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Shrestha B, Yang S, Griffith L, Ma J, Wang F, Liu H, Zhao Q, Du Y, Zhang J, Chang J, Guo JT. Discovery of hepatitis B virus subviral particle biogenesis inhibitors from a bioactive compound library. Antiviral Res 2024; 228:105955. [PMID: 38964614 DOI: 10.1016/j.antiviral.2024.105955] [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: 05/09/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
High levels of hepatitis B virus (HBV) surface antigen (HBsAg) in the blood of chronic HBV carriers are considered to drive the exhaustion of antigen-specific T and B lymphocytes and thus responsible for the persistence of infection. Accordingly, therapeutic elimination of HBsAg may facilitate the activation of adaptive antiviral immune responses against HBV and achieve a functional cure of chronic hepatitis B. We discovered recently that an amphipathic alpha helix spanning W156 to R169 of HBV small envelope (S) protein plays an essential role in the morphogenesis of subviral particles (SVPs) and metabolism of S protein. We thus hypothesized that pharmacological disruption of SVP morphogenesis may induce intracellular degradation of S protein and reduce HBsAg secretion. To identify inhibitors of SVP biogenesis, we screened 4417 bioactive compounds with a HepG2-derived cell line expressing HBV S protein and efficiently secreting small spherical SVPs. The screen identified 24 compounds that reduced intracellular SVPs and secreted HBsAg in a concentration-dependent manner. However, 18 of those compounds inhibited the secretion of HBsAg and HBeAg in HBV replicon transfected HepG2 cells at similar efficiency, suggesting each of those compounds may disrupt a common cellular function required for the synthesis and/or secretion of these viral proteins. Interestingly, lycorine more efficiently inhibited the secretion of HBsAg in HepG2 cells transfected with HBV replicons, HepG2.2.15 cells and HBV infected - HepG2 cells expressing sodium taurocholate cotransporting polypeptide (NTCP). The structure activity relationship and antiviral mechanism of lycorine against HBV have been determined.
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Affiliation(s)
| | - Sisi Yang
- Baruch S. Blumberg Institute, Doylestown, PA, USA; Department of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | | | - Julia Ma
- Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Fuxuan Wang
- Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Hui Liu
- Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Qiong Zhao
- Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Yanming Du
- Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | | | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Doylestown, PA, USA.
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Le NTH, Janssen K, Kirchmair J, Pieters L, Tuenter E. A mini-review of the anti-SARS-CoV-2 potency of Amaryllidaceae alkaloids. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 129:155576. [PMID: 38579643 DOI: 10.1016/j.phymed.2024.155576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/03/2024] [Accepted: 03/28/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Nature has perennially served as an infinite reservoir of diverse chemicals with numerous applications benefiting humankind. In recent years, due to the emerging COVID-19 pandemic, there has been a surge in studies on repurposing natural products as anti-SARS-CoV-2 agents, including plant-derived substances. Among all types of natural products, alkaloids remain one of the most important groups with various known medicinal values. The current investigation focuses on Amaryllidaceae alkaloids (AAs) since AAs have drawn significant scientific attention as anti-SARS-CoV-2 agents over the past few years. PURPOSE AND STUDY DESIGN This study serves as a mini-review, summarizing recent advances in studying the anti-SARS-CoV-2 potency of AAs, covering two aspects: structure-activity relationship and mechanism of action (MOA). METHODS The study covers the period from 2019 to 2023. The information in this review were retrieved from common databases including Web of Science, ScienceDirect, PubMed and Google scholar. Reported anti-SARS-CoV-2 potency, cytotoxicity and possible biological targets of AAs were summarized and classified into different skeletal subclasses. Then, the structure-activity relationship (SAR) was explored, pinpointing the key pharmacophore-related structural moieties. To study the mechanism of action of anti-SARS-CoV-2 AAs, possible biological targets were discussed. RESULTS In total, fourteen research articles about anti-SARS-CoV-2 was selected. From the SAR point of view, four skeletal subclasses of AAs (lycorine-, galanthamine-, crinine- and homolycorine-types) appear to be promising for further investigation as anti-SARS-CoV-2 agents despite experimental inconsistencies in determining in vitro half maximal inhibitory effective concentration (EC50). Narciclasine, haemanthamine- and montanine-type skeletons were cytotoxic and devoid of anti-SARS-CoV-2 activity. The lycorine-type scaffold was the most structurally diverse in this study and preliminary structure-activity relationships revealed the crucial role of ring C and substituents on rings A, C and D in its anti-SARS-CoV-2 activity. It also appears that two enantiomeric skeletons (haemanthamine- and crinine-types) displayed opposite activity/toxicity profiles regarding anti-SARS-CoV-2 activity. Pharmacophore-related moieties of the haemanthamine/crinine-type skeletons were the substituents on rings B, C and the dioxymethylene moiety. All galanthamine-type alkaloids in this study were devoid of cytotoxicity and it appears that varying substituents on rings C and D could enhance the anti-SARS-CoV-2 potency. Regarding MOAs, initial experimental results suggested Mpro and RdRp as possible viral targets. Dual functionality between anti-inflammatory activity on host cells and anti-SARS-CoV-2 activity on the SARS-CoV-2 virus of isoquinoline alkaloids, including AAs, were suggested as the possible MOAs to alleviate severe complications in COVID-19 patients. This dual functionality was proposed to be related to the p38 MAPK signaling pathway. CONCLUSION Overall, Amaryllidaceae alkaloids appear to be promising for further investigation as anti-SARS-CoV-2 agents. The skeletal subclasses holding the premise for further investigation are lycorine-, crinine-, galanthamine- and homolycorine-types.
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Affiliation(s)
- Ngoc-Thao-Hien Le
- Natural Products & Food Research and Analysis - Pharmaceutical Technologies (NatuRAPT), Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Université Paris Cité - INSERM Unit 1284, Paris, France.
| | - Kerrin Janssen
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria; Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria; Christian Doppler Laboratory for Molecular Informatics in the Biosciences, Department for Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Luc Pieters
- Natural Products & Food Research and Analysis - Pharmaceutical Technologies (NatuRAPT), Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Emmy Tuenter
- Natural Products & Food Research and Analysis - Pharmaceutical Technologies (NatuRAPT), Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
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Hazemann J, Kimmerlin T, Lange R, Sweeney AM, Bourquin G, Ritz D, Czodrowski P. Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches. RSC Med Chem 2024; 15:2146-2159. [PMID: 38911172 PMCID: PMC11187573 DOI: 10.1039/d4md00106k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/20/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of coronavirus disease (COVID-19) since its emergence in December 2019. As of January 2024, there has been over 774 million reported cases and 7 million deaths worldwide. While vaccination efforts have been successful in reducing the severity of the disease and decreasing the transmission rate, the development of effective therapeutics against SARS-CoV-2 remains a critical need. The main protease (Mpro) of SARS-CoV-2 is an essential enzyme required for viral replication and has been identified as a promising target for drug development. In this study, we report the identification of novel Mpro inhibitors, using a combination of deep reinforcement learning for de novo drug design with 3D pharmacophore/shape-based alignment and privileged fragment match count scoring components followed by hit expansions and molecular docking approaches. Our experimentally validated results show that 3 novel series exhibit potent inhibitory activity against SARS-CoV-2 Mpro, with IC50 values ranging from 1.3 μM to 2.3 μM and a high degree of selectivity. These findings represent promising starting points for the development of new antiviral therapies against COVID-19.
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Affiliation(s)
- Julien Hazemann
- Physical Chemistry, Chemistry Department, Johannes Gutenberg University Duesbergweg 10-14 55128 Mainz Germany
- Drug Discovery Chemistry, Idorsia Pharmaceuticals Ltd. Hegenheimermattweg 91 4123 Allschwil Switzerland
| | - Thierry Kimmerlin
- Drug Discovery Chemistry, Idorsia Pharmaceuticals Ltd. Hegenheimermattweg 91 4123 Allschwil Switzerland
| | - Roland Lange
- Drug Discovery Chemistry, Idorsia Pharmaceuticals Ltd. Hegenheimermattweg 91 4123 Allschwil Switzerland
| | - Aengus Mac Sweeney
- Drug Discovery Chemistry, Idorsia Pharmaceuticals Ltd. Hegenheimermattweg 91 4123 Allschwil Switzerland
| | - Geoffroy Bourquin
- Drug Discovery Chemistry, Idorsia Pharmaceuticals Ltd. Hegenheimermattweg 91 4123 Allschwil Switzerland
| | - Daniel Ritz
- Drug Discovery Chemistry, Idorsia Pharmaceuticals Ltd. Hegenheimermattweg 91 4123 Allschwil Switzerland
| | - Paul Czodrowski
- Physical Chemistry, Chemistry Department, Johannes Gutenberg University Duesbergweg 10-14 55128 Mainz Germany
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Zheng Y, Feng J, Ling M, Yu Y, Tao Y, Wang X. A comprehensive review on targeting cluster of differentiation: An attractive strategy for inhibiting viruses through host proteins. Int J Biol Macromol 2024; 269:132200. [PMID: 38723834 DOI: 10.1016/j.ijbiomac.2024.132200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/20/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Viral infections continue to pose a significant global public health threat. Targeting host proteins, such as cluster of differentiation (CD) macromolecules, may offer a promising alternative approach to developing antiviral treatments. CDs are cell-surface biological macromolecules mainly expressed on leukocytes that viruses can use to enter cells, thereby evading immune detection and promoting their replication. The manipulation of CDs by viruses may represent an effective and clever means of survival through the prolonged co-evolution of hosts and viruses. Targeting of CDs is anticipated to hinder the invasion of related viruses, modulate the body's immune system, and diminish the incidence of subsequent inflammation. They have become crucial for biomedical diagnosis, and some have been used as valuable tools for resisting viral infections. However, a summary of the structures and functions of CDs involved in viral infection is currently lacking. The development of drugs targeting these biological macromolecules is restricted both in terms of their availability and the number of compounds currently identified. This review provides a comprehensive analysis of the critical role of CD proteins in virus invasion and a list of relevant targeted antiviral agents, which will serve as a valuable reference for future research in this field.
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Affiliation(s)
- Youle Zheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jin Feng
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Min Ling
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yixin Yu
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yanfei Tao
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Ali MA, Sheikh H, Yaseen M, Faruqe MO, Ullah I, Kumar N, Bhat MA, Mollah MNH. Exploring the Therapeutic Potential of Petiveria alliacea L. Phytochemicals: A Computational Study on Inhibiting SARS-CoV-2's Main Protease (Mpro). Molecules 2024; 29:2524. [PMID: 38893400 PMCID: PMC11173994 DOI: 10.3390/molecules29112524] [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: 04/12/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/21/2024] Open
Abstract
The outbreak of SARS-CoV-2, also known as the COVID-19 pandemic, is still a critical risk factor for both human life and the global economy. Although, several promising therapies have been introduced in the literature to inhibit SARS-CoV-2, most of them are synthetic drugs that may have some adverse effects on the human body. Therefore, the main objective of this study was to carry out an in-silico investigation into the medicinal properties of Petiveria alliacea L. (P. alliacea L.)-mediated phytocompounds for the treatment of SARS-CoV-2 infections since phytochemicals have fewer adverse effects compared to synthetic drugs. To explore potential phytocompounds from P. alliacea L. as candidate drug molecules, we selected the infection-causing main protease (Mpro) of SARS-CoV-2 as the receptor protein. The molecular docking analysis of these receptor proteins with the different phytocompounds of P. alliacea L. was performed using AutoDock Vina. Then, we selected the three top-ranked phytocompounds (myricitrin, engeletin, and astilbin) as the candidate drug molecules based on their highest binding affinity scores of -8.9, -8.7 and -8.3 (Kcal/mol), respectively. Then, a 100 ns molecular dynamics (MD) simulation study was performed for their complexes with Mpro using YASARA software, computed RMSD, RMSF, PCA, DCCM, MM/PBSA, and free energy landscape (FEL), and found their almost stable binding performance. In addition, biological activity, ADME/T, DFT, and drug-likeness analyses exhibited the suitable pharmacokinetics properties of the selected phytocompounds. Therefore, the results of this study might be a useful resource for formulating a safe treatment plan for SARS-CoV-2 infections after experimental validation in wet-lab and clinical trials.
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Affiliation(s)
- Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
- Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Humaira Sheikh
- Department of Chemistry, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj 8100, Bangladesh;
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, Faculty of Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ihsan Ullah
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur 313001, Rajasthan, India;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
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Fukumoto Y, Suzuki N, Hara R, Tanaka YK, Ogra Y. Development of a Biosafety Level 1 Cellular Assay for Identifying Small-Molecule Antivirals Targeting the Main Protease of SARS-CoV-2: Evaluation of Cellular Activity of GC376, Boceprevir, Carmofur, Ebselen, and Selenoneine. Int J Mol Sci 2024; 25:5767. [PMID: 38891954 PMCID: PMC11172239 DOI: 10.3390/ijms25115767] [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: 04/12/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
While research has identified several inhibitors of the main protease (Mpro) of SARS-CoV-2, a significant portion of these compounds exhibit reduced activity in the presence of reducing agents, raising concerns about their effectiveness in vivo. Furthermore, the conventional biosafety level 3 (BSL-3) for cellular assays using viral particles poses a limitation for the widespread evaluation of Mpro inhibitor efficacy in a cell-based assay. Here, we established a BSL-1 compatible cellular assay to evaluate the in vivo potential of Mpro inhibitors. This assay utilizes mammalian cells expressing a tagged Mpro construct containing N-terminal glutathione S-transferase (GST) and C-terminal hemagglutinin (HA) tags and monitors Mpro autodigestion. Using this method, GC376 and boceprevir effectively inhibited Mpro autodigestion, suggesting their potential in vivo activity. Conversely, carmofur and ebselen did not exhibit significant inhibitory effects in this assay. We further investigated the inhibitory potential of selenoneine on Mpro using this approach. Computational analyses of binding energies suggest that noncovalent interactions play a critical role in facilitating the covalent modification of the C145 residue, leading to Mpro inhibition. Our method is straightforward, cost-effective, and readily applicable in standard laboratories, making it accessible to researchers with varying levels of expertise in infectious diseases.
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Grants
- 19K07079 Ministry of Education, Culture, Sports, Science and Technology
- 21H04920 Ministry of Education, Culture, Sports, Science and Technology
- 19H05772 Ministry of Education, Culture, Sports, Science and Technology
- 22K05345 Ministry of Education, Culture, Sports, Science and Technology
- 24K09793 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan; (N.S.); (Y.-k.T.); (Y.O.)
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Jayawardena TU, Merindol N, Liyanage NS, Desgagné-Penix I. Unveiling Amaryllidaceae alkaloids: from biosynthesis to antiviral potential - a review. Nat Prod Rep 2024; 41:721-747. [PMID: 38131392 DOI: 10.1039/d3np00044c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Covering: 2017 to 2023 (now)Amaryllidaceae alkaloids (AAs) are a unique class of specialized metabolites containing heterocyclic nitrogen bridging that play a distinct role in higher plants. Irrespective of their diverse structures, most AAs are biosynthesized via intramolecular oxidative coupling. The complex organization of biosynthetic pathways is constantly enlightened by new insights owing to the advancement of natural product chemistry, synthetic organic chemistry, biochemistry, systems and synthetic biology tools and applications. These promote novel compound identification, trace-level metabolite quantification, synthesis, and characterization of enzymes engaged in AA catalysis, enabling the recognition of biosynthetic pathways. A complete understanding of the pathway benefits biotechnological applications in the long run. This review emphasizes the structural diversity of the AA specialized metabolites involved in biogenesis although the process is not entirely defined yet. Moreover, this work underscores the pivotal role of synthetic and enantioselective studies in justifying biosynthetic conclusions. Their prospective candidacy as lead constituents for antiviral drug discovery has also been established. However, a complete understanding of the pathway requires further interdisciplinary efforts in which antiviral studies address the structure-activity relationship. This review presents current knowledge on the topic.
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Affiliation(s)
- Thilina U Jayawardena
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC, G8Z 4M3, Canada.
| | - Natacha Merindol
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC, G8Z 4M3, Canada.
| | - Nuwan Sameera Liyanage
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC, G8Z 4M3, Canada.
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC, G8Z 4M3, Canada.
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
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Zhang J, Zhao L, Bai Y, Li S, Zhang M, Wei B, Wang X, Xue Y, Li L, Ma G, Tang Y, Wang X. An ascidian Polycarpa aurata-derived pan-inhibitor against coronaviruses targeting M pro. Bioorg Med Chem Lett 2024; 103:129706. [PMID: 38508325 DOI: 10.1016/j.bmcl.2024.129706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
Coronaviruses (CoVs) are responsible for a wide range of illnesses in both animals and human. The main protease (Mpro) of CoVs is an attractive drug target, owing its critical and highly conserved role in viral replication. Here, we developed and refined an enzymatic technique to identify putative Mpro inhibitors from 189 marine chemicals and 46 terrestrial natural products. The IC50 values of Polycarpine (1a), a marine natural substance we studied and synthesized, are 30.0 ± 2.5 nM for SARS-CoV-2 Mpro and 0.12 ± 0.05 μM for PEDV Mpro. Our research further demonstrated that pretreatment with Polycarpine (1a) inhibited the betacoronavirus SARS-CoV-2 and alphacoronavirus PEDV multiplication in Vero-E6 cells. As a result, Polycarpine (1a), a pan-inhibitor of Mpro, will function as an effective and promising antiviral option to combat CoVs infection and as a foundation for further therapeutic research.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Lili Zhao
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
| | - Yuxin Bai
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China
| | - Shanshan Li
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Meifang Zhang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Bo Wei
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xianyang Wang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yan Xue
- Department of Physiology, School of Basic Medicine, Qingdao University, Qingdao 266000, China
| | - Li Li
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China
| | - Guiliang Ma
- Department of General Surgery, Qingdao Municipal Hospital, No. 5, Donghaizhong Road, Qingdao 266071, China.
| | - Yu Tang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
| | - Xin Wang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
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Du L, Deiter F, Bouzidi MS, Billaud JN, Simmons G, Dabral P, Selvarajah S, Lingappa AF, Michon M, Yu SF, Paulvannan K, Manicassamy B, Lingappa VR, Boushey H, Greenland JR, Pillai SK. A viral assembly inhibitor blocks SARS-CoV-2 replication in airway epithelial cells. Commun Biol 2024; 7:486. [PMID: 38649430 PMCID: PMC11035691 DOI: 10.1038/s42003-024-06130-8] [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: 05/05/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
The ongoing evolution of SARS-CoV-2 to evade vaccines and therapeutics underlines the need for innovative therapies with high genetic barriers to resistance. Therefore, there is pronounced interest in identifying new pharmacological targets in the SARS-CoV-2 viral life cycle. The small molecule PAV-104, identified through a cell-free protein synthesis and assembly screen, was recently shown to target host protein assembly machinery in a manner specific to viral assembly. In this study, we investigate the capacity of PAV-104 to inhibit SARS-CoV-2 replication in human airway epithelial cells (AECs). We show that PAV-104 inhibits >99% of infection with diverse SARS-CoV-2 variants in immortalized AECs, and in primary human AECs cultured at the air-liquid interface (ALI) to represent the lung microenvironment in vivo. Our data demonstrate that PAV-104 inhibits SARS-CoV-2 production without affecting viral entry, mRNA transcription, or protein synthesis. PAV-104 interacts with SARS-CoV-2 nucleocapsid (N) and interferes with its oligomerization, blocking particle assembly. Transcriptomic analysis reveals that PAV-104 reverses SARS-CoV-2 induction of the type-I interferon response and the maturation of nucleoprotein signaling pathway known to support coronavirus replication. Our findings suggest that PAV-104 is a promising therapeutic candidate for COVID-19 with a mechanism of action that is distinct from existing clinical management approaches.
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Affiliation(s)
- Li Du
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA
- University of California, San Francisco, CA, 94143, USA
| | - Fred Deiter
- University of California, San Francisco, CA, 94143, USA
- Veterans Administration Health Care System, 4150 Clement St., San Francisco, CA, 94121, USA
| | - Mohamed S Bouzidi
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA
- University of California, San Francisco, CA, 94143, USA
| | | | - Graham Simmons
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA
- University of California, San Francisco, CA, 94143, USA
| | - Prerna Dabral
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA
- University of California, San Francisco, CA, 94143, USA
| | | | | | - Maya Michon
- Prosetta Biosciences Inc, 670 5th St., San Francisco, CA, 94107, USA
| | - Shao Feng Yu
- Prosetta Biosciences Inc, 670 5th St., San Francisco, CA, 94107, USA
| | - Kumar Paulvannan
- Prosetta Biosciences Inc, 670 5th St., San Francisco, CA, 94107, USA
| | | | | | - Homer Boushey
- University of California, San Francisco, CA, 94143, USA
| | - John R Greenland
- University of California, San Francisco, CA, 94143, USA
- Veterans Administration Health Care System, 4150 Clement St., San Francisco, CA, 94121, USA
| | - Satish K Pillai
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA.
- University of California, San Francisco, CA, 94143, USA.
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10
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Hurwitz SJ, De R, LeCher JC, Downs-Bowen JA, Goh SL, Zandi K, McBrayer T, Amblard F, Patel D, Kohler JJ, Bhasin M, Dobosh BS, Sukhatme V, Tirouvanziam RM, Schinazi RF. Why Certain Repurposed Drugs Are Unlikely to Be Effective Antivirals to Treat SARS-CoV-2 Infections. Viruses 2024; 16:651. [PMID: 38675992 PMCID: PMC11053489 DOI: 10.3390/v16040651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Most repurposed drugs have proved ineffective for treating COVID-19. We evaluated median effective and toxic concentrations (EC50, CC50) of 49 drugs, mostly from previous clinical trials, in Vero cells. Ratios of reported unbound peak plasma concentrations, (Cmax)/EC50, were used to predict the potential in vivo efficacy. The 20 drugs with the highest ratios were retested in human Calu-3 and Caco-2 cells, and their CC50 was determined in an expanded panel of cell lines. Many of the 20 drugs with the highest ratios were inactive in human Calu-3 and Caco-2 cells. Antivirals effective in controlled clinical trials had unbound Cmax/EC50 ≥ 6.8 in Calu-3 or Caco-2 cells. EC50 of nucleoside analogs were cell dependent. This approach and earlier availability of more relevant cultures could have reduced the number of unwarranted clinical trials.
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Affiliation(s)
- Selwyn J. Hurwitz
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Julia C. LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Jessica A. Downs-Bowen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Tamara McBrayer
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Dharmeshkumar Patel
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - James J. Kohler
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Manoj Bhasin
- Center for Cystic Fibrosis & Airways Disease Research, Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis and Sleep, Emory University and Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, GA 30322, USA; (M.B.); (B.S.D.); (R.M.T.)
| | - Brian S. Dobosh
- Center for Cystic Fibrosis & Airways Disease Research, Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis and Sleep, Emory University and Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, GA 30322, USA; (M.B.); (B.S.D.); (R.M.T.)
| | - Vikas Sukhatme
- Morningside Center for Innovative and Affordable Medicine, Departments of Medicine and Hematology and Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Rabindra M. Tirouvanziam
- Center for Cystic Fibrosis & Airways Disease Research, Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis and Sleep, Emory University and Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, GA 30322, USA; (M.B.); (B.S.D.); (R.M.T.)
| | - Raymond F. Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
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11
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Shellenberger BM, Basile ON, Cassel J, Olsen MR, Salvino JM, Montaner LJ, Tietjen I, Henry GE. Synthesis, SARS-CoV-2 main protease inhibition, molecular docking and in silico ADME studies of furanochromene-quinoline hydrazone derivatives. Bioorg Med Chem Lett 2024; 102:129679. [PMID: 38423371 DOI: 10.1016/j.bmcl.2024.129679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Seven furanochromene-quinoline derivatives containing a hydrazone linker were synthesized by condensing a furanochromene hydrazide with quinoline 2-, 3-, 4-, 5-, 6-, and 8-carbaldehydes, including 8-hydroxyquinoline-2-carbaldehye. Structure-activity correlations were investigated to determine the influence of the location of the hydrazone linker on the quinoline unit on SARS-CoV-2 Mpro enzyme inhibition. The 3-, 5-, 6- and 8-substituted derivatives showed moderate inhibition of SARS-CoV-2 Mpro with IC50 values ranging from 16 to 44 μM. Additionally, all of the derivatives showed strong interaction with the SARS-CoV-2 Mpro substrate binding pocket, with docking energy scores ranging from -8.0 to -8.5 kcal/mol. These values are comparable to that of N3 peptide (-8.1 kcal/mol) and more favorable than GC-373 (-7.6 kcal/mol) and ML-188 (-7.5 kcal/mol), all of which are known SARS-CoV-2 Mpro inhibitors. Furthermore, in silico absorption, distribution, metabolism, and excretion (ADME) profiles indicate that the derivatives have good drug-likeness properties. Overall, this study highlights the potential of the furanochromene-quinoline hydrazone scaffold as a SARS-CoV-2 Mpro inhibitor.
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Affiliation(s)
- Blake M Shellenberger
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Olivia N Basile
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Joel Cassel
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Morgan R Olsen
- Department of Chemistry, Bucknell University, One Dent Drive, Lewisburg, PA 17837, USA
| | | | | | - Ian Tietjen
- The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Geneive E Henry
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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12
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Zhang R, Yan H, Zhou J, Yan G, Liu X, Shang C, Chen Y. Improved fluorescence-based assay for rapid screening and evaluation of SARS-CoV-2 main protease inhibitors. J Med Virol 2024; 96:e29498. [PMID: 38436148 DOI: 10.1002/jmv.29498] [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: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health. In parallel with vaccines, efficacious antivirals are urgently needed. SARS-CoV-2 main protease (Mpro) is an attractive drug target for antiviral development owing to its key roles in virus replication and host immune evasion. Due to the limitations of currently available methods, the development of novel high-throughput screening assays is of the highest importance for the discovery of Mpro inhibitors. In this study, we first developed an improved fluorescence-based assay for rapid screening of Mpro inhibitors from an anti-infection compound library using a versatile dimerization-dependent red fluorescent protein (ddRFP) biosensor. Utilizing this assay, we identified MG-101 as a competitive Mpro inhibitor in vitro. Moreover, our results revealed that ensitrelvir is a potent Mpro inhibitor, but baicalein, chloroquine, ebselen, echinatin, and silibinin are not. Therefore, this robust ddRFP assay provides a faithful avenue for rapid screening and evaluation of Mpro inhibitors to fight against COVID-19.
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Affiliation(s)
- Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Jiahao Zhou
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Gangan Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
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13
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Alhazmi AY, Khan FR, Rehman ZU, Hazazi A, Alotaibi BS, Alharthi NS, Alhuthali HM, Aba Alkhayl FF, Alshehri FF, Alkhoshaiban A, Al-Otaibi F. Structural and energetic analysis of NS5 protein inhibition by small molecules in Japanese encephalitis virus using machine learning and steered molecular dynamics approach. J Biomol Struct Dyn 2024:1-18. [PMID: 38407246 DOI: 10.1080/07391102.2024.2316767] [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: 09/04/2023] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
One of the viral diseases that affect millions of people around the world, particularly in developing countries, is Japanese encephalitis (JE). In this study, the conserved protein of this virus, that is, non-structural protein 5 (NS5), was used as a target protein for this study, and a compound library of 749 antiviral molecules was screened against NS5. The current study employed machine learning-based virtual screening combined with molecular docking. Here, three hits (24360, 123519051 and 213039) had lower binding energies (< -8 kcal/mol) than the control, S-Adenosyl-L-homocysteine (SAH). All the compounds showed significant H-bond interactions with functional residues, which were also observed by the control. Molecular dynamics simulation, MM/GBSA for binding free energy analysis, principal component analysis and free energy landscape were also performed to study the stability of the complex formation. All three compounds had similar root mean square deviation trends, which were comparable to the control, SAH. Post-MD, the 123519051-receptor complex had the highest number of H-bonds (4 to 5) after the control, out of which three exhibited the highest percentage occupancy (50%, 24% and 79%). Both docking and MD, 123519051 showed an H-bond with the residue Gly111, which was also found for the control-protein complex. 123519051 showed the lowest binding free energy with ΔGbind of -89 kJ/mol. Steered molecular dynamics depicted that 123519051 had the maximum magnitude of dissociation (1436.43 kJ/mol/nm), which was more than the control, validating its stable complex formation. This study concluded that 123519051 is a binder and could inhibit the protein NS5 of JE.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdulfattah Y Alhazmi
- Pharmaceutical Practices Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences - AlQuwayiyah, Shaqra University, Saudi Arabia
| | - Zia Ur Rehman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences - AlQuwayiyah, Shaqra University, Saudi Arabia
| | - Nahed S Alharthi
- Department of Medical Laboratory. College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudia Arabia
| | - Hayaa M Alhuthali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faez Falah Alshehri
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | | | - Faisal Al-Otaibi
- Department of Pharmacy Practice, College of Pharmacy, Shaqra University, Saudi Arabia
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14
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Giri-Rachman EA, Effendy VV, Azmi MHS, Yamahoki N, Stephanie R, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Aditama R, Ningrum RA, Wardiana A, Fibriani A. The SARS-CoV-2 M pro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential. ACS Synth Biol 2024; 13:509-520. [PMID: 38316139 PMCID: PMC10877612 DOI: 10.1021/acssynbio.3c00446] [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: 07/23/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024]
Abstract
The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (Mpro) dimer-based screening system (DBSS) utilizing synthetic biology in Escherichia coli BL21(DE3). We linked the SARS-CoV-2 Mpro with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-Mpro both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control (P ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 Mpro and also minimize the use of a high biosafety level laboratory.
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Affiliation(s)
| | - Vergio V. Effendy
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Muhammad H. S. Azmi
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Nicholas Yamahoki
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Rebecca Stephanie
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Dian F. Agustiyanti
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Popi H. Wisnuwardhani
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Marissa Angelina
- Research
Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency
(BRIN), Serpong 15314, Indonesia
| | - Yana Rubiyana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Reza Aditama
- Biochemistry
Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Ratih A. Ningrum
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Andri Wardiana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Azzania Fibriani
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
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15
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Allayeh AK, El-boghdady AH, Said MA, Saleh MGA, Abdel-Aal MT, Abouelenein MG. Discovery of Pyrano[2,3- c]pyrazole Derivatives as Novel Potential Human Coronavirus Inhibitors: Design, Synthesis, In Silico, In Vitro, and ADME Studies. Pharmaceuticals (Basel) 2024; 17:198. [PMID: 38399412 PMCID: PMC10892497 DOI: 10.3390/ph17020198] [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: 11/17/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
The SARS-CoV-2 pandemic at the end of 2019 had major worldwide health and economic consequences. Until effective vaccination approaches were created, the healthcare sectors endured a shortage of operative treatments that might prevent the infection's spread. As a result, academia and the pharmaceutical industry prioritized the development of SARS-CoV2 antiviral medication. Pyranopyrazoles have been shown to play a prominent function in pharmaceutical chemistry and drug sighting because of their significant bioactive properties. We provide herein a novel sequence of pyranopyrazoles and their annulated systems whose antiviral efficacy and cytotoxicity were explored versus human coronavirus 229E (HCoV-229E) Vero-E6 cell lines as a model for the Coronaviridae family. Fifteen synthetic congeners pointed out miscellaneous antiviral efficacies against HCoV-229E with variable inhibition degrees. Compound 18 showed a high selectivity index (SI = 12.6) that established spectacular inhibitory capacity against human coronavirus 229E. Compounds 6, 7, and 14 exposed moderate efficacies. Compounds 6, 7, 14, and 18 exhibited substantial antiviral action through the replication phase with reduction percentages extending from 53.6%, 60.7%, and 55% to 82.2%, correspondingly. Likewise, when assessed to the positive control tipranavir (88.6%), the inhibitory efficiency of compounds 6, 7, 14, and 18 versus the SARS-CoV2 Mpro provided high percentages of 80.4%, 73.1%, 81.4% and up to 84.5%, respectively. In silico studies were performed to investigate further the biological activity and the target compounds' physical and chemical features, including molecular dynamic (MD) simulations, protein-ligand docking, ADME studies, and density functional theory (DFT) calculations. These inquiries demonstrated that this series of metabolically stable pyranopyrazoles and their annulated systems are effective human coronavirus inhibitors that inhibit the viral Mpro protein and may have emerged as a novel COVID-19 curative option.
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Affiliation(s)
- Abdou K. Allayeh
- Environmental Virology Laboratory 176, Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre (NRC), 33 El-Behouth St., Dokki, Giza 12622, Egypt;
| | - Aliaa H. El-boghdady
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
| | - Mohamed A. Said
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt;
| | - Mahmoud G. A. Saleh
- Department of Chemistry, College of Science, Northern Border University, Arar 91431, Saudi Arabia
| | - Mohammed T. Abdel-Aal
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
| | - Mohamed G. Abouelenein
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
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16
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Parveen D, Das A, Amin S, Alam MM, Akhter M, Ahmed Khan M, Ali R, Anwer T, Sheikh KA, Azam F, Shaquiquzzaman M. Effectiveness of estrogen and its derivatives over dexamethasone in the treatment of COVID-19. J Biomol Struct Dyn 2024; 42:1858-1874. [PMID: 37129196 DOI: 10.1080/07391102.2023.2205944] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/08/2023] [Indexed: 05/03/2023]
Abstract
Coronavirus disease (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus and dexamethasone is a glucocorticoid widely used for its treatment. Dexamethasone is not used in non-severe cases due to its immunosuppressant action. So, considering this, Estrogen and Estetrol were tested for the treatment of COVID-19 as they all possess a common steroid ring and dislike dexamethasone, they are immunoenhancer. Virtual screening of test ligands was performed through molecular docking, MM-GBSA, simulations, in silico ADMET and drug-likeness prediction to identify their potential to inhibit the effects of SARS-CoV-2. Results showed that test ligands possess drug-like properties and they are safe as drug candidates. The protein-ligand interaction study revealed that they bind with the amino acid residues at the active site of the target proteins and the test ligands possess better binding potential than Dexamethasone. With protein Mpro, Estetrol and Estrogen showed docking score of -7.240 and -5.491 kcal/mol, and with protein ACE2, Estetrol and Estrogen showed docking score of -5.269 and -4.732 kcal/mol, respectively. Further, MD Simulation was carried out and most of the interactions of molecular docking are preserved during simulation. The prominent interactions that our test ligands showed during MD Simulation are similar to drugs that possess in vitro anticovid activity as shown in recent studies. Hence, our test ligands possessed potential for anticovid activity and they should be further tested through in vitro and in vivo studies for their activity against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Darakhshan Parveen
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
| | - Anwesha Das
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
| | - Shaista Amin
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
| | - M Mumtaz Alam
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
| | - Mymoona Akhter
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
| | - Mohammad Ahmed Khan
- Department of Pharmacology, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
| | - Ruhi Ali
- Department of Pharmaceutical Chemistry, DIPSAR, Delhi Pharmaceutical Science and Research University (DPSRU), New Delhi, India
| | - Tarique Anwer
- Department of Pharmacology, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Khursheed A Sheikh
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - M Shaquiquzzaman
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
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17
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Haghir Ebrahim Abadi MH, Ghasemlou A, Bayani F, Sefidbakht Y, Vosough M, Mozaffari-Jovin S, Uversky VN. AI-driven covalent drug design strategies targeting main protease (m pro) against SARS-CoV-2: structural insights and molecular mechanisms. J Biomol Struct Dyn 2024:1-29. [PMID: 38287509 DOI: 10.1080/07391102.2024.2308769] [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: 11/09/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
The emergence of new SARS-CoV-2 variants has raised concerns about the effectiveness of COVID-19 vaccines. To address this challenge, small-molecule antivirals have been proposed as a crucial therapeutic option. Among potential targets for anti-COVID-19 therapy, the main protease (Mpro) of SARS-CoV-2 is important due to its essential role in the virus's life cycle and high conservation. The substrate-binding region of the core proteases of various coronaviruses, including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), could be used for the generation of new protease inhibitors. Various drug discovery methods have employed a diverse range of strategies, targeting both monomeric and dimeric forms, including drug repurposing, integrating virtual screening with high-throughput screening (HTS), and structure-based drug design, each demonstrating varying levels of efficiency. Covalent inhibitors, such as Nirmatrelvir and MG-101, showcase robust and high-affinity binding to Mpro, exhibiting stable interactions confirmed by molecular docking studies. Development of effective antiviral drugs is imperative to address potential pandemic situations. This review explores recent advances in the search for Mpro inhibitors and the application of artificial intelligence (AI) in drug design. AI leverages vast datasets and advanced algorithms to streamline the design and identification of promising Mpro inhibitors. AI-driven drug discovery methods, including molecular docking, predictive modeling, and structure-based drug repurposing, are at the forefront of identifying potential candidates for effective antiviral therapy. In a time when COVID-19 potentially threat global health, the quest for potent antiviral solutions targeting Mpro could be critical for inhibiting the virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sina Mozaffari-Jovin
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
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18
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Outteridge M, Nunn CM, Devine K, Patel B, McLean GR. Antivirals for Broader Coverage against Human Coronaviruses. Viruses 2024; 16:156. [PMID: 38275966 PMCID: PMC10820748 DOI: 10.3390/v16010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.
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Affiliation(s)
- Mia Outteridge
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Christine M. Nunn
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Kevin Devine
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Bhaven Patel
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
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Lima Neto JX, Bezerra KS, Barbosa ED, Araujo RL, Galvão DS, Lyra ML, Oliveira JIN, Akash S, Jardan YAB, Nafidi HA, Bourhia M, Fulco UL. Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2. Front Mol Biosci 2024; 10:1325588. [PMID: 38304231 PMCID: PMC10830813 DOI: 10.3389/fmolb.2023.1325588] [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: 10/21/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
Background: The RNA-dependent RNA polymerase (RdRp) complex, essential in viral transcription and replication, is a key target for antiviral therapeutics. The core unit of RdRp comprises the nonstructural protein NSP12, with NSP7 and two copies of NSP8 (NSP81 and NSP82) binding to NSP12 to enhance its affinity for viral RNA and polymerase activity. Notably, the interfaces between these subunits are highly conserved, simplifying the design of molecules that can disrupt their interaction. Methods: We conducted a detailed quantum biochemical analysis to characterize the interactions within the NSP12-NSP7, NSP12-NSP81, and NSP12-NSP82 dimers. Our objective was to ascertain the contribution of individual amino acids to these protein-protein interactions, pinpointing hotspot regions crucial for complex stability. Results: The analysis revealed that the NSP12-NSP81 complex possessed the highest total interaction energy (TIE), with 14 pairs of residues demonstrating significant energetic contributions. In contrast, the NSP12-NSP7 complex exhibited substantial interactions in 8 residue pairs, while the NSP12-NSP82 complex had only one pair showing notable interaction. The study highlighted the importance of hydrogen bonds and π-alkyl interactions in maintaining these complexes. Intriguingly, introducing the RNA sequence with Remdesivir into the complex resulted in negligible alterations in both interaction energy and geometric configuration. Conclusion: Our comprehensive analysis of the RdRp complex at the protein-protein interface provides invaluable insights into interaction dynamics and energetics. These findings can guide the design of small molecules or peptide/peptidomimetic ligands to disrupt these critical interactions, offering a strategic pathway for developing effective antiviral drugs.
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Affiliation(s)
- José Xavier Lima Neto
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Katyanna Sales Bezerra
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Emmanuel Duarte Barbosa
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Roniel Lima Araujo
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
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20
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De Luca V, Angeli A, Nocentini A, Gratteri P, Pratesi S, Tanini D, Carginale V, Capperucci A, Supuran CT, Capasso C. Leveraging SARS-CoV-2 Main Protease (M pro) for COVID-19 Mitigation with Selenium-Based Inhibitors. Int J Mol Sci 2024; 25:971. [PMID: 38256046 PMCID: PMC10815619 DOI: 10.3390/ijms25020971] [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: 12/07/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The implementation of innovative approaches is crucial in an ongoing endeavor to mitigate the impact of COVID-19 pandemic. The present study examines the strategic application of the SARS-CoV-2 Main Protease (Mpro) as a prospective instrument in the repertoire to combat the virus. The cloning, expression, and purification of Mpro, which plays a critical role in the viral life cycle, through heterologous expression in Escherichia coli in a completely soluble form produced an active enzyme. The hydrolysis of a specific substrate peptide comprising a six-amino-acid sequence (TSAVLQ) linked to a p-nitroaniline (pNA) fragment together with the use of a fluorogenic substrate allowed us to determine effective inhibitors incorporating selenium moieties, such as benzoselenoates and carbamoselenoates. The new inhibitors revealed their potential to proficiently inhibit Mpro with IC50-s in the low micromolar range. Our study contributes to the development of a new class of protease inhibitors targeting Mpro, ultimately strengthening the antiviral arsenal against COVID-19 and possibly, related coronaviruses.
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Affiliation(s)
- Viviana De Luca
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, 80131 Naples, Italy; (V.D.L.); (V.C.)
| | - Andrea Angeli
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (A.N.); (P.G.)
| | - Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (A.N.); (P.G.)
| | - Paola Gratteri
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (A.N.); (P.G.)
| | - Silvia Pratesi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy (D.T.); (A.C.)
| | - Damiano Tanini
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy (D.T.); (A.C.)
| | - Vincenzo Carginale
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, 80131 Naples, Italy; (V.D.L.); (V.C.)
| | - Antonella Capperucci
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy (D.T.); (A.C.)
| | - Claudiu T. Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (A.N.); (P.G.)
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, 80131 Naples, Italy; (V.D.L.); (V.C.)
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21
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Gavilán E, Medina-Guzman R, Bahatyrevich-Kharitonik B, Ruano D. Protein Quality Control Systems and ER Stress as Key Players in SARS-CoV-2-Induced Neurodegeneration. Cells 2024; 13:123. [PMID: 38247815 PMCID: PMC10814689 DOI: 10.3390/cells13020123] [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: 11/29/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic has brought to the forefront the intricate relationship between SARS-CoV-2 and its impact on neurological complications, including potential links to neurodegenerative processes, characterized by a dysfunction of the protein quality control systems and ER stress. This review article explores the role of protein quality control systems, such as the Unfolded Protein Response (UPR), the Endoplasmic Reticulum-Associated Degradation (ERAD), the Ubiquitin-Proteasome System (UPS), autophagy and the molecular chaperones, in SARS-CoV-2 infection. Our hypothesis suggests that SARS-CoV-2 produces ER stress and exploits the protein quality control systems, leading to a disruption in proteostasis that cannot be solved by the host cell. This disruption culminates in cell death and may represent a link between SARS-CoV-2 and neurodegeneration.
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Affiliation(s)
- Elena Gavilán
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Rafael Medina-Guzman
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
| | - Bazhena Bahatyrevich-Kharitonik
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Diego Ruano
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
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22
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Dinata R, Nisa N, Arati C, Rasmita B, Uditraj C, Siddhartha R, Bhanushree B, Saeed-Ahmed L, Manikandan B, Bidanchi RM, Abinash G, Pori B, Khushboo M, Roy VK, Gurusubramanian G. Repurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods. J Biomol Struct Dyn 2024; 42:43-81. [PMID: 37021347 DOI: 10.1080/07391102.2023.2192797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
The COVID-19 pandemic has caused adverse health (severe respiratory, enteric and systemic infections) and environmental impacts that have threatened public health and the economy worldwide. Drug repurposing and small molecule multi-target directed herbal medicine therapeutic approaches are the most appropriate exploration strategies for SARS-CoV-2 drug discovery. This study identified potential multi-target-directed Parkia bioactive entities against SARS-CoV-2 receptors (S-protein, ACE2, TMPRSS2, RBD/ACE2, RdRp, MPro, and PLPro) using ADMET, drug-likeness, molecular docking (AutoDock, FireDock and HDOCK), molecular dynamics simulation and MM-PBSA tools. One thousand Parkia bioactive entities were screened out by virtual screening and forty-five bioactive phytomolecules were selected based on favorable binding affinity and acceptable pharmacokinetic and pharmacodynamics properties. The binding affinity values of Parkia phyto-ligands (AutoDock: -6.00--10.40 kcal/mol; FireDock: -31.00--62.02 kcal/mol; and HDOCK: -150.0--294.93 kcal/mol) were observed to be higher than the reference antiviral drugs (AutoDock: -5.90--9.10 kcal/mol; FireDock: -35.64--59.35 kcal/mol; and HDOCK: -132.82--211.87 kcal/mol), suggesting a potent modulatory action of Parkia bioactive entities against the SARS-CoV-2. Didymin, rutin, epigallocatechin gallate, epicatechin-3-0-gallate, hyperin, ursolic acid, lupeol, stigmasta-5,24(28)-diene-3-ol, ellagic acid, apigenin, stigmasterol, and campesterol strongly bound with the multiple targets of the SARS-CoV-2 receptors, inhibiting viral entry, attachment, binding, replication, transcription, maturation, packaging and spread. Furthermore, ACE2, TMPRSS2, and MPro receptors possess significant molecular dynamic properties, including stability, compactness, flexibility and total binding energy. Residues GLU-589, and LEU-95 of ACE2, GLN-350, HIS-186, and ASP-257 of TMPRSS2, and GLU-14, MET-49, and GLN-189 of MPro receptors contributed to the formation of hydrogen bonds and binding interactions, playing vital roles in inhibiting the activity of the receptors. Promising results were achieved by developing multi-targeted antiviral Parkia bioactive entities as lead and prospective candidates under a small molecule strategy against SARS-CoV-2 pathogenesis. The antiviral activity of Parkia bioactive entities needs to be further validated by pre-clinical and clinical trials.
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Affiliation(s)
- Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Nisekhoto Nisa
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Chettri Arati
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Chetia Uditraj
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | | | | | - Bose Manikandan
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Giri Abinash
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Buragohain Pori
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Maurya Khushboo
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Vikas Kumar Roy
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
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23
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Chaudhury S, Kaur P, Gupta D, Anand P, Chaudhary M, Tiwari S, Mittal A, Gupta J, Kaur S, Singh VD, Dhawan D, Singh P, Sahu SK. Therapeutic Management with Repurposing Approaches: A Mystery During COVID-19 Outbreak. Curr Mol Med 2024; 24:712-733. [PMID: 37312440 DOI: 10.2174/1566524023666230613141746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/15/2023]
Abstract
The ubiquitous pandemic that emerged due to COVID-19 affected the whole planet. People all over the globe became vulnerable to the unpredictable emergence of coronavirus. The sudden emergence of respiratory disease in coronavirus infected several patients. This affected human life drastically, from mild symptoms to severe illness, leading to mortality. COVID-19 is an exceptionally communicable disease caused by SARS-CoV-2. According to a genomic study, the viral spike RBD interactions with the host ACE2 protein from several coronavirus strains and the interaction between RBD and ACE2 highlighted the potential change in affinity from the virus causing the COVID-19 outbreak to a progenitor type of SARS-CoV-2. SARS-CoV-2, which could be the principal reservoir, is phylogenetically related to the SARS-like bat virus. Other research works reported that intermediary hosts for the transmission of viruses to humans could include cats, bats, snakes, pigs, ferrets, orangutans, and monkeys. Even with the arrival of vaccines and individuals getting vaccinated and treated with FDAapproved repurposed drugs like Remdesivir, the first and foremost steps aimed towards the possible control and minimization of community transmission of the virus include social distancing, self-realization, and self-health care. In this review paper, we discussed and summarized various approaches and methodologies adopted and proposed by researchers all over the globe to help with the management of this zoonotic outbreak by following repurposed approaches.
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Affiliation(s)
- Soumik Chaudhury
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Paranjeet Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Deepali Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Palak Anand
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Manish Chaudhary
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Siddhita Tiwari
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Amit Mittal
- Faculty of Pharmaceutical Sciences, Desh Bhagat University, Amloh Road, Mandi Gobindgarh, 147301, Punjab, India
| | - Jeena Gupta
- School of Bioscience, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Sukhmeen Kaur
- Department of Opthalmology, Punjab Institute of Medical Sciences, Jalandhar, 144001, Punjab, India
| | - Varsh Deep Singh
- American University of Barbados, Wildey, St. Michael, BB11100, Barbados
| | - Dakshita Dhawan
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Princejyot Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Sanjeev Kumar Sahu
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
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24
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Ali IH, Elkashlan AM, Hammad MA, Hamdi M. Antimicrobial and anti-SARS-CoV-2 activities of smart daclatasvir-chitosan/gelatin nanoparticles-in-PLLA nanofibrous medical textiles; in vitro, and in vivo study. Int J Biol Macromol 2023; 253:127350. [PMID: 37838117 DOI: 10.1016/j.ijbiomac.2023.127350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/19/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
This study aims at the development of electrospun polylactic acid nanofibers (PLLA NFs) incorporating smart daclatasvir-loaded chitosan gelatin nanoparticles to be used as medical textiles. First, smart nanoparticles were prepared through ionic gelation and optimized using Design Expert® software where daclatasvir (DAC), chitosan (CS), and gelatin (GL) amounts were selected to be the independent variables. DAC was used owing to its reported Anti-SARS-CoV-2 activity, CS was chosen due to its antimicrobial activity and GL was used owing to its sensitivity to be hydrolyzed upon exposure to Papain-like protease enzyme (PLpro). The optimum DAC-CS/TAN NPs possessed 109 nm size and 94.44 % entrapment efficiency in addition to sustained drug release for 14 days. Furthermore, upon exposure to PLpro, smart DAC-CS/GL NPs released the whole DAC amount within 3 h. Then, DAC-CS/GL NPs were incorporated within PLLA NFs through electrospinning. Swellability was found to increase gradually reflecting the controlled release of DAC from nanofibers within 3 weeks. Cell viability assessments using human fibroblasts showed that the developed nanofibers possess high biocompatibility. An in-vivo animal model for skin irritation was carried out for two weeks where visual inspection and histopathological investigations showed that neither edema nor erythema were observed.
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Affiliation(s)
- Isra H Ali
- Department of Pharmaceutics, Faculty of Pharmacy, University of Sadat City, P.O. Box 32897, Sadat City, Egypt.
| | - Akram M Elkashlan
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, P.O. Box 32897, Sadat City, Egypt
| | - Mohamed A Hammad
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Sadat City, P.O. Box 32897, Sadat City, Egypt
| | - Mohamed Hamdi
- Department of Pharmaceutics, Faculty of Pharmacy, University of Sadat City, P.O. Box 32897, Sadat City, Egypt
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25
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Pennisi R, Gentile D, Rescifina A, Napoli E, Trischitta P, Piperno A, Sciortino MT. An Integrated In Silico and In Vitro Approach for the Identification of Natural Products Active against SARS-CoV-2. Biomolecules 2023; 14:43. [PMID: 38254643 PMCID: PMC10813393 DOI: 10.3390/biom14010043] [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: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has provoked a global health crisis due to the absence of a specific therapeutic agent. 3CLpro (also known as the main protease or Mpro) and PLpro are chymotrypsin-like proteases encoded by the SARS-CoV-2 genome, and play essential roles during the virus lifecycle. Therefore, they are recognized as a prospective therapeutic target in drug discovery against SARS-CoV-2 infection. Thus, this work aims to collectively present potential natural 3CLpro and PLpro inhibitors by in silico simulations and in vitro entry pseudotype-entry models. We screened luteolin-7-O-glucuronide (L7OG), cynarin (CY), folic acid (FA), and rosmarinic acid (RA) molecules against PLpro and 3CLpro through a luminogenic substrate assay. We only reported moderate inhibitory activity on the recombinant 3CLpro and PLpro by L7OG and FA. Afterward, the entry inhibitory activity of L7OG and FA was tested in cell lines transduced with the two different SARS-CoV-2 pseudotypes harboring alpha (α) and omicron (o) spike (S) protein. The results showed that both compounds have a consistent inhibitory activity on the entry for both variants. However, L7OG showed a greater degree of entry inhibition against α-SARS-CoV-2. Molecular modeling studies were used to determine the inhibitory mechanism of the candidate molecules by focusing on their interactions with residues recognized by the protease active site and receptor-binding domain (RBD) of spike SARS-CoV-2. This work allowed us to identify the binding sites of FA and L7OG within the RBD domain in the alpha and omicron variants, demonstrating how FA is active in both variants. We have confidence that future in vivo studies testing the safety and effectiveness of these natural compounds are warranted, given that they are effective against a variant of concerns.
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Affiliation(s)
- Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
| | - Davide Gentile
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, V.le A. Doria 6, 95125 Catania, Italy;
| | - Edoardo Napoli
- Istituto di Chimica Biomolecolare—Consiglio Nazionale delle Ricerche, 95126 Catania, Italy;
| | - Paola Trischitta
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
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Liu W, Mu G, Jia Y, Yu M, Zhang S, Wang Z, Fang S. The role of IBV PL1pro in virus replication and suppression of host innate immune responses. BMC Vet Res 2023; 19:270. [PMID: 38087313 PMCID: PMC10717896 DOI: 10.1186/s12917-023-03839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Coronavirus papain-like proteases (PLpros) play a crucial role in virus replication and the evasion of the host immune response. Infectious bronchitis virus (IBV) encodes a proteolytically defective remnant of PL1pro and an active PL2pro. However, the function of PL1pro in IBV remains largely unknown. This study aims to explore the effect of PL1pro on virus replication and underlying mechanisms. RESULTS The recombinant viruses rIBV-ΔPL1pro and rIBV-ΔPL1pro-N were obtained using reverse genetic techniques through the deletion of the IBV PL1pro domain and the N-terminal conserved sequence of PL1pro (PL1pro-N). We observed significantly lower replication of rIBV-ΔPL1pro and rIBV-ΔPL1pro-N than wild-type IBV. Further investigation revealed that the lack of PL1pro-N in IBV decreased virus resistance to interferon (IFN) while also inducing host immune response by enhancing the production of IFN-β and activating the downstream STAT1 signaling pathway of IFNs. In addition, the overexpression of PL1pro-N significantly suppressed type I IFN response by down-regulating the expressions of genes in the IFN pathway. CONCLUSIONS Our data demonstrated that IBV PL1pro plays a crucial role in IBV replication and the suppression of host innate immune responses, suggesting that IBV PL1pro could serve as a promising molecular target for antiviral therapy.
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Affiliation(s)
- Weirong Liu
- Yangtze University Health Science Center, Jingzhou, Hubei Province, China
| | - Ge Mu
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, Hubei Province, 434025, China
| | - Yiquan Jia
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, Hubei Province, 434025, China
| | - Mengting Yu
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, Hubei Province, 434025, China
| | - Songbai Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, Hubei Province, China
| | - Zhen Wang
- Yangtze University Health Science Center, Jingzhou, Hubei Province, China
| | - Shouguo Fang
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, Hubei Province, 434025, China.
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Mysorekar I, Michita R, Tran L, Bark S, Kumar D, Toner S, Jose J, Narayanan A. Zika Virus NS1 Drives Tunneling Nanotube Formation for Mitochondrial Transfer, Enhanced Survival, Interferon Evasion, and Stealth Transmission in Trophoblasts. RESEARCH SQUARE 2023:rs.3.rs-3674059. [PMID: 38106210 PMCID: PMC10723532 DOI: 10.21203/rs.3.rs-3674059/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Zika virus (ZIKV) infection continues to pose a significant public health concern due to limited available preventive measures and treatments. ZIKV is unique among flaviviruses in its vertical transmission capacity (i.e., transmission from mother to fetus) yet the underlying mechanisms remain incompletely understood. Here, we show that both African and Asian lineages of ZIKV induce tunneling nanotubes (TNTs) in placental trophoblasts and multiple other mammalian cell types. Amongst investigated flaviviruses, only ZIKV strains trigger TNTs. We show that ZIKV-induced TNTs facilitate transfer of viral particles, proteins, and RNA to neighboring uninfected cells. ZIKV TNT formation is driven exclusively via its non-structural protein 1 (NS1); specifically, the N-terminal region (50 aa) of membrane-bound NS1 is necessary and sufficient for triggering TNT formation in host cells. Using affinity purification-mass spectrometry of cells infected with wild-type NS1 or non-TNT forming NS1 (pNS1ΔTNT) proteins, we found mitochondrial proteins are dominant NS1-interacting partners, consistent with the elevated mitochondrial mass we observed in infected trophoblasts. We demonstrate that mitochondria are siphoned via TNTs from healthy to ZIKV-infected cells, both homotypically and heterotypically, and inhibition of mitochondrial respiration reduced viral replication in trophoblast cells. Finally, ZIKV strains lacking TNT capabilities due to mutant NS1 elicited a robust antiviral IFN-λ 1/2/3 response, indicating ZIKV's TNT-mediated trafficking also allows ZIKV cell-cell transmission that is camouflaged from host defenses. Together, our findings identify a new stealth mechanism that ZIKV employs for intercellular spread among placental trophoblasts, evasion of antiviral interferon response, and the hijacking of mitochondria to augment its propagation and survival. Discerning the mechanisms of ZIKV intercellular strategies offers a basis for novel therapeutic developments targeting these interactions to limit its dissemination.
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Bischof E. Mitigating COVID-19 Mortality and Morbidity in China's Aging Population: A Focus on Available Medications and Future Developments. Aging Dis 2023; 14:1967-1976. [PMID: 37199593 PMCID: PMC10676792 DOI: 10.14336/ad.2023.0318] [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: 02/15/2023] [Accepted: 03/18/2023] [Indexed: 05/19/2023] Open
Abstract
The COVID-19 pandemic, often referred to as the geropandemic, has put immense pressure on global healthcare systems worldwide, leading to a rush in the development and approval of medications for the treatment of the viral infection. Clinical trials on efficacy and safety had a limited spectrum on inclusion and endpoints because of the urgent need for fast results. The chronologically and biologically aged population is especially at risk for severe or lethal disease, as well as treatment-associated toxicity. In China, the growing elderly population segment has been a focus in public health measurements of COVID-19, guiding towards herd immunity with a mild variant, thus minimizing overall deaths and morbidity. While the COVID-19 pandemic has now been reclassified and the virus weakened, there is a clear need for novel therapies to protect the elderly. This paper reviews the current safety and efficacy of available COVID-19 medications in China, with a specific focus on 3CL protease inhibitors and the aging population. The current COVID wave in China has demonstrated a significant impact on the elderly and the need for new drugs that are effective at low doses and can be used alone, without harmful side effects, generation of viral resistance, and drug-drug interactions. The rush to develop and approve COVID-19 medications has brought up important questions about the balance between speed and caution, resulting in a pipeline of novel therapies now moving through clinical trials, including third-generation 3CL protease inhibitors. A majority of those therapeutics are being developed in China.
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Affiliation(s)
- Evelyne Bischof
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Department of Advanced Biomedical Sciences, Federico II University of Naples, Naples, Italy.
- Shanghai University of Medicine and Health Sciences, Shanghai, China.
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Chakraborty C, Bhattacharya M, Alshammari A, Alharbi M, Albekairi TH, Zheng C. Exploring the structural and molecular interaction landscape of nirmatrelvir and Mpro complex: The study might assist in designing more potent antivirals targeting SARS-CoV-2 and other viruses. J Infect Public Health 2023; 16:1961-1970. [PMID: 37883855 DOI: 10.1016/j.jiph.2023.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Several therapeutics have been developed and approved against SARS-CoV-2 occasionally; nirmatrelvir is one of them. The drug target of nirmatrelvir is Mpro, and therefore, it is necessary to comprehend the structural and molecular interaction of the Mpro-nirmatrelvir complex. METHODS Integrative bioinformatics, system biology, and statistical models were used to analyze the macromolecular complex. RESULTS Using two macromolecular complexes, the study illustrated the interactive residues, H-bonds, and interactive interfaces. It informed of six and nine H-bond formations for the first and second complex, respectively. The maximum bond length was observed as 3.33 Å. The ligand binding pocket's surface area and volume were noted as 303.485 Å2 and 295.456 Å3 for the first complex and 308.397 Å2 and 304.865 Å3 for the second complex. The structural proteome dynamics were evaluated by analyzing the complex's NMA mobility, eigenvalues, deformability, and B-factor. Conversely, a model was created to assess the therapeutic status of nirmatrelvir. CONCLUSIONS Our study reveals the structural and molecular interaction landscape of Mpro-nirmatrelvir complex. The study will guide researchers in designing more broad-spectrum antiviral molecules mimicking nirmatrelvir, which assist in fighting against SARS-CoV-2 and other infectious viruses. It will also help to prepare for future epidemics or pandemics.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Thamer H Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Chunfu Zheng
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao 028000, China; Department of Microbiology, Immunology & Infection Diseases, University of Calgary, Health Research Innovation Centre, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
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30
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Xu F, Yang Z, Wang L, Meng D, Long J. MESPool: Molecular Edge Shrinkage Pooling for hierarchical molecular representation learning and property prediction. Brief Bioinform 2023; 25:bbad423. [PMID: 38048081 PMCID: PMC10753536 DOI: 10.1093/bib/bbad423] [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: 06/15/2023] [Revised: 09/18/2023] [Accepted: 10/29/2023] [Indexed: 12/05/2023] Open
Abstract
Identifying task-relevant structures is important for molecular property prediction. In a graph neural network (GNN), graph pooling can group nodes and hierarchically represent the molecular graph. However, previous pooling methods either drop out node information or lose the connection of the original graph; therefore, it is difficult to identify continuous subtructures. Importantly, they lacked interpretability on molecular graphs. To this end, we proposed a novel Molecular Edge Shrinkage Pooling (MESPool) method, which is based on edges (or chemical bonds). MESPool preserves crucial edges and shrinks others inside the functional groups and is able to search for key structures without breaking the original connection. We compared MESPool with various well-known pooling methods on different benchmarks and showed that MESPool outperforms the previous methods. Furthermore, we explained the rationality of MESPool on some datasets, including a COVID-19 drug dataset.
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Affiliation(s)
- Fanding Xu
- School of Life Science and Technology, Xi’an Jiaotong University, 710049 Shaanxi, China
| | - Zhiwei Yang
- School of Physics, Xi’an Jiaotong University, 710049 Shaanxi, China
| | - Lizhuo Wang
- School of Life Science and Technology, Xi’an Jiaotong University, 710049 Shaanxi, China
| | - Deyu Meng
- Rearch Institute for Mathematics and Mathematical Technology, Xi’an Jiaotong University, 710049 Shaanxi, China
- School of Mathematics and Statistics, Henan University, 475004 Henan, China
| | - Jiangang Long
- School of Life Science and Technology, Xi’an Jiaotong University, 710049 Shaanxi, China
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Ghosh AK, Shahabi D, Imhoff MEC, Kovela S, Sharma A, Hattori SI, Higashi-Kuwata N, Mitsuya H, Mesecar AD. SARS-CoV-2 papain-like protease (PLpro) inhibitory and antiviral activity of small molecule derivatives for drug leads. Bioorg Med Chem Lett 2023; 96:129489. [PMID: 37770002 PMCID: PMC10842477 DOI: 10.1016/j.bmcl.2023.129489] [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: 08/29/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
We report here the synthesis and biological evaluation of a series of small molecule SARS-CoV-2 PLpro inhibitors. We compared the activity of selected compounds in both SARS-CoV-1 and SARS-CoV-2 PLpro inhibitory and antiviral assays. We have synthesized and evaluated several new structural variants of previous leads against SARS-CoV-2 PLpro. The replacement of the carboxamide functionality with sulfonamide derivatives resulted in PLpro inhibitors with potent PLpro inhibitory and antiviral activity in VeroE6 cells similar to GRL0617. To obtain molecular insight, we created an optimized model of a potent sulfonamide derivative in the SARS-CoV-2 PLpro active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA.
| | - Dana Shahabi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | | | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Ashish Sharma
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655 Japan; Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556 Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892 USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
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Kaboudi N, Krüger N, Hamzeh-Mivehroud M. Development of novel ligands against SARS-CoV-2 M pro enzyme: an in silico and in vitro Study. Mol Inform 2023; 42:e202300120. [PMID: 37590494 DOI: 10.1002/minf.202300120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/22/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Despite tremendous efforts made by scientific community during the outbreak of COVID-19 pandemic, this disease still remains as a public health concern. Although different types of vaccines were globally used to reduce the mortality, emergence of new variants of SARS-CoV-2 is a challenging issue in COVID-19 pharmacotherapy. In this context, target therapy of SARS-CoV-2 by small ligands is a promising strategy. METHODS In this investigation, we applied ligand-based virtual screening for finding novel molecules based on nirmatrelvir structure. Various criteria including drug-likeness, ADME, and toxicity properties were applied for filtering the compounds. The selected candidate molecules were subjected to molecular docking and dynamics simulation for predicting the binding mode and binding free energy, respectively. Then the molecules were experimentally evaluated in terms of antiviral activity against SARS-CoV-2 and toxicity assessment. RESULTS The results demonstrated that the identified compounds showed inhibitory activity towards SARS-CoV-2 Mpro . CONCLUSION In summary, the introduced compounds may provide novel scaffold for further structural modification and optimization with improved anti SARS-CoV-2 Mpro activity.
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Affiliation(s)
- Navid Kaboudi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nadine Krüger
- Platform Infection Models, German Primate Center-Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Mushebenge AGA, Ugbaja SC, Mbatha NA, B. Khan R, Kumalo HM. Assessing the Potential Contribution of In Silico Studies in Discovering Drug Candidates That Interact with Various SARS-CoV-2 Receptors. Int J Mol Sci 2023; 24:15518. [PMID: 37958503 PMCID: PMC10647470 DOI: 10.3390/ijms242115518] [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: 08/03/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The COVID-19 pandemic has spurred intense research efforts to identify effective treatments for SARS-CoV-2. In silico studies have emerged as a powerful tool in the drug discovery process, particularly in the search for drug candidates that interact with various SARS-CoV-2 receptors. These studies involve the use of computer simulations and computational algorithms to predict the potential interaction of drug candidates with target receptors. The primary receptors targeted by drug candidates include the RNA polymerase, main protease, spike protein, ACE2 receptor, and transmembrane protease serine 2 (TMPRSS2). In silico studies have identified several promising drug candidates, including Remdesivir, Favipiravir, Ribavirin, Ivermectin, Lopinavir/Ritonavir, and Camostat Mesylate, among others. The use of in silico studies offers several advantages, including the ability to screen a large number of drug candidates in a relatively short amount of time, thereby reducing the time and cost involved in traditional drug discovery methods. Additionally, in silico studies allow for the prediction of the binding affinity of the drug candidates to target receptors, providing insight into their potential efficacy. This study is aimed at assessing the useful contributions of the application of computational instruments in the discovery of receptors targeted in SARS-CoV-2. It further highlights some identified advantages and limitations of these studies, thereby revealing some complementary experimental validation to ensure the efficacy and safety of identified drug candidates.
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Affiliation(s)
- Aganze Gloire-Aimé Mushebenge
- Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa;
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Faculty of Pharmaceutical Sciences, University of Lubumbashi, Lubumbashi 1825, Democratic Republic of the Congo
| | - Samuel Chima Ugbaja
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Africa Health Research Institute, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nonkululeko Avril Mbatha
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
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Xu L, Chen R, Liu J, Patterson TA, Hong H. Analyzing 3D structures of the SARS-CoV-2 main protease reveals structural features of ligand binding for COVID-19 drug discovery. Drug Discov Today 2023; 28:103727. [PMID: 37516343 DOI: 10.1016/j.drudis.2023.103727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) main protease has an essential role in viral replication and has become a major target for coronavirus 2019 (COVID-19) drug development. Various inhibitors have been discovered or designed to bind to the main protease. The availability of more than 550 3D structures of the main protease provides a wealth of structural details on the main protease in both ligand-free and ligand-bound states. Therefore, we examined these structures to ascertain the structural features for the role of the main protease in the cleavage of polyproteins, the alternative conformations during main protease maturation, and ligand interactions in the main protease. The structural features unearthed could promote the development of COVID-19 drugs targeting the SARS-CoV-2 main protease.
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Affiliation(s)
- Liang Xu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Ru Chen
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jie Liu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Tucker A Patterson
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
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Tran N, Dasari S, Barwell SAE, McLeod MJ, Kalyaanamoorthy S, Holyoak T, Ganesan A. The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nat Commun 2023; 14:5625. [PMID: 37699927 PMCID: PMC10497556 DOI: 10.1038/s41467-023-40023-4] [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: 08/24/2022] [Accepted: 07/04/2023] [Indexed: 09/14/2023] Open
Abstract
The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro's susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of an Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrate a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild type enzyme. We show that other point mutations also significantly shift the equilibrium towards this state by altering conformational free energies. Unique avenues of SARS-CoV-2 research can be explored by understanding how H163 modulates this equilibrium.
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Affiliation(s)
- Norman Tran
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sathish Dasari
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sarah A E Barwell
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | | | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Todd Holyoak
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
| | - Aravindhan Ganesan
- ArGan's Lab, School of Pharmacy, Faculty of Science, University of Waterloo, 10A Victoria Street South, Kitchener, ON, N2G 1C5, Canada.
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D′Oliviera A, Dai X, Mottaghinia S, Geissler EP, Etienne L, Zhang Y, Mugridge JS. Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529306. [PMID: 36865253 PMCID: PMC9980103 DOI: 10.1101/2023.02.20.529306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is critical for the production of functional viral proteins during infection and, like many viral proteases, can also target host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes global protein synthesis and cellular redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain required for tRNA modification activity in cells. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 may be resistant to cleavage. In primates, regions outside the cleavage site with rapid evolution could indicate adaptation to ancient viral pathogens. We determined the structure of a TRMT1 peptide in complex with Mpro, revealing a substrate binding conformation distinct from the majority of available Mpro-peptide complexes. Kinetic parameters for peptide cleavage showed that the TRMT1(526-536) sequence is cleaved with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage that could help inform future therapeutic design and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection suppresses protein translation and oxidative stress response to impact viral pathogenesis.
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Affiliation(s)
- Angel D′Oliviera
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Xuhang Dai
- Department of Chemistry, New York University, New York, NY 10003
| | - Saba Mottaghinia
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Evan P. Geissler
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Lucie Etienne
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003
- Simons Center for Computational Physical Chemistry at New York University, New York, NY 10003
| | - Jeffrey S. Mugridge
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
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Maus H, Müller P, Meta M, Hoba SN, Hammerschmidt SJ, Zimmermann RA, Zimmer C, Fuchs N, Schirmeister T, Barthels F. Next Generation of Fluorometric Protease Assays: 7-Nitrobenz-2-oxa-1,3-diazol-4-yl-amides (NBD-Amides) as Class-Spanning Protease Substrates. Chemistry 2023; 29:e202301855. [PMID: 37313627 DOI: 10.1002/chem.202301855] [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: 06/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/15/2023]
Abstract
Fluorometric assays are one of the most frequently used methods in medicinal chemistry. Over the last 50 years, the reporter molecules for the detection of protease activity have evolved from first-generation colorimetric p-nitroanilides, through FRET substrates, and 7-amino-4-methyl coumarin (AMC)-based substrates. The aim of further substrate development is to increase sensitivity and reduce vulnerability to assay interferences. Herein, we describe a new generation of substrates for protease assays based on 7-nitrobenz-2-oxa-1,3-diazol-4-yl-amides (NBD-amides). In this study, we synthesized and tested substrates for 10 different proteases from the serine-, cysteine-, and metalloprotease classes. Enzyme- and substrate-specific parameters as well as the inhibitory activity of literature-known inhibitors confirmed their suitability for application in fluorometric assays. Hence, we were able to present NBD-based alternatives for common protease substrates. In conclusion, these NBD substrates are not only less susceptible to common assay interference, but they are also able to replace FRET-based substrates with the requirement of a prime site amino acid residue.
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Affiliation(s)
- Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Sabrina N Hoba
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
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Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol 2023; 97:e0059723. [PMID: 37578235 PMCID: PMC10506478 DOI: 10.1128/jvi.00597-23] [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: 04/20/2023] [Accepted: 06/11/2023] [Indexed: 08/15/2023] Open
Abstract
Multiple coronaviruses (CoVs) can cause respiratory diseases in humans. While prophylactic vaccines designed to prevent infection are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), incomplete vaccine efficacy, vaccine hesitancy, and the threat of other pathogenic CoVs for which vaccines do not exist have highlighted the need for effective antiviral therapies. While antiviral compounds targeting the viral polymerase and protease are already in clinical use, their sensitivity to potential resistance mutations as well as their breadth against the full range of human and preemergent CoVs remain incompletely defined. To begin to fill that gap in knowledge, we report here the development of an improved, noninfectious, cell-based fluorescent assay with high sensitivity and low background that reports on the activity of viral proteases, which are key drug targets. We demonstrate that the assay is compatible with not only the SARS-CoV-2 Mpro protein but also orthologues from a range of human and nonhuman CoVs as well as clinically reported SARS-CoV-2 drug-resistant Mpro variants. We then use this assay to define the breadth of activity of two clinically used protease inhibitors, nirmatrelvir and ensitrelvir. Continued use of this assay will help define the strengths and limitations of current therapies and may also facilitate the development of next-generation protease inhibitors that are broadly active against both currently circulating and preemergent CoVs. IMPORTANCE Coronaviruses (CoVs) are important human pathogens with the ability to cause global pandemics. Working in concert with vaccines, antivirals specifically limit viral disease in people who are actively infected. Antiviral compounds that target CoV proteases are already in clinical use; their efficacy against variant proteases and preemergent zoonotic CoVs, however, remains incompletely defined. Here, we report an improved, noninfectious, and highly sensitive fluorescent method of defining the sensitivity of CoV proteases to small molecule inhibitors. We use this approach to assay the activity of current antiviral therapies against clinically reported SARS-CoV-2 protease mutants and a panel of highly diverse CoV proteases. Additionally, we show this system is adaptable to other structurally nonrelated viral proteases. In the future, this assay can be used to not only better define the strengths and limitations of current therapies but also help develop new, broadly acting inhibitors that more broadly target viral families.
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Affiliation(s)
- Rebecca A. Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vishwas N. Rao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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Bagdonas M, Čerepenkaitė K, Mickevičiūtė A, Kananavičiūtė R, Grybaitė B, Anusevičius K, Rukšėnaitė A, Kojis T, Gedgaudas M, Mickevičius V, Matulis D, Zubrienė A, Matulienė J. Screening, Synthesis and Biochemical Characterization of SARS-CoV-2 Protease Inhibitors. Int J Mol Sci 2023; 24:13491. [PMID: 37686295 PMCID: PMC10488051 DOI: 10.3390/ijms241713491] [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: 07/19/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
The severe acute respiratory syndrome-causing coronavirus 2 (SARS-CoV-2) papain-like protease (PLpro) and main protease (Mpro) play an important role in viral replication events and are important targets for anti-coronavirus drug discovery. In search of these protease inhibitors, we screened a library of 1300 compounds using a fluorescence thermal shift assay (FTSA) and identified 53 hits that thermally stabilized or destabilized PLpro. The hit compounds structurally belonged to two classes of small molecules: thiazole derivatives and symmetrical disulfide compounds. Compound dissociation constants (Kd) were determined using an enzymatic inhibition method. Seven aromatic disulfide compounds were identified as efficient PLpro inhibitors with Kd values in the micromolar range. Two disulfides displayed six-fold higher potency for PLpro (Kd = 0.5 µM) than for Mpro. The disulfide derivatives bound covalently to both proteases, as confirmed through mass spectrometry. The identified compounds can serve as lead compounds for further chemical optimization toward anti-COVID-19 drugs.
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Affiliation(s)
- Martynas Bagdonas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Kamilė Čerepenkaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Rūta Kananavičiūtė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
| | - Birutė Grybaitė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilenų pl. 19, LT-50254 Kaunas, Lithuania; (B.G.); (K.A.); (V.M.)
| | - Kazimieras Anusevičius
- Department of Organic Chemistry, Kaunas University of Technology, Radvilenų pl. 19, LT-50254 Kaunas, Lithuania; (B.G.); (K.A.); (V.M.)
| | - Audronė Rukšėnaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania;
| | - Tautvydas Kojis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Marius Gedgaudas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Vytautas Mickevičius
- Department of Organic Chemistry, Kaunas University of Technology, Radvilenų pl. 19, LT-50254 Kaunas, Lithuania; (B.G.); (K.A.); (V.M.)
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Jurgita Matulienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
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Soleimani Asl S, Roozbahani MH. A novel robust inhibitor of papain-like protease (PLpro) as a COVID-19 drug. J Biomol Struct Dyn 2023:1-8. [PMID: 37578047 DOI: 10.1080/07391102.2023.2245474] [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: 04/09/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023]
Abstract
Regarding the significance of SARS-CoV-2, scientists have shown considerable interest in developing effective drugs. Inhibitors for PLpro are the primary strategies for locating suitable COVID-19 drugs. Natural compounds comprise the majority of COVID-19 drugs. Due to limitations on the safety of clinical trials in cases of COVID, computational methods are typically utilized for inhibition studies. Whereas papain is highly similar to PLpro and is entirely safe, the current study aimed to examine several plant secondary metabolites to identify the most effective papain inhibitor and validate the results using molecular dynamics and docking. This simulation was conducted identically for PLpro and the optimal inhibitor. The results indicated that the experimental results are comparable to those obtained In-Silico, and the inhibition effects of Chlorogenic acid (CGA) on papain attained in the experiment were validated (IC50=0.54 mM). CGA as an inhibitor was located in the active site of PLpro and papain (total energy -2009410 and -456069 kJ/mol, respectively) at the desired location and distance. The study revealed that CGA and its derivatives are effective PLpro inhibitors against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saeed Soleimani Asl
- Iran Digital Twin Laboratory (IDT-Lab)- Incubator Center, Iran University of Science and Technology, Tehran, Iran
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Hamdi M, Elkashlan AM, Hammad MA, Ali IH. SARS-CoV-2 Papain-like Protease Responsive ZnO/Daclatasvir-Loaded Chitosan/Gelatin Nanofibers as Smart Antimicrobial Medical Textiles: In Silico, In Vitro and Cell Studies. Pharmaceutics 2023; 15:2074. [PMID: 37631287 PMCID: PMC10457880 DOI: 10.3390/pharmaceutics15082074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
A significant number of deaths are reported annually worldwide due to microbial and viral infections. The development of protective medical textiles for patients and healthcare professionals has attracted many researchers' attention. Therefore, this study aims to develop smart drug-eluting nanofibrous matrices to be used as a basic material for medical textile fabrication. First, chitosan/gelatin nanofibers were selected as the basic material owing to the wide antimicrobial activity of chitosan and the capability of gelatin to be hydrolyzed in the abundance of the papain-like protease (PLpro) enzyme secreted by SARS-CoV-2. Daclatasvir (DAC), an NS5A inhibitor, was selected as the model drug based on in silico studies where it showed high anti-SARS-CoV-2 potential compared to FDA-approved references. Due to their reported antimicrobial and antiviral activities, ZnO NPs were successfully prepared and incorporated with daclatasvir in chitosan/gelatin nanofibrous matrices through electrospinning. Afterward, an in vitro release study in a simulated buffer revealed the controlled release of DAC over 21 days from the nanofibers compared to only 6 h for free DAC. On the other hand, the abundance of PLpro induced the complete release of DAC from the nanofibers in only 4-8 h. Finally, the nanofibers demonstrated a wide antimicrobial activity against S. aureus, E. coli, and C. albicans.
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Affiliation(s)
- Mohamed Hamdi
- Department of Pharmaceutics, Faculty of Pharmacy, University of Sadat City, Sadat City P.O. Box 32897, Egypt;
| | - Akram M. Elkashlan
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City P.O. Box 32897, Egypt;
| | - Mohamed A. Hammad
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat City P.O. Box 32897, Egypt;
| | - Isra H. Ali
- Department of Pharmaceutics, Faculty of Pharmacy, University of Sadat City, Sadat City P.O. Box 32897, Egypt;
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Jan Z, Geethakumari AM, Biswas KH, Jithesh PV. Protegrin-2, a potential inhibitor for targeting SARS-CoV-2 main protease M pro. Comput Struct Biotechnol J 2023; 21:3665-3671. [PMID: 37576748 PMCID: PMC10412832 DOI: 10.1016/j.csbj.2023.07.020] [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: 03/24/2023] [Revised: 07/03/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023] Open
Abstract
Background SARS-CoV-2 variants continue to spread throughout the world and cause waves of COVID-19 infections. It is important to find effective antiviral drugs to combat SARS-CoV-2 and its variants. The main protease (Mpro) of SARS-CoV-2 is a promising therapeutic target due to its crucial role in viral replication and its conservation in all the variants. Therefore, the aim of this work was to identify an effective inhibitor of Mpro. Methods We studied around 200 antimicrobial peptides using in silico methods including molecular docking and allergenicity and toxicity prediction. One selected antiviral peptide was studied experimentally using a Bioluminescence Resonance Energy Transfer (BRET)-based Mpro biosensor, which reports Mpro activity through a decrease in energy transfer. Results Molecular docking identified one natural antimicrobial peptide, Protegrin-2, with high binding affinity and stable interactions with Mpro allosteric residues. Furthermore, free energy calculations and molecular dynamics simulation illustrated a high affinity interaction between the two. We also determined the impact of the binding of Protegrin-2 to Mpro using a BRET-based assay, showing that it inhibits the proteolytic cleavage activity of Mpro. Conclusions Our in silico and experimental studies identified Protegrin-2 as a potent inhibitor of Mpro that could be pursued further towards drug development against COVID-19 infection.
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Affiliation(s)
- Zainab Jan
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha 34110, Qatar
| | - Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha 34110, Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha 34110, Qatar
| | - Puthen Veettil Jithesh
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha 34110, Qatar
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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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Zhu B, Ouda R, de Figueiredo P, Kobayashi KS. ORF6, a repressor of the MHC class I pathway: new molecular target for SARS-CoV-2 drug discovery? Expert Opin Ther Targets 2023; 27:639-644. [PMID: 37602463 DOI: 10.1080/14728222.2023.2248377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 07/19/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Affiliation(s)
- Baohui Zhu
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Ryota Ouda
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Paul de Figueiredo
- Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, and Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Koichi S Kobayashi
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
- Hokkaido University, Institute for Vaccine Research and Development (HU-IVReD), Sapporo, Japan
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, USA
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Mani S, Kaur A, Jakhar K, Kumari G, Sonar S, Kumar A, Das S, Kumar S, Kumar V, Kundu R, Pandey AK, Singh UP, Majumdar T. Targeting DPP4-RBD interactions by sitagliptin and linagliptin delivers a potential host-directed therapy against pan-SARS-CoV-2 infections. Int J Biol Macromol 2023; 245:125444. [PMID: 37385308 PMCID: PMC10293653 DOI: 10.1016/j.ijbiomac.2023.125444] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023]
Abstract
Highly mutated SARS-CoV-2 is known aetiological factor for COVID-19. Here, we have demonstrated that the receptor binding domain (RBD) of the spike protein can interact with human dipeptidyl peptidase 4 (DPP4) to facilitate virus entry, in addition to the usual route of ACE2-RBD binding. Significant number of residues of RBD makes hydrogen bonds and hydrophobic interactions with α/β-hydrolase domain of DPP4. With this observation, we created a strategy to combat COVID-19 by circumventing the catalytic activity of DPP4 using its inhibitors. Sitagliptin, linagliptin or in combination disavowed RBD to establish a heterodimer complex with both DPP4 and ACE2 which is requisite strategy for virus entry into the cells. Both gliptins not only impede DPP4 activity, but also prevent ACE2-RBD interaction, crucial for virus growth. Sitagliptin, and linagliptin alone or in combination have avidity to impede the growth of pan-SARS-CoV-2 variants including original SARS-CoV-2, alpha, beta, delta, and kappa in a dose dependent manner. However, these drugs were unable to alter enzymatic activity of PLpro and Mpro. We conclude that viruses hijack DPP4 for cell invasion via RBD binding. Impeding RBD interaction with both DPP4 and ACE2 selectively by sitagliptin and linagliptin is an potential strategy for efficiently preventing viral replication.
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Affiliation(s)
- Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Kamini Jakhar
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Sudipta Sonar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Amit Kumar
- National Institute of Immunology, New Delhi, India
| | - Sudesna Das
- CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Vijay Kumar
- National Institute of Immunology, New Delhi, India
| | - Rakesh Kundu
- Department of Zoology, Visva-Bharati University, Santiniketan, West Bengal, India
| | - Anil Kumar Pandey
- Department of Physiology, ESIC Medical College & Hospital, Faridabad, India
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Varikoti RA, Schultz KJ, Kombala CJ, Kruel A, Brandvold KR, Zhou M, Kumar N. Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV-2 main protease. J Comput Aided Mol Des 2023:10.1007/s10822-023-00509-1. [PMID: 37314632 DOI: 10.1007/s10822-023-00509-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) models followed by experimental validation in an iterative manner. Generative deep learning models can generate thousands of new candidates, however, their physiochemical and biochemical properties are typically not fully optimized. Using our recently developed deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 Mpro that preserve the core scaffold. We utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure-activity relationships, multi-parameter optimization, and graph neural networks on generated candidates to predict biological activity and binding affinity in advance. As a result of these combined computational endeavors, eight promising candidates were singled out and put through experimental testing using Native Mass Spectrometry and FRET-based functional assays. Two of the tested compounds with quinazoline-2-thiol and acetylpiperidine core moieties showed IC[Formula: see text] values in the low micromolar range: [Formula: see text] [Formula: see text]M and 3.41±0.0015 [Formula: see text]M, respectively. Molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations within the chain B and the interface domains of the Mpro. Our integrated approach provides a platform for data driven lead optimization with rapid characterization and experimental validation in a closed loop that could be applied to other potential protein targets.
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Affiliation(s)
- Rohith Anand Varikoti
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99352, USA
| | - Katherine J Schultz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99352, USA
| | - Chathuri J Kombala
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99352, USA
| | - Agustin Kruel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99352, USA
| | - Kristoffer R Brandvold
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99352, USA
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99352, USA
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99352, USA.
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Farkaš B, Minneci M, Misevicius M, Rozas I. A Tale of Two Proteases: M Pro and TMPRSS2 as Targets for COVID-19 Therapies. Pharmaceuticals (Basel) 2023; 16:834. [PMID: 37375781 DOI: 10.3390/ph16060834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Considering the importance of the 2019 outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulting in the coronavirus disease 2019 (COVID-19) pandemic, an overview of two proteases that play an important role in the infection by SARS-CoV-2, the main protease of SARS-CoV-2 (MPro) and the host transmembrane protease serine 2 (TMPRSS2), is presented in this review. After summarising the viral replication cycle to identify the relevance of these proteases, the therapeutic agents already approved are presented. Then, this review discusses some of the most recently reported inhibitors first for the viral MPro and next for the host TMPRSS2 explaining the mechanism of action of each protease. Afterward, some computational approaches to design novel MPro and TMPRSS2 inhibitors are presented, also describing the corresponding crystallographic structures reported so far. Finally, a brief discussion on a few reports found some dual-action inhibitors for both proteases is given. This review provides an overview of two proteases of different origins (viral and human host) that have become important targets for the development of antiviral agents to treat COVID-19.
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Affiliation(s)
- Barbara Farkaš
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Marco Minneci
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Matas Misevicius
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
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48
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Xue Y, Mei H, Chen Y, Griffin JD, Liu Q, Weisberg E, Yang J. Repurposing clinically available drugs and therapies for pathogenic targets to combat SARS-CoV-2. MedComm (Beijing) 2023; 4:e254. [PMID: 37193304 PMCID: PMC10183156 DOI: 10.1002/mco2.254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/11/2023] [Accepted: 03/07/2023] [Indexed: 05/18/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected a large portion of the global population, both physically and mentally. Current evidence suggests that the rapidly evolving coronavirus subvariants risk rendering vaccines and antibodies ineffective due to their potential to evade existing immunity, with enhanced transmission activity and higher reinfection rates that could lead to new outbreaks across the globe. The goal of viral management is to disrupt the viral life cycle as well as to relieve severe symptoms such as lung damage, cytokine storm, and organ failure. In the fight against viruses, the combination of viral genome sequencing, elucidation of the structure of viral proteins, and identifying proteins that are highly conserved across multiple coronaviruses has revealed many potential molecular targets. In addition, the time- and cost-effective repurposing of preexisting antiviral drugs or approved/clinical drugs for these targets offers considerable clinical advantages for COVID-19 patients. This review provides a comprehensive overview of various identified pathogenic targets and pathways as well as corresponding repurposed approved/clinical drugs and their potential against COVID-19. These findings provide new insight into the discovery of novel therapeutic strategies that could be applied to the control of disease symptoms emanating from evolving SARS-CoV-2 variants.
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Affiliation(s)
- Yiying Xue
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Husheng Mei
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
| | - Yisa Chen
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - James D. Griffin
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
- Hefei Cancer HospitalChinese Academy of SciencesHefeiChina
| | - Ellen Weisberg
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jing Yang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
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49
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Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Mol Aspects Med 2023; 91:101151. [PMID: 36371228 PMCID: PMC9613808 DOI: 10.1016/j.mam.2022.101151] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.
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Affiliation(s)
- Yash Gupta
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Oleksandr V Savytskyi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; In Vivo Biosystems, Eugene, OR, USA
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vasili Pleqi
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Caleb A Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Rohit Chitale
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA; The Council on Strategic Risks, 1025 Connecticut Ave NW, Washington, DC, USA
| | - Ravi Durvasula
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | | | - Prakasha Kempaiah
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of QHS Computational Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA.
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50
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Pillai S, Du L, Deiter F, Bouzidi M, Billaud JN, Graham S, Prerna D, Selvarajah S, Lingappa A, Michon M, Yu S, Paulvannan K, Lingappa V, Boushey H, Greenland J. A Novel Viral Assembly Inhibitor Blocks SARS-CoV-2 Replication in Airway Epithelial Cells. RESEARCH SQUARE 2023:rs.3.rs-2887435. [PMID: 37292622 PMCID: PMC10246244 DOI: 10.21203/rs.3.rs-2887435/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ongoing evolution of SARS-CoV-2 to evade vaccines and therapeutics underlines the need for novel therapies with high genetic barriers to resistance. The small molecule PAV-104, identified through a cell-free protein synthesis and assembly screen, was recently shown to target host protein assembly machinery in a manner specific to viral assembly. Here, we investigated the capacity of PAV-104 to inhibit SARS-CoV-2 replication in human airway epithelial cells (AECs). Our data demonstrate that PAV-104 inhibited > 99% of infection with diverse SARS-CoV-2 variants in primary and immortalized human AECs. PAV-104 suppressed SARS-CoV-2 production without affecting viral entry or protein synthesis. PAV-104 interacted with SARS-CoV-2 nucleocapsid (N) and interfered with its oligomerization, blocking particle assembly. Transcriptomic analysis revealed that PAV-104 reversed SARS-CoV-2 induction of the Type-I interferon response and the 'maturation of nucleoprotein' signaling pathway known to support coronavirus replication. Our findings suggest that PAV-104 is a promising therapeutic candidate for COVID-19.
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Affiliation(s)
| | - Li Du
- Vitalant Research Institute/UCSF
| | - Fred Deiter
- Veterans Administration Health Care System/UCSF
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