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Stratton C, Christensen A, Jordan C, Salvatore BA, Mahdavian E. An interdisciplinary course on computer-aided drug discovery to broaden student participation in original scientific research. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 52:276-290. [PMID: 38308532 PMCID: PMC11251704 DOI: 10.1002/bmb.21811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 11/13/2023] [Accepted: 12/30/2023] [Indexed: 02/04/2024]
Abstract
We present a new highly interdisciplinary project-based course in computer aided drug discovery (CADD). This course was developed in response to a call for alternative pedagogical approaches during the COVID-19 pandemic, which caused the cancellation of a face-to-face summer research program sponsored by the Louisiana Biomedical Research Network (LBRN). The course integrates guided research and educational experiences for chemistry, biology, and computer science students. We implement research-based methods with publicly available tools in bioinformatics and molecular modeling to identify and prioritize promising antiviral drug candidates for COVID-19. The purpose of this course is three-fold: I. Implement an active learning and inclusive pedagogy that fosters student engagement and research mindset; II. Develop student interdisciplinary research skills that are highly beneficial in a broader scientific context; III. Demonstrate that pedagogical shifts (initially incurred during the COVID-19 pandemic) can furnish longer-term instructional benefits. The course, which has now been successfully taught a total of five times, incorporates four modules, including lectures/discussions, live demos, inquiry-based assignments, and science communication.
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Affiliation(s)
- Christopher Stratton
- Department of Biological Science, LSU Shreveport, One University Place, Shreveport, Louisiana, USA
| | - Avery Christensen
- Department of Biological Science, LSU Shreveport, One University Place, Shreveport, Louisiana, USA
| | - Chelsey Jordan
- Department of Biological Science, LSU Shreveport, One University Place, Shreveport, Louisiana, USA
| | - Brian A Salvatore
- Department of Chemistry & Physics, LSU Shreveport, One University Place, Shreveport, Louisiana, USA
| | - Elahe Mahdavian
- Department of Biological Science, LSU Shreveport, One University Place, Shreveport, Louisiana, USA
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2
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Wu A, Shi K, Wang J, Zhang R, Wang Y. Targeting SARS-CoV-2 entry processes: The promising potential and future of host-targeted small-molecule inhibitors. Eur J Med Chem 2024; 263:115923. [PMID: 37981443 DOI: 10.1016/j.ejmech.2023.115923] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/28/2023] [Indexed: 11/21/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has had a huge impact on global health. To respond to rapidly mutating viruses and to prepare for the next pandemic, there is an urgent need to develop small molecule therapies that target critical stages of the SARS-CoV-2 life cycle. Inhibiting the entry process of the virus can effectively control viral infection and play a role in prevention and treatment. Host factors involved in this process, such as ACE2, TMPRSS2, ADAM17, furin, PIKfyve, TPC2, CTSL, AAK1, V-ATPase, HSPG, and NRP1, have been found to be potentially good targets with stability. Through further exploration of the cell entry process of SARS-CoV-2, small-molecule drugs targeting these host factors have been developed. This review focuses on the structural functions of potential host cell targets during the entry of SARS-CoV-2 into host cells. The research progress, chemical structure, structure-activity relationship, and clinical value of small-molecule inhibitors against COVID-19 are reviewed to provide a reference for the development of small-molecule drugs against COVID-19.
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Affiliation(s)
- Aijia Wu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Kunyu Shi
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Ruofei Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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3
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Goyal S, Singh M, Thirumal D, Sharma P, Mujwar S, Mishra KK, Singh TG, Singh R, Singh V, Singh T, Ahmad SF. In Silico Approaches to Developing Novel Glycogen Synthase Kinase 3β (GSK-3β). Biomedicines 2023; 11:2784. [PMID: 37893156 PMCID: PMC10604233 DOI: 10.3390/biomedicines11102784] [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: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Alzheimer's disease (AD) is caused by plaque agglomeration and entanglement in several areas of the neural cells, which leads to apoptosis. The main etiology of AD is senile dementia, which is linked to amyloid-beta (Aβ) deregulation and tau perivascular pathogeny. Hyperphosphorylated tau has a propensity for microtubules, which elevate the instability and tau-protein congregates, leading to accumulation of neurofibrillary tangles (NFTs). Tau hyperphosphorylation is susceptible to GSK-3, which has led to an emerging hypothesis regarding the pathogenesis of AD. Accordingly, attempts have been made to conduct investigations and achieve further advancements on new analogues capable of inhibiting the GSK-3 protein, which are currently in the clinical trials. In this analysis, we have evaluated certain GSK-3 inhibitor variants utilising scaffolding and framework devised techniques with pharmacological characteristics, accompanied by computational screenings (pharmacokinetics and docking). The structure-based designed analogues interacted effectively with the active amino acids of GSK-3β target protein. The in silico pharmacokinetic studies revealed their drug-like properties. The analogues with best interactions and binding scores will be considered in the future to completely demonstrate their potential relevance as viable GSK-3 inhibitors.
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Affiliation(s)
- Shuchi Goyal
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (S.G.); (S.M.); (R.S.)
| | - Manjinder Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (S.G.); (S.M.); (R.S.)
| | - Divya Thirumal
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (S.G.); (S.M.); (R.S.)
| | - Pratibha Sharma
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (S.G.); (S.M.); (R.S.)
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (S.G.); (S.M.); (R.S.)
| | - Krishna Kumar Mishra
- Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura 140401, Punjab, India;
| | - Thakur Gurjeet Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (S.G.); (S.M.); (R.S.)
| | - Ravinder Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (S.G.); (S.M.); (R.S.)
| | - Varinder Singh
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda 151001, Punjab, India;
| | - Tanveer Singh
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A & M Health Science Center, Bryan, TX 77807, USA;
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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Murali M, Nair B, Vishnu VR, Aneesh TP, Nath LR. 2,4-Dihydroxycinnamic acid as spike ACE2 inhibitor and apigenin as RdRp inhibitor in Nimbamritadi Panchatiktam Kashayam against COVID-19: an in silico and in vitro approach. Mol Divers 2023; 27:2353-2363. [PMID: 36357813 PMCID: PMC9648999 DOI: 10.1007/s11030-022-10552-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
Nimbamritadi Panchatiktam Kashayam (NPK) is an ayurvedic formulation composed of ingredients with potent anti-viral activities. We studied the interaction energy of 144 phytoconstituents present in NPK against spike receptor-binding domain (RBD) complexed with ACE2 protein (PDB ID: 6LZG) and RNA-dependent RNA polymerase protein (PDB ID: 7BTF) using Biovia Drug Discovery studio. The result indicated that 2,4-hydroxycinnamic acid exerts more significant binding affinities (28.43 kcal/mol) than Umifenovir (21.24 kcal/mol) against spike ACE2. Apigenin exhibited the highest binding affinities (54.63 kcal/mol) compared with Remdesivir (24.52 kcal/mol) against RdRp. An in vitro analysis showed a reduction in the number of lentiviral particles on transfected HEK293T-hACE2 cells as assessed by pseudovirus inhibition assay. At the same time, the tested compounds showed non-toxic up to 100 µg/ml in normal cells by MTT assay. The study highlights the plausible clinical utility of this traditional medicine against SARS CoV2.
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Affiliation(s)
- Maneesha Murali
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - Bhagyalakshmi Nair
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - V R Vishnu
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - T P Aneesh
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India.
| | - Lekshmi R Nath
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India.
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5
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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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Bhatia S, Singh M, Sharma P, Mujwar S, Singh V, Mishra KK, Singh TG, Singh T, Ahmad SF. Scaffold Morphing and In Silico Design of Potential BACE-1 (β-Secretase) Inhibitors: A Hope for a Newer Dawn in Anti-Alzheimer Therapeutics. Molecules 2023; 28:6032. [PMID: 37630283 PMCID: PMC10459662 DOI: 10.3390/molecules28166032] [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: 07/24/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Alzheimer's disease (AD) is the prime cause of 65-80% of dementia cases and is caused by plaque and tangle deposition in the brain neurons leading to brain cell degeneration. β-secretase (BACE-1) is a key enzyme responsible for depositing extracellular plaques made of β-amyloid protein. Therefore, efforts are being applied to develop novel BACE-1 enzyme inhibitors to halt plaque build-up. In our study, we analyzed some Elenbecestat analogues (a BACE-1 inhibitor currently in clinical trials) using a structure-based drug design and scaffold morphing approach to achieve a superior therapeutic profile, followed by in silico studies, including molecular docking and pharmacokinetics methodologies. Among all the designed compounds, SB306 and SB12 showed good interactions with the catalytic dyad motifs (Asp228 and Asp32) of the BACE-1 enzyme with drug-likeliness properties and a high degree of thermodynamic stability confirmed by the molecular dynamic and stability of the simulated system indicating the inhibitory nature of the SB306 and SB12 on BACE 1.
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Affiliation(s)
- Shiveena Bhatia
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Manjinder Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Pratibha Sharma
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Varinder Singh
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda 151001, Punjab, India;
| | - Krishna Kumar Mishra
- Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura 140401, Punjab, India;
| | - Thakur Gurjeet Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India (P.S.); (S.M.); (T.G.S.)
| | - Tanveer Singh
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M Health Science Center, College Station, TX 77807, USA
| | - Sheikh Fayaz Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
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Sha A, Chen H. Infection routes, invasion mechanisms, and drug inhibition pathways of human coronaviruses on the nervous system. Front Neurosci 2023; 17:1169740. [PMID: 37139519 PMCID: PMC10150004 DOI: 10.3389/fnins.2023.1169740] [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: 02/20/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
So far, numerous studies have reported on how coronaviruses affect the human nervous system. However, these studies mainly focused on the impact of a single coronavirus on the nervous system, and failed to fully report the invasion mechanisms and the rules of symptoms of the seven human coronaviruses. This research can assist medical professionals in identifying the regularity of coronavirus invasion into the nervous system by examining the impacts of human coronaviruses on the nervous system. Meanwhile, the discovery also helps humans to prevent the damage to the human nervous system caused by the more novel coronavirus in advance, thus reducing the rate of disease transmission and fatality caused by such viruses. In addition to describing the structures, routes of infection, and symptomatic manifestations of human coronaviruses, this review also finds that the structures of human coronaviruses correlate with virulence, pathways of infection, and blocking mechanisms of drugs. This review can provide a theoretical basis for the research and development of related drugs, promote the prevention and treatment of coronavirus infectious diseases, and contribute to global epidemic prevention.
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Affiliation(s)
- Ailong Sha
- School of Teacher Education, Chongqing Three Gorges University, Chongqing, China
- School of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Hongrun Chen
- School of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
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Mudi PK, Mahanty AK, Kotakonda M, Prasad S, Bhattacharyya S, Biswas B. A benzimidazole scaffold as a promising inhibitor against SARS-CoV-2. J Biomol Struct Dyn 2023; 41:1798-1810. [PMID: 35000553 DOI: 10.1080/07391102.2021.2024448] [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
The manuscript reports the green-chemical synthesis of a new diindole-substituted benzimidazole compound, B1 through a straightforward route in coupling between indolyl-3-carboxaldehyde and o-phenylenediamine in water medium under the aerobic condition at 75 ºC. The single crystal X-ray structural analysis of B1 suggests that the disubstituted benzimidazole compound crystallizes in a monoclinic system and the indole groups exist in a perpendicular fashion with respect to benzimidazole moiety. The SARS-CoV-2 screening activity has been studied against 1 × 10e4 VeroE6 cells in a dose-dependent manner following Hoechst 33342 and nucleocapsid staining activity with respect to remdesivir. The compound exhibits 92.4% cell viability for 30 h and 35.1% inhibition against VeroE6 cells at non-cytotoxic concentration. Molecular docking studies predict high binding propensities of B1 with the main protease (Mpro) and non-structural (nsp2 and nsp7-nsp8) proteins of SARS-CoV-2 through a number of non-covalent interactions. Molecular dynamics (MD) simulation analysis for 100 ns confirms the formation of stable conformations of B1-docked proteins with significant changes of binding energy, attributing the potential inhibition properties of the synthetic benzimidazole scaffold against SARS-CoV-2. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prafullya Kumar Mudi
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | - Ayan Kumar Mahanty
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | | | - Sunnapu Prasad
- Department of Pharmaceutical Chemistry, Sri Ramakrishna Institute of Paramedical Science, Coimbatore, India
| | - Subires Bhattacharyya
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | - Bhaskar Biswas
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
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Mahnam K, Ghobadi Z. Finding a prospective dual-target drug for the treatment of coronavirus disease by theoretical study. J Biomol Struct Dyn 2022; 40:12621-12641. [PMID: 34514953 DOI: 10.1080/07391102.2021.1973910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Spike protein of coronavirus is a key protein in binding and entrance of virus to the human cell via binding to the receptor-binding domain (RBD) domain of S1 subunit to peptidase domain region of ACE2 receptor. In this study, the possible effect of 24 antiviral drugs on the RBD domain of spike protein was investigated via docking and molecular dynamics simulation for finding a dual-target drug. At first, all drugs were docked to the RBD domain of spike protein, and then all complexes and free RBD domains were separately used for molecular dynamics simulation for 50 ns via amber18 software. The simulation results showed that 10 ligands from 28 ligands were separated from the RBD domain, and among 18 remained ligands, baloxavir marboxil, and danoprevir drugs, besides endonuclease activity and protease inhibitory, can bind to key residues of the RBD domain. Then these drugs have a dual target and should be more effective than current drugs, and experimental studies should be done on baloxavir marboxil and danoprevir as more potential drugs for coronavirus disease Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karim Mahnam
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.,Nanotechnology Research Center, Shahrekord University, Shahrekord, Iran
| | - Zahra Ghobadi
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
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Sharun K, Tiwari R, Yatoo MI, Natesan S, Megawati D, Singh KP, Michalak I, Dhama K. A comprehensive review on pharmacologic agents, immunotherapies and supportive therapeutics for COVID-19. NARRA J 2022; 2:e92. [PMID: 38449903 PMCID: PMC10914132 DOI: 10.52225/narra.v2i3.92] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 03/08/2024]
Abstract
The emergence of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected many countries throughout the world. As urgency is a necessity, most efforts have focused on identifying small molecule drugs that can be repurposed for use as anti-SARS-CoV-2 agents. Although several drug candidates have been identified using in silico method and in vitro studies, most of these drugs require the support of in vivo data before they can be considered for clinical trials. Several drugs are considered promising therapeutic agents for COVID-19. In addition to the direct-acting antiviral drugs, supportive therapies including traditional Chinese medicine, immunotherapies, immunomodulators, and nutritional therapy could contribute a major role in treating COVID-19 patients. Some of these drugs have already been included in the treatment guidelines, recommendations, and standard operating procedures. In this article, we comprehensively review the approved and potential therapeutic drugs, immune cells-based therapies, immunomodulatory agents/drugs, herbs and plant metabolites, nutritional and dietary for COVID-19.
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Affiliation(s)
- Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Mohd I. Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Alusteng Srinagar, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir, India
| | - Senthilkumar Natesan
- Department of Infectious Diseases, Indian Institute of Public Health Gandhinagar, Opp to Airforce station HQ, Gandhinagar, India
| | - Dewi Megawati
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Indonesia
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
| | - Karam P. Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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11
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Lu D, Liu D, Wang X, Liu Y, Liu Y, Ren R, Pang G. Kinetics of Drug Molecule Interactions with a Newly Developed Nano-Gold-Modified Spike Protein Electrochemical Receptor Sensor. BIOSENSORS 2022; 12:888. [PMID: 36291025 PMCID: PMC9599096 DOI: 10.3390/bios12100888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
In March 2020, the World Health Organization (WHO) declared COVID-19 a pandemic, and the spike protein has been reported to be an important drug target for anti-COVID-19 treatment. As such, in this study, we successfully developed a novel electrochemical receptor biosensor by immobilizing the SARS-CoV-2 spike protein and using AuNPs-HRP as an electrochemical signal amplification system. Moreover, the time-current method was used to quantify seven antiviral drug compounds, such as arbidol and chloroquine diphosphate. The results show that the spike protein and the drugs are linearly correlated within a certain concentration range and that the detection sensitivity of the sensor is extremely high. In the low concentration range of linear response, the kinetics of receptor-ligand interactions are similar to that of an enzymatic reaction. Among the investigated drug molecules, bromhexine exhibits the smallest Ka value, and thus, is most sensitively detected by the sensor. Hydroxychloroquine exhibits the largest Ka value. Molecular docking simulations of the spike protein with six small-molecule drugs show that residues of this protein, such as Asp, Trp, Asn, and Gln, form hydrogen bonds with the -OH or -NH2 groups on the branched chains of small-molecule drugs. The electrochemical receptor biosensor can directly quantify the interaction between the spike protein and drugs such as abidor and hydroxychloroquine and perform kinetic studies with a limit of detection 3.3 × 10-20 mol/L, which provides a new research method and idea for receptor-ligand interactions and pharmacodynamic evaluation.
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Affiliation(s)
- Dingqiang Lu
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
- Tianjin Key Laboratory of Food Biotechnology, Tianjin 300134, China
| | - Danyang Liu
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xinqian Wang
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yujiao Liu
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yixuan Liu
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Ruijuan Ren
- Tianjin Institute for Food Safety Inspection Technology, Tianjin 300134, China
| | - Guangchang Pang
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
- Tianjin Key Laboratory of Food Biotechnology, Tianjin 300134, China
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12
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Kumar S, Paul P, Yadav P, Kaul R, Maitra SS, Jha SK, Chaari A. A multi-targeted approach to identify potential flavonoids against three targets in the SARS-CoV-2 life cycle. Comput Biol Med 2022; 142:105231. [PMID: 35032740 PMCID: PMC8750703 DOI: 10.1016/j.compbiomed.2022.105231] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 02/07/2023]
Abstract
The advent and persistence of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2)-induced Coronavirus Disease (COVID-19) pandemic since December 2019 has created the largest public health emergency in over a century. Despite the administration of multiple vaccines across the globe, there continues to be a lack of approved efficacious non-prophylactic interventions for the disease. Flavonoids are a class of phytochemicals with historically established antiviral, anti-inflammatory and antioxidative properties that are effective against cancers, type 2 diabetes mellitus, and even other human coronaviruses. To identify the most promising bioactive flavonoids against the SARS-CoV-2, this article screened a virtual library of 46 bioactive flavonoids against three promising targets in the SARS-CoV-2 life cycle: human TMPRSS2 protein, 3CLpro, and PLpro. By examining the effects of glycosylation and other structural-activity relationships, the presence of sugar moiety in flavonoids significantly reduces its binding energy. It increases the solubility of flavonoids leading to reduced toxicity and higher bioavailability. Through protein-ligand contact profiling, it was concluded that naringin formed more hydrogen bonds with TMPRSS2 and 3CLpro. In contrast, hesperidin formed a more significant number of hydrogen bonds with PLpro. These observations were complimented by the 100 ns molecular dynamics simulation and binding free energy analysis, which showed a considerable stability of docked bioflavonoids in the active site of SARS-CoV-2 target proteins. Finally, the binding affinity and stability of the selected docked complexes were compared with the reference ligands (camostat for TMPRSS2, GC376 for 3CLpro, and GRL0617 for PLpro) that strongly inhibit their respective SARS-COV-2 targets. Overall analysis revealed that the selected flavonoids could be potential therapeutic agents against SARS-CoV-2. Naringin showed better affinity and stability for TMPRSS2 and 3CLpro, whereas hesperidin showed a better binding relationship and stability for PLpro.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India; Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.
| | - Pradipta Paul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
| | - Pardeep Yadav
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India; Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Ridhima Kaul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
| | - S S Maitra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Ali Chaari
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
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13
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Ning Q, Wu D, Wang X, Xi D, Chen T, Chen G, Wang H, Lu H, Wang M, Zhu L, Hu J, Liu T, Ma K, Han M, Luo X. The mechanism underlying extrapulmonary complications of the coronavirus disease 2019 and its therapeutic implication. Signal Transduct Target Ther 2022; 7:57. [PMID: 35197452 PMCID: PMC8863906 DOI: 10.1038/s41392-022-00907-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is a highly transmissible disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that poses a major threat to global public health. Although COVID-19 primarily affects the respiratory system, causing severe pneumonia and acute respiratory distress syndrome in severe cases, it can also result in multiple extrapulmonary complications. The pathogenesis of extrapulmonary damage in patients with COVID-19 is probably multifactorial, involving both the direct effects of SARS-CoV-2 and the indirect mechanisms associated with the host inflammatory response. Recognition of features and pathogenesis of extrapulmonary complications has clinical implications for identifying disease progression and designing therapeutic strategies. This review provides an overview of the extrapulmonary complications of COVID-19 from immunological and pathophysiologic perspectives and focuses on the pathogenesis and potential therapeutic targets for the management of COVID-19.
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Affiliation(s)
- Qin Ning
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Di Wu
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojing Wang
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dong Xi
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Chen
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guang Chen
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongwu Wang
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huiling Lu
- National Medical Center for Major Public Health Events, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Wang
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Zhu
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junjian Hu
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Liu
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Ma
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meifang Han
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Luo
- National Medical Center for Major Public Health Events, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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14
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Barrett R, Hodgkinson J. Impact of the COVID-19 pandemic on cardiovascular heart disease medication use: time-series analysis of England's prescription data during the COVID-19 pandemic (January 2019 to October 2020). Ther Adv Cardiovasc Dis 2022; 16:17539447221137170. [PMID: 36420815 PMCID: PMC9702971 DOI: 10.1177/17539447221137170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 10/19/2022] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Management of high blood pressure (BP) typically requires adherence to medication regimes. However, it is known that the COVID-19 pandemic both interrupted access to some routine prescriptions and changed some patient health behaviours. AIM This study, therefore, retrospectively investigated prescription reimbursement of cardiovascular (CVD) medicines as a proxy measure for patient adherence and access to medicines during the pandemic. METHODS A cohort study of all primary care patients in England prescribed CVD medicines. The exposure was to the global pandemic. Prescriptions were compared before and after the pandemic's onset. Statistical variation was the outcome of interest. RESULTS Descriptive statistics show changes to monthly prescriptions, with wide confidence intervals indicating varying underlying practice. Analysis of variance reveals statistically significant differences for bendroflumethiazide, potassium-sparing diuretics, nicorandil, ezetimibe, ivabradine, ranolazine, colesevelam and midodrine. After the pandemic began (March-October 2020), negative parameters are observed for ACE inhibitors, beta-blockers, calcium channel blockers, statins, antiplatelet, antithrombotics, ARBs, loop diuretics, doxazosin, bendroflumethiazide, nitrates and indapamide, indicating decelerating monthly prescription items (statistically significant declines of calcium channel blockers, antithrombotic, adrenoreceptor blockers and diuretics) of CVD medicines within the general population. Many data points are not statistically significant, but fluctuations remain clinically important for the large population of patients taking these medications. CONCLUSION A concerning decline in uptake of CVD therapies for chronic heart disease was observed. Accessible screening and treatment alongside financial relief on prescription levies are needed. A video abstract is (4 min 51 s) available: https://bit.ly/39gvEHi.
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Affiliation(s)
- Ravina Barrett
- School of Applied Sciences, University of
Brighton, Cockcroft Building, Lewes Road, Moulsecoomb, Brighton BN2 4GJ,
UK
| | - James Hodgkinson
- Murray Learning Centre, Institute of Applied
Health Research, College of Medical and Dental Sciences, University of
Birmingham, Birmingham, UK
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15
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Mahato RK, Mahanty AK, Kotakonda M, Prasad S, Bhattacharyya S, Biswas B. A hydrated 2,3-diaminophenazinium chloride as a promising building block against SARS-CoV-2. Sci Rep 2021; 11:23122. [PMID: 34848758 PMCID: PMC8633378 DOI: 10.1038/s41598-021-02280-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022] Open
Abstract
Phenazine scaffolds are the versatile secondary metabolites of bacterial origin. It functions in the biological control of plant pathogens and contributes to the producing strains ecological fitness and pathogenicity. In the light of the excellent therapeutic properties of phenazine, we have synthesized a hydrated 2,3-diaminophenazinium chloride (DAPH+Cl-·3H2O) through direct catalytic oxidation of o-phenylenediamine with an iron(III) complex, [Fe(1,10-phenanthroline)2Cl2]NO3 in ethanol under aerobic condition. The crystal structure, molecular complexity and supramolecular aspects of DAPH+Cl- were confirmed and elucidated with different spectroscopic methods and single crystal X-ray structural analysis. Crystal engineering study on DAPH+Cl- exhibits a fascinating formation of (H2O)2…Cl-…(H2O) cluster and energy framework analysis of defines the role of chloride ions in the stabilization of DAPH+Cl-. The bactericidal efficiency of the compound has been testified against few clinical bacteria like Streptococcus pneumoniae, Escherichia coli, K. pneumoniae using the disc diffusion method and the results of high inhibition zone suggest its excellent antibacterial properties. The phenazinium chloride exhibits a significant percentage of cell viability and a considerable inhibition property against SARS-CoV-2 at non-cytotoxic concentration compared to remdesivir. Molecular docking studies estimate a good binding propensity of DAPH+Cl- with non-structural proteins (nsp2 and nsp7-nsp-8) and the main protease (Mpro) of SARS-CoV-2. The molecular dynamics simulation studies attribute the conformationally stable structures of the DAPH+Cl- bound Mpro and nsp2, nsp7-nsp8 complexes as evident from the considerable binding energy values, - 19.2 ± 0.3, - 25.7 ± 0.1, and - 24.5 ± 0.7 kcal/mol, respectively.
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Affiliation(s)
- Rajani Kanta Mahato
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India
| | - Ayan Kumar Mahanty
- Department of Biotechnology, University of North Bengal, Darjeeling, 734013, India
| | | | - Sunnapu Prasad
- Department of Pharmaceutical Chemistry, Sri Ramakrishna Institute of Paramedical Science, Coimbatore, 641044, India
| | | | - Bhaskar Biswas
- Department of Chemistry, University of North Bengal, Darjeeling, 734013, India.
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16
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Nath V, Rohini A, Kumar V. Identification of M pro inhibitors of SARS-CoV-2 using structure based computational drug repurposing. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021; 37:102178. [PMID: 34611467 PMCID: PMC8483991 DOI: 10.1016/j.bcab.2021.102178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/03/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022]
Abstract
The recent outbreak of COVID-19, caused by the novel pathogen SARS-coronavirus 2 (SARS-CoV-2) is a severe health emergency. In this pandemic, drug repurposing seems to be the most promising alternative to identify effective therapeutic agents for immediate treatment of infected patients. The present study aimed to evaluate all the drugs present in drug bank as potential novel SARS-CoV-2 inhibitors, using computational drug repurposing studies. Docking-based virtual screening and binding energy prediction were performed, followed by Absorption Distribution Metabolism Excretion calculation. Hydroxychloroquine and Nelfinavir have been identified as the best potential inhibitor against the SARS-CoV-2, therefore, they were used as reference compounds in computational DR studies. The docking study revealed 13 best compounds based on their highest binding affinity, binding energy, and dock score concerning the other screened compounds. Out of 13, only 4 compounds were further shortlisted based on their binding energy and best ADME properties. The hierarchical virtual screening yielded the best 04 drugs, DB07042 (compound 2), DB13035 (compound 3), DB13604 (compound 5) and DB08253 (compound 6), with commendable binding energies in kcal/mol, i.e. −65.45, −62.01, −52.09 and −51.70 respectively. Further, Molecular dynamics simulation with 04 best-retrieved hits has confirmed stable trajectories in protein in terms of root mean square deviation and root mean square fluctuation. During 30 ns simulation, the interactions were also found similar to the docking-based studies. However, clinical studies are necessary to investigate their therapeutic use against this outbreak.
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Key Words
- ACE, Angiotensin-Converting Enzyme
- ADME, Absorption Distribution Metabolism Excretion
- Binding energy
- CDR, Computational Drug Repurposing
- COVID
- CoV, Corona Virus
- Docking
- Drug repurposing
- HTVS, High-throughput virtual screening
- MMGBSA, Molecular mechanics generalized born surface area
- OPLS, Optimized Potentials for Liquid Simulations
- PDB, Protein data bank
- SARS, Severe Acute Respiratory Syndrome
- SP, Standard Precision
- Virtual screening
- XP, Extra precision
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Affiliation(s)
- Virendra Nath
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer, India
| | - A Rohini
- College of Pharmacy, JSS Academy of Technical Sciences, Noida, Uttar Pradesh, India
| | - Vipin Kumar
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer, India
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17
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Rossi FV, Gentili D, Marcantoni E. Metal-Promoted Heterocyclization: A Heterosynthetic Approach to Face a Pandemic Crisis. Molecules 2021; 26:2620. [PMID: 33947170 PMCID: PMC8124705 DOI: 10.3390/molecules26092620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022] Open
Abstract
The outbreak of SARS-CoV-2 has drastically changed our everyday life and the life of scientists from all over the world. In the last year, the scientific community has faced this worldwide threat using any tool available in order to find an effective response. The recent formulation, production, and ongoing administration of vaccines represent a starting point in the battle against SARS-CoV-2, but they cannot be the only aid available. In this regard, the use of drugs capable to mitigate and fight the virus is a crucial aspect of the pharmacological strategy. Among the plethora of approved drugs, a consistent element is a heterocyclic framework inside its skeleton. Heterocycles have played a pivotal role for decades in the pharmaceutical industry due to their high bioactivity derived from anticancer, antiviral, and anti-inflammatory capabilities. In this context, the development of new performing and sustainable synthetic strategies to obtain heterocyclic molecules has become a key focus of scientists. In this review, we present the recent trends in metal-promoted heterocyclization, and we focus our attention on the construction of heterocycles associated with the skeleton of drugs targeting SARS-CoV-2 coronavirus.
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Affiliation(s)
- Federico Vittorio Rossi
- Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (D.G.); (E.M.)
- Laboratori Alchemia Srl, Via San Faustino, 20134 Milano, Italy
| | - Dario Gentili
- Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (D.G.); (E.M.)
| | - Enrico Marcantoni
- Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy; (D.G.); (E.M.)
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18
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Singh N, Villoutreix BO. Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. Comput Struct Biotechnol J 2021; 19:2537-2548. [PMID: 33936562 PMCID: PMC8074526 DOI: 10.1016/j.csbj.2021.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
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Affiliation(s)
- Natesh Singh
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Bruno O. Villoutreix
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
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19
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Kalra RS, Kumar V, Dhanjal JK, Garg S, Li X, Kaul SC, Sundar D, Wadhwa R. COVID19-inhibitory activity of withanolides involves targeting of the host cell surface receptor ACE2: insights from computational and biochemical assays. J Biomol Struct Dyn 2021; 40:7885-7898. [PMID: 33797339 PMCID: PMC8022344 DOI: 10.1080/07391102.2021.1902858] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 outbreak in China in December 2019 and its spread as worldwide pandemic has been a major global health crisis. Extremely high infection and mortality rate has severely affected all sectors of life and derailed the global economy. While drug and vaccine development have been prioritized and have made significant progression, use of phytochemicals and herbal constituents is deemed as a low-cost, safer and readily available alternative. We investigated therapeutic efficacy of eight withanolides (derived from Ashwagandha) against the angiotensin-converting enzyme 2 (ACE2) proteins, a target cell surface receptor for SARS-CoV-2 and report results on the (i) computational analyses including binding affinity and stable interactions with ACE2, occupancy of ACE2 residues in making polar and nonpolar interactions with different withanolides/ligands and (2) in vitro mRNA and protein analyses using human cancer (A549, MCF7 and HSC3) cells. We found that among all withanolides, Withaferin-A, Withanone, Withanoside-IV and Withanoside-V significantly inhibited the ACE2 expression. Analysis of withanolides-rich aqueous extracts derived from Ashwagandha leaves and stem showed a higher ACE2 inhibitory potency of stem-derived extracts. Taken together, we demonstrated the inhibitory potency of Ashwagandha withanolides and its aqueous extracts against ACE2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Rajkumar Singh Kalra
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Vipul Kumar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
| | - Jaspreet Kaur Dhanjal
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Sukant Garg
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Xiaoshuai Li
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Sunil C Kaul
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
| | - Renu Wadhwa
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
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20
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Born J, Manica M, Cadow J, Markert G, Mill NA, Filipavicius M, Janakarajan N, Cardinale A, Laino T, Rodríguez Martínez M. Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abe808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Bridging systems biology and drug design, we propose a deep learning framework for de novo discovery of molecules tailored to bind with given protein targets. Our methodology is exemplified by the task of designing antiviral candidates to target SARS-CoV-2 related proteins. Crucially, our framework does not require fine-tuning for specific proteins but is demonstrated to generalize in proposing ligands with high predicted binding affinities against unseen targets. Coupling our framework with the automatic retrosynthesis prediction of IBM RXN for Chemistry, we demonstrate the feasibility of swift chemical synthesis of molecules with potential antiviral properties that were designed against a specific protein target. In particular, we synthesize an antiviral candidate designed against the host protein angiotensin converting enzyme 2 (ACE2); a surface receptor on human respiratory epithelial cells that facilitates SARS-CoV-2 cell entry through its spike glycoprotein.
This is achieved as follows. First, we train a multimodal ligand–protein binding affinity model on predicting affinities of bioactive compounds to target proteins and couple this model with pharmacological toxicity predictors. Exploiting this multi-objective as a reward function of a conditional molecular generator that consists of two variational autoencoders (VAE), our framework steers the generation toward regions of the chemical space with high-reward molecules. Specifically, we explore a challenging setting of generating ligands against unseen protein targets by performing a leave-one-out-cross-validation on 41 SARS-CoV-2-related target proteins. Using deep reinforcement learning, it is demonstrated that in 35 out of 41 cases, the generation is biased towards sampling binding ligands, with an average increase of 83% comparing to an unbiased VAE. The generated molecules exhibit favorable properties in terms of target binding affinity, selectivity and drug-likeness. We use molecular retrosynthetic models to provide a synthetic accessibility assessment of the best generated hit molecules. Finally, with this end-to-end framework, we synthesize 3-Bromobenzylamine, a potential inhibitor of the host ACE2 protein, solely based on the recommendations of a molecular retrosynthesis model and a synthesis protocol prediction model. We hope that our framework can contribute towards swift discovery of de novo molecules with desired pharmacological properties.
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21
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Hedman HD, Krawczyk E, Helmy YA, Zhang L, Varga C. Host Diversity and Potential Transmission Pathways of SARS-CoV-2 at the Human-Animal Interface. Pathogens 2021; 10:180. [PMID: 33567598 PMCID: PMC7915269 DOI: 10.3390/pathogens10020180] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Emerging infectious diseases present great risks to public health. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), has become an urgent public health issue of global concern. It is speculated that the virus first emerged through a zoonotic spillover. Basic research studies have suggested that bats are likely the ancestral reservoir host. Nonetheless, the evolutionary history and host susceptibility of SARS-CoV-2 remains unclear as a multitude of animals has been proposed as potential intermediate or dead-end hosts. SARS-CoV-2 has been isolated from domestic animals, both companion and livestock, as well as in captive wildlife that were in close contact with human COVID-19 cases. Currently, domestic mink is the only known animal that is susceptible to a natural infection, develop severe illness, and can also transmit SARS-CoV-2 to other minks and humans. To improve foundational knowledge of SARS-CoV-2, we are conducting a synthesis review of its host diversity and transmission pathways. To mitigate this COVID-19 pandemic, we strongly advocate for a systems-oriented scientific approach that comprehensively evaluates the transmission of SARS-CoV-2 at the human and animal interface.
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Affiliation(s)
- Hayden D. Hedman
- Summit County Local Public Health Agency, Summit County, Frisco, CO 80443, USA;
| | - Eric Krawczyk
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Yosra A. Helmy
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA;
| | - Lixin Zhang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA;
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Csaba Varga
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA
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22
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Bobrowski T, Chen L, Eastman RT, Itkin Z, Shinn P, Chen CZ, Guo H, Zheng W, Michael S, Simeonov A, Hall MD, Zakharov AV, Muratov EN. Synergistic and Antagonistic Drug Combinations against SARS-CoV-2. Mol Ther 2021; 29:873-885. [PMID: 33333292 PMCID: PMC7834738 DOI: 10.1016/j.ymthe.2020.12.016] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/15/2020] [Accepted: 12/09/2020] [Indexed: 01/15/2023] Open
Abstract
Antiviral drug development for coronavirus disease 2019 (COVID-19) is occurring at an unprecedented pace, yet there are still limited therapeutic options for treating this disease. We hypothesized that combining drugs with independent mechanisms of action could result in synergy against SARS-CoV-2, thus generating better antiviral efficacy. Using in silico approaches, we prioritized 73 combinations of 32 drugs with potential activity against SARS-CoV-2 and then tested them in vitro. Sixteen synergistic and eight antagonistic combinations were identified; among 16 synergistic cases, combinations of the US Food and Drug Administration (FDA)-approved drug nitazoxanide with remdesivir, amodiaquine, or umifenovir were most notable, all exhibiting significant synergy against SARS-CoV-2 in a cell model. However, the combination of remdesivir and lysosomotropic drugs, such as hydroxychloroquine, demonstrated strong antagonism. Overall, these results highlight the utility of drug repurposing and preclinical testing of drug combinations for discovering potential therapies to treat COVID-19.
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Affiliation(s)
- Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Richard T Eastman
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Zina Itkin
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Paul Shinn
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Hui Guo
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, MD 20850, USA.
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.
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23
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Target SARS-CoV-2: computation of binding energies with drugs of dexamethasone/umifenovir by molecular dynamics using OPLS-AA force field. RESEARCH ON BIOMEDICAL ENGINEERING 2021. [PMCID: PMC7791166 DOI: 10.1007/s42600-020-00119-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction In recent times, myriads of public have been infected with a novel SARS-CoV-2, and the fatality toll has reached thousands and been mounting step by step, which is a major crisis in the world. The challenge for this burning issue pertinent to repurposed medicines which prevent novel coronavirus is of immense concern for all scientists around the globe until the arrival of the vaccine. Methods Because of the global high priority rating on the search for the repurposed drugs which outfits clinical suitability to SARS-CoV-2, a unique theoretical methodology is proposed. The approach is based on explorations of biothermodynamics computed via molecular dynamics, root-mean-square deviation (RMSD), radius of gyration (Rg) and interactions. This unique methodology is tested for umifenovir/dexamethasone drugs on (SARS-CoV-2) main protease. Results This theoretical exploration not only suggested the presence of strong interactions between (SARS-CoV-2 + umifenovir/dexamethasone) but also emphasized the clinical suitability of dexamethasone over umifenovir to treat SARS-CoV-2. This supremacy of dexamethasone is well supported by the results of global clinical trials and COVID-19 therapeutic approved management guidelines of countries. Conclusions Thus, this work will pave a way for incremental advancement towards future design and development of more specific inhibitors for the treatment of SARS-CoV-2 infection in humans.
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24
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Shayan S, Jamaran S, Askandar RH, Rahimi A, Elahi A, Farshadfar C, Ardalan N. The SARS-Cov-2 Proliferation Blocked by a Novel and Potent Main Protease Inhibitor via Computer-aided Drug Design. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:399-418. [PMID: 34903997 PMCID: PMC8653640 DOI: 10.22037/ijpr.2021.114846.15061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The recent prevalence of novel "coronavirus disease 2019" has expanded quickly globally, causing a universal pandemic. Herein, an effort was constructed to design a potent drug to inhibit the main protease of SARS-Cov-2 (3CLp) by means of structure-based drug design. A large library of the compounds was used for virtual screening. After molecular docking and ADME studies, we selected a compound with a better binding affinity to the 3CLp active site and acceptable ADME properties compared to the selected positive control drug. Molecular dynamic (MD) simulation (200 ns) and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) were used for further analysis. MD simulation outcomes have proved that the 3CLp-ZINC31157475 complex possesses a considerable value of dynamic properties such as flexibility, stability, compactness, and binding energy. Our MM-PBSA computation illustrates that ZINC31157475 is more potent (-88.03 kcal mol-1) than nelfinavir (-19.54 kcal mol-1) against COVID-19 3CLp. Further, we have determined that the main residues of the 3CLp interact with ligands from per-residue binding energy. In conclusion, we suggest that ZINC31157475 can potentially treat COVID-19 by inhibition of the 3CLp. However, in-vitro and in-vivo study is essential for approval of this suggestion.
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Affiliation(s)
- Sepideh Shayan
- Department of Biochemistry, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran.
| | - Shahab Jamaran
- Department of Microbiology, Faculty of Biological Sciences, Arak Branch, Islamic Azad University, Arak, Iran.
| | | | - Arian Rahimi
- Young Researchers and Elite Club, East Tehran Branch, Islamic Azad University, Tehran, Iran.
| | - Azam Elahi
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Chiako Farshadfar
- Department of Biochemistry, Faculty of Biological Sciences, Science and Research Branch, Islamic Azad University, Sanandaj, Iran.
| | - Noeman Ardalan
- Department of Microbiology, Faculty of Biological Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran.
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Buitrón-González I, Aguilera-Durán G, Romo-Mancillas A. In-silico drug repurposing study: Amprenavir, enalaprilat, and plerixafor, potential drugs for destabilizing the SARS-CoV-2 S-protein-angiotensin-converting enzyme 2 complex. RESULTS IN CHEMISTRY 2020; 3:100094. [PMID: 33520633 PMCID: PMC7834266 DOI: 10.1016/j.rechem.2020.100094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/22/2020] [Indexed: 01/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that leads to coronavirus disease (COVID-19) has put public health at risk in 2020. The spike protein (SP) in SARS-CoV-2 is primarily responsible for the attachment and entry of the virus into the cell, which binds to the angiotensin-converting enzyme 2 (ACE2). Owing to the lack of an effective therapy, drug repositioning is an opportunity to search for molecules with pharmacological potential for the treatment of COVID-19. In this study, three candidates with the potential to destabilize the SP-ACE2 complex are reported. Through molecular docking, 147 drugs were evaluated and their possible binding sites in the interface region of the SP-ACE2 complex and the SP of SARS-CoV-2 were identified. The five best candidate molecules were selected for molecular dynamics studies to observe changes in interactions between SP-ACE2 and ligands with the SP-ACE2 complex. Using umbrella sampling molecular dynamics simulations, the binding energy of SP with ACE2 (−29.58 kcal/mol) without ligands, and in complex with amprenavir (−20.13 kcal/mol), enalaprilat (–23.84 kcal/mol), and plerixafor (−19.72 kcal/mol) were calculated. These drugs are potential candidates for the treatment of COVID-19 as they destabilize the SP-ACE2 complex; the binding energy of SP is decreased in the presence of these drugs and may prevent the virus from entering the cell. Plerixafor is the drug with the greatest potential to destabilize the SP-ACE2 complex, followed by amprenavir and enalaprilat; thus, these three drugs are proposed for future in vitro and in vivo evaluations.
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Affiliation(s)
- Ivonne Buitrón-González
- Laboratorio de Diseño Asistido por Computadora y Síntesis de Fármacos, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico
| | - Giovanny Aguilera-Durán
- Laboratorio de Diseño Asistido por Computadora y Síntesis de Fármacos, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico
| | - Antonio Romo-Mancillas
- Laboratorio de Diseño Asistido por Computadora y Síntesis de Fármacos, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico
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26
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Chan SW. Current and Future Direct-Acting Antivirals Against COVID-19. Front Microbiol 2020; 11:587944. [PMID: 33262747 PMCID: PMC7688518 DOI: 10.3389/fmicb.2020.587944] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/23/2020] [Indexed: 01/18/2023] Open
Abstract
The coronavirus disease of 2019 (COVID-19) has caused an unprecedented global crisis. The etiological agent is a new virus called the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). As of October, 2020 there have been 45.4 million confirmed cases with a mortality rate of 2.6% globally. With the lack of a vaccine and effective treatments, the race is on to find a cure for the virus infection using specific antivirals. The viral RNA-dependent RNA polymerase, proteases, spike protein-host angiotensin-converting enzyme 2 binding and fusion have presented as attractive targets for pan-coronavirus and broad spectrum direct-acting antivirals (DAAs). This review presents a perspective on current re-purposing treatments and future DAAs.
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27
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Bojkova D, Bechtel M, McLaughlin KM, McGreig JE, Klann K, Bellinghausen C, Rohde G, Jonigk D, Braubach P, Ciesek S, Münch C, Wass MN, Michaelis M, Cinatl J. Aprotinin Inhibits SARS-CoV-2 Replication. Cells 2020; 9:E2377. [PMID: 33143316 PMCID: PMC7692688 DOI: 10.3390/cells9112377] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/15/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome virus 2 (SARS-CoV-2) is the cause of the current coronavirus disease 19 (COVID-19) pandemic. Protease inhibitors are under consideration as virus entry inhibitors that prevent the cleavage of the coronavirus spike (S) protein by cellular proteases. Herein, we showed that the protease inhibitor aprotinin (but not the protease inhibitor SERPINA1/alpha-1 antitrypsin) inhibited SARS-CoV-2 replication in therapeutically achievable concentrations. An analysis of proteomics and translatome data indicated that SARS-CoV-2 replication is associated with a downregulation of host cell protease inhibitors. Hence, aprotinin may compensate for downregulated host cell proteases during later virus replication cycles. Aprotinin displayed anti-SARS-CoV-2 activity in different cell types (Caco2, Calu-3, and primary bronchial epithelial cell air-liquid interface cultures) and against four virus isolates. In conclusion, therapeutic aprotinin concentrations exert anti-SARS-CoV-2 activity. An approved aprotinin aerosol may have potential for the early local control of SARS-CoV-2 replication and the prevention of COVID-19 progression to a severe, systemic disease.
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Affiliation(s)
- Denisa Bojkova
- Institute for Medical Virology, University Hospital, Goethe University, 60596 Frankfurt am Main, Germany; (D.B.); (M.B.); (S.C.)
| | - Marco Bechtel
- Institute for Medical Virology, University Hospital, Goethe University, 60596 Frankfurt am Main, Germany; (D.B.); (M.B.); (S.C.)
| | - Katie-May McLaughlin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (K.-M.M.); (J.E.M.)
| | - Jake E. McGreig
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (K.-M.M.); (J.E.M.)
| | - Kevin Klann
- Faculty of Medicine, Institute of Biochemistry II, Goethe University, 60590 Frankfurt am Main, Germany; (K.K.); (C.M.)
| | - Carla Bellinghausen
- Department of Respiratory Medicine and Allergology, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany; (C.B.); (G.R.)
| | - Gernot Rohde
- Department of Respiratory Medicine and Allergology, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany; (C.B.); (G.R.)
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School (MHH), 30625 Hannover, Germany; (D.J.); (P.B.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), The German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Peter Braubach
- Institute of Pathology, Hannover Medical School (MHH), 30625 Hannover, Germany; (D.J.); (P.B.)
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), The German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University, 60596 Frankfurt am Main, Germany; (D.B.); (M.B.); (S.C.)
- German Center for Infection Research, DZIF, External Partner Site, 60596 Frankfurt am Main, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine und Pharmacology, 60596 Frankfurt am Main, Germany
| | - Christian Münch
- Faculty of Medicine, Institute of Biochemistry II, Goethe University, 60590 Frankfurt am Main, Germany; (K.K.); (C.M.)
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University, 60590 Frankfurt am Main, Germany
| | - Mark N. Wass
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (K.-M.M.); (J.E.M.)
| | - Martin Michaelis
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (K.-M.M.); (J.E.M.)
| | - Jindrich Cinatl
- Institute for Medical Virology, University Hospital, Goethe University, 60596 Frankfurt am Main, Germany; (D.B.); (M.B.); (S.C.)
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28
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Anklesaria Z, Frankman J, Gordin J, Zhan J, Liu AK. Fatal Rhabdomyolysis in a COVID-19 Patient on Rosuvastatin. Cureus 2020; 12:e11186. [PMID: 33133803 PMCID: PMC7593204 DOI: 10.7759/cureus.11186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It is well-established by now that COVID-19 can have a wide variety of neuromuscular manifestations, including rhabdomyolysis. Weakness and elevated creatinine kinase (CK) have been documented as the initial presentation of COVID-19. Myopathy from statin use has also been well-established since the introduction of this class of medication, and the common pathologic mechanism of both entities may have been mitochondrial dysfunction. We present here the case of a COVID-19 patient on rosuvastatin who developed rhabdomyolysis with CK above 1,000,000 units/L. The patient did not present with any respiratory difficulty and responded poorly to treatment, resulting in his untimely demise. COVID-19 may have accentuated an otherwise survivable condition by means of extra stress on mitochondrial homeostasis. Understanding the actual mechanism will be important in the development and utilization of medications in the fight against COVID-19.
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Affiliation(s)
- Zafia Anklesaria
- Pulmonary and Critical Care, California Hospital Medical Center, Los Angeles, USA
| | - Jonathan Frankman
- Family Medicine, California Hospital Medical Center, Los Angeles, USA
| | - Jonathan Gordin
- Cardiology, California Hospital Medical Center, Los Angeles, USA
| | - Jennifer Zhan
- Emergency Medicine, California Hospital Medical Center, Los Angeles, USA
| | - Antonio K Liu
- Neurology, Adventist Health White Memorial, Los Angeles, USA
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