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Shawky AM, Almalki FA, Alzahrani HA, Abdalla AN, Youssif BGM, Ibrahim NA, Gamal M, El-Sherief HAM, Abdel-Fattah MM, Hefny AA, Abdelazeem AH, Gouda AM. Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions. Eur J Med Chem 2024; 277:116704. [PMID: 39121741 DOI: 10.1016/j.ejmech.2024.116704] [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: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Since 2020, many compounds have been investigated for their potential use in the treatment of SARS-CoV-2 infection. Among these agents, a huge number of natural products and FDA-approved drugs have been evaluated as potential therapeutics for SARS-CoV-2 using virtual screening and docking studies. However, the identification of the molecular targets involved in viral replication led to the development of rationally designed anti-SARS-CoV-2 agents. Among these targets, the main protease (Mpro) is one of the key enzymes needed in the replication of the virus. The data gleaned from the crystal structures of SARS-CoV-2 Mpro complexes with small-molecule covalent inhibitors has been used in the design and discovery of many highly potent and broad-spectrum Mpro inhibitors. The current review focuses mainly on the covalent type of SARS-CoV-2 Mpro inhibitors. The design, chemistry, and classification of these inhibitors were also in focus. The biological activity of these inhibitors, including their inhibitory activities against Mpro, their antiviral activities, and the SAR studies, were discussed. The review also describes the potential mechanism of the interaction between these inhibitors and the catalytic Cys145 residue in Mpro. Moreover, the binding modes and key binding interactions of these covalent inhibitors were also illustrated. The covalent inhibitors discussed in this review were of diverse chemical nature and origin. Their antiviral activity was mediated mainly by the inhibition of SARS-CoV-2 Mpro, with IC50 values in the micromolar to the nanomolar range. Many of these inhibitors exhibited broad-spectrum inhibitory activity against the Mpro enzymes of other coronaviruses (SARS-CoV-1 and MERS-CoV). The dual inhibition of the Mpro and PLpro enzymes of SARS-CoV-2 could also provide higher therapeutic benefits than Mpro inhibition. Despite the approval of nirmatrelvir by the FDA, many mutations in the Mpro enzyme of SARS-CoV-2 have been reported. Although some of these mutations did not affect the potency of nirmatrelvir, there is an urgent need to develop a second generation of Mpro inhibitors. We hope that the data summarized in this review could help researchers in the design of a new potent generation of SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Hayat Ali Alzahrani
- Applied Medical Science College, Medical Laboratory Technology Department, Northern Border University, Arar, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia; Department of Pharmacology and Toxicology, Medicinal And Aromatic Plants Research Institute, National Center for Research, Khartoum, 2404, Sudan
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt.
| | - Nashwa A Ibrahim
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Mohammed Gamal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Ahmed A Hefny
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; School of Pharmacy, University of Waterloo, Kitchener, Ontario, N2G 1C5, Canada
| | - Ahmed H Abdelazeem
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; Pharmacy Department, College of Pharmacy, Nursing and Medical Sciences, Riyadh Elm University, Riyadh, 11681, Saudi Arabia
| | - Ahmed M Gouda
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
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2
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Badawy AM, Donia MSM, Hamdy NG, El-Ayouty MM, Mohamed OG, Darwish KM, Tripathi A, Ahmed SA. Dual SARS-CoV-2 and MERS-CoV inhibitors from Artemisia monosperma: isolation, structure elucidation, molecular modelling studies, and in vitro activities. Org Biomol Chem 2024; 22:7006-7016. [PMID: 39135436 DOI: 10.1039/d4ob00929k] [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: 08/29/2024]
Abstract
The COVID-19 pandemic has spread throughout the whole globe, so it is imperative that all available resources be used to treat this scourge. In reality, the development of new pharmaceuticals has mostly benefited from natural products. The widespread medicinal usage of species in the Asteraceae family is extensively researched. In this study, compounds isolated from methanolic extract of Artemisia monosperma Delile, a wild plant whose grows in Egypt's Sinai Peninsula. Three compounds, stigmasterol 3-O-β-D-glucopyranoside 1, rhamnetin 3, and padmatin 6, were first isolated from this species. In addition, five previously reported compounds, arcapillin 2, jaceosidin 4, hispidulin 5, 7-O-methyleriodictyol 7, and eupatilin 8, were isolated. Applying molecular modelling simulations revealed two compounds, arcapillin 2 and rhamnetin 3 with the best docking interactions and energies within SARS-CoV-2 Mpro-binding site (-6.16, and -6.70 kcal mol-1, respectively). The top-docked compounds (2-3) were further evaluated for inhibitory concentrations (IC50), and half-maximal cytotoxicity (CC50) of both SARS-CoV-2 and MERS-CoV. Interestingly, arcapillin showed high antiviral activity towards SARS-CoV-2 and MERS-CoV, with IC50 values of 190.8 μg mL-1 and 16.58 μg mL-1, respectively. These findings may hold promise for further preclinical and clinical research, particularly on arcapillin itself or in collaboration with other drugs for COVID-19 treatment.
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Affiliation(s)
- Ahmed M Badawy
- Department of Pharmacognosy, Faculty of Pharmacy, Sinai University, El-Arish 45511, Egypt.
| | - Marwa Samir M Donia
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt.
| | - Nehal G Hamdy
- Department of Pharmacognosy, Faculty of Pharmacy, Sinai University, El-Arish 45511, Egypt.
| | - Mayada M El-Ayouty
- Department of Pharmacognosy, Faculty of Pharmacy, Sinai University, El-Arish 45511, Egypt.
| | - Osama G Mohamed
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr el Aini St., Cairo 11562, Egypt.
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt.
| | - Ashootosh Tripathi
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Safwat A Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt.
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3
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Yu S, Gong L, Han YC, Yang L, Li J, Hoffmann AA, Luo GH, Yuan GR, Fang JC, Ji R. Oral secretions from striped stem borer (Chilo suppressalis) induce defenses in rice. PEST MANAGEMENT SCIENCE 2024. [PMID: 39152725 DOI: 10.1002/ps.8376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND The striped stem borer (SSB, Chilo suppressalis) is one of the most destructive insect pests on rice. As a chewing insect, SSB larval feeding causes a dramatic increase in rice defense responses. However, the effects of oral secretions (OSs) during SSB feeding on rice defense remain largely unexplored. RESULTS In this study, based on transcriptome analysis results, treatment with SSB OSs regulated the expression of genes involved in the plant defense-related pathways of calcium, mitogen-activated protein kinases, reactive oxygen species, jasmonic acid (JA), herbivore-induced plant volatiles (HIPVs), and protease inhibitors. Unsurprisingly, treatment with SSB OSs elicited the accumulation of JA and JA-isoleucine in rice. The defense mechanisms activated by the cascade not only induced the expression of trypsin inhibitors, inhibiting the normal growth of SSB larvae but also induced HIPVs emission, rendering rice attractive to a common larval parasitoid. High-throughput proteome sequencing of SSB OSs led to 534 proteins being identified and 343 proteins with two or more unique peptides being detected. CONCLUSION The study demonstrates that SSB OSs trigger both direct and indirect defense mechanisms in rice, akin to the effects of SSB feeding. It identifies specific proteins in SSB OSs that may influence the interactions between SSB and rice during feeding, providing valuable insights for effectors research. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Shan Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety (State Key Laboratory Cultivation Base of Ministry of Science and Technology), Nanjing, China
| | - Lei Gong
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety (State Key Laboratory Cultivation Base of Ministry of Science and Technology), Nanjing, China
| | - Yang-Chun Han
- Laboratory for Quarantine of Alien Species, Integrated Technical Service Center of Jiangyin Customs, Jiangyin, China
| | - Lei Yang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety (State Key Laboratory Cultivation Base of Ministry of Science and Technology), Nanjing, China
| | - Jing Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety (State Key Laboratory Cultivation Base of Ministry of Science and Technology), Nanjing, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Guang-Hua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety (State Key Laboratory Cultivation Base of Ministry of Science and Technology), Nanjing, China
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Ji-Chao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety (State Key Laboratory Cultivation Base of Ministry of Science and Technology), Nanjing, China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety (State Key Laboratory Cultivation Base of Ministry of Science and Technology), Nanjing, China
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Shayo MJ, Samwel B, Shadrack DM, Cassel J, Salvino JM, Montaner LJ, Deogratias G, Tietjen I, Kiruri L, Hilonga S, Innocent E. Drug repositioning identifies salvinorin A and deacetylgedunin (DCG) enriched plant extracts as novel inhibitors of Mpro, RBD-ACE2 and TMPRRS2 proteins. RSC Adv 2024; 14:21203-21212. [PMID: 38966817 PMCID: PMC11223729 DOI: 10.1039/d4ra02593h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/21/2024] [Indexed: 07/06/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) has spread worldwide with severe health, social, and economic repercussions. Although vaccines have significantly reduced the severity of symptoms and deaths, alternative medications derived from natural products (NPs) are vital to further decrease fatalities, especially in regions with low vaccine uptake. When paired with the latest computational developments, NPs, which have been used to cure illnesses and infections for thousands of years, constitute a renewed resource for drug discovery. In the present report, a combination of computational and in vitro methods reveals the repositioning of NPs and identifies salvinorin A and deacetylgedunin (DCG) as having potential anti-SARS-CoV-2 activities. Salvinorin A was found both in silico and in vitro to inhibit both SARS-CoV-2 spike/host ACE2 protein interactions, consistent with blocking viral cell entry, and well as live virus replication. Plant extracts from Azadirachta indica and Cedrela odorata, which contain high levels of DCG, inhibited viral cell replication by targeting the main protease (Mpro) and/or inhibited viral cell entry by blocking the interaction between spike RBD-ACE2 protein at concentrations lower than salvinorin A. Our findings suggest that salvinorin A represent promising chemical starting points where further optimization may result in effective natural product-derived and potent anti-SARS-CoV-2 inhibitors to supplement vaccine efforts.
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Affiliation(s)
- Mariana J Shayo
- Department of Biological and Pre-clinical Studies, Institute of Traditional Medicine, Muhimbili University of Health and Allied Sciences P.O.Box 65001 Dar es Salaam Tanzania
| | - Baraka Samwel
- Department of Natural Products, Institute of Traditional Medicines, Muhimbili University of Health and Allied Sciences P.O.Box 65001 Dar es Salaam Tanzania
| | - Daniel M Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania P.O.Box 47 Dodoma Tanzania
- School of Life Science and Bio-engineering, Nelson Mandela African Institute of Science and Technology P.O.Box 447 Arusha Tanzania
| | - Joel Cassel
- The Wistar Institute 3601 Spruce Street Philadelphia PA 19104 USA
| | - Joseph M Salvino
- The Wistar Institute 3601 Spruce Street Philadelphia PA 19104 USA
| | - Luis J Montaner
- The Wistar Institute 3601 Spruce Street Philadelphia PA 19104 USA
| | - Geradius Deogratias
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam P.O.Box 35061 Dar es Salaam Tanzania
| | - Ian Tietjen
- The Wistar Institute 3601 Spruce Street Philadelphia PA 19104 USA
| | - Lucy Kiruri
- Kenyata University, Department of Chemistry P.O.Box 43844-00100 Nairobi Kenya
| | - Samson Hilonga
- Department of Medical Botany, Plant Breeding and Agronomy, Institute of Traditional Medicine, Muhimbili University of Health and Allied Sciences P.O.Box 65001 Dar es Salaam Tanzania
| | - Ester Innocent
- Department of Biological and Pre-clinical Studies, Institute of Traditional Medicine, Muhimbili University of Health and Allied Sciences P.O.Box 65001 Dar es Salaam Tanzania
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Alugubelli Y, Xiao J, Khatua K, Kumar S, Sun L, Ma Y, Ma XR, Vulupala VR, Atla S, Blankenship LR, Coleman D, Xie X, Neuman BW, Liu WR, Xu S. Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease. J Med Chem 2024; 67:6495-6507. [PMID: 38608245 PMCID: PMC11056980 DOI: 10.1021/acs.jmedchem.3c02416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
We have witnessed three coronavirus (CoV) outbreaks in the past two decades, including the COVID-19 pandemic caused by SARS-CoV-2. Main protease (MPro), a highly conserved protease among various CoVs, is essential for viral replication and pathogenesis, making it a prime target for antiviral drug development. Here, we leverage proteolysis targeting chimera (PROTAC) technology to develop a new class of small-molecule antivirals that induce the degradation of SARS-CoV-2 MPro. Among them, MPD2 was demonstrated to effectively reduce MPro protein levels in 293T cells, relying on a time-dependent, CRBN-mediated, and proteasome-driven mechanism. Furthermore, MPD2 exhibited remarkable efficacy in diminishing MPro protein levels in SARS-CoV-2-infected A549-ACE2 cells. MPD2 also displayed potent antiviral activity against various SARS-CoV-2 strains and exhibited enhanced potency against nirmatrelvir-resistant viruses. Overall, this proof-of-concept study highlights the potential of targeted protein degradation of MPro as an innovative approach for developing antivirals that could fight against drug-resistant viral variants.
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Affiliation(s)
- Yugendar
R. Alugubelli
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jing Xiao
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kaustav Khatua
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Sathish Kumar
- Department
of Biology, Texas A&M University, College Station, Texas 77843, United States
| | - Long Sun
- Department
of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Yuying Ma
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xinyu R. Ma
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Veerabhadra R. Vulupala
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Sandeep Atla
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren R. Blankenship
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Demonta Coleman
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xuping Xie
- Department
of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Benjamin W. Neuman
- Department
of Biology, Texas A&M University, College Station, Texas 77843, United States
- Texas
A&M Global Health Research Complex, Texas A&M University, College
Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, Texas 77843, United States
| | - Shiqing Xu
- Texas
A&M Drug Discovery Center, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
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6
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El-Hddad SSA, Sobhy MH, El-Morsy A, Shoman NA, El-Adl K. Quinazolines and thiazolidine-2,4-dions as SARS-CoV-2 inhibitors: repurposing, in silico molecular docking and dynamics simulation. RSC Adv 2024; 14:13237-13250. [PMID: 38655479 PMCID: PMC11037030 DOI: 10.1039/d4ra02029d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
This paper presents an extensive analysis of COVID-19 with a specific focus on VEGFR-2 inhibitors as potential treatments. The investigation includes an overview of computational methodologies employed in drug repurposing and highlights in silico research aimed at developing treatments for SARS-CoV-2. The study explores the possible effects of twenty-eight established VEGFR-2 inhibitors, which include amide and urea linkers, against SARS-CoV-2. Among these, nine inhibitors exhibit highly promising in silico outcomes (designated as 3-6, 11, 24, 26, 27, and sorafenib) and are subjected to extensive molecular dynamics (MD) simulations to evaluate the binding modes and affinities of these inhibitors to the SARS-CoV-2 Mpro across a 100 ns timeframe. Additionally, MD simulations are conducted to ascertain the binding free energy of the most compelling ligand-pocket complexes identified through docking studies. The findings provide valuable understanding regarding the dynamic and thermodynamic properties of the interactions between ligands and pockets, reinforcing the outcomes of the docking studies and presenting promising prospects for the creation of therapeutic treatments targeting COVID-19.
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Affiliation(s)
- Sanadelaslam S A El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University Al Bayda 991 Libya
| | - Mohamed H Sobhy
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development Cairo Egypt
| | - Ahmed El-Morsy
- Pharmaceutical Chemistry Department, College of Pharmacy, The Islamic University Najaf Iraq
| | - Nabil A Shoman
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Ahram Canadian University Giza Egypt
| | - Khaled El-Adl
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development Cairo Egypt
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University Cairo11884 Egypt
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7
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Nguyen TH, Thai QM, Pham MQ, Minh PTH, Phung HTT. Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds. Mol Divers 2024; 28:553-561. [PMID: 36823394 PMCID: PMC9950021 DOI: 10.1007/s11030-023-10601-1] [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: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 02/25/2023]
Abstract
To date, the COVID-19 pandemic has still been infectious around the world, continuously causing social and economic damage on a global scale. One of the most important therapeutic targets for the treatment of COVID-19 is the main protease (Mpro) of SARS-CoV-2. In this study, we combined machine-learning (ML) model with atomistic simulations to computationally search for highly promising SARS-CoV-2 Mpro inhibitors from the representative natural compounds of the National Cancer Institute (NCI) Database. First, the trained ML model was used to scan the library quickly and reliably for possible Mpro inhibitors. The ML output was then confirmed using atomistic simulations integrating molecular docking and molecular dynamic simulations with the linear interaction energy scheme. The results turned out to show that there was evidently good agreement between ML and atomistic simulations. Ten substances were proposed to be able to inhibit SARS-CoV-2 Mpro. Seven of them have high-nanomolar affinity and are very potential inhibitors. The strategy has been proven to be reliable and appropriate for fast prediction of SARS-CoV-2 Mpro inhibitors, benefiting for new emerging SARS-CoV-2 variants in the future accordingly.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Quynh Mai Thai
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Thi Hong Minh
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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8
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Tamil Selvan S, Dharmalingam Jothinathan MK. Eco-Technological Evaluation of Natural Phytochemicals Potential Drug Molecules Against Main Protease: A Machine Learning Algorithm. Cureus 2024; 16:e57151. [PMID: 38681365 PMCID: PMC11055964 DOI: 10.7759/cureus.57151] [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: 01/02/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction: The global viral pandemic has rapidly spread, leading to many individuals experiencing the infection. Coronaviruses (CoVs) are among many viral families that infect different types of mammals. They can spread to humans and cause gastrointestinal, neurological, and respiratory problems. The present investigation has discovered flavonoid compounds as promising molecular agents with potential antiviral activity against virus proteins, specifically main protease (Mpro). Methodology: A comprehensive in silico screening of natural compounds derived from medicinal plants was performed in the present study. It included parameter assessments such as drug-likeness, pharmacokinetics, molecular docking, toxicity evaluations, bioavailability assessments, and molecular target exploration. In this systematic approach, the primary objective was to identify potential lead compounds. These phytochemicals were investigated as drug candidates to provide a detailed understanding of their molecular properties. Results: The Mpro binding energy values were -10.637, -12.752, -7.813, -15.732, -6.449, -5.578, -8.037, and -8.52 kcal/mol for isoquercetin, narirutin, myricetin, hesperidin, silibinin, baicalein, taxifolin, and petunidin. Molecular simulations were conducted on two flavonoid compounds - hesperidin and narirutin - stable over 100 nanoseconds in the Coronavirus protein. Conclusions: The computational study we conducted is promising, but to validate the action of these compounds, further experimental studies are needed, with a critical component of the research being the conduct of in vitro and in vivo experiments.
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Affiliation(s)
- Silambarasan Tamil Selvan
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, IND
| | - Mukesh Kumar Dharmalingam Jothinathan
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, IND
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9
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Sheng YJ, Kuo STA, Yang T, Russell DH, Yan X, Xu S, Liu WR, Fierke CA. BRD4354 Is a Potent Covalent Inhibitor against the SARS-CoV-2 Main Protease. Biochemistry 2024:10.1021/acs.biochem.3c00685. [PMID: 38329238 PMCID: PMC11306412 DOI: 10.1021/acs.biochem.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Numerous organic molecules are known to inhibit the main protease (MPro) of SARS-CoV-2, the pathogen of Coronavirus Disease 2019 (COVID-19). Guided by previous research on zinc-ligand inhibitors of MPro and zinc-dependent histone deacetylases (HDACs), we identified BRD4354 as a potent inhibitor of MPro. The in vitro protease activity assays show that BRD4354 displays time-dependent inhibition against MPro with an IC50 (concentration that inhibits activity by 50%) of 0.72 ± 0.04 μM after 60 min of incubation. Inactivation follows a two-step process with an initial rapid binding step with a KI of 1.9 ± 0.5 μM followed by a second slow inactivation step, kinact,max of 0.040 ± 0.002 min-1. Native mass spectrometry studies indicate that a covalent intermediate is formed where the ortho-quinone methide fragment of BRD4354 forms a covalent bond with the catalytic cysteine C145 of MPro. Based on these data, a Michael-addition reaction mechanism between MPro C145 and BRD4354 was proposed. These results suggest that both preclinical testing of BRD4354 and structure-activity relationship studies based on BRD4354 are warranted to develop more effective anti-COVID therapeutics.
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Affiliation(s)
- Yan J. Sheng
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Syuan-Ting Alex Kuo
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Tingyuan Yang
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Xin Yan
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
- Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Carol A. Fierke
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
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10
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Wang Q, Lu X, Jia R, Yan X, Wang J, Zhao L, Zhong R, Sun G. Recent advances in chemometric modelling of inhibitors against SARS-CoV-2. Heliyon 2024; 10:e24209. [PMID: 38293468 PMCID: PMC10826659 DOI: 10.1016/j.heliyon.2024.e24209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused great harm to all countries worldwide. This disease can be prevented by vaccination and managed using various treatment methods, including injections, oral medications, or aerosol therapies. However, the selection of suitable compounds for the research and development of anti-SARS-CoV-2 drugs is a daunting task because of the vast databases of available compounds. The traditional process of drug research and development is time-consuming, labour-intensive, and costly. The application of chemometrics can significantly expedite drug R&D. This is particularly necessary and important for drug development against pandemic public emergency diseases, such as COVID-19. Through various chemometric techniques, such as quantitative structure-activity relationship (QSAR) modelling, molecular docking, and molecular dynamics (MD) simulations, compounds with inhibitory activity against SARS-CoV-2 can be quickly screened, allowing researchers to focus on the few prioritised candidates. In addition, the ADMET properties of the screened candidate compounds should be further explored to promote the successful discovery of anti-SARS-CoV-2 drugs. In this case, considerable time and economic costs can be saved while minimising the need for extensive animal experiments, in line with the 3R principles. This paper focuses on recent advances in chemometric modelling studies of COVID-19-related inhibitors, highlights current limitations, and outlines potential future directions for development.
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Affiliation(s)
- Qianqian Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Xinyi Lu
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Runqing Jia
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Xinlong Yan
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Jianhua Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing 100124, PR China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
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11
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Martinusen SG, Slaton EW, Nelson SE, Pulgar MA, Besu JT, Simas CF, Denard CA. Modular and integrative activity reporters enhance biochemical studies in the yeast ER. Protein Eng Des Sel 2024; 37:gzae008. [PMID: 38696722 DOI: 10.1093/protein/gzae008] [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: 07/13/2023] [Revised: 03/31/2024] [Accepted: 05/01/2024] [Indexed: 05/04/2024] Open
Abstract
The yeast endoplasmic reticulum sequestration and screening (YESS) system is a broadly applicable platform to perform high-throughput biochemical studies of post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CLpro), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.
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Affiliation(s)
| | - Ethan W Slaton
- Department of Chemical Engineering, University of Florida, Gainesville, 32611, USA
| | - Sage E Nelson
- Department of Chemical Engineering, University of Florida, Gainesville, 32611, USA
| | - Marian A Pulgar
- Department of Chemical Engineering, University of Florida, Gainesville, 32611, USA
| | - Julia T Besu
- Department of Biology, University of Florida, Gainesville, 32611, USA
| | - Cassidy F Simas
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, 32611, USA
| | - Carl A Denard
- Department of Chemical Engineering, University of Florida, Gainesville, 32611, USA
- UF Health Cancer Center, University of Florida, Gainesville, 32611, USA
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12
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Tiwari G, Chauhan MS, Sharma D. In silico study of inhibition activity of boceprevir drug against 2019-nCoV main protease. Z NATURFORSCH C 2024; 79:1-12. [PMID: 38156366 DOI: 10.1515/znc-2023-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Boceprevir drug is a ketoamide serine protease inhibitor with a linear peptidomimetic structure that exhibits inhibition activity against 2019-nCoV main protease. This paper reports electronic properties of boceprevir and its molecular docking as well as molecular dynamics simulation analysis with protein receptor. For this, the equilibrium structure of boceprevir has been obtained by DFT at B3LYP and ωB97XD levels with 6-311+G(d,p) basis set in gas and water mediums. HOMO-LUMO and absorption spectrum analysis have been used to evaluate the boceprevir's toxicity and photosensitivity, respectively. Molecular docking simulation has been performed to test the binding affinity of boceprevir with 2019-nCoV MPRO; which rendered a variety of desirable binding locations between the ligand and target protein's residue positions. The optimum binding location has been considered for molecular dynamics simulation. The findings have been addressed to clarify the boceprevir drug efficacy against the 2019-nCoV MPRO.
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Affiliation(s)
- Gargi Tiwari
- Department of Physics, Patna University, Patna-800005, India
| | | | - Dipendra Sharma
- Department of Physics, DDU Gorakhpur University, Gorakhpur-273009, India
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13
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Pandit S, Duchow M, Chao W, Capasso A, Samanta D. DNA-Barcoded Plasmonic Nanostructures for Activity-Based Protease Sensing. Angew Chem Int Ed Engl 2024; 63:e202310964. [PMID: 37985161 DOI: 10.1002/anie.202310964] [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: 07/31/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
We report the development of a new class of protease activity sensors called DNA-barcoded plasmonic nanostructures. These probes are comprised of gold nanoparticles functionalized with peptide-DNA conjugates (GPDs), where the peptide is a substrate of the protease of interest. The DNA acts as a barcode identifying the peptide and facilitates signal amplification. Protease-mediated peptide cleavage frees the DNA from the nanoparticle surface, which is subsequently measured via a CRISPR/Cas12a-based assay as a proxy for protease activity. As proof-of-concept, we show activity-based, multiplexed detection of the SARS-CoV-2-associated protease, 3CL, and the apoptosis marker, caspase 3, with high sensitivity and selectivity. GPDs yield >25-fold turn-on signals, 100-fold improved response compared to commercial probes, and detection limits as low as 58 pM at room temperature. Moreover, nanomolar concentrations of proteases can be detected visually by leveraging the aggregation-dependent color change of the gold nanoparticles. We showcase the clinical potential of GPDs by detecting a colorectal cancer-associated protease, cathepsin B, in three different patient-derived cell lines. Taken together, GPDs detect physiologically relevant concentrations of active proteases in challenging biological samples, require minimal sample processing, and offer unmatched multiplexing capabilities (mediated by DNA), making them powerful chemical tools for biosensing and disease diagnostics.
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Affiliation(s)
- Subrata Pandit
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
| | - Mark Duchow
- Department of Oncology, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Austin, TX 78712, USA
| | - Wilson Chao
- Department of Biochemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
| | - Anna Capasso
- Department of Oncology, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Austin, TX 78712, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
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14
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Cai L, Han F, Ji B, He X, Wang L, Niu T, Zhai J, Wang J. In Silico Screening of Natural Flavonoids against 3-Chymotrypsin-like Protease of SARS-CoV-2 Using Machine Learning and Molecular Modeling. Molecules 2023; 28:8034. [PMID: 38138524 PMCID: PMC10745665 DOI: 10.3390/molecules28248034] [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: 11/07/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The "Long-COVID syndrome" has posed significant challenges due to a lack of validated therapeutic options. We developed a novel multi-step virtual screening strategy to reliably identify inhibitors against 3-chymotrypsin-like protease of SARS-CoV-2 from abundant flavonoids, which represents a promising source of antiviral and immune-boosting nutrients. We identified 57 interacting residues as contributors to the protein-ligand binding pocket. Their energy interaction profiles constituted the input features for Machine Learning (ML) models. The consensus of 25 classifiers trained using various ML algorithms attained 93.9% accuracy and a 6.4% false-positive-rate. The consensus of 10 regression models for binding energy prediction also achieved a low root-mean-square error of 1.18 kcal/mol. We screened out 120 flavonoid hits first and retained 50 drug-like hits after predefined ADMET filtering to ensure bioavailability and safety profiles. Furthermore, molecular dynamics simulations prioritized nine bioactive flavonoids as promising anti-SARS-CoV-2 agents exhibiting both high structural stability (root-mean-square deviation < 5 Å for 218 ns) and low MM/PBSA binding free energy (<-6 kcal/mol). Among them, KB-2 (PubChem-CID, 14630497) and 9-O-Methylglyceofuran (PubChem-CID, 44257401) displayed excellent binding affinity and desirable pharmacokinetic capabilities. These compounds have great potential to serve as oral nutraceuticals with therapeutic and prophylactic properties as care strategies for patients with long-COVID syndrome.
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Affiliation(s)
| | | | | | | | | | | | | | - Junmei Wang
- School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; (L.C.); (F.H.); (B.J.); (X.H.); (L.W.); (T.N.); (J.Z.)
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15
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He Q, Zhao X, Wu D, Jia S, Liu C, Cheng Z, Huang F, Chen Y, Lu T, Lu S. Hydrophobic tag-based protein degradation: Development, opportunity and challenge. Eur J Med Chem 2023; 260:115741. [PMID: 37607438 DOI: 10.1016/j.ejmech.2023.115741] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023]
Abstract
Targeted protein degradation (TPD) has emerged as a promising approach for drug development, particularly for undruggable targets. TPD technology has also been instrumental in overcoming drug resistance. While some TPD molecules utilizing proteolysis-targeting chimera (PROTACs) or molecular glue strategies have been approved or evaluated in clinical trials, hydrophobic tag-based protein degradation (HyT-PD) has also gained significant attention as a tool for medicinal chemists. The increasing number of reported HyT-PD molecules possessing high efficiency in degrading protein and good pharmacokinetic (PK) properties, has further fueled interest in this approach. This review aims to present the design rationale, hydrophobic tags in use, and diverse mechanisms of action of HyT-PD. Additionally, the advantages and disadvantages of HyT-PD in protein degradation are discussed. This review may help inspire the development of more HyT-PDs with superior drug-like properties for clinical evaluation.
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Affiliation(s)
- Qindi He
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Xiaofei Zhao
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Donglin Wu
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Siming Jia
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Canlin Liu
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Zitian Cheng
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Fei Huang
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Tao Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Shuai Lu
- School of Science, China Pharmaceutical University, Nanjing, 211198, PR China.
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16
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El-Hddad S, Sobhy M, Ayoub A, El-Adl K. In silico molecular docking, dynamics simulation and repurposing of some VEGFR-2 inhibitors based on the SARS-CoV-2-main-protease inhibitor N3. J Biomol Struct Dyn 2023; 41:9267-9281. [PMID: 36399002 DOI: 10.1080/07391102.2022.2148000] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022]
Abstract
The global and rapid spread of the novel human coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has brought immediate urgency to the discovery of favorable targets for COVID-19 treatment. Here, we consider drug reuse as an attractive methodology for drug discovery by reusing existing drugs to treat diseases other than their initial indications. Here, we review current information concerning the global health issue of COVID-19 including VEGFR-2 inhibitors. Besides, we describe computational approaches to be used in drug repurposing and highlight examples of in silico studies of drug development efforts against SARS-CoV-2. The present study suggests the potential anti-SARS-CoV-2 activities of 35 reported VEGFR-2 inhibitors containing the amide and urea linkers. Nineteen members revealed the best in silico results and hence, were subjected to further molecular dynamics (MD) simulation for their inhibitory activities against SARS-CoV-2 Mpro across 100 ns. Furthermore, MD simulations followed by calculations of the free energy of binding were also carried out for the most promising ligand-pocket complexes from docking studies to clarify some information on their dynamic and thermodynamic properties and approve the docking results. These results we obtained probably provided an excellent lead candidate for the development of therapeutic drugs against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanadelaslam El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University, Al Bayda, Libya
| | - Mohamed Sobhy
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Ahmed Ayoub
- HTuO Biosciences Inc., Vancouver, BC, Canada
| | - Khaled El-Adl
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
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17
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Hegazy GE, Abu-Serie MM, Soliman NA, Teleb M, Abdel-Fattah YR. Superior anti-pulmonary viral potential of Natrialba sp. M6-producing surfactin and C50 carotenoid pigment with unveiling its action modes. Virol J 2023; 20:249. [PMID: 37904234 PMCID: PMC10614327 DOI: 10.1186/s12985-023-02215-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Respiratory viruses, particularly adenoviruses (ADV), influenza A virus (e.g., H1N1), and coronaviruses (e.g., HCoV-229E and SARS-CoV-2) pose a global public health problem. Therefore, developing natural wide-spectrum antiviral compounds for disrupting the viral life cycle with antioxidant activity provides an efficient treatment approach. Herein, biosurfactant (Sur) and C50 carotenoid pigment (Pig) of haloalkaliphilic archaeon Natrialba sp. M6 which exhibited potent efficacy against hepatitis and anti-herpes simplex viruses, were investigated against pulmonary viruses. METHODS The cytotoxicity of the extracted Sur and Pig was examined on susceptible cell lines for ADV, HIN1, HCoV-229E, and SARS-CoV-2. Their potential against the cytopathic activity of these viruses was detected with investigating the action modes (including, virucidal, anti-adsorption, and anti-replication), unveiling the main mechanisms, and using molecular docking analysis. Radical scavenging activity was determined and HPLC analysis for potent extract (Sur) was performed. RESULTS All current investigations stated higher anti-pulmonary viruses of Sur than Pig via mainly virucidal and/or anti-replicative modes. Moreover, Sur had stronger ADV's capsid protein binding, ADV's DNA polymerase inhibition, suppressing hemagglutinin and neuraminidase of H1N1, and inhibiting chymotrypsin-like (3CL) protease of SARS-CoV-2, supporting with in-silico analysis, as well as radical scavenging activity than Pig. HPLC analysis of Sur confirmed the predominate presence of surfactin in it. CONCLUSION This study declared the promising efficacy of Sur as an efficient pharmacological treatment option for these pulmonary viruses and considered as guide for further in vivo research.
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Affiliation(s)
- Ghada E Hegazy
- National Institute of Oceanography and Fisheries, NIOF, Cairo, Egypt.
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, Alexandria, Egypt.
| | - Marwa M Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, Alexandria, Egypt.
| | - Nadia A Soliman
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, Alexandria, Egypt.
| | - Mohamed Teleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Yasser R Abdel-Fattah
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, Alexandria, Egypt.
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18
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Sokouti B. A review on in silico virtual screening methods in COVID-19 using anticancer drugs and other natural/chemical inhibitors. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:994-1026. [PMID: 38023988 PMCID: PMC10651357 DOI: 10.37349/etat.2023.00177] [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: 12/30/2022] [Accepted: 05/22/2023] [Indexed: 12/01/2023] Open
Abstract
The present coronavirus disease 2019 (COVID-19) pandemic scenario has posed a difficulty for cancer treatment. Even under ideal conditions, malignancies like small cell lung cancer (SCLC) are challenging to treat because of their fast development and early metastases. The treatment of these patients must not be jeopardized, and they must be protected as much as possible from the continuous spread of the COVID-19 infection. Initially identified in December 2019 in Wuhan, China, the contagious coronavirus illness 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Finding inhibitors against the druggable targets of SARS-CoV-2 has been a significant focus of research efforts across the globe. The primary motivation for using molecular modeling tools against SARS-CoV-2 was to identify candidates for use as therapeutic targets from a pharmacological database. In the published study, scientists used a combination of medication repurposing and virtual drug screening methodologies to target many structures of SARS-CoV-2. This virus plays an essential part in the maturation and replication of other viruses. In addition, the total binding free energy and molecular dynamics (MD) modeling findings showed that the dynamics of various medications and substances were stable; some of them have been tested experimentally against SARS-CoV-2. Different virtual screening (VS) methods have been discussed as potential means by which the evaluated medications that show strong binding to the active site might be repurposed for use against SARS-CoV-2.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz 5165665813, Iran
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19
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Alugubelli YR, Xiao J, Khatua K, Kumar S, Ma Y, Ma XR, Vulupala VR, Atla SR, Blankenship L, Coleman D, Neuman BW, Liu WR, Xu S. Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560163. [PMID: 37808777 PMCID: PMC10557696 DOI: 10.1101/2023.09.29.560163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
We have witnessed three coronavirus (CoV) outbreaks in the past two decades, including the COVID-19 pandemic caused by SARS-CoV-2. Main protease (M Pro ) is a highly conserved and essential protease that plays key roles in viral replication and pathogenesis among various CoVs, representing one of the most attractive drug targets for antiviral drug development. Traditional antiviral drug development strategies focus on the pursuit of high-affinity binding inhibitors against M Pro . However, this approach often suffers from issues such as toxicity, drug resistance, and a lack of broad-spectrum efficacy. Targeted protein degradation represents a promising strategy for developing next-generation antiviral drugs to combat infectious diseases. Here we leverage the proteolysis targeting chimera (PROTAC) technology to develop a new class of small-molecule antivirals that induce the degradation of SARS-CoV-2 M Pro . Our previously developed M Pro inhibitors MPI8 and MPI29 were used as M Pro ligands to conjugate a CRBN E3 ligand, leading to compounds that can both inhibit and degrade SARS-CoV-2 M Pro . Among them, MDP2 was demonstrated to effectively reduce M Pro protein levels in 293T cells (DC 50 = 296 nM), relying on a time-dependent, CRBN-mediated, and proteasome-driven mechanism. Furthermore, MPD2 exhibited remarkable efficacy in diminishing M Pro protein levels in SARS-CoV-2-infected A549-ACE2 cells, concurrently demonstrating potent anti-SARS-CoV-2 activity (EC 50 = 492 nM). This proof-of-concept study highlights the potential of PROTAC-mediated targeted protein degradation of M Pro as an innovative and promising approach for COVID-19 drug discovery.
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20
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Purohit P, Panda M, Muya JT, Bandyopadhyay P, Meher BR. Theoretical insights into the binding interaction of Nirmatrelvir with SARS-CoV-2 Mpro mutants (C145A and C145S): MD simulations and binding free-energy calculation to understand drug resistance. J Biomol Struct Dyn 2023:1-20. [PMID: 37599474 DOI: 10.1080/07391102.2023.2248519] [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: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Mpro, the main protease and a crucial enzyme in SARS-CoV-2 is the most fascinating molecular target for pharmacological treatment and is also liable for viral protein maturation. For antiviral therapy, no drugs have been approved clinically to date. Targeting the Mpro with a compound having inhibitory properties against it can hinder viral replication. The therapeutic potential of the antiviral compound Nirmatrelvir (NMV) against SARS-CoV-2 Mpro was investigated using a systematic approach of molecular docking, MD simulations, and binding free energy calculation based on the MM-GBSA method. NMV, a covalent inhibitor with a recently revealed chemical structure, is a promising oral antiviral clinical candidate with significant in vitro anti-SARS-CoV-2 action in third-phase clinical trials. To explore the therapeutic ability and possible drug resistance, the Mpro system was studied for WT and two of its primary mutants (C145A & C145S). The protein-ligand (Mpro/NMV) complexes were further examined through long MD simulations to check the possible drug resistance in the mutants. To understand the binding affinity, the MM-GBSA method was applied to the Mpro/NMV complexes. Moreover, PCA analysis confirms the detachment of the linker region from the major domains in C145S and C145A mutants allowing for conformational alterations in the active-site region. Based on the predicted biological activities and binding affinities of NMV to WT and mutant (C145A & C145S) Mpro, it can be stipulated that NMV may have conventional potency to act as an anti-viral agent against WT Mpro, while the catalytic-dyad mutations may show substantial mutation-induced drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Jules Tshishimbi Muya
- Faculte of Science, Research Centre for Theoretical Chemistry and Physics in Central Africa, University of Kinshasa, Kinshasa, Congo
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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21
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Martinusen SG, Slaton EW, Nelson SE, Pulgar MA, Besu JT, Simas CF, Denard CA. Modular and integrative activity reporters enhance biochemical studies in the yeast ER. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548713. [PMID: 37502857 PMCID: PMC10369952 DOI: 10.1101/2023.07.12.548713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The yeast endoplasmic reticulum sequestration and screening (YESS) system is a generalizable platform that has become highly useful to investigate post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CL pro ), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.
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22
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Chen D, Zheng R, Su J, Lai J, Chen H, Ning Z, Liu X, Zhu B, Li Y. Inhibition of H1N1 Influenza Virus-induced Apoptosis by Ebselen Through ROS-mediated ATM/ATR Signaling Pathways. Biol Trace Elem Res 2023; 201:2811-2822. [PMID: 35896885 PMCID: PMC9330958 DOI: 10.1007/s12011-022-03369-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/23/2022] [Indexed: 11/24/2022]
Abstract
Influenza A viruses can cause global outbreaks and seasonal pandemics. However, the use of conventional anti-influenza drugs leads to an increase in drug-resistant mutations in influenza viruses worldwide. Therefore, numerous studies have focused on developing effective anti-influenza drugs. It is feasible to treat influenza by targeting influenza-mediated oxidative damage. Ebselen is a synthetic organoselenium compound which provides glutathione peroxidase-like activity. It has been shown to play a role in anti-influenza therapy, but the mechanism remains to be further explored. This experiment verified the anti-influenza effect of ebselen. CCK-8 and PCR showed that ebselen had a significant inhibitory effect on virus replication compared with the virus group. In addition, the mechanistic investigations revealed that ebselen could inhibit influenza-mediated apoptosis, mitochondrial damage, accumulation of reactive oxygen species, and DNA breakage. At the same time, ebselen significantly inhibited the phosphorylation of ATM and ATR and promoted the activation of PARP and Caspase-3. Ebselen, on the other hand, reduced the inflammatory response caused by influenza. These results suggest that ebselen is a promising inhibitor for H1N1.
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Affiliation(s)
- Danyang Chen
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China
| | - Ruilin Zheng
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China
| | - Jingyao Su
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China
| | - Jia Lai
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China
| | - Haitian Chen
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China
| | - Zhihui Ning
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China
| | - Xia Liu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China
| | - Bing Zhu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China
| | - Yinghua Li
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Yuexiu District, No 318 Renminzhong Road, Guangzhou, 510120, China.
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23
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Kumar D, Shandilya AK, Srivastava S. The journey of F1000Research since inception: through bibliometric analysis. F1000Res 2023; 12:516. [PMID: 37274828 PMCID: PMC10238821 DOI: 10.12688/f1000research.134244.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2023] [Indexed: 06/07/2023] Open
Abstract
Background: Bibliometric analysis is an approach adopted by researchers to understand the various analytics such as year-wise publications, their citations, most impactful authors and their contributions, identification of emerging keywords, multiple themes (niche, motor, basic, and emerging or declining) etc. F1000Research is one of the Q1 category journals that publishes articles in various domains, but a detailed journal analysis is yet to be done. Methods: This study is an effort to extract the F1000Research journey information through bibliometric analysis using VOS-viewer and Biblioshiny (R-studio) interface. The F1000Research journal started its journey in 2012; since then, 5767 articles have been published until the end of 2022. Most of the published articles are from medical science, covering Biochemistry, Genetics & Molecular Biology, Immunology & Pharmacology, Toxicology & Pharmaceutics. To understand the research journey, various analyses such as publication & citation trends, leading authors, institutions, countries, most frequent keywords, bibliographic coupling between authors, countries and documents, emerging research themes, and trending keywords were performed. Results: The United States is the biggest contributor, and COVID-19 is the most commonly occurred keyword. Conclusions: The present study may help future researchers to understand the emerging medical science domain. It will also help the editors and journal to focus more on developing or emerging areas and to understand their importance towards society. Future researchers can contribute their quality research studies, focusing on emerging themes. These authors' research can guide future researchers to develop their research area around the most impacted articles. They can collaborate with them to bring that emerging theme forward.
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Affiliation(s)
- Dilip Kumar
- Welcomgroup Graduate School of Hotel Administration, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Abhinav Kumar Shandilya
- Department of Hotel Management and Catering Technology, Birla Institute of Technology, Ranchi, Jharkhand, 835215, India
| | - Sandeep Srivastava
- Welcomgroup Graduate School of Hotel Administration, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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24
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Raghav PK, Mann Z, Ahluwalia SK, Rajalingam R. Potential treatments of COVID-19: Drug repurposing and therapeutic interventions. J Pharmacol Sci 2023; 152:1-21. [PMID: 37059487 PMCID: PMC9930377 DOI: 10.1016/j.jphs.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The infection is caused when Spike-protein (S-protein) present on the surface of SARS-CoV-2 interacts with human cell surface receptor, Angiotensin-converting enzyme 2 (ACE2). This binding facilitates SARS-CoV-2 genome entry into the human cells, which in turn causes infection. Since the beginning of the pandemic, many different therapies have been developed to combat COVID-19, including treatment and prevention. This review is focused on the currently adapted and certain other potential therapies for COVID-19 treatment, which include drug repurposing, vaccines and drug-free therapies. The efficacy of various treatment options is constantly being tested through clinical trials and in vivo studies before they are made medically available to the public.
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Affiliation(s)
- Pawan Kumar Raghav
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
| | | | - Simran Kaur Ahluwalia
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh, India
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
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25
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Kalita P, Tripathi T, Padhi AK. Computational Protein Design for COVID-19 Research and Emerging Therapeutics. ACS CENTRAL SCIENCE 2023; 9:602-613. [PMID: 37122454 PMCID: PMC10042144 DOI: 10.1021/acscentsci.2c01513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Indexed: 05/03/2023]
Abstract
As the world struggles with the ongoing COVID-19 pandemic, unprecedented obstacles have continuously been traversed as new SARS-CoV-2 variants continually emerge. Infectious disease outbreaks are unavoidable, but the knowledge gained from the successes and failures will help create a robust health management system to deal with such pandemics. Previously, scientists required years to develop diagnostics, therapeutics, or vaccines; however, we have seen that, with the rapid deployment of high-throughput technologies and unprecedented scientific collaboration worldwide, breakthrough discoveries can be accelerated and insights broadened. Computational protein design (CPD) is a game-changing new technology that has provided alternative therapeutic strategies for pandemic management. In addition to the development of peptide-based inhibitors, miniprotein binders, decoys, biosensors, nanobodies, and monoclonal antibodies, CPD has also been used to redesign native SARS-CoV-2 proteins and human ACE2 receptors. We discuss how novel CPD strategies have been exploited to develop rationally designed and robust COVID-19 treatment strategies.
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Affiliation(s)
- Parismita Kalita
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
- Regional
Director’s Office, Indira Gandhi
National Open University, Regional Centre Kohima, Kenuozou, Kohima 797001, India
| | - Aditya K. Padhi
- Laboratory
for Computational Biology & Biomolecular Design, School of Biochemical
Engineering, Indian Institute of Technology
(BHU), Varanasi 221005, Uttar Pradesh, India
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26
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Shi Y, Dong L, Ju Z, Li Q, Cui Y, Liu Y, He J, Ding X. Exploring potential SARS-CoV-2 Mpro non-covalent inhibitors through docking, pharmacophore profile matching, molecular dynamic simulation, and MM-GBSA. J Mol Model 2023; 29:138. [PMID: 37055578 PMCID: PMC10100623 DOI: 10.1007/s00894-023-05534-3] [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: 01/06/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023]
Abstract
CONTEXT In the replication of SARS-CoV-2, the main protease (Mpro/3CLpro) is significant. It is conserved in a number of novel coronavirus variations, and no known human proteases share its cleavage sites. Therefore, 3CLpro is an ideal target. In the report, we screened five potential inhibitors (1543, 2308, 3717, 5606, and 9000) of SARS-CoV-2 Mpro through a workflow. The calculation of MM-GBSA binding free energy showed that three of the five potential inhibitors (1543, 2308, 5606) had similar inhibitor effects to X77 against Mpro of SARS-CoV-2. In conclusion, the manuscript lays the groundwork for the design of Mpro inhibitors. METHODS In the virtual screening phase, we used structure-based virtual screening (Qvina2.1) and ligand-based virtual screening (AncPhore). In the molecular dynamic simulation part, we used the Amber14SB + GAFF force field to perform molecular dynamic simulation of the complex for 100 ns (Gromacs2021.5) and performed MM-GBSA binding free energy calculation according to the simulation trajectory.
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Affiliation(s)
- Yunfan Shi
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.
- Joint Key Lab of Sichuan & Chongqing, Bioresource Res & Utilizat, Chongqing, China.
| | - Liting Dong
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Zhuang Ju
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Joint Key Lab of Sichuan & Chongqing, Bioresource Res & Utilizat, Chongqing, China
| | - Qiufu Li
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Joint Key Lab of Sichuan & Chongqing, Bioresource Res & Utilizat, Chongqing, China
| | - Yanru Cui
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Joint Key Lab of Sichuan & Chongqing, Bioresource Res & Utilizat, Chongqing, China
| | - Yiran Liu
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Joint Key Lab of Sichuan & Chongqing, Bioresource Res & Utilizat, Chongqing, China
| | - Jiaoyu He
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Joint Key Lab of Sichuan & Chongqing, Bioresource Res & Utilizat, Chongqing, China
| | - Xianping Ding
- College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.
- Joint Key Lab of Sichuan & Chongqing, Bioresource Res & Utilizat, Chongqing, China.
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27
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Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
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28
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Fuertes MA, Alonso C. New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome. Curr Genomics 2023; 23:424-440. [PMID: 37920558 PMCID: PMC10173420 DOI: 10.2174/1389202924666230202152351] [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: 04/27/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Background The coronavirus disease has led to an exhaustive exploration of the SARS-CoV-2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention. Objective The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome. Methods A method in which 14 trinucleotide families, each characterized by being composed of triplets with identical nucleotides in all possible configurations, was used to find short peptides with biological relevance. The novelty of the approach lies in using these families to search how they are distributed across genomes of different CoV genera and then to compare the distributions of these families with each other. Results We identified distributions of trinucleotide families in different CoV genera and also how they are related, using a selection criterion that identified short RNA motifs. The motifs were reported to be conserved in SARS-CoVs; in the remaining CoV genomes analysed, motifs contained, exclusively, different configurations of the trinucleotides A, T, G and A, C, G. Eighty-eight short RNA motifs, ranging in length from 12 to 49 nucleotides, were found: 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf, and 6 in the nucleocapsid-encoding orf. Although some motifs (~27%) were found to be intercalated or attached to functional peptides, most of them have not yet been associated with any known functions. Conclusion Some of the trinucleotide family distributions in different CoV genera are not random; they are present in short peptides that, in many cases, are intercalated or attached to functional sites of the proteome.
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Affiliation(s)
- Miguel Angel Fuertes
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, Madrid, 28049, Spain
| | - Carlos Alonso
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, Madrid, 28049, Spain
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29
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Pauly I, Kumar Singh A, Kumar A, Singh Y, Thareja S, Kamal MA, Verma A, Kumar P. Current Insights and Molecular Docking Studies of the Drugs under Clinical Trial as RdRp Inhibitors in COVID-19 Treatment. Curr Pharm Des 2023; 28:3677-3705. [PMID: 36345244 DOI: 10.2174/1381612829666221107123841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/10/2022]
Abstract
Study Background & Objective: After the influenza pandemic (1918), COVID-19 was declared a Vth pandemic by the WHO in 2020. SARS-CoV-2 is an RNA-enveloped single-stranded virus. Based on the structure and life cycle, Protease (3CLpro), RdRp, ACE2, IL-6, and TMPRSS2 are the major targets for drug development against COVID-19. Pre-existing several drugs (FDA-approved) are used to inhibit the above targets in different diseases. In coronavirus treatment, these drugs are also in different clinical trial stages. Remdesivir (RdRp inhibitor) is the only FDA-approved medicine for coronavirus treatment. In the present study, by using the drug repurposing strategy, 70 preexisting clinical or under clinical trial molecules were used in scrutiny for RdRp inhibitor potent molecules in coronavirus treatment being surveyed via docking studies. Molecular simulation studies further confirmed the binding mechanism and stability of the most potent compounds. MATERIAL AND METHODS Docking studies were performed using the Maestro 12.9 module of Schrodinger software over 70 molecules with RdRp as the target and remdesivir as the standard drug and further confirmed by simulation studies. RESULTS The docking studies showed that many HIV protease inhibitors demonstrated remarkable binding interactions with the target RdRp. Protease inhibitors such as lopinavir and ritonavir are effective. Along with these, AT-527, ledipasvir, bicalutamide, and cobicistat showed improved docking scores. RMSD and RMSF were further analyzed for potent ledipasvir and ritonavir by simulation studies and were identified as potential candidates for corona disease. CONCLUSION The drug repurposing approach provides a new avenue in COVID-19 treatment.
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Affiliation(s)
- Irine Pauly
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Yogesh Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Mohammad A Kamal
- King Fahd Medical Research Center, King Abdulaziz University, Jaddah, Saudi Arabia.,Enzymoics, 7 Peterlee Place, Hebersham, NSW 2770, Australia.,Novel Global Community Educational Foundation, Australia Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, Australia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, 211007, India
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
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30
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Malik A, Kohli M, Jacob NA, Kayal A, Raj TK, Kulkarni N, Chandramohan V. In silico screening of phytochemical compounds and FDA drugs as potential inhibitors for NSP16/10 5' methyl transferase activity. J Biomol Struct Dyn 2023; 41:221-233. [PMID: 34844519 DOI: 10.1080/07391102.2021.2005680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The recent global pandemic associated with the highly contagious novel coronavirus (SARS-CoV-2) has led to an unpredictable loss of life and economy worldwide, and the discovery of antiviral drugs is an urgent necessity. For the discovery of new drug leads and for the treatment of various diseases, natural products and purified photochemical from medicinal plants are used. The RNA cap was methylated by two S-adenosyl-L-methionine (SAM)-dependent methyltransferases of SARS coronavirus (SARS-CoV-2), catalyzed by NSP16 2'-O-Mtase. Natural substrate SAM, 128 Phytocompounds retrieved from the Phytocompounds database, and 11 standard FDA-approved HIV drugs reclaimed from the PubChem database are subjected to docking analysis. The docking study was done using AutoDock Vina. Further, admetSAR and DruLiTO servers are used to analyze the drug-likeness properties. The NSP16/10 structure and natural substrate SAM, Phytocompounds Withanolide (WTL), and HIV standard drug Dolutegravir (DLT) as hit compounds were identified by molecular dynamics using the Gromacs GPU-enabled package. To examine the effectiveness of the identified drugs versus COVID-19, further in vitro and in vivo studies are required. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mayank Kohli
- Biotechnology Skill Enhancement Programme, Department of Biotechnology, Siddaganga Institute of Technology, Karnataka, India
| | - Neethu Anju Jacob
- Biotechnology Skill Enhancement Programme, Department of Biotechnology, Siddaganga Institute of Technology, Karnataka, India
| | | | | | | | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Karnataka, India
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31
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Multicriteria group decision making via generalized trapezoidal intuitionistic fuzzy number-based novel similarity measure and its application to diverse COVID-19 scenarios. Artif Intell Rev 2023; 56:3543-3617. [PMID: 36092823 PMCID: PMC9450847 DOI: 10.1007/s10462-022-10251-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Havoc, brutality, economic breakdown, and vulnerability are the terms that can be rightly associated with COVID-19, for the kind of impact it is having on the whole world for the last two years. COVID-19 came as a nightmare and it is still not over yet, changing its form factor with each mutation. Moreover, each unpredictable mutation causes more severeness. In the present article, we outline a decision support algorithm using Generalized Trapezoidal Intuitionistic Fuzzy Numbers (GTrIFNs) to deal with various facets of COVID-19 problems. Intuitionistic fuzzy sets (IFSs) and their continuous counterparts, viz., the intuitionistic fuzzy numbers (IFNs), have the flexibility and effectiveness to handle the uncertainty and fuzziness associated with real-world problems. Although a meticulous amount of research works can be found in the literature, a wide majority of them are based mainly on normalized IFNs rather than the more generalized approach, and most of them had several limitations. Therefore, we have made a sincere attempt to devise a novel Similarity Measure (SM) which considers the evaluation of two prominent features of GTrIFNs, which are their expected values and variances. Then, to establish the superiority of our approach we present a comparative analysis of our method with several other established similarity methods considering ten different profiles of GTrIFNs. The proposed SM is then validated for feasibility and applicability, by elaborating a Fuzzy Multicriteria Group Decision Making (FMCGDM) algorithm and it is supportedby a suitable illustrative example. Finally, the proposed SM approach is applied to tackle some significant concerns due to COVID-19. For instance, problems like the selection of best medicine for COVID-19 infected patients; proper healthcare waste disposal technique; and topmost government intervention measures to prevent the COVID-19 spread, are some of the burning issues which are handled with our newly proposed SM approach. Graphical abstract
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32
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Therapeutic Potential of the Purinergic System in Major Depressive Disorder Associated with COVID-19. Cell Mol Neurobiol 2023; 43:621-637. [PMID: 35348977 PMCID: PMC8960668 DOI: 10.1007/s10571-022-01215-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 03/18/2022] [Indexed: 12/23/2022]
Abstract
Neuroinflammation is closely related to the development of depression, since the latter is caused, among other factors, by inflammatory processes, mainly related to the activation of microglia and expression of specific genes, which occurs during the neuroinflammatory process. Thus, COVID-19 is an important risk factor for the development of depression, since in addition to generating the feeling of stress, which also increases the activity of the immune system, it is also the cause of pathological processes and physiological ones that lead to the development of neuroinflammation, microglial activation, gene expression dysfunction and decreased concentration of available serotonin. That said, drugs are being used to combat COVID-19 to reduce the oxidative stress presented in the disease. Thus, tramadol and fluoxetine are highlighted as drugs used, however, although they present some positive results, such as the reduction of pro-inflammatory cytokines, they are also associated with negative effects such as dependence, pulmonary, cardiac and brain impairment. From this, the purinergic system is highlighted in the literature as a possible therapeutic target. This is because its mechanisms are related to the regulation of microglia, astrocytes and the physiology of important neurotransmitters and hormones. Added to this, there is a modulation of inflammatory activity, especially with regard to the P2X7 receptors of this system. The latter is an important target for the treatment of depression and COVID-19, since positive results were obtained through the genetic exclusion of this receptor and the use of selective antagonists.
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33
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Gouhar SA, Elshahid ZA. Molecular docking and simulation studies of synthetic protease inhibitors against COVID-19: a computational study. J Biomol Struct Dyn 2022; 40:13976-13996. [PMID: 34738871 DOI: 10.1080/07391102.2021.1997822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19 is the most recent threat to global health. Many people preferred treatment in case of infection instead of vaccination. The inhibition of viral replication is a good strategy for the treatment of COVID-19 infection. 3CLpro and PLpro are two important viral proteases responsible for proteolysis, infection, and replication of the virus. Therefore, targeting of these two enzymes is an attractive way to deal with COVID-19. The aim of this study was to screen some synthetic protease inhibitors to determine an appropriate hit molecule against COVID-19 using molecular docking and molecular dynamic simulations. The strategy depends on docking existing synthetic compounds mostly HIV protease inhibitors against two COVID-19 proteases to identify promising drugs for the treatment of COVID-19. We used protein data bank to obtain the X-ray crystal structure of the most important COVID-19 proteases 3CL pro (PDB ID: 6M2N) and PL pro (PDB ID: 6WX4). In this conceptual context, an attempt has been made to suggest an in silico computational relationship between 50 synthetic protease inhibitors and COVID-19 proteases. Out of 50 screened compounds, the best docking scores were found for these five protease inhibitors BDBM7021, BDBM698, BDBM694, BDBM93239, BDBM700. A 100-ns MD simulation was carried out to assess the stability of COVID-19 proteases and inhibitors, revealing an average RMSD value of 0.7 and favorable binding free energy (MM-GBSA) for all complexes confirming their potency as powerful binders in the COVID-19 proteases' binding pocket. Furthermore, the current results must be confirmed using in-vitro and in-vivo antiviral methods.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shaimaa A Gouhar
- Medical Biochemistry Department, Medical Research Division, National Research Centre, Cairo, Egypt
| | - Zeinab A Elshahid
- Chemistry of Natural and Microbial Products, Pharmaceutical Industry Research Division, National Research Center, Cairo, Egypt
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Vergoten G, Bailly C. Interaction of the renin inhibitor aliskiren with the SARS-CoV-2 main protease: a molecular docking study. J Biomol Struct Dyn 2022; 40:12714-12722. [PMID: 34514971 DOI: 10.1080/07391102.2021.1976673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The renin protein is an upstream enzymatic regulator of the renin-aldosterone-angiotensin system (RAAS) essential for the maintenance of blood pressure. The angiotensin-converting enzyme-2 (ACE2) is a major component of the RAAS and a cell surface receptor exploited by the SARS-CoV-2 virus to enter host cells. A recent molecular modeling study has revealed that the direct renin peptide inhibitor remikiren can bind to the catalytic site of SARS-CoV-2 main protease (Mpro). By analogy, we postulated that the non-peptidic drug aliskiren, a more potent renin inhibitor than remikiren and a drug routinely used to treat hypertension, may also be able to interact with Mpro. An in silico comparison of the binding of the two compounds to Mpro indicates that aliskiren (ΔE = -75.9 kcal/mol) can form stable complexes with the main viral protease, binding to the active site, as remikiren (ΔE = -83.2 kcal/mol). The comparison with a panoply of 30 references compounds (mainly antiviral drugs) indicated that remikiren is a potent Mpro binder comparable to drugs like glecaprevir and pibrentasvir (ΔE = -96.5 kcal/mol). The energy of interaction (ΔE) of aliskiren with Mpro is about 10% lower than with remikiren, comparable to that calculated with drugs like velpatasvir and sofosbuvir. A model is proposed to define the drug binding site, with the best binders (including remikiren) penetrating deeply into the site, whereas the less potent binders (including aliskiren) interact more superficially with the protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gérard Vergoten
- Inserm, INFINITE - U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, University of Lille, Lille, France
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Zhao W, Song D, Wang P, Tian Y, Chang S, Li W. Mechanism and Experimental Verification of the Use of Rhodiola crenulata to Cytokine Storm Based on Network Pharmacology and Molecular Docking. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221142790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Objective: To identify the potential biological mechanisms by which Rhodiola crenulata (RC) treats cytokine storm (CS) using network pharmacology, molecular docking, and experimental verification. Methods: The ingredients and targets of RC were collected from the Organchem database. CS-related genes were collected using the GeneCards and OMIM databases. Cytoscape 3.7.2 software was used to construct the RC-CS network diagram. These data were inputted into the STRING database to construct a protein–protein interaction network. we performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment analysis using DAVID and R software. Molecular docking of the active ingredient and pathway-related targets was carried out using AutoDock Vina and PyMOL, and then a CS model was established in rats induced by lipopolysaccharide for in vivo experimental verification. Results: The network pharmacology results showed that kaempferol was the most important active component of RC in the treatment of CS, and IL6 and STAT3 were identified as key targets. Molecular docking results showed that RC active components kaempferol had a good binding ability to IL6/STAT3. At the same time, compared with the model group, different doses of kaempferol could down-regulate the expression of inflammatory factors ( P < .05), and protect against systemic inflammatory response multiple organ damage. Conclusion: This study preliminarily revealed that RC can prevent and treat CS by regulating the expression of inflammatory factors, inhibiting the systemic inflammatory response induced by lipopolysaccharide, and providing a theoretical basis for the study of its pharmacodynamic material basis and mechanism of action.
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Affiliation(s)
- Wanhua Zhao
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Dan Song
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Pingyi Wang
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Yu Tian
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Senhao Chang
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Wenhua Li
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
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Sharun K, Tiwari R, Yatoo MI, Natesan S, Megawati D, Singh KP, Michalak I, Dhama K. A comprehensive review on pharmacologic agents, immunotherapies and supportive therapeutics for COVID-19. NARRA J 2022; 2:e92. [PMID: 38449903 PMCID: PMC10914132 DOI: 10.52225/narra.v2i3.92] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 03/08/2024]
Abstract
The emergence of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected many countries throughout the world. As urgency is a necessity, most efforts have focused on identifying small molecule drugs that can be repurposed for use as anti-SARS-CoV-2 agents. Although several drug candidates have been identified using in silico method and in vitro studies, most of these drugs require the support of in vivo data before they can be considered for clinical trials. Several drugs are considered promising therapeutic agents for COVID-19. In addition to the direct-acting antiviral drugs, supportive therapies including traditional Chinese medicine, immunotherapies, immunomodulators, and nutritional therapy could contribute a major role in treating COVID-19 patients. Some of these drugs have already been included in the treatment guidelines, recommendations, and standard operating procedures. In this article, we comprehensively review the approved and potential therapeutic drugs, immune cells-based therapies, immunomodulatory agents/drugs, herbs and plant metabolites, nutritional and dietary for COVID-19.
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Affiliation(s)
- Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Mohd I. Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Alusteng Srinagar, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir, India
| | - Senthilkumar Natesan
- Department of Infectious Diseases, Indian Institute of Public Health Gandhinagar, Opp to Airforce station HQ, Gandhinagar, India
| | - Dewi Megawati
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Indonesia
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
| | - Karam P. Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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Structure-Based Virtual Screening and Functional Validation of Potential Hit Molecules Targeting the SARS-CoV-2 Main Protease. Biomolecules 2022; 12:biom12121754. [PMID: 36551182 PMCID: PMC9775371 DOI: 10.3390/biom12121754] [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: 09/29/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/29/2022] Open
Abstract
The recent global health emergency caused by the coronavirus disease 2019 (COVID-19) pandemic has taken a heavy toll, both in terms of lives and economies. Vaccines against the disease have been developed, but the efficiency of vaccination campaigns worldwide has been variable due to challenges regarding production, logistics, distribution and vaccine hesitancy. Furthermore, vaccines are less effective against new variants of the SARS-CoV-2 virus and vaccination-induced immunity fades over time. These challenges and the vaccines' ineffectiveness for the infected population necessitate improved treatment options, including the inhibition of the SARS-CoV-2 main protease (Mpro). Drug repurposing to achieve inhibition could provide an immediate solution for disease management. Here, we used structure-based virtual screening (SBVS) to identify natural products (from NP-lib) and FDA-approved drugs (from e-Drug3D-lib and Drugs-lib) which bind to the Mpro active site with high-affinity and therefore could be designated as potential inhibitors. We prioritized nine candidate inhibitors (e-Drug3D-lib: Ciclesonide, Losartan and Telmisartan; Drugs-lib: Flezelastine, Hesperidin and Niceverine; NP-lib: three natural products) and predicted their half maximum inhibitory concentration using DeepPurpose, a deep learning tool for drug-target interactions. Finally, we experimentally validated Losartan and two of the natural products as in vitro Mpro inhibitors, using a bioluminescence resonance energy transfer (BRET)-based Mpro sensor. Our study suggests that existing drugs and natural products could be explored for the treatment of COVID-19.
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Mahgoub RE, Mohamed FE, Alzyoud L, Ali BR, Ferreira J, Rabeh WM, AlNeyadi SS, Atatreh N, Ghattas MA. The Discovery of Small Allosteric and Active Site Inhibitors of the SARS-CoV-2 Main Protease via Structure-Based Virtual Screening and Biological Evaluation. Molecules 2022; 27:molecules27196710. [PMID: 36235244 PMCID: PMC9572942 DOI: 10.3390/molecules27196710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
The main protease enzyme (Mpro) of SARS-CoV-2 is one of the most promising targets for COVID-19 treatment. Accordingly, in this work, a structure-based virtual screening of 3.8 million ligand libraries was carried out. After rigorous filtering, docking, and post screening assessments, 78 compounds were selected for biological evaluation, 3 of which showed promising inhibition of the Mpro enzyme. The obtained hits (CB03, GR04, and GR20) had reasonable potencies with Ki values in the medium to high micromolar range. Interestingly, while our most potent hit, GR20, was suggested to act via a reversible covalent mechanism, GR04 was confirmed as a noncompetitive inhibitor that seems to be one of a kind when compared to the other allosteric inhibitors discovered so far. Moreover, all three compounds have small sizes (~300 Da) with interesting fittings in their relevant binding sites, and they possess lead-like characteristics that can introduce them as very attractive candidates for the future development of COVID-19 treatments.
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Affiliation(s)
- Radwa E. Mahgoub
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Feda E. Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Lara Alzyoud
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Bassam R. Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
- Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Wael M. Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Shaikha S. AlNeyadi
- Department of Chemistry, College of Science, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Mohammad A. Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- Correspondence: ; Tel.: +971-26133275
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Copertino DC, Casado Lima BC, Duarte RRR, Powell TR, Ormsby CE, Wilkin T, Gulick RM, de Mulder Rougvie M, Nixon DF. Antiretroviral drug activity and potential for pre-exposure prophylaxis against COVID-19 and HIV infection. J Biomol Struct Dyn 2022; 40:7367-7380. [PMID: 33734021 PMCID: PMC8448789 DOI: 10.1080/07391102.2021.1901144] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/24/2021] [Indexed: 12/18/2022]
Abstract
COVID-19 is the disease caused by SARS-CoV-2 which has led to 2,643,000 deaths worldwide, a number which is rapidly increasing. Urgent studies to identify new antiviral drugs, repurpose existing drugs, or identify drugs that can target the overactive immune response are ongoing. Antiretroviral drugs (ARVs) have been tested in past human coronavirus infections, and also against SARS-CoV-2, but a trial of lopinavir and ritonavir failed to show any clinical benefit in COVID-19. However, there is limited data as to the course of COVID-19 in people living with HIV, with some studies showing a decreased mortality for those taking certain ARV regimens. We hypothesized that ARVs other than lopinavir and ritonavir might be responsible for some protection against the progression of COVID-19. Here, we used chemoinformatic analyses to predict which ARVs would bind and potentially inhibit the SARS-CoV-2 main protease (Mpro) or RNA-dependent-RNA-polymerase (RdRp) enzymes in silico. The drugs predicted to bind the SARS-CoV-2 Mpro included the protease inhibitors atazanavir and indinavir. The ARVs predicted to bind the catalytic site of the RdRp included Nucleoside Reverse Transcriptase Inhibitors, abacavir, emtricitabine, zidovudine, and tenofovir. Existing or new combinations of antiretroviral drugs could potentially prevent or ameliorate the course of COVID-19 if shown to inhibit SARS-CoV-2 in vitro and in clinical trials. Further studies are needed to establish the activity of ARVs for treatment or prevention of SARS-CoV-2 infection .Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dennis C. Copertino
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bruno C. Casado Lima
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Rodrigo R. R. Duarte
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Timothy R. Powell
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher E. Ormsby
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Timothy Wilkin
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Roy M. Gulick
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - Douglas F. Nixon
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
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Kashyap P, Thakur M, Singh N, Shikha D, Kumar S, Baniwal P, Yadav YS, Sharma M, Sridhar K, Inbaraj BS. In Silico Evaluation of Natural Flavonoids as a Potential Inhibitor of Coronavirus Disease. Molecules 2022; 27:molecules27196374. [PMID: 36234910 PMCID: PMC9572657 DOI: 10.3390/molecules27196374] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 01/08/2023] Open
Abstract
The recent coronavirus disease (COVID-19) outbreak in Wuhan, China, has led to millions of infections and the death of approximately one million people. No targeted therapeutics are currently available, and only a few efficient treatment options are accessible. Many researchers are investigating active compounds from natural plant sources that may inhibit COVID-19 proliferation. Flavonoids are generally present in our diet, as well as traditional medicines and are effective against various diseases. Thus, here, we reviewed the potential of flavonoids against crucial proteins involved in the coronavirus infectious cycle. The fundamentals of coronaviruses, the structures of SARS-CoV-2, and the mechanism of its entry into the host’s body have also been discussed. In silico studies have been successfully employed to study the interaction of flavonoids against COVID-19 Mpro, spike protein PLpro, and other interactive sites for its possible inhibition. Recent studies showed that many flavonoids such as hesperidin, amentoflavone, rutin, diosmin, apiin, and many other flavonoids have a higher affinity with Mpro and lower binding energy than currently used drugs such as hydroxylchloroquine, nelfinavir, ritonavir, and lopinavir. Thus, these compounds can be developed as specific therapeutic agents against COVID-19, but need further in vitro and in vivo studies to validate these compounds and pave the way for drug discovery.
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Affiliation(s)
- Piyush Kashyap
- Department of Food Technology and Nutrition, School of Agriculture, Lovely Professional University, Phagwara 144401, India
| | - Mamta Thakur
- Department of Food Technology, School of Sciences, ITM University, Gwalior 474001, India
| | - Nidhi Singh
- Centre of Bioinformatics, University of Allahabad, Prayraj 211002, India
| | - Deep Shikha
- Department of Food Technology, Bhai Gurdas Institute of Engineering and Technology, Sangrur 148001, India
| | - Shiv Kumar
- MMICT & BM (HM), Maharishi Markandeshwar Deemed to be University, Mullana, Ambala 133207, India
- Correspondence: (S.K.); or (K.S.); or (B.S.I.)
| | - Poonam Baniwal
- Department of Quality Control, Food Corporation of India, New Delhi 110001, India
| | - Yogender Singh Yadav
- Department of Dairy Engineering, College of Dairy Science and Technology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
| | - Minaxi Sharma
- Laboratoire de Chimieverte et Produits Biobasés, Département AgroBioscience et Chimie, Haute Ecole Provinciale du Hainaut-Condorcet, 11, 7800 ATH Rue de la Sucrerie, Belgium
| | - Kandi Sridhar
- UMR1253, Science et Technologie du Lait et de l’œuf, INRAE, L’InstitutAgro, Rennes-Angers, 65 Rue de Saint Brieuc, F-35042 Rennes, France
- Correspondence: (S.K.); or (K.S.); or (B.S.I.)
| | - Baskaran Stephen Inbaraj
- Department of Food Science, Fu Jen Catholic University, New Taipei City 242 05, Taiwan
- Correspondence: (S.K.); or (K.S.); or (B.S.I.)
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Strömich L, Wu N, Barahona M, Yaliraki SN. Allosteric Hotspots in the Main Protease of SARS-CoV-2. J Mol Biol 2022; 434:167748. [PMID: 35843284 PMCID: PMC9288249 DOI: 10.1016/j.jmb.2022.167748] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023]
Abstract
Inhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph-theoretical methods: Bond-to-bond propensity, which has been previously successful in identifying allosteric sites in extensive benchmark data sets without a priori knowledge, and Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. Using statistical bootstrapping, we score the highest ranking sites against random sites at similar distances, and we identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.
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Affiliation(s)
- Léonie Strömich
- Department of Chemistry Imperial College London, United Kingdom
| | - Nan Wu
- Department of Chemistry Imperial College London, United Kingdom
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Pekel H, Ilter M, Sensoy O. Inhibition of SARS-CoV-2 main protease: a repurposing study that targets the dimer interface of the protein. J Biomol Struct Dyn 2022; 40:7167-7182. [PMID: 33847241 PMCID: PMC8054500 DOI: 10.1080/07391102.2021.1910571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/28/2021] [Indexed: 11/22/2022]
Abstract
Coronavirus disease-2019 (COVID-19) was firstly reported in Wuhan, China, towards the end of 2019, and emerged as a pandemic. The spread and lethality rates of the COVID-19 have ignited studies that focus on the development of therapeutics for either treatment or prophylaxis purposes. In parallel, drug repurposing studies have also come into prominence. Herein, we aimed at having a holistic understanding of conformational and dynamical changes induced by an experimentally characterized inhibitor on main protease (Mpro) which would enable the discovery of novel inhibitors. To this end, we performed molecular dynamics simulations using crystal structures of apo and α-ketoamide 13b-bound Mpro homodimer. Analysis of trajectories pertaining to apo Mpro revealed a new target site, which is located at the homodimer interface, next to the catalytic dyad. Thereafter, we performed ensemble-based virtual screening by exploiting the ZINC and DrugBank databases and identified three candidate molecules, namely eluxadoline, diosmin, and ZINC02948810 that could invoke local and global conformational rearrangements which were also elicited by α-ketoamide 13b on the catalytic dyad of Mpro. Furthermore, ZINC23881687 stably interacted with catalytically important residues Glu166 and Ser1 and the target site throughout the simulation. However, it gave positive binding energy, presumably, due to displaying higher flexibility that might dominate the entropic term, which is not included in the MM-PBSA method. Finally, ZINC20425029, whose mode of action was different, modulated dynamical properties of catalytically important residue, Ala285. As such, this study presents valuable findings that might be used in the development of novel therapeutics against Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hanife Pekel
- Department of Pharmacy Services, Vocational School of Health Services, Istanbul Medipol University, Istanbul, Turkey
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Metehan Ilter
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Ozge Sensoy
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
- Department of Computer Engineering, School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
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Shi FS, Yu Y, Li YL, Cui L, Zhao Z, Wang M, Wang B, Zhang R, Huang YW. Expression Profile and Localization of SARS-CoV-2 Nonstructural Replicase Proteins in Infected Cells. Microbiol Spectr 2022; 10:e0074422. [PMID: 35730969 PMCID: PMC9431475 DOI: 10.1128/spectrum.00744-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is responsible for the COVID-19 pandemic that has caused unprecedented loss of life and economic trouble all over the world, though the mechanism of its replication remains poorly understood. In this study, antibodies were generated and used to systematically determine the expression profile and subcellular distribution of 11 SARS-CoV-2 nonstructural replicase proteins (nsp1, nsp2, nsp3, nsp5, nsp7, nsp8, nsp9, nsp10, nsp13, nsp14, and nsp15) by Western blot and immunofluorescence assay. Nsp3, nsp5, and nsp8 were detected in perinuclear foci at different time points, with diffusion and stronger fluorescence observed over time. In particular, colocalization of nsp8 and nsp13 with different replicase proteins suggested viral protein-protein interaction, which may be key to understanding their functions and potential molecular mechanisms. Viral intermediate dsRNA was detected in perinuclear foci as early as 2-h postinfection, indicating the initiation of virus replication. With the passage of time, these perinuclear dsRNA foci became larger and brighter, and nearly all colocalized with N protein, consistent with viral growth over time. Thus, the development of these anti-nsp antibodies provides basic tools for the further study of replication and diagnosis of SARS-CoV-2. IMPORTANCE The intracellular localization of SARS-CoV-2 replicase nonstructural proteins (nsp) during infection has not been fully elucidated. In this study, we systematically analyzed the expression and subcellular localization of 11 distinct viral nsp and dsRNA over time in SARS-CoV-2-infected cells by using individual antibody against these replicase proteins. The data indicated that nsp gene expression is highly regulated in space and time, which could be useful to understand the function of viral replicases and future development of diagnostics and potential antiviral strategies against SARS-CoV-2.
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Affiliation(s)
- Fang-Shu Shi
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Yin Yu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, China
| | - Ya-Li Li
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Lilan Cui
- Novoprotein Scientific Inc., Shanghai, China
| | - Zhuangzhuang Zhao
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Mi Wang
- Novoprotein Scientific Inc., Shanghai, China
| | - Bin Wang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Rong Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Ávila-Gálvez MÁ, Rafael-Pita C, Fernández N, Baixinho J, Anastácio JD, Cankar K, Bosch D, Nunes Dos Santos C. Targeting proteases involved in the viral replication of SARS-CoV-2 by sesquiterpene lactones from chicory ( Cichorium intybus L.). Food Funct 2022; 13:8977-8988. [PMID: 35938740 DOI: 10.1039/d2fo00933a] [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: 11/21/2022]
Abstract
SARS-CoV-2 is a highly transmissible and pathogenic coronavirus causing a respiratory disease that emerged in 2019, leading to a public health emergency situation which continues to date. The treatment options are still very limited and vaccines available are less effective against new variants. SARS-CoV-2 enzymes, namely main protease (Mpro) and papain-like protease (PLpro), play a pivotal role in the viral life cycle, making them a putative drug target. Here, we described for the first time the potential inhibitory activity of chicory extract against both proteases. Besides, we have identified that the four most abundant sesquiterpene lactones in chicory inhibited these proteases, showing an effective binding in the active sites of Mpro and PLpro. This paper provides new insight for further drug development or food-based strategies for the prevention of SARS-CoV-2 by targeting viral proteases.
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Affiliation(s)
- María Ángeles Ávila-Gálvez
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Carlos Rafael-Pita
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Naiara Fernández
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
| | - João Baixinho
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - José D Anastácio
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Katarina Cankar
- Wageningen University and Research, Wageningen Plant Research, BU Bioscience, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Dirk Bosch
- Wageningen University and Research, Wageningen Plant Research, BU Bioscience, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Cláudia Nunes Dos Santos
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
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45
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Gyebi GA, Ogunyemi OM, Adefolalu AA, Rodríguez-Martínez A, López-Pastor JF, Banegas-Luna AJ, Pérez-Sánchez H, Adegunloye AP, Ogunro OB, Afolabi SO. African derived phytocompounds may interfere with SARS-CoV-2 RNA capping machinery via inhibition of 2'-O-ribose methyltransferase: An in silico perspective. J Mol Struct 2022; 1262:133019. [PMID: 35431328 PMCID: PMC9002684 DOI: 10.1016/j.molstruc.2022.133019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 02/07/2023]
Abstract
Despite the ongoing vaccination against the life-threatening COVID-19, there is need for viable therapeutic interventions. The S-adenosyl-l-Methionine (SAM) dependent 2-O'-ribose methyltransferase (2'-O-MTase) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a therapeutic target against COVID-19 infection. In a bid to profile bioactive principles from natural sources, a custom-made library of 226 phytochemicals from African medicinal plants with especially anti-malarial activity was screened for direct interactions with SARS-CoV-2 2'-O-MTase (S2RMT) using molecular docking and molecular dynamics (MD) simulations as well as binding free energies methods. Based on minimal binding energy lower than sinefungin (a reference methyl-transferase inhibitor) and binding mode analysis at the catalytic site of S2RMT, a list of 26 hit phytocompounds was defined. The interaction of these phytocompounds was compared with the 2'-O-MTase of SARS-CoV and MERS-CoV. Among these compounds, the lead phytocompounds (LPs) viz: mulberrofuran F, 24-methylene cycloartenol, ferulate, 3-benzoylhosloppone and 10-hydroxyusambarensine interacted strongly with the conserved KDKE tetrad within the substrate binding pocket of the 2'-O-MTase of the coronavirus strains which is critical for substrate binding. The thermodynamic parameters analyzed from the MD simulation trajectories of the LPs-S2RMT complexes presented an eminent structural stability and compactness. These LPs demonstrated favorable druggability and in silico ADMET properties over a diverse array of molecular computing descriptors. The LPs show promising prospects in the disruption of S2RMT capping machinery in silico. However, these LPs should be validated via in vitro and in vivo experimental models.
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Affiliation(s)
- Gideon A. Gyebi
- Department of Biochemistry, Bingham University, Karu, Nigeria,Corresponding authors
| | - Oludare M. Ogunyemi
- Human Nutraceuticals and Bioinformatics Research Unit, Department of Biochemistry, Salem University, Lokoja, Nigeria
| | | | - Alejandro Rodríguez-Martínez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), Spain
| | - Juan F. López-Pastor
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), Spain
| | - Antonio J. Banegas-Luna
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), Spain,Corresponding authors
| | | | - Olalekan B. Ogunro
- Department of Biological Sciences, KolaDaisi University, Ibadan, Nigeria
| | - Saheed O. Afolabi
- Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences University of Ilorin, Ilorin, Nigeria
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46
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Gupta A, Sahu N, Singh AP, Singh VK, Singh SC, Upadhye VJ, Mathew AT, Kumar R, Sinha RP. Exploration of Novel Lichen Compounds as Inhibitors of SARS-CoV-2 Mpro: Ligand-Based Design, Molecular Dynamics, and ADMET Analyses. Appl Biochem Biotechnol 2022; 194:6386-6406. [PMID: 35921031 PMCID: PMC9346229 DOI: 10.1007/s12010-022-04103-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2022] [Indexed: 11/02/2022]
Abstract
In the year 2019-2020, the whole world witnessed the spread of a disease called COVID-19 caused by SARS-CoV-2. A number of effective drugs and vaccine has been formulated to combat this outbreak. For the development of anti-COVID-19 drugs, the main protease (Mpro) is considered a key target as it has rare mutations and plays a crucial role in the replication of the SARS CoV-2. In this study, a library of selected lichen compounds was prepared and used for virtual screening against SARS-CoV-2 Mpro using molecular docking, and several hits as potential inhibitors were identified. Remdesivir was used as a standard inhibitor of Mpro for its comparison with the identified hits. Twenty-six compounds were identified as potential hits against Mpro, and these were subjected to in silico ADMET property prediction, and the compounds having favorable properties were selected for further analysis. After manual inspection of their interaction with the binding pocket of Mpro and binding affinity score, four compounds, namely, variolaric acid, cryptostictinolide, gyrophoric acid, and usnic acid, were selected for molecular dynamics study to evaluate the stability of complex. The molecular dynamics results indicated that except cryptostictinolide, all the three compounds made a stable complex with Mpro throughout a 100-ns simulation time period. Among all, usnic acid seems to be more stable and effective against SARS-CoV-2 Mpro. In summary, our findings suggest that usnic acid, variolaric acid, and gyrophoric acid have potential to inhibit SARS-Cov-2 Mpro and act as a lead compounds for the development of antiviral drug candidates against SARS-CoV-2.
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Affiliation(s)
- Amit Gupta
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Niharika Sahu
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ashish P Singh
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vinay Kumar Singh
- School of Biotechnology, Centre for Bioinformatics, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Suresh C Singh
- Pathkits Healthcare Pvt. Ltd, Electronic City Sector-18, Gurgaon, 122001, India
| | - Vijay J Upadhye
- Parul University (Waghodia), Vadodara, 391760, Gujarat, India
| | - Alen T Mathew
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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47
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More-Adate P, Lokhande KB, Swamy KV, Nagar S, Baheti A. GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 Mpro. Comput Biol Med 2022; 147:105679. [PMID: 35667152 PMCID: PMC9158327 DOI: 10.1016/j.compbiomed.2022.105679] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 was originally identified in Wuhan city of China in December 2019 and it spread rapidly throughout the globe, causing a threat to human life. Since targeted therapies are deficient, scientists all over the world have an opportunity to develop novel drug therapies to combat COVID-19. After the declaration of a global medical emergency, it was established that the Food and Drug Administration (FDA) could permit the use of emergency testing, treatments, and vaccines to decrease suffering, and loss of life, and restore the nation's health and security. The FDA has approved the use of remdesivir and its analogs as an antiviral medication, to treat COVID-19. The primary protease of SARS-CoV-2, which has the potential to regulate coronavirus proliferation, has been a viable target for the discovery of medicines against SARS-CoV-2. The present research deals with the in silico technique to screen phytocompounds from a traditional medicinal plant, Bauhinia variegata for potential inhibitors of the SARS-CoV-2 main protease. Dried leaves of the plant B. variegata were used to prepare aqueous and methanol extract and the constituents were analyzed using the GC-MS technique. A total of 57 compounds were retrieved from the aqueous and methanol extract analysis. Among these, three lead compounds (2,5 dimethyl 1-H Pyrrole, 2,3 diphenyl cyclopropyl methyl phenyl sulphoxide, and Benzonitrile m phenethyl) were shown to have the highest binding affinity (−5.719 to −5.580 kcal/mol) towards SARS-CoV-2 Mpro. The post MD simulation results also revealed the favorable confirmation and stability of the selected lead compounds with Mpro as per trajectory analysis. The Prime MM/GBSA binding free energy supports this finding, the top lead compound 2,3 diphenyl cyclopropyl methyl phenyl sulphoxide showed high binding free energy (−64.377 ± 5.24 kcal/mol) towards Mpro which reflects the binding stability of the molecule with Mpro. The binding free energy of the complexes was strongly influenced by His, Gln, and Glu residues. All of the molecules chosen are found to have strong pharmacokinetic characteristics and show drug-likeness properties. The lead compounds present acute toxicity (LD50) values ranging from 670 mg/kg to 2500 mg/kg; with toxicity classifications of 4 and 5 classes. Thus, these compounds could behave as probable lead candidates for treatment against SARS-CoV-2. However further in vitro and in vivo studies are required for the development of medication against SARS-CoV-2.
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48
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Alzyoud L, Ghattas MA, Atatreh N. Allosteric Binding Sites of the SARS-CoV-2 Main Protease: Potential Targets for Broad-Spectrum Anti-Coronavirus Agents. Drug Des Devel Ther 2022; 16:2463-2478. [PMID: 35941927 PMCID: PMC9356625 DOI: 10.2147/dddt.s370574] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/23/2022] [Indexed: 12/23/2022] Open
Abstract
The current pandemic caused by the COVID-19 disease has reached everywhere in the world and has affected every aspect of our lives. As of the current data, the World Health Organization (WHO) has reported more than 300 million confirmed COVID-19 cases worldwide and more than 5 million deaths. Mpro is an enzyme that plays a key role in the life cycle of the SARS-CoV-2 virus, and it is vital for the disease progression. The Mpro enzyme seems to have several allosteric sites that can hinder the enzyme catalytic activity. Furthermore, some of these allosteric sites are located at or nearby the dimerization interface which is essential for the overall Mpro activity. In this review paper, we investigate the potential of the Mpro allosteric site to act as a drug target, especially since they interestingly appear to be resistant to mutation. The work is illustrated through three subsequent sections: First, the two main categories of Mpro allosteric sites have been explained and discussed. Second, a total of six pockets have been studied and evaluated for their druggability and cavity characteristics. Third, the experimental and computational attempts for the discovery of new allosteric inhibitors have been illustrated and discussed. To sum up, this review paper gives a detailed insight into the feasibility of developing new Mpro inhibitors to act as a potential treatment for the COVID-19 disease.
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Affiliation(s)
- Lara Alzyoud
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- Correspondence: Mohammad A Ghattas; Noor Atatreh, Email ;
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
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49
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Mahmood RA, Hasan A, Rahmatullah M, Paul AK, Jahan R, Jannat K, Bondhon TA, Mahboob T, Nissapatorn V, de Lourdes Pereira M, Paul TK, Rumi OH, Wiart C, Wilairatana P. Solanaceae Family Phytochemicals as Inhibitors of 3C-Like Protease of SARS-CoV-2: An In Silico Analysis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154739. [PMID: 35897915 PMCID: PMC9331421 DOI: 10.3390/molecules27154739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022]
Abstract
COVID-19, caused by the coronavirus SARS-CoV-2, emerged in late December 2019 in Wuhan, China. As of 8 April 2022, the virus has caused a global pandemic, resulting in 494,587,638 infections leading to 6,170,283 deaths around the world. Although several vaccines have received emergency authorization from USA and UK drug authorities and two more in Russia and China, it is too early to comment on the prolonged effectiveness of the vaccines, their availability, and affordability for the developing countries of the world, and the daunting task to vaccinate 7 billion people of the world with two doses of the vaccine with additional booster doses. As a result, it is still worthwhile to search for drugs and several promising leads have been found, mainly through in silico studies. In this study, we have examined the binding energies of several alkaloids and anthocyanin derivatives from the Solanaceae family, a family which contains common consumable vegetables and fruit items such as eggplant, pepper, and tomatoes. Our study demonstrates that Solanaceae family alkaloids such as incanumine and solaradixine, as well as anthocyanins and anthocyanidins, have very high predicted binding energies for the 3C-like protease of SARS-CoV-2 (also known as Mpro). Since Mpro is vital for SARS-CoV-2 replication, the compounds merit potential for further antiviral research towards the objective of obtaining affordable drugs.
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Affiliation(s)
- Raisul Awal Mahmood
- Department of Chemistry, Bangladesh University of Engineering & Technology, Dhaka 1000, Bangladesh;
| | - Anamul Hasan
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
- Correspondence: (M.R.); (M.d.L.P.)
| | - Alok K. Paul
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, TAS 7001, Australia
| | - Rownak Jahan
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Khoshnur Jannat
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Tohmina Afroze Bondhon
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Tooba Mahboob
- School of Allied Health Sciences and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat 80160, Thailand; (T.M.); (V.N.)
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat 80160, Thailand; (T.M.); (V.N.)
| | - Maria de Lourdes Pereira
- Department of Medical Sciences, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (M.R.); (M.d.L.P.)
| | - Tridib K. Paul
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Ommay Hany Rumi
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Christophe Wiart
- Institute for Tropical Biology and Conservation, Universiti Malaysia, Kota Kinabalu 88400, Sabah, Malaysia;
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
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50
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Bio-Guided Isolation of SARS-CoV-2 Main Protease Inhibitors from Medicinal Plants: In Vitro Assay and Molecular Dynamics. PLANTS 2022; 11:plants11151914. [PMID: 35893619 PMCID: PMC9332707 DOI: 10.3390/plants11151914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022]
Abstract
Since the emergence of the pandemic of the coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the discovery of antiviral phytoconstituents from medicinal plants against SARS-CoV-2 has been comprehensively researched. In this study, thirty-three plants belonging to seventeen different families used traditionally in Saudi Arabia were tested in vitro for their ability to inhibit the SARS-CoV-2 main protease (MPRO). Major constituents of the bio-active extracts were isolated and tested for their inhibition potential against this enzyme; in addition, their antiviral activity against the SARS-CoV-2 Egyptian strain was assessed. Further, the thermodynamic stability of the best active compounds was studied through focused comparative insights for the active metabolites regarding ligand–target binding characteristics at the molecular level. Additionally, the obtained computational findings provided useful directions for future drug optimization and development. The results revealed that Psiadia punctulata, Aframomum melegueta, and Nigella sativa extracts showed a high percentage of inhibition of 66.4, 58.7, and 31.5%, against SARS-CoV-2 MPRO, respectively. The major isolated constituents of these plants were identified as gardenins A and B (from P. punctulata), 6-gingerol and 6-paradol (from A. melegueta), and thymoquinone (from N. sativa). These compounds are the first to be tested invitro against SARS-CoV-2 MPRO. Among the isolated compounds, only thymoquinone (THY), gardenin A (GDA), 6-gingerol (GNG), and 6-paradol (PAD) inhibited the SARS-CoV-2 MPRO enzyme with inhibition percentages of 63.21, 73.80, 65.2, and 71.8%, respectively. In vitro assessment of SARS-CoV-2 (hCoV-19/Egypt/NRC-03/2020 (accession number on GSAID: EPI_ISL_430820) revealed a strong-to-low antiviral activity of the isolated compounds. THY showed relatively high cytotoxicity and was anti-SARS-CoV-2, while PAD demonstrated a cytotoxic effect on the tested VERO cells with a selectivity index of CC50/IC50 = 1.33 and CC50/IC50 = 0.6, respectively. Moreover, GNG had moderate activity at non-cytotoxic concentrations in vitro with a selectivity index of CC50/IC50 = 101.3/43.45 = 2.3. Meanwhile, GDA showed weak activity with a selectivity index of CC50/IC50 = 246.5/83.77 = 2.9. The thermodynamic stability of top-active compounds revealed preferential stability and SARS-CoV-2 MPRO binding affinity for PAD through molecular-docking-coupled molecular dynamics simulation. The obtained results suggest the treating potential of these plants and/or their active metabolites for COVID-19. However, further in-vivo and clinical investigations are required to establish the potential preventive and treatment effectiveness of these plants and/or their bio-active compounds in COVID-19.
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