmakers to identify optimal response strategies minimizing emergency impacts. Scenarios developed from two public emergencies: the 2011 Fukushima nuclear power plant accidents and the Covid-19 pandemic, are utilized to illustrate the framework in this paper. Capabilities of the framework in supporting decision making in both events illustrate its generality and adaptability when dealing with complex real-world situations. Our analysis results reveal many similarities between these two seemingly distinct events. This indicates that seemingly unrelated emergencies can share many common features beyond their idiosyncratic characteristics. Valuable mitigation insights can be obtained by analyzing a broad range of past emergencies systematically.
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Affiliation(s)
- Yinan Cai
- Department of Nuclear Science and EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Michael W. Golay
- Department of Nuclear Science and EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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16
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Velagacherla V, Suresh A, Mehta CH, Nayak UY, Nayak Y. Multi-Targeting Approach in Selection of Potential Molecule for COVID-19 Treatment. Viruses 2023; 15:213. [PMID: 36680253 PMCID: PMC9861341 DOI: 10.3390/v15010213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The coronavirus disease (COVID-19) is a pandemic that started in the City of Wuhan, Hubei Province, China, caused by the spread of coronavirus (SARS-CoV-2). Drug discovery teams around the globe are in a race to develop a medicine for its management. It takes time for a novel molecule to enter the market, and the ideal way is to exploit the already approved drugs and repurpose them therapeutically. We have attempted to screen selected molecules with an affinity towards multiple protein targets in COVID-19 using the Schrödinger suit for in silico predictions. The proteins selected were angiotensin-converting enzyme-2 (ACE2), main protease (MPro), and spike protein. The molecular docking, prime MM-GBSA, induced-fit docking (IFD), and molecular dynamics (MD) simulations were used to identify the most suitable molecule that forms a stable interaction with the selected viral proteins. The ligand-binding stability for the proteins PDB-IDs 1ZV8 (spike protein), 5R82 (Mpro), and 6M1D (ACE2), was in the order of nintedanib > quercetin, nintedanib > darunavir, nintedanib > baricitinib, respectively. The MM-GBSA, IFD, and MD simulation studies imply that the drug nintedanib has the highest binding stability among the shortlisted. Nintedanib, primarily used for idiopathic pulmonary fibrosis, can be considered for repurposing for us against COVID-19.
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Affiliation(s)
- Varalakshmi Velagacherla
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
| | - Akhil Suresh
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
| | - Chetan Hasmukh Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
| | - Usha Y. Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Udupi 576104, India
| | - Yogendra Nayak
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Udupi 576104, India
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
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17
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Jamshidi E, Asgary A, Kharrazi AY, Tavakoli N, Zali A, Mehrazi M, Jamshidi M, Farrokhi B, Maher A, von Garnier C, Rahi SJ, Mansouri N. Personalized predictions of adverse side effects of the COVID-19 vaccines. Heliyon 2023; 9:e12753. [PMID: 36597482 PMCID: PMC9800018 DOI: 10.1016/j.heliyon.2022.e12753] [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: 11/01/2021] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Background Misconceptions about adverse side effects are thought to influence public acceptance of the Coronavirus disease 2019 (COVID-19) vaccines negatively. To address such perceived disadvantages of vaccines, a novel machine learning (ML) approach was designed to generate personalized predictions of the most common adverse side effects following injection of six different COVID-19 vaccines based on personal and health-related characteristics. Methods Prospective data of adverse side effects following COVID-19 vaccination in 19943 participants from Iran and Switzerland was utilized. Six vaccines were studied: The AZD1222, Sputnik V, BBIBP-CorV, COVAXIN, BNT162b2, and the mRNA-1273 vaccine. The eight side effects were considered as the model output: fever, fatigue, headache, nausea, chills, joint pain, muscle pain, and injection site reactions. The total input parameters for the first and second dose predictions were 46 and 54 features, respectively, including age, gender, lifestyle variables, and medical history. The performances of multiple ML models were compared using Area Under the Receiver Operating Characteristic Curve (ROC-AUC). Results The total number of people receiving the first dose of the AZD1222, Sputnik V, BBIBP-CorV, COVAXIN, BNT162b2, and mRNA-1273 were 6022, 7290, 5279, 802, 277, and 273, respectively. For the second dose, the numbers were 2851, 5587, 3841, 599, 242 and 228. The Logistic Regression model for predicting different side effects of the first dose achieved ROC-AUCs of 0.620-0.686, 0.685-0.716, 0.632-0.727, 0.527-0.598, 0.548-0.655, 0.545-0.712 for the AZD1222, Sputnik V, BBIBP-CorV, COVAXIN, BNT162b2 and mRNA-1273 vaccines, respectively. The second dose models yielded ROC-AUCs of 0.777-0.867, 0.795-0.848, 0.857-0.906, 0.788-0.875, 0.683-0.850, and 0.486-0.680, respectively. Conclusions Using a large cohort of recipients vaccinated with COVID-19 vaccines, a novel and personalized strategy was established to predict the occurrence of the most common adverse side effects with high accuracy. This technique can serve as a tool to inform COVID-19 vaccine selection and generate personalized factsheets to curb concerns about adverse side effects.
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Affiliation(s)
- Elham Jamshidi
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhossein Asgary
- Department of Biotechnology, College of Sciences, University of Tehran, Tehran, Iran
| | | | - Nader Tavakoli
- Trauma and Injury Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Zali
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Mehrazi
- Trauma and Injury Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Masoud Jamshidi
- Department of Exercise Physiology, Tehran University, Tehran, Iran
| | - Babak Farrokhi
- Health Network Administration Center, Undersecretary for Health Affairs, Ministry of Health and Medical Education, Tehran, Iran
| | - Ali Maher
- School of Management and Medical Education, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Christophe von Garnier
- Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Sahand Jamal Rahi
- Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nahal Mansouri
- Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Research Group on Artificial Intelligence in Pulmonary Medicine, Division of Pulmonary Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
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18
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Kasabe B, Ahire G, Patil P, Punekar M, Davuluri KS, Kakade M, Alagarasu K, Parashar D, Cherian S. Drug repurposing approach against chikungunya virus: an in vitro and in silico study. Front Cell Infect Microbiol 2023; 13:1132538. [PMID: 37180434 PMCID: PMC10174255 DOI: 10.3389/fcimb.2023.1132538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
The chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes mosquitoes. There are no licenced antivirals or vaccines for treatment or prevention. Drug repurposing approach has emerged as a novel concept to find alternative uses of therapeutics to battle pathogens. In the present study, anti CHIKV activity of fourteen FDA-approved drugs was investigated by in vitro and in silico approaches. Focus-forming unit assay, immunofluorescence test, and quantitative RT-PCR assay were used to assess the in vitro inhibitory effect of these drugs against CHIKV in Vero CCL-81 cells. The findings showed that nine compounds, viz., temsirolimus, 2-fluoroadenine, doxorubicin, felbinac, emetine, lomibuvir, enalaprilat, metyrapone and resveratrol exhibit anti chikungunya activity. Furthermore, in silico molecular docking studies performed by targeting CHIKV structural and non-structural proteins revealed that these drugs can bind to structural protein targets such as envelope protein, and capsid, and non-structural proteins NSP2, NSP3 and NSP4 (RdRp). Findings from in vitro and in silico studies reveal that these drugs can suppress the infection and replication of CHIKV and further in vivo studies followed by clinical trials are warranted.
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Affiliation(s)
- Bhagyashri Kasabe
- Bioinformatics Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
| | - Gunwant Ahire
- Dengue & Chikungunya Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
| | - Poonam Patil
- Dengue & Chikungunya Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
| | - Madhura Punekar
- Dengue & Chikungunya Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
| | - Kusuma Sai Davuluri
- Dengue & Chikungunya Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
| | - Mahadeo Kakade
- Dengue & Chikungunya Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
| | - Kalichamy Alagarasu
- Dengue & Chikungunya Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
| | - Deepti Parashar
- Dengue & Chikungunya Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
- *Correspondence: Deepti Parashar, ; Sarah Cherian,
| | - Sarah Cherian
- Bioinformatics Group, Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, Maharashtra, India
- *Correspondence: Deepti Parashar, ; Sarah Cherian,
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Fico G, Isayeva U, De Prisco M, Oliva V, Solè B, Montejo L, Grande I, Arbelo N, Gomez-Ramiro M, Pintor L, Carpiniello B, Manchia M, Vieta E, Murru A. Psychotropic drug repurposing for COVID-19: A Systematic Review and Meta-Analysis. Eur Neuropsychopharmacol 2023; 66:30-44. [PMID: 36399837 PMCID: PMC9581805 DOI: 10.1016/j.euroneuro.2022.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 01/11/2023]
Abstract
Several psychotropic drugs, including antidepressants (AD), mood stabilizers, and antipsychotics (AP) have been suggested to have favorable effects in the treatment of COVID-19. The aim of this systematic review and meta-analysis was to collect evidence from studies concerning the scientific evidence for the repurposing of psychotropic drugs in COVID-19 treatment. Two independent authors searched PubMed-MEDLINE, Scopus, PsycINFO, and ClinicalTrials.gov databases, and reviewed the reference lists of articles for eligible articles published up to 13th December 2021. All computational, preclinical and clinical (observational and/or RCTs) studies on the effect of any psychotropic drug on Sars-CoV-2 or patients with COVID-19 were considered for inclusion. We conducted random effect meta-analyses on clinical studies reporting the effect of AD or AP on COVID-19 outcomes. 29 studies were included in the synthesis: 15 clinical, 9 preclinical, and 5 computational studies. 9 clinical studies could be included in the quantitative analyses. AD did not increase the risk of severe COVID-19 (RR= 1.71; CI 0.65-4.51) or mortality (RR=0.94; CI 0.81-1.09). Fluvoxamine was associated with a reduced risk of mortality for COVID-19 (OR=0.15; CI 0.02-0.95). AP increased the risk of severe COVID-19 (RR=3.66; CI 2.76-4.85) and mortality (OR=1.53; CI 1.15-2.03). Fluvoxamine might be a possible candidate for psychotropic drug repurposing in COVID-19 due to its anti-inflammatory and antiviral potential, while evidence on other AD is still controversial. Although AP are associated with worse COVID-19 outcomes, their use should be evaluated case to case and ongoing treatment with antipsychotics should be not discontinued in psychiatric patients.
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Affiliation(s)
- Giovanna Fico
- Bipolar and Depressive Disorders Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain
| | - Ulker Isayeva
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Via Liguria 13, 09121, Cagliari, Italy
| | - Michele De Prisco
- Bipolar and Depressive Disorders Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain; Section of Psychiatry, Department of Neuroscience, Reproductive Science and Odontostomatology, Federico II University of Naples, Naples, Italy
| | - Vincenzo Oliva
- Bipolar and Depressive Disorders Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Brisa Solè
- Bipolar and Depressive Disorders Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain
| | - Laura Montejo
- Bipolar and Depressive Disorders Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain
| | - Iria Grande
- Bipolar and Depressive Disorders Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain
| | - Nestor Arbelo
- Barcelona Clínic Schizophrenia Unit, Department of Clinical Foundations, Pharmacology Unit, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Catalonia, Spain; Consultation-Liaison Psychiatry Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain
| | - Marta Gomez-Ramiro
- Barcelona Clínic Schizophrenia Unit, Department of Clinical Foundations, Pharmacology Unit, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Catalonia, Spain; Department of Psychiatry, Servizo Galego de Saúde (SERGAS), Pontevedra, Spain; Psychiatric Diseases Research Group, Galicia Sur Health Research Institute, Vigo, Spain
| | - Luis Pintor
- Consultation-Liaison Psychiatry Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain
| | - Bernardo Carpiniello
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Via Liguria 13, 09121, Cagliari, Italy
| | - Mirko Manchia
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Via Liguria 13, 09121, Cagliari, Italy; Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Eduard Vieta
- Bipolar and Depressive Disorders Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain.
| | - Andrea Murru
- Bipolar and Depressive Disorders Unit, Institute of Neurosciences, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, 170 Villarroel st, 12-0, 08036, Barcelona, Catalonia, Spain
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20
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Han I, Mumtaz S, Choi EH. Nonthermal Biocompatible Plasma Inactivation of Coronavirus SARS-CoV-2: Prospects for Future Antiviral Applications. Viruses 2022; 14:2685. [PMID: 36560689 PMCID: PMC9785490 DOI: 10.3390/v14122685] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The coronavirus disease (COVID-19) pandemic has placed a massive impact on global civilization. Finding effective treatments and drugs for these viral diseases was crucial. This paper outlined and highlighted key elements of recent advances in nonthermal biocompatible plasma (NBP) technology for antiviral applications. We searched for papers on NBP virus inactivation in PubMed ePubs, Scopus, and Web of Science databases. The data and relevant information were gathered in order to establish a mechanism for NBP-based viral inactivation. NBP has been developed as a new, effective, and safe strategy for viral inactivation. NBP may be used to inactivate viruses in an ecologically friendly way as well as activate animal and plant viruses in a number of matrices. The reactive species have been shown to be the cause of viral inactivation. NBP-based disinfection techniques provide an interesting solution to many of the problems since they are simply deployable and do not require the resource-constrained consumables and reagents required for traditional decontamination treatments. Scientists are developing NBP technology solutions to assist the medical community in dealing with the present COVID-19 outbreak. NBP is predicted to be the most promising strategy for battling COVID-19 and other viruses in the future.
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Affiliation(s)
- Ihn Han
- Department of Plasma Bio-Display, Kwangwoon University, Seoul 01897, Republic of Korea
- Plasma Bioscience Research Center (PBRC), Applied Plasma Medicine Center, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Sohail Mumtaz
- Plasma Bioscience Research Center (PBRC), Applied Plasma Medicine Center, Kwangwoon University, Seoul 01897, Republic of Korea
- Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Eun Ha Choi
- Department of Plasma Bio-Display, Kwangwoon University, Seoul 01897, Republic of Korea
- Plasma Bioscience Research Center (PBRC), Applied Plasma Medicine Center, Kwangwoon University, Seoul 01897, Republic of Korea
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21
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Miandad K, Ullah A, Bashir K, Khan S, Abideen SA, Shaker B, Alharbi M, Alshammari A, Ali M, Haleem A, Ahmad S. Virtual Screening of Artemisia annua Phytochemicals as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228103. [PMID: 36432204 PMCID: PMC9695405 DOI: 10.3390/molecules27228103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human coronaviruses that emerged in China at Wuhan city, Hubei province during December 2019. Subsequently, SARS-CoV-2 has spread worldwide and caused millions of deaths around the globe. Several compounds and vaccines have been proposed to tackle this crisis. Novel recommended in silico approaches have been commonly used to screen for specific SARS-CoV-2 inhibitors of different types. Herein, the phytochemicals of Pakistani medicinal plants (especially Artemisia annua) were virtually screened to identify potential inhibitors of the SARS-CoV-2 main protease enzyme. The X-ray crystal structure of the main protease of SARS-CoV-2 with an N3 inhibitor was obtained from the protein data bank while A. annua phytochemicals were retrieved from different drug databases. The docking technique was carried out to assess the binding efficacy of the retrieved phytochemicals; the docking results revealed that several phytochemicals have potential to inhibit the SARS-CoV-2 main protease enzyme. Among the total docked compounds, the top-10 docked complexes were considered for further study and evaluated for their physiochemical and pharmacokinetic properties. The top-3 docked complexes with the best binding energies were as follows: the top-1 docked complex with a -7 kcal/mol binding energy score, the top-2 docked complex with a -6.9 kcal/mol binding energy score, and the top-3 docked complex with a -6.8 kcal/mol binding energy score. These complexes were subjected to a molecular dynamic simulation analysis for further validation to check the dynamic behavior of the selected top-complexes. During the whole simulation time, no major changes were observed in the docked complexes, which indicated complex stability. Additionally, the free binding energies for the selected docked complexes were also estimated via the MM-GB/PBSA approach, and the results revealed that the total delta energies of MMGBSA were -24.23 kcal/mol, -26.38 kcal/mol, and -25 kcal/mol for top-1, top-2, and top-3, respectively. MMPBSA calculated the delta total energy as -17.23 kcal/mol (top-1 complex), -24.75 kcal/mol (top-2 complex), and -24.86 kcal/mol (top-3 complex). This study explored in silico screened phytochemicals against the main protease of the SARS-CoV-2 virus; however, the findings require an experimentally based study to further validate the obtained results.
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Affiliation(s)
- Khalid Miandad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Kashif Bashir
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda 24461, Pakistan
| | - Syed Ainul Abideen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mahwish Ali
- Department of Biological Science, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Abdul Haleem
- Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
- Correspondence:
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22
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Nascimento IJDS, de Aquino TM, da Silva-Júnior EF. The New Era of Drug Discovery: The Power of Computer-aided Drug
Design (CADD). LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220405225817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
Drug design and discovery is a process that requires high financial costs and is timeconsuming.
For many years, this process focused on empirical pharmacology. However, over the years,
the target-based approach allowed a significant discovery in this field, initiating the rational design era. In
view, to decrease the time and financial cost, rational drug design is benefited by increasing computer
engineering and software development, and computer-aided drug design (CADD) emerges as a promising
alternative. Since the 1970s, this approach has been able to identify many important and revolutionary
compounds, like protease inhibitors, antibiotics, and others. Many anticancer compounds identified
through this approach have shown their importance, being CADD essential in any drug discovery campaign.
Thus, this perspective will present the prominent successful cases utilizing this approach and entering
into the next stage of drug design. We believe that drug discovery will follow the progress in bioinformatics,
using high-performance computing with molecular dynamics protocols faster and more effectively.
In addition, artificial intelligence and machine learning will be the next process in the rational design
of new drugs. Here, we hope that this paper generates new ideas and instigates research groups
worldwide to use these methods and stimulate progress in drug design.
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Affiliation(s)
| | | | - Edeildo Ferreira da Silva-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Maceió, Brazil
- Laboratory of Medicinal
Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
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23
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Gu Y, Zheng S, Yin Q, Jiang R, Li J. REDDA: Integrating multiple biological relations to heterogeneous graph neural network for drug-disease association prediction. Comput Biol Med 2022; 150:106127. [PMID: 36182762 DOI: 10.1016/j.compbiomed.2022.106127] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/27/2022] [Accepted: 09/18/2022] [Indexed: 11/03/2022]
Abstract
Computational drug repositioning is an effective way to find new indications for existing drugs, thus can accelerate drug development and reduce experimental costs. Recently, various deep learning-based repurposing methods have been established to identify the potential drug-disease associations (DDA). However, effective utilization of the relations of biological entities to capture the biological interactions to enhance the drug-disease association prediction is still challenging. To resolve the above problem, we proposed a heterogeneous graph neural network called REDDA (Relations-Enhanced Drug-Disease Association prediction). Assembled with three attention mechanisms, REDDA can sequentially learn drug/disease representations by a general heterogeneous graph convolutional network-based node embedding block, a topological subnet embedding block, a graph attention block, and a layer attention block. Performance comparisons on our proposed benchmark dataset show that REDDA outperforms 8 advanced drug-disease association prediction methods, achieving relative improvements of 0.76% on the area under the receiver operating characteristic curve (AUC) score and 13.92% on the precision-recall curve (AUPR) score compared to the suboptimal method. On the other benchmark dataset, REDDA also obtains relative improvements of 2.48% on the AUC score and 4.93% on the AUPR score. Specifically, case studies also indicate that REDDA can give valid predictions for the discovery of -new indications for drugs and new therapies for diseases. The overall results provide an inspiring potential for REDDA in the in silico drug development. The proposed benchmark dataset and source code are available in https://github.com/gu-yaowen/REDDA.
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Affiliation(s)
- Yaowen Gu
- Institute of Medical Information (IMI), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100020, China
| | - Si Zheng
- Institute of Medical Information (IMI), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100020, China; Institute for Artificial Intelligence, Department of Computer Science and Technology, BNRist, Tsinghua University, Beijing, 100084, China
| | - Qijin Yin
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Jiao Li
- Institute of Medical Information (IMI), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100020, China.
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24
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Mangione W, Falls Z, Samudrala R. Optimal COVID-19 therapeutic candidate discovery using the CANDO platform. Front Pharmacol 2022; 13:970494. [PMID: 36091793 PMCID: PMC9452636 DOI: 10.3389/fphar.2022.970494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/07/2022] [Indexed: 01/22/2023] Open
Abstract
The worldwide outbreak of SARS-CoV-2 in early 2020 caused numerous deaths and unprecedented measures to control its spread. We employed our Computational Analysis of Novel Drug Opportunities (CANDO) multiscale therapeutic discovery, repurposing, and design platform to identify small molecule inhibitors of the virus to treat its resulting indication, COVID-19. Initially, few experimental studies existed on SARS-CoV-2, so we optimized our drug candidate prediction pipelines using results from two independent high-throughput screens against prevalent human coronaviruses. Ranked lists of candidate drugs were generated using our open source cando.py software based on viral protein inhibition and proteomic interaction similarity. For the former viral protein inhibition pipeline, we computed interaction scores between all compounds in the corresponding candidate library and eighteen SARS-CoV proteins using an interaction scoring protocol with extensive parameter optimization which was then applied to the SARS-CoV-2 proteome for prediction. For the latter similarity based pipeline, we computed interaction scores between all compounds and human protein structures in our libraries then used a consensus scoring approach to identify candidates with highly similar proteomic interaction signatures to multiple known anti-coronavirus actives. We published our ranked candidate lists at the very beginning of the COVID-19 pandemic. Since then, 51 of our 276 predictions have demonstrated anti-SARS-CoV-2 activity in published clinical and experimental studies. These results illustrate the ability of our platform to rapidly respond to emergent pathogens and provide greater evidence that treating compounds in a multitarget context more accurately describes their behavior in biological systems.
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Affiliation(s)
| | | | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
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25
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regCOVID: Tracking publications of registered COVID-19 studies. BMC Med Res Methodol 2022; 22:221. [PMID: 35948881 PMCID: PMC9364859 DOI: 10.1186/s12874-022-01703-9] [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: 02/10/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
Background In response to the COVID-19 pandemic many clinical studies have been initiated leading to the need for efficient ways to track and analyze study results. We expanded our previous project that tracked registered COVID-19 clinical studies to also track result articles generated from these studies. Our objective was to develop a data science approach to identify and analyze all publications linked to COVID-19 clinical studies and generate a prioritized list of publications for efficient understanding of the state of COVID-19 clinical research. Methods We conducted searches of ClinicalTrials.gov and PubMed to identify articles linked to COVID-19 studies, and developed criteria based on the trial phase, intervention, location, and record recency to develop a prioritized list of result publications. Results The performed searchers resulted in 1 022 articles linked to 565 interventional trials (17.8% of all 3 167 COVID-19 interventional trials as of 31 January 2022). 609 publications were identified via abstract-link in PubMed and 413 via registry-link in ClinicalTrials.gov, with 27 articles linked from both sources. Of the 565 trials publishing at least one article, 197 (34.9%) had multiple linked publications. An attention score was assigned to each publication to develop a prioritized list of all publications linked to COVID-19 trials and 83 publications were identified that are result articles from late phase (Phase 3) trials with at least one US site and multiple study record updates. For COVID-19 vaccine trials, 108 linked result articles for 64 trials (14.7% of 436 total COVID-19 vaccine trials) were found. Conclusions Our method allows for the efficient identification of important COVID-19 articles that report results of registered clinical trials and are connected via a structured article-trial link. Our data science methodology also allows for consistent and as needed data updates and is generalizable to other conditions of interest.
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Karakkadparambil Sankaran S, Nair AS. Molecular dynamics and docking studies on potentially active natural phytochemicals for targeting SARS-CoV-2 main protease. J Biomol Struct Dyn 2022:1-17. [PMID: 35930306 DOI: 10.1080/07391102.2022.2107573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
In the present study, we screened eighty seven novel phytochemical compounds from four popular herbs, such as, Aegle Marmelos, Coleus Amboinicus, Aerva Lanata and Biophytum Sensitivum and identified the best three for targeting the main protease (Mpro) receptor of SARS-CoV-2. After categorizing all the phytochemicals based upon LibDock scores and hydrogen bonding interactions, the top ranked 26 compounds were further subjected for detailed Molecular dynamics (MD) study. From these screening we identified that Aegelinosides B leads the list with a high LibDock value of 142.50 (binding energy: -8.54 kcal/mol), which is better than several popular reference compounds namely, Tipranavir (LibDock score, 141.50), Saquinavir (125.34), Zopicole (122.9), Pirenepine (122.70), (115.37), Metixene (109.18), Oxiconazole Pimozide (138.00) and Rimonabant (91.88). Detailed analysis for structural stability (RMSD), Cα fluctuations (RMSF), intermolecular hydrogen bond interactions, effect of solvent accessibility (SASA) and compactness (Rg) factors were performed for the best six compounds and it is found that they are very stable and exhibit folding behavior. Apart from the docking and MD tests, through further drug-likeness and toxicity tests, three compounds, such as, Aegelinosides B, Epicatechin, and Feruloyltyramine (LibDock scores, respectively, 142.50, 124.33 and 129.06) can be suggested for fighting SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
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27
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Abdelmalik M, Beraima M, Fadlalmola HA, Mariod AA, Masaad H, Ahmed M, Mohammead M, Mohammed A, Fadlalla A, Rahama E, Abbakr I, Saeed A, Sambu B. Misconceptions and associated factors of COVID-19 infection among internally displaced persons in Sudan. J Public Health Afr 2022; 13:2051. [PMID: 36051511 PMCID: PMC9425959 DOI: 10.4081/jphia.2022.2051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 05/04/2022] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a global public health threat that has spread rapidly and caused morbidity and mortality worldwide. Reducing the myths about infectious diseases is vital for controlling transmission. This study explored the level of misconceptions and associated factors of COVID-19 among internally displaced persons in Sudan. This study is a cross-sectional, descriptive design and community-based study. We collected the data using a self-administered questionnaire via the convenience sampling technique among internally displaced persons in the camps of Zalingei town in the central Darfur region of Sudan. The total mean score of the respondents’ misconception was 3.1725 (SD=0.59) with 63.2%, indicating moderate misunderstanding of COVID- 19. Multiple linear regression revealed the independent variables together had a significant impact on a misconception, F(14,116)=2.429, p<0.005. The regression model explains 22.7% of the variance in misunderstanding. Analysis of the influence of single factors on the dependent variable showed that people aged 31–40 years had significantly higher levels of misconception, 0.381 (t=2.116, p<0.037), than those aged over 60 years, and university graduates had considerably lower levels of misunderstanding, −0.061 (t=−2.091, p<0.03) than non-graduates. This study found a moderate level of misconception of COVID-19. Non-graduates had higher levels of misunderstanding than graduates. The results suggest that an education campaign should focus on people with low levels of education to correct their misconceptions regarding the prevention of COVID-19 infection.
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28
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Piplani S, Singh P, Winkler DA, Petrovsky N. Potential COVID-19 Therapies from Computational Repurposing of Drugs and Natural Products against the SARS-CoV-2 Helicase. Int J Mol Sci 2022; 23:7704. [PMID: 35887049 PMCID: PMC9322913 DOI: 10.3390/ijms23147704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023] Open
Abstract
Repurposing of existing drugs is a rapid way to find potential new treatments for SARS-CoV-2. Here, we applied a virtual screening approach using Autodock Vina and molecular dynamic simulation in tandem to screen and calculate binding energies of repurposed drugs against the SARS-CoV-2 helicase protein (non-structural protein nsp13). Amongst the top hits from our study were antivirals, antihistamines, and antipsychotics, plus a range of other drugs. Approximately 30% of our top 87 hits had published evidence indicating in vivo or in vitro SARS-CoV-2 activity. Top hits not previously reported to have SARS-CoV-2 activity included the antiviral agents, cabotegravir and RSV-604; the NK1 antagonist, aprepitant; the trypanocidal drug, aminoquinuride; the analgesic, antrafenine; the anticancer intercalator, epirubicin; the antihistamine, fexofenadine; and the anticoagulant, dicoumarol. These hits from our in silico SARS-CoV-2 helicase screen warrant further testing as potential COVID-19 treatments.
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Affiliation(s)
- Sakshi Piplani
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
| | - Puneet Singh
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
| | - David A. Winkler
- Biochemistry and Chemistry Department, La Trobe University, Kingsbury Drive, Melbourne 3086, Australia;
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Nikolai Petrovsky
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
- Department of Diabetes and Endocrinology, Flinders Medical Centre, Flinders University, 1 Flinders Drive, Adelaide 5042, Australia
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29
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Chiu W, Verschueren L, Van den Eynde C, Buyck C, De Meyer S, Jochmans D, Bojkova D, Ciesek S, Cinatl J, De Jonghe S, Leyssen P, Neyts J, Van Loock M, Van Damme E. Development and optimization of a high-throughput screening assay for in vitro anti-SARS-CoV-2 activity: Evaluation of 5676 Phase 1 Passed Structures. J Med Virol 2022; 94:3101-3111. [PMID: 35229317 PMCID: PMC9088669 DOI: 10.1002/jmv.27683] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 01/09/2023]
Abstract
Although vaccines are currently used to control the coronavirus disease 2019 (COVID-19) pandemic, treatment options are urgently needed for those who cannot be vaccinated and for future outbreaks involving new severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) strains or coronaviruses not covered by current vaccines. Thus far, few existing antivirals are known to be effective against SARS-CoV-2 and clinically successful against COVID-19. As part of an immediate response to the COVID-19 pandemic, a high-throughput, high content imaging-based SARS-CoV-2 infection assay was developed in VeroE6 African green monkey kidney epithelial cells expressing a stable enhanced green fluorescent protein (VeroE6-eGFP cells) and was used to screen a library of 5676 compounds that passed Phase 1 clinical trials. Eight drugs (nelfinavir, RG-12915, itraconazole, chloroquine, hydroxychloroquine, sematilide, remdesivir, and doxorubicin) were identified as inhibitors of in vitro anti-SARS-CoV-2 activity in VeroE6-eGFP and/or Caco-2 cell lines. However, apart from remdesivir, toxicity and pharmacokinetic data did not support further clinical development of these compounds for COVID-19 treatment.
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Affiliation(s)
- Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
| | | | | | | | | | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
| | - Denisa Bojkova
- Institute of Medical VirologyUniversity Hospital Frankfurt, Goethe UniversityFrankfurt am MainGermany
| | - Sandra Ciesek
- Institute of Medical VirologyUniversity Hospital Frankfurt, Goethe UniversityFrankfurt am MainGermany
| | - Jindrich Cinatl
- Institute of Medical VirologyUniversity Hospital Frankfurt, Goethe UniversityFrankfurt am MainGermany
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
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Eskandarzade N, Ghorbani A, Samarfard S, Diaz J, Guzzi PH, Fariborzi N, Tahmasebi A, Izadpanah K. Network for network concept offers new insights into host- SARS-CoV-2 protein interactions and potential novel targets for developing antiviral drugs. Comput Biol Med 2022; 146:105575. [PMID: 35533462 PMCID: PMC9055686 DOI: 10.1016/j.compbiomed.2022.105575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, the causal agent of COVID-19, is primarily a pulmonary virus that can directly or indirectly infect several organs. Despite many studies carried out during the current COVID-19 pandemic, some pathological features of SARS-CoV-2 have remained unclear. It has been recently attempted to address the current knowledge gaps on the viral pathogenicity and pathological mechanisms via cellular-level tropism of SARS-CoV-2 using human proteomics, visualization of virus-host protein-protein interactions (PPIs), and enrichment analysis of experimental results. The synergistic use of models and methods that rely on graph theory has enabled the visualization and analysis of the molecular context of virus/host PPIs. We review current knowledge on the SARS-COV-2/host interactome cascade involved in the viral pathogenicity through the graph theory concept and highlight the hub proteins in the intra-viral network that create a subnet with a small number of host central proteins, leading to cell disintegration and infectivity. Then we discuss the putative principle of the "gene-for-gene and "network for network" concepts as platforms for future directions toward designing efficient anti-viral therapies.
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Affiliation(s)
- Neda Eskandarzade
- Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran,Corresponding author
| | - Samira Samarfard
- Berrimah Veterinary Laboratory, Department of Primary Industry and Resources, Berrimah, NT, 0828, Australia
| | - Jose Diaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Pietro H. Guzzi
- Department of Medical and Surgical Sciences, Laboratory of Bioinformatics Unit, Italy
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Tahmasebi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
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31
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Suresh N, Chinnakonda Ashok Kumar N, Subramanian S, Srinivasa G. Memory augmented recurrent neural networks for de-novo drug design. PLoS One 2022; 17:e0269461. [PMID: 35737661 PMCID: PMC9223405 DOI: 10.1371/journal.pone.0269461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 05/22/2022] [Indexed: 12/01/2022] Open
Abstract
A recurrent neural network (RNN) is a machine learning model that learns the relationship between elements of an input series, in addition to inferring a relationship between the data input to the model and target output. Memory augmentation allows the RNN to learn the interrelationships between elements of the input over a protracted length of the input series. Inspired by the success of stack augmented RNN (StackRNN) to generate strings for various applications, we present two memory augmented RNN-based architectures: the Neural Turing Machine (NTM) and the Differentiable Neural Computer (DNC) for the de-novo generation of small molecules. We trained a character-level convolutional neural network (CNN) to predict the properties of a generated string and compute a reward or loss in a deep reinforcement learning setup to bias the Generator to produce molecules with the desired property. Further, we compare the performance of these architectures to gain insight to their relative merits in terms of the validity and novelty of the generated molecules and the degree of property bias towards the computational generation of de-novo drugs. We also compare the performance of these architectures with simpler recurrent neural networks (Vanilla RNN, LSTM, and GRU) without an external memory component to explore the impact of augmented memory in the task of de-novo generation of small molecules.
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Affiliation(s)
- Naveen Suresh
- PES Center for Pattern Recognition and Department of Computer Science and Engineering, PES University, Bengaluru, Karnataka, India
| | - Neelesh Chinnakonda Ashok Kumar
- PES Center for Pattern Recognition and Department of Computer Science and Engineering, PES University, Bengaluru, Karnataka, India
| | - Srikumar Subramanian
- PES Center for Pattern Recognition and Department of Computer Science and Engineering, PES University, Bengaluru, Karnataka, India
| | - Gowri Srinivasa
- PES Center for Pattern Recognition and Department of Computer Science and Engineering, PES University, Bengaluru, Karnataka, India
- * E-mail:
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32
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Wang X, Chen L, Wang X, Zhang M, Yang F, Wu F, Liu J, Lu L, Pang Y. Long-Acting Protective Ocular Surface by Instilling Adhesive Dual-Antiviral Nanoparticles. Adv Healthc Mater 2022; 11:e2200283. [PMID: 35579101 DOI: 10.1002/adhm.202200283] [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: 02/04/2022] [Revised: 04/29/2022] [Indexed: 11/08/2022]
Abstract
The eye is susceptible to viral infections, causing severe ocular symptoms or even respiratory diseases. Methods capable of protecting the eye from external viral invasion in a long-term and highly effective way are urgently needed but have been proved to be extremely challenging. Here, a strategy of forming a long-acting protective ocular surface is described by instilling adhesive dual-antiviral nanoparticles. Taking pseudotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a model virus, antiviral agent-loaded nanoparticles are coated with a "double-lock" hybrid cell membrane abundant with integrin-β1 and angiotensin converting enzyme II (ACE2). After instillation, the presence of integrin-β1 endows coated nanoparticles with steady adhesion via specific binding to Arg-Gly-Asp sequence on the fibronectin of ocular epithelium, achieving durable retention on the ocular surface. In addition to loaded inhibitors, the exposure of ACE2 can trap SARS-CoV-2 and subsequently neutralize the associated spike protein, playing a dual antiviral effect of the resulting nanoparticles. Adhesive dual-antiviral nanoparticles enabled by coating with a "double-lock" hybrid cell membrane could be a versatile platform for topical long-acting protection against viral infection of the eye.
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Affiliation(s)
- Xinyue Wang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Liangbo Chen
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology Department of Ophthalmology Shanghai Ninth People's Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200011 P. R. China
| | - Xinling Wang
- Key Laboratory of Medical Molecular Virology of MOE/MOH School of Basic Medical Sciences and Shanghai Public Health Clinical Center Fudan University Shanghai 200032 P. R. China
| | - Mengmeng Zhang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Fengmin Yang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Feng Wu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Jinyao Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Institute of Molecular Medicine State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 P. R. China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of MOE/MOH School of Basic Medical Sciences and Shanghai Public Health Clinical Center Fudan University Shanghai 200032 P. R. China
| | - Yan Pang
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology Department of Ophthalmology Shanghai Ninth People's Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200011 P. R. China
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Drug Repurposing for COVID-19: A Review and a Novel Strategy to Identify New Targets and Potential Drug Candidates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092723. [PMID: 35566073 PMCID: PMC9099573 DOI: 10.3390/molecules27092723] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023]
Abstract
In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) was first identified in the province of Wuhan, China. Since then, there have been over 400 million confirmed cases and 5.8 million deaths by COVID-19 reported worldwide. The urgent need for therapies against SARS-CoV-2 led researchers to use drug repurposing approaches. This strategy allows the reduction in risks, time, and costs associated with drug development. In many cases, a repurposed drug can enter directly to preclinical testing and clinical trials, thus accelerating the whole drug discovery process. In this work, we will give a general overview of the main developments in COVID-19 treatment, focusing on the contribution of the drug repurposing paradigm to find effective drugs against this disease. Finally, we will present our findings using a new drug repurposing strategy that identified 11 compounds that may be potentially effective against COVID-19. To our knowledge, seven of these drugs have never been tested against SARS-CoV-2 and are potential candidates for in vitro and in vivo studies to evaluate their effectiveness in COVID-19 treatment.
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34
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Guevara‐Pulido J, Jiménez RA, Morantes SJ, Jaramillo DN, Acosta‐Guzmán P. Design, Synthesis, and Development of 4‐[(7‐Chloroquinoline‐4‐yl)amino]phenol as a Potential SARS‐CoV‐2 Mpro Inhibitor. ChemistrySelect 2022; 7:e202200125. [PMID: 35601684 PMCID: PMC9111044 DOI: 10.1002/slct.202200125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
A series of chloroquine analogs were designed to search for a less toxic chloroquine derivative as a potential SARS‐CoV‐2 Mpro inhibitor. Herein, an ANN‐based QSAR model was built to predict the IC50 values of each analog using the experimental values of other 4‐aminoquinolines as the training set. Subsequently, molecular docking was used to evaluate each analog's binding affinity to Mpro. The analog that showed the greatest affinity and lowest IC50 values was synthesized and characterized for its posterior incorporation into a polycaprolactone‐based nanoparticulate system. After characterizing the loaded nanoparticles, an in vitro drug release assay was carried out, and the cytotoxicity of the analog and loaded nanoparticles was evaluated using murine fibroblast (L929) and human lung adenocarcinoma (A549) cell lines. Results show that the synthesized analog is much less toxic than chloroquine and that the nanoparticulate system allowed for the prolonged release of the analog without evidence of adverse effects on the cell lines used; therefore, suggesting that the analog could be a potential therapeutic option for COVID‐19.
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35
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Hua Y, Dai X, Xu Y, Xing G, Liu H, Lu T, Chen Y, Zhang Y. Drug repositioning: Progress and challenges in drug discovery for various diseases. Eur J Med Chem 2022; 234:114239. [PMID: 35290843 PMCID: PMC8883737 DOI: 10.1016/j.ejmech.2022.114239] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022]
Abstract
Compared with traditional de novo drug discovery, drug repurposing has become an attractive drug discovery strategy due to its low-cost and high efficiency. Through a comprehensive analysis of the candidates that have been identified with drug repositioning potentials, it is found that although some drugs do not show obvious advantages in the original indications, they may exert more obvious effects in other diseases. In addition, some drugs have a synergistic effect to exert better clinical efficacy if used in combination. Particularly, it has been confirmed that drug repositioning has benefits and values on the current public health emergency such as the COVID-19 pandemic, which proved the great potential of drug repositioning. In this review, we systematically reviewed a series of representative drugs that have been repositioned for different diseases and illustrated successful cases in each disease. Especially, the mechanism of action for the representative drugs in new indications were explicitly explored for each disease, we hope this review can provide important insights for follow-up research.
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Affiliation(s)
- Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Xiaowen Dai
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Yuan Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Guomeng Xing
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
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Osewe PL, Peters MA. Prioritizing Global Public Health Investments for COVID-19 Response in Real Time: Results from a Delphi Exercise. Health Secur 2022; 20:137-146. [PMID: 35420445 PMCID: PMC9081018 DOI: 10.1089/hs.2021.0142] [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] [Indexed: 11/24/2022] Open
Abstract
In the first months of the COVID-19 pandemic, there was a lack of guidance on how to channel the unprecedented amount of health financing toward the pandemic response. We employed a multistep, interactive Delphi process to reach consensus on a “menu” of priority COVID-19 response interventions. In all, 27 health security experts—representing national governments, bilateral and multilateral organizations, academia, technical agencies, and nongovernmental organizations—participated in the exercise. The experts rated 11 technical investment areas and 37 interventions on a 5-point scale in terms of their importance to COVID-19 response. Initial findings were discussed at a virtual meeting where experts suggested modifications. A group of 19 experts then rated a revised list of 11 technical areas and 39 interventions. Consensus was defined as at least 80% of experts agreeing on the importance of a technical area or intervention; stability of scores across the rounds was identified using Wilcoxon matched-pairs and unpaired signed rank tests. Between the initial and final menu, 3 technical areas and 7 interventions were slightly modified, 3 interventions were added, and 1 intervention was removed. Consensus was reached on all 11 technical areas and 35 of the final 39 interventions, and between 34 and 37 interventions were stable across rounds depending on the test used. In this exercise, the health security experts agreed that COVID-19 response financing should prioritize interventions that enhance a country's capacity to test, trace, and treat high-risk populations. Simultaneously, supportive systems (eg, risk communication, community engagement, public health infrastructure, information systems, policy and coordination, workforce capacity, other social protections) should be developed to ensure that nonpharmaceutical and medical interventions can maximize the effectiveness of these systems.
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Affiliation(s)
- Patrick L Osewe
- Patrick L. Osewe, MD, MPH, is Chief of Health Sector Group, Asian Development Bank, Manila, Philippines
| | - Michael A Peters
- Michael A. Peters, MSPH, PhD, was a Consultant, Asian Development Bank, Manila, Philippines. He is now Associate Faculty, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models. Bioengineering (Basel) 2022; 9:bioengineering9030118. [PMID: 35324806 PMCID: PMC8945737 DOI: 10.3390/bioengineering9030118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 11/25/2022] Open
Abstract
Protein structure prediction is an important issue in structural bioinformatics. In this process, model quality assessment (MQA), which estimates the accuracy of the predicted structure, is also practically important. Currently, the most commonly used dataset to evaluate the performance of MQA is the critical assessment of the protein structure prediction (CASP) dataset. However, the CASP dataset does not contain enough targets with high-quality models, and thus cannot sufficiently evaluate the MQA performance in practical use. Additionally, most application studies employ homology modeling because of its reliability. However, the CASP dataset includes models generated by de novo methods, which may lead to the mis-estimation of MQA performance. In this study, we created new benchmark datasets, named a homology models dataset for model quality assessment (HMDM), that contain targets with high-quality models derived using homology modeling. We then benchmarked the performance of the MQA methods using the new datasets and compared their performance to that of the classical selection based on the sequence identity of the template proteins. The results showed that model selection by the latest MQA methods using deep learning is better than selection by template sequence identity and classical statistical potentials. Using HMDM, it is possible to verify the MQA performance for high-accuracy homology models.
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Ratajczak F, Joblin M, Ringsquandl M, Hildebrandt M. Task-driven knowledge graph filtering improves prioritizing drugs for repurposing. BMC Bioinformatics 2022; 23:84. [PMID: 35246025 PMCID: PMC8894843 DOI: 10.1186/s12859-022-04608-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/09/2021] [Indexed: 02/07/2023] Open
Abstract
Background Drug repurposing aims at finding new targets for already developed drugs. It becomes more relevant as the cost of discovering new drugs steadily increases. To find new potential targets for a drug, an abundance of methods and existing biomedical knowledge from different domains can be leveraged. Recently, knowledge graphs have emerged in the biomedical domain that integrate information about genes, drugs, diseases and other biological domains. Knowledge graphs can be used to predict new connections between compounds and diseases, leveraging the interconnected biomedical data around them. While real world use cases such as drug repurposing are only interested in one specific relation type, widely used knowledge graph embedding models simultaneously optimize over all relation types in the graph. This can lead the models to underfit the data that is most relevant for the desired relation type. For example, if we want to learn embeddings to predict links between compounds and diseases but almost the entirety of relations in the graph is incident to other pairs of entity types, then the resulting embeddings are likely not optimised to predict links between compounds and diseases. We propose a method that leverages domain knowledge in the form of metapaths and use them to filter two biomedical knowledge graphs (Hetionet and DRKG) for the purpose of improving performance on the prediction task of drug repurposing while simultaneously increasing computational efficiency. Results We find that our method reduces the number of entities by 60% on Hetionet and 26% on DRKG, while leading to an improvement in prediction performance of up to 40.8% on Hetionet and 14.2% on DRKG, with an average improvement of 20.6% on Hetionet and 8.9% on DRKG. Additionally, prioritization of antiviral compounds for SARS CoV-2 improves after task-driven filtering is applied. Conclusion Knowledge graphs contain facts that are counter productive for specific tasks, in our case drug repurposing. We also demonstrate that these facts can be removed, resulting in an improved performance in that task and a more efficient learning process. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04608-y.
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Affiliation(s)
- Florin Ratajczak
- Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Munich, Germany. .,Digital Technology and Innovation, Siemens Healthineers, Erlangen, Germany.
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Kebria MM, Milan PB, Peyravian N, Kiani J, Khatibi S, Mozafari M. Stem cell therapy for COVID-19 pneumonia. MOLECULAR BIOMEDICINE 2022; 3:6. [PMID: 35174448 PMCID: PMC8850486 DOI: 10.1186/s43556-021-00067-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is a highly contagious microorganism, and despite substantial investigation, no progress has been achieved in treating post-COVID complications. However, the virus has made various mutations and has spread around the world. Researchers have tried different treatments to reduce the side effects of the COVID-19 symptoms. One of the most common and effective treatments now used is steroid therapy to reduce the complications of this disease. Long-term steroid therapy for chronic inflammation following COVID-19 is harmful and increases the risk of secondary infection, and effective treatment remains challenging owing to fibrosis and severe inflammation and infection. Sometimes our immune system can severely damage ourselves in disease. In the past, many researchers have conducted various studies on the immunomodulatory properties of stem cells. This property of stem cells led them to modulate the immune system of autoimmune diseases like diabetes, multiple sclerosis, and Parkinson's. Because of their immunomodulatory properties, stem cell-based therapy employing mesenchymal or hematopoietic stem cells may be a viable alternative treatment option in some patients. By priming the immune system and providing cytokines, chemokines, and growth factors, stem cells can be employed to build a long-term regenerative and protective response. This review addresses the latest trends and rapid progress in stem cell treatment for Acute Respiratory Distress Syndrome (ARDS) following COVID-19.
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Affiliation(s)
- Maziar Malekzadeh Kebria
- Cellular and Molecular Research Centre, Iran University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Peiman Brouki Milan
- Cellular and Molecular Research Centre, Iran University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Noshad Peyravian
- Cellular and Molecular Research Centre, Iran University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Present Address: Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Soheil Khatibi
- Babol University of Medical Sciences, Infection Diseases Centre, Mazandaran, Iran
| | - Masoud Mozafari
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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Dhameliya TM, Nagar PR, Gajjar ND. Systematic virtual screening in search of SARS CoV-2 inhibitors against spike glycoprotein: pharmacophore screening, molecular docking, ADMET analysis and MD simulations. Mol Divers 2022; 26:2775-2792. [PMID: 35132518 PMCID: PMC8821869 DOI: 10.1007/s11030-022-10394-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/22/2022] [Indexed: 01/08/2023]
Abstract
In the absence of efficient anti-viral medications, the coronavirus disease 2019 (COVID-19), stemming from severe acute respiratory syndrome coronavirus-2 (SARS CoV-2), has spawned a worldwide catastrophe and global emergency. Amidst several anti-viral targets of COVID-19, spike glycoprotein has been recognized as an essential target for the viral entry into the host cell. In the search of effective SARS CoV-2 inhibitors acting against spike glycoprotein, the virtual screening of 175,851 ligands from the 2020.1 Asinex BioDesign library has been performed using in silico tools like SiteMap analysis, pharmacophore-based screening, molecular docking using different levels of precision, such as high throughput virtual screening, standard precision and extra precision, followed by absorption, distribution, metabolism, excretion and toxicity analysis, and molecular dynamics (MD) simulation. Following a molecular docking study, seventeen molecules (with a docking score of less than - 6.0) were identified having the substantial interactions with the catalytic amino acid and nucleic acid residues of spike glycoprotein at the binding site. In investigations using MD simulations for 10 ns, the hit molecules (1 and 2) showed adequate compactness and uniqueness, as well as satisfactory stability. These computational research findings have offered a key starting point in the field of design and development of novel SARS CoV-2 entry inhibitors with appropriate drug likeliness.
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Affiliation(s)
- Tejas M Dhameliya
- L. M. College of Pharmacy, Navrangpura, Ahmedabad, Gujarat, 380009, India.
| | - Prinsa R Nagar
- L. M. College of Pharmacy, Navrangpura, Ahmedabad, Gujarat, 380009, India
| | - Normi D Gajjar
- L. M. College of Pharmacy, Navrangpura, Ahmedabad, Gujarat, 380009, India
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41
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Vivek-Ananth RP, Krishnaswamy S, Samal A. Potential phytochemical inhibitors of SARS-CoV-2 helicase Nsp13: a molecular docking and dynamic simulation study. Mol Divers 2022; 26:429-442. [PMID: 34117992 PMCID: PMC8196922 DOI: 10.1007/s11030-021-10251-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 helicase Nsp13 is a promising target for developing anti-COVID drugs. In the present study, we have identified potential natural product inhibitors of SARS-CoV-2 Nsp13 targeting the ATP-binding site using molecular docking and molecular dynamics (MD) simulations. MD simulation of the prepared crystal structure of SARS-CoV-2 Nsp13 was performed to generate an ensemble of structures of helicase Nsp13 capturing the conformational diversity of the ATP-binding site. A natural product library of more than 14,000 phytochemicals from Indian medicinal plants was used to perform virtual screening against the ensemble of Nsp13 structures. Subsequently, a two-stage filter, first based on protein-ligand docking binding energy value and second based on protein residues in the ligand-binding site and non-covalent interactions between the protein residues and the ligand in the best-docked pose, was used to identify 368 phytochemicals as potential inhibitors of SARS-CoV-2 helicase Nsp13. MD simulations of the top inhibitors complexed with protein were performed to confirm stable binding, and to compute MM-PBSA based binding energy. From among the 368 potential phytochemical inhibitors, the top identified potential inhibitors of SARS-CoV-2 helicase Nsp13 namely, Picrasidine M, (+)-Epiexcelsin, Isorhoeadine, Euphorbetin and Picrasidine N, can be taken up initially for experimental studies.
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Affiliation(s)
- R P Vivek-Ananth
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | | | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India.
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India.
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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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Al-Shuhaib MBS, Hashim HO, Al-Shuhaib JMB, Obayes DH. Artecanin of Laurus nobilis is a novel inhibitor of SARS-CoV-2 main protease with highly desirable druglikeness. J Biomol Struct Dyn 2022; 41:2355-2367. [PMID: 35067202 DOI: 10.1080/07391102.2022.2030801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Main protease (Mpro) is a critical enzyme in the life cycle of severe acute respiratory syndrome Coronavirus -2 (SARS-CoV-2). Due to its essential role in the maturation of the polyproteins, the necessity to inhibit Mpro is one of the essential means to prevent the outbreak of COVID-19. In this context, this study was conducted on the natural compounds of medicinal plants that are commonly available in the Middle East to find out the most potent one to inhibit Mpro with the best bioavailability and druglikeness properties. A total of 3392 compounds of sixty-six medicinal plants were retrieved from PubChem database and docked against Mpro. Thirty compounds with the highest docking scores with Mpro were chosen for further virtual screening. Variable druglikeness and toxicity potentials of these compounds were evaluated using SwissADME and Protox servers respectively. Out of these virtually screened compounds, artecanin was predicted to exhibit the most favourable druglikeness potentials, accompanied by no predicted hepatoxicity, carcinogenicity, mutagenicity, and cytotoxicity. Molecular dynamics (MD) simulations showed that Mpro-artecanin complex exhibited comparable stability with that observed in the ligand-free Mpro. This study revealed for the first time that artecanin from Laurus nobilis provided a novel static and dynamic inhibition for Mpro with excellent safety, oral bioavailability, and pharmacokinetic profile. This study suggested the ability of artecanin to be used as a potential natural inhibitor that can be used to block or at least counteract the SARS-CoV-2 invasion.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Hayder O. Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil, Iraq
| | | | - Daniel H. Obayes
- Babylon Directorate of Education, Ministry of Education, Babil, Iraq
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Yu Y, Fang Y, Tang R, Xu D, Dai S, Zhang W. Electrochemical oxidative sulfonylation of N‐arylamides/amine with sodium sulfinates. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202100805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yingliang Yu
- Anhui Normal University College of Chemistry and Materials Science CHINA
| | - Yang Fang
- Anhui Normal University College of Chemistry and Materials Science CHINA
| | - Rumeng Tang
- Anhui Normal University College of Chemistry and Materials Science CHINA
| | - Dongping Xu
- Anhui Normal University College of Chemistry and Materials Science CHINA
| | - Shuaishuai Dai
- Anhui Normal University College of Chemistry and Materials Science CHINA
| | - Wu Zhang
- Anhui Normal University College of Chemistry and Materials Science 1 Beijing Eastroad 241000 Wuhu CHINA
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Abstract
Coronavirus disease 2019 (COVID-19) is still propagating a year after the start of the pandemic. Besides the complications patients face during the COVID-19 disease period, there is an accumulating body of evidence concerning the late-onset complications of COVID-19, of which autoimmune manifestations have attracted remarkable attention from the first months of the pandemic. Autoimmune hemolytic anemia, immune thrombocytopenic purpura, autoimmune thyroid diseases, Kawasaki disease, Guillain-Barre syndrome, and the detection of autoantibodies are the cues to the discovery of the potential of COVID-19 in inducing autoimmunity. Clarification of the pathophysiology of COVID-19 injuries to the host, whether it is direct viral injury or autoimmunity, could help to develop appropriate treatment.
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Affiliation(s)
- Niloufar Yazdanpanah
- Research Center for Immunodeficiencies, Children's Medical CenterTehran University of Medical SciencesTehranIran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical CenterTehran University of Medical SciencesTehranIran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA)Universal Scientific Education and Research Network (USERN)TehranIran
- Department of Immunology, School of MedicineTehran University of Medical SciencesTehranIran
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Wu J, Chen Z, Han X, Chen Q, Wang Y, Feng T. SARS-CoV-2 RNA-dependent RNA polymerase as a target for high-throughput drug screening. Future Virol 2022:10.2217/fvl-2021-0335. [PMID: 36794167 PMCID: PMC9910510 DOI: 10.2217/fvl-2021-0335] [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: 11/28/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023]
Abstract
The ongoing COVID-19 pandemic caused by the SARS-CoV-2 has necessitated rapid development of drug screening tools. RNA-dependent RNA polymerase (RdRp) is a promising target due to its essential functions in replication and transcription of viral genome. To date, through minimal RNA synthesizing machinery established from cryo-electron microscopy structural data, there has been development of high-throughput screening assays for directly screening inhibitors that target the SARS-CoV-2 RdRp. Here, we analyze and present verified techniques that could be used to discover potential anti-RdRp agents or repurposing of approved drugs to target the SARS-CoV-2 RdRp. In addition, we highlight the characteristics and application value of cell-free or cell-based assays in drug discovery.
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Affiliation(s)
- Jiahui Wu
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Zhiqiang Chen
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China,2Department of Nuclear Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province, China
| | - Xue Han
- 3Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, 59 Haier Road, Qingdao, 266000, Shandong Province, China
| | - Qiaoqiao Chen
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Yintao Wang
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Tingting Feng
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China,Author for correspondence: Tel.: +86 512 6588 2429;
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Molecular docking and molecular dynamic simulation approaches for drug development and repurposing of drugs for severe acute respiratory syndrome-Coronavirus-2. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300476 DOI: 10.1016/b978-0-323-91172-6.00007-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Shen L, Liu F, Huang L, Liu G, Zhou L, Peng L. VDA-RWLRLS: An anti-SARS-CoV-2 drug prioritizing framework combining an unbalanced bi-random walk and Laplacian regularized least squares. Comput Biol Med 2022; 140:105119. [PMID: 34902608 PMCID: PMC8664497 DOI: 10.1016/j.compbiomed.2021.105119] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/08/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND A new coronavirus disease named COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is rapidly spreading worldwide. However, there is currently no effective drug to fight COVID-19. METHODS In this study, we developed a Virus-Drug Association (VDA) identification framework (VDA-RWLRLS) combining unbalanced bi-Random Walk, Laplacian Regularized Least Squares, molecular docking, and molecular dynamics simulation to find clues for the treatment of COVID-19. First, virus similarity and drug similarity are computed based on genomic sequences, chemical structures, and Gaussian association profiles. Second, an unbalanced bi-random walk is implemented on the virus network and the drug network, respectively. Third, the results of the random walks are taken as the input of Laplacian regularized least squares to compute the association score for each virus-drug pair. Fourth, the final associations are characterized by integrating the predictions from the virus network and the drug network. Finally, molecular docking and molecular dynamics simulation are implemented to measure the potential of screened anti-COVID-19 drugs and further validate the predicted results. RESULTS In comparison with six state-of-the-art association prediction models (NGRHMDA, SMiR-NBI, LRLSHMDA, VDA-KATZ, VDA-RWR, and VDA-BiRW), VDA-RWLRLS demonstrates superior VDA prediction performance. It obtains the best AUCs of 0.885 8, 0.835 5, and 0.862 5 on the three VDA datasets. Molecular docking and dynamics simulations demonstrated that remdesivir and ribavirin may be potential anti-COVID-19 drugs. CONCLUSIONS Integrating unbalanced bi-random walks, Laplacian regularized least squares, molecular docking, and molecular dynamics simulation, this work initially screened a few anti-SARS-CoV-2 drugs and may contribute to preventing COVID-19 transmission.
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Affiliation(s)
- Ling Shen
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China
| | - Fuxing Liu
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China
| | - Li Huang
- Academy of Arts and Design, Tsinghua University, Beijing, 10 084, Beijing, China; The Future Laboratory, Tsinghua University, Beijing, 10 084, Beijing, China
| | - Guangyi Liu
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China.
| | - Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China; College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412 007, Hunan, China.
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In search of SARS CoV-2 replication inhibitors: Virtual screening, molecular dynamics simulations and ADMET analysis. J Mol Struct 2021; 1246:131190. [PMID: 34334813 PMCID: PMC8313085 DOI: 10.1016/j.molstruc.2021.131190] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/11/2021] [Accepted: 07/24/2021] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome has relapsed recently as novel coronavirus causing a life threat to the entire world in the absence of an effective therapy. To hamper the replication of the deadly SARS CoV-2 inside the host cells, systematic in silico virtual screening of total 267,324 ligands from Asinex EliteSynergy and BioDesign libraries has been performed using AutoDock Vina against RdRp. The molecular modeling studies revealed the identification of twenty-one macrocyclic hits (2-22) with better binding energy than remdesivir (1), marketed SARS CoV-2 inhibitor. Further, the analysis using rules for drug-likeness and their ADMET profile revealed the candidature of these hits due to superior oral bioavailability and druggability. Further, the MD simulation studies of top two hits (2 and 3) performed using GROMACS 2020.1 for 10 ns revealed their stability into the docked complexes. These results provide an important breakthrough in the design of macrocyclic hits as SARS CoV-2 RNA replicase inhibitor.
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Key Words
- ACE2, angiotensin converting enzyme 2
- ADMET assay
- ADMET, absorption, distribution, metabolism, excretion and toxicity
- BBB, blood-brain barrier
- BOILED, brain or intestinal estimated permeation method
- COVID-19
- COVID-19, corona virus disease 2019
- E, envelope protein
- FDA, food and drugs administration
- HBA, hydrogen bond acceptor
- HBD, hydrogen bond donor
- HERG, human ether-a-go-go-related gene
- LOAEL, oral rat chronic toxicity
- M, membrane protein
- MD simulations
- MD, molecular dynamics
- Molecular docking
- N, nucleocapsid protein
- NSPs, non-structural proteins
- RdRp
- RdRp, RNA dependent RNA polymerase
- S, spike glycoprotein
- SARS CoV-2
- SARS CoV-2, severe acute respiratory syndrome 2
- UTR, untranslated region
- WHO, world health organization
- pp1a/b, polyproteins
- ssRNA, single stranded ribonucleic acid
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Structural modification of antineoplastic drug carmofur designed to the inhibition of SARS-CoV-2 main protease: A theoretical investigation. RESULTS IN CHEMISTRY 2021; 4:100259. [PMID: 34904062 PMCID: PMC8656244 DOI: 10.1016/j.rechem.2021.100259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
A coherent account of the reaction mechanistic details, structural modifications, and inhibition potentials of antineoplastic drug carmofur and its modified analogs to inhibition of SARS-CoV-2 main protease (Mpro) is reported. The survey is performed by integrating the density functional based tight binding (DFTB3) with density functional theory (DFT) calculations. The inhibition process commences with nucleophilic attack from the sulfur atom on the carbonyl group, yielding a C-S bond formation, followed by a bond formation of the H-O9 by 2.07 Å, which results in a transition state contains a ring of six atoms. We found that although the direct addition of sulfhydryl group hydrogen to the N3 position is likely to happen, the proper position of the hydrogen to O9 decreases its accessibility. The thermodynamic stability of the complex was calculated to be highly sensitive to the substituent on the N11 position. Compounds with CH2NH2 and CH2F at N11 positions of carmofur revealed high thermodynamic stability to complexation with Mpro but induced no change in substrate-binding pocket comparable to carmofur. Replacing the N11 of carmofur with carbon (C-carmofur) was effective in terms of complexation stability at CH2CH2CH2F and CH2CH2CH2OH substitutions and occupation of S1 subsite by these structures in addition to the S2 subsite. Based on the resulted data, increasing the length of the carbon chain at introduced substitutions in N-carmofur almost decreases the complexation stability while in C-carmofur the trend is reversed. Throughout these information outputs, it was suggested that compounds d, e, i′, and k′ might be novel and more efficacious drug candidates instead of carmofur. We believe that our characterization of mechanistic details and structural modification on Mpro/carmofur complex will significantly intensify researchers' understanding of this system, and consequently help them to take advantage of results into practice and design various valuable derivatives for inhibition of SARS-CoV-2 main protease.
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