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Yu W, Yi SZ, Jiang CY, Guan JW, Xue R, Zhang XX, Zeng T, Tang H, Chen W, Han B. Biosensor-based active ingredient recognition system for screening potential small molecular Severe acute respiratory syndrome coronavirus 2 entry blockers targeting the spike protein from Rugosa rose. Biomed Chromatogr 2024:e5987. [PMID: 39126351 DOI: 10.1002/bmc.5987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
The traditional formulation Hanchuan zupa granules (HCZPs) have been widely used for controlling coronavirus disease 2019 (COVID-19). However, its active components remain unknown. Here, HCZP components targeting the spike receptor-binding domain (S-RBD) of SARS-CoV-2 were investigated using a surface plasmon resonance (SPR) biosensor-based active ingredient recognition system (SPR-AIRS). Recombinant S-RBD proteins were immobilized on the SPR chip by amine coupling for the prescreening of nine HCZP medicinal herbs. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) identified gallic acid (GA) and methyl gallate (MG) from Rosa rugosa as S-RBD ligands, with KD values of 2.69 and 0.95 μM, respectively, as shown by SPR. Molecular dynamics indicated that GA formed hydrogen bonds with G496, N501, and Y505 of S-RBD, and MG with G496 and Y505, inhibiting S-RBD binding to angiotensin-converting enzyme 2 (ACE2). SPR-based competition analysis verified that both compounds blocked S-RBD and ACE2 binding, and SPR demonstrated that GA and MG bound to ACE2 (KD = 5.10 and 4.05 μM, respectively), suggesting that they blocked the receptor and neutralized SARS-CoV-2. Infection with SARS-CoV-2 pseudovirus showed that GA and MG suppressed viral entry into 293T-ACE2 cells. These S-RBD inhibitors have potential for drug design, while the findings provide a reference on HCZP composition and its use for treating COVID-19.
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Affiliation(s)
- Wei Yu
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Sheng-Zhe Yi
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Cheng-Yu Jiang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Jia-Wei Guan
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Rui Xue
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Xu-Xuan Zhang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Tao Zeng
- Corps Center for Food and Drug Evaluation and Verification, Xinjiang Production and Construction Corps Market Supervision Administration, Urumqi, China
| | - Hui Tang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Wen Chen
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Bo Han
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
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Saldarriaga-Córdoba M, Clavero-León C, Rey-Suarez P, Nuñez-Rangel V, Avendaño-Herrera R, Solano-González S, Alzate JF. Unveiling Novel Kunitz- and Waprin-Type Toxins in the Micrurus mipartitus Coral Snake Venom Gland: An In Silico Transcriptome Analysis. Toxins (Basel) 2024; 16:224. [PMID: 38787076 PMCID: PMC11126030 DOI: 10.3390/toxins16050224] [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: 03/06/2024] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Kunitz-type peptide expression has been described in the venom of snakes of the Viperidae, Elapidae and Colubridae families. This work aimed to identify these peptides in the venom gland transcriptome of the coral snake Micrurus mipartitus. Transcriptomic analysis revealed a high diversity of venom-associated Kunitz serine protease inhibitor proteins (KSPIs). A total of eight copies of KSPIs were predicted and grouped into four distinctive types, including short KSPI, long KSPI, Kunitz-Waprin (Ku-WAP) proteins, and a multi-domain Kunitz-type protein. From these, one short KSPI showed high identity with Micrurus tener and Austrelaps superbus. The long KSPI group exhibited similarity within the Micrurus genus and showed homology with various elapid snakes and even with the colubrid Pantherophis guttatus. A third group suggested the presence of Kunitz domains in addition to a whey-acidic-protein-type four-disulfide core domain. Finally, the fourth group corresponded to a transcript copy with a putative 511 amino acid protein, formerly annotated as KSPI, which UniProt classified as SPINT1. In conclusion, this study showed the diversity of Kunitz-type proteins expressed in the venom gland transcriptome of M. mipartitus.
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Affiliation(s)
| | - Claudia Clavero-León
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Santiago 8320000, Chile
| | - Paola Rey-Suarez
- Grupo de Investigación en Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 50010, Colombia; (P.R.-S.); (V.N.-R.)
| | - Vitelbina Nuñez-Rangel
- Grupo de Investigación en Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 50010, Colombia; (P.R.-S.); (V.N.-R.)
- Escuela de Microbiología, Universidad de Antioquia, Medellín 50010, Colombia
| | - Ruben Avendaño-Herrera
- Facultad de Ciencias de la Vida & Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Viña del Mar 2531015, Chile;
| | - Stefany Solano-González
- Laboratorio de Bioinformática Aplicada, Escuela de Ciencias Biológicas, Universidad Nacional, Heredia 86-3000, Costa Rica
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín 50010, Colombia;
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Anwar HM, Salem GEM, Abd El-Latief HM, Osman AAE, Ghanem SK, Khan H, Chavanich S, Darwish A. Therapeutic potential of proteases in acute lung injury and respiratory distress syndrome via TLR4/Nrf2/NF-kB signaling modulation. Int J Biol Macromol 2024; 267:131153. [PMID: 38574930 DOI: 10.1016/j.ijbiomac.2024.131153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/02/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
The COVID-19 pandemic has drawn attention to acute lung injury and respiratory distress syndrome as major causes of death, underscoring the urgent need for effective treatments. Protease enzymes possess a wide range of beneficial effects, including antioxidant, anti-inflammatory, antifibrotic, and fibrinolytic effects. This study aimed to evaluate the potential therapeutic effects of bacterial protease and chymotrypsin in rats in mitigating acute lung injury induced by lipopolysaccharide. Molecular docking was employed to investigate the inhibitory effect of bacterial protease and chymotrypsin on TLR-4, the receptor for lipopolysaccharide. Bacterial protease restored TLR-4, Nrf2, p38 MAPK, NF-kB, and IKK-β levels to normal levels, while chymotrypsin normalized TLR-4, IKK-β, IL-6, and IL-17 levels. The expression of TGF-β, caspase-3, and VEGF in the bacterial protease- and chymotrypsin-treated groups was markedly reduced. Our results suggest that both therapies ameliorate LPS-induced acute lung injury and modulate the TLR4/Nrf2/NF-k signaling pathway. Each protease exhibited distinct mechanisms, with bacterial protease showing a better response to oxidative stress, edema, and fibrosis, whereas chymotrypsin provided a better response in the acute phase and innate immunity. These findings highlight the potential of each protease as a promising therapeutic option for acute lung injury and respiratory distress syndrome.
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Affiliation(s)
- Hend Mohamed Anwar
- Department of Biochemistry, Egyptian Drug Authority (EDA), Former National Organization for Drug Control and Research (NODCAR), Giza 11221, Egypt
| | - Gad Elsayed Mohamed Salem
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hanan M Abd El-Latief
- Zoology Department, Women's College for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - Amany Abd Elhameid Osman
- Zoology Department, Women's College for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - Sahar K Ghanem
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Sohag University, Egypt
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan 23200, Pakistan.
| | - Suchana Chavanich
- Reef Biology Research Group, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand.
| | - Alshaymaa Darwish
- Biochemistry Department, Faculty of Pharmacy, Sohag University, Sohag, Egypt.
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Mushtaq M, Ali B, Ali M, BiBi N, Raut R, Suliman GM, Swelum AA. Different levels of single-strain probiotic (Bacillus subtilis) with proteolytic enzyme (serratiopeptidase) can be used as an alternative to antibiotic growth promoters in broiler. Poult Sci 2024; 103:103400. [PMID: 38295498 PMCID: PMC10844863 DOI: 10.1016/j.psj.2023.103400] [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: 11/25/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024] Open
Abstract
In the current study, the proteolytic enzyme (serratiopeptidase) was used to enhance the efficacy of Bacillus subtilis (B. subtilis) probiotic as a growth promotor in broiler chicken. The effects of serratiopeptidase on the efficacy of different levels of B. subtilis as a growth promotor in broiler chicks were evaluated regarding growth performance traits, villus histomorphometric characterization, and intestinal microbiota count. Day-old broiler chicks (n = 120) were allocated into 4 groups having 3 replicates/group. In the control group (C), the basal diet was kept without supplementation. In treatment groups (P100, P150, and P200), the basal diet was supplemented with 100, 150, and 200 mg probiotics, respectively besides 30 mg proteolytic enzyme in the 3 treated groups for 4 wk. The performance parameters were significantly affected by the supplementation of serratiopeptidase to the B. subtilis treatment groups. Feed intake (FI), body weight gain (WG), feed conversion ratio (FCR), and dressing percent were significantly improved in the treatment groups as compared to the control group. Significantly, the lowest feed intake was recorded for the P200 group. The highest body weight gain and dressing percentage were recorded for the P200 group. An improved FCR was recorded in the P200 group (1.7) as compared to the control group. The different levels of B. subtilis supplemented with serratiopeptidase revealed significant improvements (P<0.05) in the morphology of the intestine by showing increases in villus height and width and crypt depth of the small intestine. The microbial count revealed that E. coli and salmonella colonies were significantly reduced in the P200 group as compared to the control and other treatment groups. In conclusion, the supplementation of B. subtilis with serratiopeptidase as a growth promoter in broiler chicks significantly improved the overall performance, and intestinal health and reduced microbial load contributing to optimizing the performance of broiler chickens. The greatest improvement was observed in the P200 group fed with B. subtilis as a probiotic and serratiopeptidase enzyme (200 mg:30 mg).
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Affiliation(s)
- Muhammad Mushtaq
- Faculty of Animal Husbandry and Veterinary Sciences, University of Agriculture, Peshawar, Pakistan
| | - Baseerat Ali
- Faculty of Animal Husbandry and Veterinary Sciences, University of Agriculture, Peshawar, Pakistan
| | - Majid Ali
- Faculty of Animal Husbandry and Veterinary Sciences, University of Agriculture, Peshawar, Pakistan
| | - Neelam BiBi
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Rabin Raut
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 3720 USA
| | - Gamaleldin M Suliman
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ayman A Swelum
- Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
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5
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Zhang Y, Bharathi V, Dokoshi T, de Anda J, Ursery LT, Kulkarni NN, Nakamura Y, Chen J, Luo EWC, Wang L, Xu H, Coady A, Zurich R, Lee MW, Matsui T, Lee H, Chan LC, Schepmoes AA, Lipton MS, Zhao R, Adkins JN, Clair GC, Thurlow LR, Schisler JC, Wolfgang MC, Hagan RS, Yeaman MR, Weiss TM, Chen X, Li MMH, Nizet V, Antoniak S, Mackman N, Gallo RL, Wong GCL. Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes. Proc Natl Acad Sci U S A 2024; 121:e2300644120. [PMID: 38306481 PMCID: PMC10861912 DOI: 10.1073/pnas.2300644120] [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: 01/14/2023] [Accepted: 10/28/2023] [Indexed: 02/04/2024] Open
Abstract
It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to the strong but ineffective inflammatory response that characterizes severe Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse cell types, including cells without angiotensin-converting enzyme 2 receptors necessary for infection. Proteolytic degradation of SARS-CoV-2 virions is a milestone in host viral clearance, but the impact of remnant viral peptide fragments from high viral loads is not known. Here, we examine the inflammatory capacity of fragmented viral components from the perspective of supramolecular self-organization in the infected host environment. Interestingly, a machine learning analysis to SARS-CoV-2 proteome reveals sequence motifs that mimic host antimicrobial peptides (xenoAMPs), especially highly cationic human cathelicidin LL-37 capable of augmenting inflammation. Such xenoAMPs are strongly enriched in SARS-CoV-2 relative to low-pathogenicity coronaviruses. Moreover, xenoAMPs from SARS-CoV-2 but not low-pathogenicity homologs assemble double-stranded RNA (dsRNA) into nanocrystalline complexes with lattice constants commensurate with the steric size of Toll-like receptor (TLR)-3 and therefore capable of multivalent binding. Such complexes amplify cytokine secretion in diverse uninfected cell types in culture (epithelial cells, endothelial cells, keratinocytes, monocytes, and macrophages), similar to cathelicidin's role in rheumatoid arthritis and lupus. The induced transcriptome matches well with the global gene expression pattern in COVID-19, despite using <0.3% of the viral proteome. Delivery of these complexes to uninfected mice boosts plasma interleukin-6 and CXCL1 levels as observed in COVID-19 patients.
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Affiliation(s)
- Yue Zhang
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
- Biomedical Engineering, School of Engineering, Westlake University, Hangzhou, Zhejiang310012, China
| | - Vanthana Bharathi
- University of North Carolina Blood Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Tatsuya Dokoshi
- Department of Dermatology, University of California San Diego, La Jolla, CA92093
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Lauryn Tumey Ursery
- University of North Carolina Blood Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Nikhil N. Kulkarni
- Department of Dermatology, University of California San Diego, La Jolla, CA92093
| | - Yoshiyuki Nakamura
- Department of Dermatology, University of California San Diego, La Jolla, CA92093
| | - Jonathan Chen
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Elizabeth W. C. Luo
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Lamei Wang
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Hua Xu
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Alison Coady
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Raymond Zurich
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Michelle W. Lee
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
| | - HongKyu Lee
- Division of Molecular Medicine, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
| | - Liana C. Chan
- Division of Molecular Medicine, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
- Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Institute for Infection & Immunity, Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, CA90502
| | - Athena A. Schepmoes
- Environmental Molecular Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Mary S. Lipton
- Environmental Molecular Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Rui Zhao
- Environmental Molecular Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Joshua N. Adkins
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Geremy C. Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Lance R. Thurlow
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jonathan C. Schisler
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Matthew C. Wolfgang
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Robert S. Hagan
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Michael R. Yeaman
- Division of Molecular Medicine, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
- Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Institute for Infection & Immunity, Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, CA90502
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
| | - Xinhua Chen
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Melody M. H. Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Silvio Antoniak
- Department of Pathology and Laboratory Medicine, University of North Carolina Blood Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Nigel Mackman
- University of North Carolina Blood Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Richard L. Gallo
- Department of Dermatology, University of California San Diego, La Jolla, CA92093
| | - Gerard C. L. Wong
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
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Alzyoud L, Mahgoub RE, Mohamed FE, Ali BR, Ferreira J, Rabeh WM, Atatreh N, Ghattas MA. The Discovery of Novel Small Oxindole-Based Inhibitors Targeting the SARS-CoV-2 Main Protease (M pro ). Chem Biodivers 2023; 20:e202301176. [PMID: 37861105 DOI: 10.1002/cbdv.202301176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/14/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
With the potential for coronaviruses to re-emerge and trigger future pandemics, the urgent development of antiviral inhibitors against SARS-CoV-2 is essential. The Mpro enzyme is crucial for disease progression and the virus's life cycle. It possesses allosteric sites that can hinder its catalytic activity, with some of these sites located at or near the dimerization interface. Among them, sites #2 and #5 possess druggable pockets and are predicted to bind drug-like molecules. Consequently, a commercially available ligand library containing ~7 million ligands was used to target site #2 via structure-based virtual screening. After extensive filtering, docking, and post-docking analyses, 53 compounds were chosen for biological testing. An oxindole derivative was identified as a Mpro non-competitive reversible inhibitor with a Ki of 115 μM and an IC50 of 101.9 μM. Throughout the 200 ns-long MD trajectories, our top hit has shown a very stable binding mode, forming several interactions with residues in sites #2 and #5. Moreover, derivatives of our top hit were acquired for biological testing to gain deeper insights into their structure-activity relationship. To sum up, drug-like allosteric inhibitors seem promising and can provide us with an additional weapon in our war against the recent pandemic, and possibly other coronaviruses-caused diseases.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
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7
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Jain R, Mathew D. Mechanisms influencing the high prevalence of COVID-19 in diabetics: A systematic review. MEDICAL RESEARCH ARCHIVES 2023; 11:4540. [PMID: 38933091 PMCID: PMC11198970 DOI: 10.18103/mra.v11i10.4540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Diabetics have an increased risk of contracting COVID-19 infection and tend to have more severe symptoms. This systematic review explores the potential mechanisms influencing the high prevalence of COVID-19 infections in individuals with diabetes. It reviews the emerging evidence about the interactions between viral and diabetic pathways, particularly how diabetes physiology could contribute to higher viral reception, viral entry and pathogenicity, and the severity of disease symptoms. Finally, it examines the challenges we face in studying these mechanisms and offers new strategies that might assist our fight against current and future pandemics.
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Affiliation(s)
- Roshni Jain
- Cell and Molecular Biology Program, University of Nevada, Reno, NV 89557
- Department of Biology, University of Nevada, Reno, NV 89557
| | - Dennis Mathew
- Cell and Molecular Biology Program, University of Nevada, Reno, NV 89557
- Department of Biology, University of Nevada, Reno, NV 89557
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8
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Wang Y, Guo H, Wang G, Zhai J, Du B. COVID-19 as a Trigger for Type 1 Diabetes. J Clin Endocrinol Metab 2023; 108:2176-2183. [PMID: 36950864 DOI: 10.1210/clinem/dgad165] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Type 1 diabetes (T1D) is usually caused by immune-mediated destruction of islet β cells, and genetic and environmental factors are thought to trigger autoimmunity. Convincing evidence indicates that viruses are associated with T1D development and progression. During the COVID-19 pandemic, cases of hyperglycemia, diabetic ketoacidosis, and new diabetes increased, suggesting that SARS-CoV-2 may be a trigger for or unmask T1D. Possible mechanisms of β-cell damage include virus-triggered cell death, immune-mediated loss of pancreatic β cells, and damage to β cells because of infection of surrounding cells. This article examines the potential pathways by which SARS-CoV-2 affects islet β cells in these 3 aspects. Specifically, we emphasize that T1D can be triggered by SARS-CoV-2 through several autoimmune mechanisms, including epitope spread, molecular mimicry, and bystander activation. Given that the development of T1D is often a chronic, long-term process, it is difficult to currently draw firm conclusions as to whether SARS-CoV-2 causes T1D. This area needs to be focused on in terms of the long-term outcomes. More in-depth and comprehensive studies with larger cohorts of patients and long-term clinical follow-ups are required.
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Affiliation(s)
- Yichen Wang
- Department of Endocrinology, Lequn Branch, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hui Guo
- Department of Endocrinology, Lequn Branch, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Gongquan Wang
- Department of Cardiology, Lequn Branch, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Jiawei Zhai
- Department of Cardiology, Lequn Branch, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Bing Du
- Department of Cardiology, Lequn Branch, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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9
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Dileepan KN, Raveendran VV, Sharma R, Abraham H, Barua R, Singh V, Sharma R, Sharma M. Mast cell-mediated immune regulation in health and disease. Front Med (Lausanne) 2023; 10:1213320. [PMID: 37663654 PMCID: PMC10470157 DOI: 10.3389/fmed.2023.1213320] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/17/2023] [Indexed: 09/05/2023] Open
Abstract
Mast cells are important components of the immune system, and they perform pro-inflammatory as well as anti-inflammatory roles in the complex process of immune regulation in health and disease. Because of their strategic perivascular localization, sensitivity and adaptability to the microenvironment, and ability to release a variety of preformed and newly synthesized effector molecules, mast cells perform unique functions in almost all organs. Additionally, Mast cells express a wide range of surface and cytoplasmic receptors which enable them to respond to a variety of cytokines, chemicals, and pathogens. The mast cell's role as a cellular interface between external and internal environments as well as between vasculature and tissues is critical for protection and repair. Mast cell interactions with different immune and nonimmune cells through secreted inflammatory mediators may also turn in favor of disease promoting agents. First and forefront, mast cells are well recognized for their multifaceted functions in allergic diseases. Reciprocal communication between mast cells and endothelial cells in the presence of bacterial toxins in chronic/sub-clinical infections induce persistent vascular inflammation. We have shown that mast cell proteases and histamine induce endothelial inflammatory responses that are synergistically amplified by bacterial toxins. Mast cells have been shown to exacerbate vascular changes in normal states as well as in chronic or subclinical infections, particularly among cigarette smokers. Furthermore, a potential role of mast cells in SARS-CoV-2-induced dysfunction of the capillary-alveolar interface adds to the growing understanding of mast cells in viral infections. The interaction between mast cells and microglial cells in the brain further highlights their significance in neuroinflammation. This review highlights the significant role of mast cells as the interface that acts as sensor and early responder through interactions with cells in systemic organs and the nervous system.
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Affiliation(s)
- Kottarappat N. Dileepan
- Division of Allergy, Clinical Immunology and Rheumatology, Department of Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Vineesh V. Raveendran
- Division of Allergy, Clinical Immunology and Rheumatology, Department of Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Rishi Sharma
- Department of Medicine, School of Medicine, University of Missouri, Kansas City, MO, United States
| | - Harita Abraham
- Division of Allergy, Clinical Immunology and Rheumatology, Department of Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Rajat Barua
- Cardiology Section, Kansas City Veterans Affairs Medical Center, Kansas City, MO, United States
| | - Vikas Singh
- Neurology Section, Kansas City Veterans Affairs Medical Center, Kansas City, MO, United States
| | - Ram Sharma
- Research and Development Service, Kansas City Veterans Affairs Medical Center, Kansas City, MO, United States
| | - Mukut Sharma
- Research and Development Service, Kansas City Veterans Affairs Medical Center, Kansas City, MO, United States
- Midwest Veterans’ Biomedical Research Foundation (MVBRF), Kansas City VA Medical Center, Kansas, MO, United States
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10
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Neves RL, Branquinho J, Arata JG, Bittencourt CA, Gomes CP, Riguetti M, da Mata GF, Fernandes DE, Icimoto MY, Kirsztajn GM, Pesquero JB. ACE2, ACE, DPPIV, PREP and CAT L enzymatic activities in COVID-19: imbalance of ACE2/ACE ratio and potential RAAS dysregulation in severe cases. Inflamm Res 2023; 72:1719-1731. [PMID: 37537367 DOI: 10.1007/s00011-023-01775-3] [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: 05/19/2023] [Revised: 07/07/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
OBJECTIVE AND DESIGN Circulating enzymatic activity and RAAS regulation in severe cases of COVID-19 remains unclear, therefore we measured the serum activity of several proteases as potential targets to control the SARS-CoV-2 infection. MATERIAL OR SUBJECTS 152 patients with COVID-19-like symptoms were grouped according to the severity of symptoms (COVID-19 negative, mild, moderate and severe). METHODS Serum samples of COVID-19 patients and controls were subjected to biochemical analysis and enzymatic assays of ACE2, ACE, DPPIV, PREP and CAT L. One-way ANOVA and multivariate logistic regression analysis were used. Statistical significance was accepted at p < 0.05. RESULTS We detected a positive correlation among comorbidities, higher C-reactive protein (CRP) and D-dimer levels with disease severity. Enzymatic assays revealed an increase in serum ACE2 and CAT L activities in severe COVID-19 patients, while ACE, DPPIV and PREP activities were significantly reduced. Notably, analysis of ACE2/ACE activity ratio suggests a possible imbalance of ANG II/ANG(1-7) ratio, in a positive association with the disease severity. CONCLUSION Our findings reveal a correlation between proteases activity and the severity of COVID-19. These enzymes together contribute to the activation of pro-inflammatory pathways, trigger a systemic activation of inflammatory mediators, leading to a RAAS dysregulation and generating a significant damage in several organs, contributing to poor outcomes of severe cases.
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Affiliation(s)
- Raquel Leão Neves
- Department of Biophysics, Center for Research and Molecular Diagnostic of Genetic Diseases, Federal University of São Paulo, São Paulo, Brazil
| | - Jéssica Branquinho
- Department of Biophysics, Center for Research and Molecular Diagnostic of Genetic Diseases, Federal University of São Paulo, São Paulo, Brazil
| | - Júlia Galanakis Arata
- Department of Biophysics, Center for Research and Molecular Diagnostic of Genetic Diseases, Federal University of São Paulo, São Paulo, Brazil
| | - Clarissa Azevedo Bittencourt
- Department of Biophysics, Center for Research and Molecular Diagnostic of Genetic Diseases, Federal University of São Paulo, São Paulo, Brazil
| | - Caio Perez Gomes
- Department of Biophysics, Center for Research and Molecular Diagnostic of Genetic Diseases, Federal University of São Paulo, São Paulo, Brazil
| | - Michelle Riguetti
- Division of Nephrology, Department of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Gustavo Ferreira da Mata
- Division of Nephrology, Department of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | | | | | | | - João Bosco Pesquero
- Department of Biophysics, Center for Research and Molecular Diagnostic of Genetic Diseases, Federal University of São Paulo, São Paulo, Brazil.
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11
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Song JY, Huang JY, Hsu YC, Lo MT, Lin C, Shen TC, Liao MT, Lu KC. Coronavirus disease 2019 and cardiovascular disease. Tzu Chi Med J 2023; 35:213-220. [PMID: 37545802 PMCID: PMC10399840 DOI: 10.4103/tcmj.tcmj_219_22] [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: 08/13/2022] [Revised: 10/28/2022] [Accepted: 05/17/2023] [Indexed: 08/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus behind the coronavirus disease 2019 (COVID-19) pandemic, is a type of RNA virus that is nonsegmented. Cardiovascular diseases (CVDs) increase the mortality risk of patients. In this review article, we overview the existing evidence regarding the potential mechanisms of myocardial damage in coronavirus disease 2019 (COVID-19) patients. Having a comprehensive knowledge of the cardiovascular damage caused by SARS-CoV-2 and its underlying mechanisms is essential for providing prompt and efficient treatment, ultimately leading to a reduction in mortality rates. Severe COVID-19 causes acute respiratory distress syndrome and shock in patients. In addition, awareness regarding COVID-19 cardiovascular manifestations has increased, including the adverse impact on prognosis with cardiovascular involvement. Angiotensin-converting enzyme 2 receptor may play a role in acute myocardial injury caused by SARS-CoV-2 infection. COVID-19 patients experiencing heart failure may have their condition exacerbated by various contributing factors and mechanisms. Increased oxygen demand, myocarditis, stress cardiomyopathy, elevated pulmonary pressures, and venous thrombosis are potential health issues. The combination of these factors may lead to COVID-19-related cardiogenic shock, resulting in acute systolic heart failure. Extracorporeal membrane oxygenation (ECMO) and left ventricular assist devices (LVADs) are treatment options when inotropic support fails for effective circulatory support. To ensure effective COVID-19-related cardiovascular disease (CVD) surveillance, it is crucial to closely monitor the future host adaptation, viral evolution, and transmissibility of SARS-CoV-2, given the virus's pandemic potential.
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Affiliation(s)
- Jenn-Yeu Song
- Division of Cardiovascular Surgery, Department of Surgery, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Jian-You Huang
- School of Medicine, Tzu Chi University, Hualien, Taiwan
- Department of Anesthesiology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Yi-Chiung Hsu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Men-Tzung Lo
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Chen Lin
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Ta-Chung Shen
- Division of Cardiovascular Surgery, Department of Surgery, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Min-Tser Liao
- Department of Pediatrics, Taoyuan Armed Forces General Hospital Hsinchu Branch, Hsinchu, Taiwan
- Department of Pediatrics, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
- Department of Pediatrics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
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12
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Pal T, Anand U, Sikdar Mitra S, Biswas P, Tripathi V, Proćków J, Dey A, Pérez de la Lastra JM. Harnessing and bioprospecting botanical-based herbal medicines against potential drug targets for COVID-19: a review coupled molecular docking studies. J Biomol Struct Dyn 2023:1-23. [PMID: 37105230 DOI: 10.1080/07391102.2023.2187634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Since the end of February 2020, the world has come to a standstill due to the virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Since then, the global scientific community has explored various remedies and treatments against this virus, including natural products that have always been a choice because of their many benefits. Various known phytochemicals are well documented for their antiviral properties. Research is being carried out to discover new natural plant products or existing ones as a treatment measure for this disease. The three important targets in this regard are-papain like protease (PLpro), spike protein, and 3 chymotrypsin like proteases (3CLpro). Various docking studies are also being elucidated to identify the phytochemicals that modulate crucial proteins of the virus. The paper is simultaneously a comprehensive review that covers recent advances in the domain of the effect of various botanically derived natural products as an alternative treatment approach against Coronavirus Disease 2019 (COVID-19). Furthermore, the docking analyses revealed that rutin (inhibitor of the major protease of SARS-CoV-2), gallocatechin (e.g., interacting with 03 hydrogen bonds with a spike-like protein), lycorine (showing the best binding affinity with amino acids GLN498, THR500 and GLY446 of the spike-like protein), and quercetrin (inhabiting at its residues ASP216, PHE219, and ILE259) are promising inhibitors of SARS‑CoV‑2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tarun Pal
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | | | - Shreya Sikdar Mitra
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Protha Biswas
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - José M Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología, IPNA-CSIC, Tenerife, Spain
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13
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Sb-doped FeOCl nanozyme-based biosensor for highly sensitive colorimetric detection of glutathione. Anal Bioanal Chem 2023; 415:1205-1219. [PMID: 36625896 DOI: 10.1007/s00216-022-04503-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/28/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023]
Abstract
Nanozymes have been emerging as substitutes for natural enzymes to construct biosensors towards biomolecular detection. However, the detection of glutathione (GSH) by nanozyme-based biosensors still remains a great challenge for research on catalytic activity enhancement and the detection mechanism. In this work, Sb-doped iron oxychloride (Sb-FeOCl) with a well-defined nanorod-like structure is prepared by high-temperature calcination. Sb-FeOCl nanorods have high peroxidase-like activity, which can catalyze the decomposition of H2O2 into ·OH and then oxidize 3,3',5,5'-tetramethylbenzidine (TMB). In view of these intriguing observations, a reliable colorimetric method with a simple mixing and detection strategy is developed for the detection of GSH. The linear range of GSH detection is 1-36 μM. The detection limit of GSH reaches a low level of 0.495 μM (3σ/slope). The GSH sensing system also exhibits excellent specificity and anti-interference. Taking advantage of the advantages of the Sb-FeOCl nanorod-based biosensor, it can be used to quantitatively detect GSH levels in human serum. It can be anticipated that the Sb-FeOCl nanorods have broad prospects in the field of enzymatic biochemical reactions.
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14
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Khan S, Nasrullah, Hussain A, Asif M, Sattar FA, Audhal FA, Qadir MI, Hamdard MH. In-silico studies of inhibitory compounds against protease enzymes of SARS-CoV-2. Medicine (Baltimore) 2023; 102:e31318. [PMID: 36820539 PMCID: PMC9907915 DOI: 10.1097/md.0000000000031318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
In December 2019, a COVID-19 outbreak caused by SARS-CoV-2 raised worldwide health concerns. In this case, molecular docking and drug repurposing computational approaches were engaged to check the efficiency of plant-based inhibitory compounds against SARS-CoV-2 main protease enzyme and papain-like protease enzyme. Twenty phytochemical inhibitory compounds were collected. Then these compounds were screened based on Lipinski's rule. As a result of this screening eleven compounds were further selected. Quantitative structure-activity relationships analysis was done before molecular docking to check especially the antiviral activity of inhibitory compounds. Docking validation of these compounds was checked by using online server Database of Useful Decoys: Enhanced. Binding affinity value, and pharmacokinetic properties of Aloin compound indicated that it can be used against main protease enzyme of SARS-CoV-2. So, it makes it a promising compound to follow further in cell and biochemical-based assays to explore its potential use against COVID-19.
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Affiliation(s)
- Saba Khan
- Institute of Molecular Biology & Biotechnology Bahauddin Zakariya University Multan, Multan, Pakistan
| | - Nasrullah
- Department of Molecular Biology and Biotechnology, CASVAB, Quetta, Pakistan
| | - Abrar Hussain
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | | | | | | | - Muhammad Imran Qadir
- Institute of Molecular Biology & Biotechnology Bahauddin Zakariya University Multan, Multan, Pakistan
| | - Muhammad Hamid Hamdard
- Faculty of Biology, Kabul University, Kabul, Afghanistan
- * Correspondence: Muahmmad Hamid Hamdard, Faculty of Biology, Kabul University, Kabul, Afghanistan (e-mail: )
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15
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Klimova EM, Bozhkov AI, Lavinska OV, Drozdova LA, Kurhuzova NI. Low molecular weight cytotoxic components (DAMPs) form the post-COVID-19 syndrome. Immunobiology 2023; 228:152316. [PMID: 36565610 PMCID: PMC9764760 DOI: 10.1016/j.imbio.2022.152316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/25/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
We studied the role of cytotoxic components (DAMPs) formed in the body of patients with COVID-19 in ensuring the long-term preservation of post-COVID-19 manifestations and the possibility of creating an experimental model by transferring DAMPs to rats. In patients with post-COVID-19 syndrome (PCS) 2 months after SARS-CoV-2 infection we determined the presence of cytotoxic components in the blood serum (Terasaki test, Dunaliella viridis test and content of DAMPs). In post-COVID-19 syndrome patients with a high content of serum cytotoxic oligopeptide fraction (selective group, n = 16) we determined the number of leukocytes, lymphocytes, neutrophil granulocytes and monocytes in the blood, the content of C-reactive protein (CRP), the concentration of C3 and C4 complement components and circulating immune complexes, the serum content of IL-6, IL -10, IL-18, TNF-α, phagocytic activity of neutrophils, presence of neutrophil traps and autoantibodies ANA. It has been shown that in patients with PCS, there are components with cytotoxicity in the blood serum, form specific immunopathological patterns, which are characterized by: an increased content of CRP, complement system components C3 and C4 and cytokines (TNF-α, IL-6, IL-10, IL-18) activation, the formation of a wide range of autoantibodies ANA, the low efficiency of endocytosis in oxygen-independent phagocytosis; their phagocytic activity reaches its functional limit, and against this background, activation of neutrophil traps occurs, which can contribute to further induction of DAMPs. This self-sustaining cell-killing activation provided long-term preservation of PCS symptoms. The transfer of blood serum components from selective group patients with PCS to rats was accompanied by the appearance of cytotoxic components in them which induced sensitization and immunopathological reactions. Preventive administration of a biologically active substance with polyfunctional properties MF to experimental animals "corrected" the initial functional state of the body's immune-metabolic system and eliminated or facilitated immuno-inflammatory reactions.
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Affiliation(s)
- Elena M Klimova
- Department of Molecular Biology and Biotechnology, V.N. Karazin National University, 4 Pl. Svobody, 61022 Kharkiv, Ukraine; Diagnostic Laboratory with Enzyme Immunoassay and Immunofluorescence Analysis, State Institution "Zaycev V.T. Institute of General and Urgent Surgery of National Academy of Medical Sciences of Ukraine", Balakireva vyizd, 1, 61103 Kharkiv, Ukraine
| | - Anatoly I Bozhkov
- Department of Molecular Biology and Biotechnology, V.N. Karazin National University, 4 Pl. Svobody, 61022 Kharkiv, Ukraine.
| | - Olena V Lavinska
- Department of Molecular Biology and Biotechnology, V.N. Karazin National University, 4 Pl. Svobody, 61022 Kharkiv, Ukraine; Diagnostic Laboratory with Enzyme Immunoassay and Immunofluorescence Analysis, State Institution "Zaycev V.T. Institute of General and Urgent Surgery of National Academy of Medical Sciences of Ukraine", Balakireva vyizd, 1, 61103 Kharkiv, Ukraine.
| | - Larisa A Drozdova
- Diagnostic Laboratory with Enzyme Immunoassay and Immunofluorescence Analysis, State Institution "Zaycev V.T. Institute of General and Urgent Surgery of National Academy of Medical Sciences of Ukraine", Balakireva vyizd, 1, 61103 Kharkiv, Ukraine
| | - Nataliia I Kurhuzova
- Department of Molecular Biology and Biotechnology, V.N. Karazin National University, 4 Pl. Svobody, 61022 Kharkiv, Ukraine.
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16
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Al Adem K, Ferreira JC, Fadl S, Rabeh WM. pH profiles of 3-chymotrypsin-like protease (3CLpro) from SARS-CoV-2 elucidate its catalytic mechanism and a histidine residue critical for activity. J Biol Chem 2022; 299:102790. [PMID: 36509143 PMCID: PMC9733303 DOI: 10.1016/j.jbc.2022.102790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
3-Chymotrypsin-like protease (3CLpro) is a promising drug target for coronavirus disease 2019 and related coronavirus diseases because of the essential role of this protease in processing viral polyproteins after infection. Understanding the detailed catalytic mechanism of 3CLpro is essential for designing effective inhibitors of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular dynamics studies have suggested pH-dependent conformational changes of 3CLpro, but experimental pH profiles of SARS-CoV-2 3CLpro and analyses of the conserved active-site histidine residues have not been reported. In this work, pH-dependence studies of the kinetic parameters of SARS-CoV-2 3CLpro revealed a bell-shaped pH profile with 2 pKa values (6.9 ± 0.1 and 9.4 ± 0.1) attributable to ionization of the catalytic dyad His41 and Cys145, respectively. Our investigation of the roles of conserved active-site histidines showed that different amino acid substitutions of His163 produced inactive enzymes, indicating a key role of His163 in maintaining catalytically active SARS-CoV-2 3CLpro. By contrast, the H164A and H172A mutants retained 75% and 26% of the activity of WT, respectively. The alternative amino acid substitutions H172K and H172R did not recover the enzymatic activity, whereas H172Y restored activity to a level similar to that of the WT enzyme. The pH profiles of H164A, H172A, and H172Y were similar to those of the WT enzyme, with comparable pKa values for the catalytic dyad. Taken together, the experimental data support a general base mechanism of SARS-CoV-2 3CLpro and indicate that the neutral states of the catalytic dyad and active-site histidine residues are required for maximum enzyme activity.
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17
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Sanusi ZK, Lobb KA. Insights into the Dynamics and Binding of Two Polyprotein Substrate Cleavage Points in the Context of the SARS-CoV-2 Main and Papain-like Proteases. Molecules 2022; 27:8251. [PMID: 36500348 PMCID: PMC9740519 DOI: 10.3390/molecules27238251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022] Open
Abstract
It is well known that vital enzymes in the replication process of the coronavirus are the SARS-CoV-2 PLpro and SARS-CoV-2 3CLpro, both of which are important targets in the search for anti-coronavirus agents. These two enzymes are responsible for cleavage at various polyprotein sites in the SARS-CoV-2 lifecycle. Herein, the dynamics of the polyprotein cleavage sequences for the boundary between non-structural proteins Nsp1 and Nsp2 (CS1) and between Nsp2 and Nsp3 (CS2) in complex with both the papain-like protein PLpro and the main protease 3CLpro were explored using computational methods. The post dynamics analysis reveals that CS1 and CS2 both have greater stability when complexed with PLpro. Of these two, greater stability is observed for the CS1-PLpro complex, while destabilization resulting in loss of CS2 from the PLpro active site is observed for CS2-PLpro, suggesting the rate of exchange by the papain-like protease is faster for CS2 compared to CS1. On the other hand, the 3CLpro main protease also reveals stability for CS1 suggesting that the main protease could also play a potential role in the cleavage at point CS1. However, destabilization occurs early in the simulation for the complex CLpro-CS2 suggesting a poor interaction and non-plausible protease cleavage of the polyprotein at CS2 by the main protease. These findings could be used as a guide in the development and design of potent COVID-19 antiviral inhibitors that mimic the CS1 cleavage site.
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Affiliation(s)
| | - Kevin Alan Lobb
- Department of Chemistry, Rhodes University, Makhanda 6140, South Africa
- Research Unit in Bioinformatics (RUBi), Rhodes University, Makhanda 6140, South Africa
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18
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Mondal S, Chen Y, Lockbaum GJ, Sen S, Chaudhuri S, Reyes AC, Lee JM, Kaur AN, Sultana N, Cameron MD, Shaffer SA, Schiffer CA, Fitzgerald KA, Thompson PR. Dual Inhibitors of Main Protease (M Pro) and Cathepsin L as Potent Antivirals against SARS-CoV2. J Am Chem Soc 2022; 144:21035-21045. [PMID: 36356199 PMCID: PMC9662648 DOI: 10.1021/jacs.2c04626] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Indexed: 11/12/2022]
Abstract
Given the current impact of SARS-CoV2 and COVID-19 on human health and the global economy, the development of direct acting antivirals is of paramount importance. Main protease (MPro), a cysteine protease that cleaves the viral polyprotein, is essential for viral replication. Therefore, MPro is a novel therapeutic target. We identified two novel MPro inhibitors, D-FFRCMKyne and D-FFCitCMKyne, that covalently modify the active site cysteine (C145) and determined cocrystal structures. Medicinal chemistry efforts led to SM141 and SM142, which adopt a unique binding mode within the MPro active site. Notably, these inhibitors do not inhibit the other cysteine protease, papain-like protease (PLPro), involved in the life cycle of SARS-CoV2. SM141 and SM142 block SARS-CoV2 replication in hACE2 expressing A549 cells with IC50 values of 8.2 and 14.7 nM. Detailed studies indicate that these compounds also inhibit cathepsin L (CatL), which cleaves the viral S protein to promote viral entry into host cells. Detailed biochemical, proteomic, and knockdown studies indicate that the antiviral activity of SM141 and SM142 results from the dual inhibition of MPro and CatL. Notably, intranasal and intraperitoneal administration of SM141 and SM142 lead to reduced viral replication, viral loads in the lung, and enhanced survival in SARS-CoV2 infected K18-ACE2 transgenic mice. In total, these data indicate that SM141 and SM142 represent promising scaffolds on which to develop antiviral drugs against SARS-CoV2.
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Affiliation(s)
- Santanu Mondal
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Yongzhi Chen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Sudeshna Sen
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Sauradip Chaudhuri
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Archie C. Reyes
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jeong Min Lee
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Arshia N. Kaur
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Nadia Sultana
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Michael D. Cameron
- Department of Molecular Medicine, The Scripps Research Institute,130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott A. Shaffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Paul R. Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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19
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Bajrai LH, Faizo AA, Alkhaldy AA, Dwivedi VD, Azhar EI. Repositioning of anti-dengue compounds against SARS-CoV-2 as viral polyprotein processing inhibitor. PLoS One 2022; 17:e0277328. [PMID: 36383621 PMCID: PMC9668197 DOI: 10.1371/journal.pone.0277328] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
A therapy for COVID-19 (Coronavirus Disease 19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) remains elusive due to the lack of an effective antiviral therapeutic molecule. The SARS-CoV-2 main protease (Mpro), which plays a vital role in the viral life cycle, is one of the most studied and validated drug targets. In Several prior studies, numerous possible chemical entities were proposed as potential Mpro inhibitors; however, most failed at various stages of drug discovery. Repositioning of existing antiviral compounds accelerates the discovery and development of potent therapeutic molecules. Hence, this study examines the applicability of anti-dengue compounds against the substrate binding site of Mpro for disrupting its polyprotein processing mechanism. An in-silico structure-based virtual screening approach is applied to screen 330 experimentally validated anti-dengue compounds to determine their affinity to the substrate binding site of Mpro. This study identified the top five compounds (CHEMBL1940602, CHEMBL2036486, CHEMBL3628485, CHEMBL200972, CHEMBL2036488) that showed a high affinity to Mpro with a docking score > -10.0 kcal/mol. The best-docked pose of these compounds with Mpro was subjected to 100 ns molecular dynamic (MD) simulation followed by MM/GBSA binding energy. This showed the maximum stability and comparable ΔG binding energy against the reference compound (X77 inhibitor). Overall, we repurposed the reported anti-dengue compounds against SARS-CoV-2-Mpro to impede its polyprotein processing for inhibiting SARS-CoV-2 infection.
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Affiliation(s)
- Leena H. Bajrai
- Special Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arwa A. Faizo
- Special Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Areej A. Alkhaldy
- Special Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Clinical Nutrition Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
- Bioinformatics Research Division, Quanta Calculus, Greater Noida, India
| | - Esam I. Azhar
- Special Infectious Agents Unit – BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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20
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De Simone G, di Masi A, Ascenzi P. Strategies of Pathogens to Escape from NO-Based Host Defense. Antioxidants (Basel) 2022; 11:2176. [PMID: 36358549 PMCID: PMC9686644 DOI: 10.3390/antiox11112176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 06/22/2024] Open
Abstract
Nitric oxide (NO) is an essential signaling molecule present in most living organisms including bacteria, fungi, plants, and animals. NO participates in a wide range of biological processes including vasomotor tone, neurotransmission, and immune response. However, NO is highly reactive and can give rise to reactive nitrogen and oxygen species that, in turn, can modify a broad range of biomolecules. Much evidence supports the critical role of NO in the virulence and replication of viruses, bacteria, protozoan, metazoan, and fungi, thus representing a general mechanism of host defense. However, pathogens have developed different mechanisms to elude the host NO and to protect themselves against oxidative and nitrosative stress. Here, the strategies evolved by viruses, bacteria, protozoan, metazoan, and fungi to escape from the NO-based host defense are overviewed.
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Affiliation(s)
| | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Via della Vasca Navale 79, 00146 Roma, Italy
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21
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Aleissa MS, AL-Zharani M, Hasnain MS, Alkahtani S. Screening, molecular simulation & in silico kinetics of virtually designed covid-19 main protease inhibitors. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022; 34:102283. [PMID: 36062199 PMCID: PMC9428119 DOI: 10.1016/j.jksus.2022.102283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/27/2022] [Accepted: 08/13/2022] [Indexed: 11/07/2022]
Abstract
Coronavirus (covid-19) infection is considered to be deadliest ever pandemic experienced by the human being. It has very badly affected the socio-economic health of human and stuck the scientific community to think and rethink about its complete eradication. But due to no effective treatment or unavailability of vaccine the health professional could not show any significant improvement to control the pandemic. The situation needs newer molecule, vaccine or effective treatment to control covid-19 infection. Different target in viruses has been explored and proteases enzymes were found to be therapeutically effective target for the design of potential anti-covid-19 molecule as it plays the vital role in viral replication and assembly. Structure-based drug design was employed to discover the small molecule of anti-covid-19. Here we considered the small library of naturally occurring polyphenolic compounds and molecular docking, Molecular dynamics (MD) simulations, free binding energy calculation and in-silico ADME calculations to identify the newer HITs. Based upon their score the two molecules were identified as promising candidate. The docking scores were found to be −7.643 and −7.065 for the HIT1 and HIT-2 respectively. In MD simulations study the RMSD values were found to be 4.3 Å & 4.9 Å respectively. To validate these results MM-GBSA was performed and their binding free energies were computationally determined. The prime energy values of identified HITs (−13412.45 & −13441.8 kJ/mole) were found to be very close proximity to reference molecule (−13493.05 kJ/mole). Then in-silico ADME calculations were performed to calculate the drug likeliness identified HITs. BY considering all the values comparative to reference molecule and obtained in-silico pharmacokinetic properties of identified HITs we can suggest that HIT-1 and HIT-2 would be the most promising molecules that can inhibit the main protease enzyme of covid-19. These two molecules would become the potential drug candidate for the treatment of covid-19 infections.
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22
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Nair SR, C SD. Serratiopeptidase: An integrated View of Multifaceted Therapeutic Enzyme. Biomolecules 2022; 12:1468. [PMID: 36291677 PMCID: PMC9599151 DOI: 10.3390/biom12101468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2023] Open
Abstract
Microbial products have been used for the treatment of different diseases for many centuries. The serratiopeptidase enzyme provides a new hope for COVID-19-infected patients. Nowadays, anti-inflammatory drugs are easy to obtain at minimal expenditure from microbial sources. Serratia sp. is identified as one of the most efficient bacteria produced from serratiopeptidase. Screening for new and efficient bacterial strains from different sources has been of interest in recent years. Serratiopeptidase remains the most well-known anti-inflammatory drug of choice. Serratiopeptidase is a cheaper and safer anti-inflammatory drug alternative to NSAIDs. The multifaceted properties of serratiopeptidase may lead towards arthritis, diabetes, cancer and thrombolytic treatments. Existing serratiopeptidase treatments in combination with antibiotics are popular in the treatment of postoperative swelling. Although an exclusive number of serratiopeptidase-producing strains have been derived, there is an urge for new recombinant strains to enhance the production of the enzyme. This review explores the properties of serratiopeptidase, different therapeutic aspects, industrial production, and various analytical techniques used in enzyme recovery. In addition, the review highlights the therapeutic and clinical aspects of the serratiopeptidase enzyme to combat COVID-19-induced respiratory syndrome.
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Affiliation(s)
| | - Subathra Devi. C
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
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23
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Negi G, Sharma A, Dey M, Dhanawat G, Parveen N. Membrane attachment and fusion of HIV-1, influenza A, and SARS-CoV-2: resolving the mechanisms with biophysical methods. Biophys Rev 2022; 14:1109-1140. [PMID: 36249860 PMCID: PMC9552142 DOI: 10.1007/s12551-022-00999-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022] Open
Abstract
Attachment to and fusion with cell membranes are two major steps in the replication cycle of many human viruses. We focus on these steps for three enveloped viruses, i.e., HIV-1, IAVs, and SARS-CoV-2. Viral spike proteins drive the membrane attachment and fusion of these viruses. Dynamic interactions between the spike proteins and membrane receptors trigger their specific attachment to the plasma membrane of host cells. A single virion on cell membranes can engage in binding with multiple receptors of the same or different types. Such dynamic and multivalent binding of these viruses result in an optimal attachment strength which in turn leads to their cellular entry and membrane fusion. The latter process is driven by conformational changes of the spike proteins which are also class I fusion proteins, providing the energetics of membrane tethering, bending, and fusion. These viruses exploit cellular and membrane factors in regulating the conformation changes and membrane processes. Herein, we describe the major structural and functional features of spike proteins of the enveloped viruses including highlights on their structural dynamics. The review delves into some of the case studies in the literature discussing the findings on multivalent binding, membrane hemifusion, and fusion of these viruses. The focus is on applications of biophysical tools with an emphasis on single-particle methods for evaluating mechanisms of these processes at the molecular and cellular levels.
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Affiliation(s)
- Geetanjali Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Manorama Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Garvita Dhanawat
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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24
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Sajid Jamal QM, Alharbi AH, Ahmad V. Identification of doxorubicin as a potential therapeutic against SARS-CoV-2 (COVID-19) protease: a molecular docking and dynamics simulation studies. J Biomol Struct Dyn 2022; 40:7960-7974. [PMID: 33826483 PMCID: PMC8043163 DOI: 10.1080/07391102.2021.1905551] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
After one year, the COVID-19 pandemic caused by SARS-CoV-2 is still the largest concern for the scientific community. Of the many recognized drug targets of SARS-CoV-2, the main protease is one of the most important target due to its function in viral replication. We conducted an in silico study with repurposing drugs of antibiotics class against virus protease and peptidase using AutoDock tool. The following significant binding energy interaction was observed with protease (PDB: 6LU7) like piperacillin -7.25; tobramycin -9.20 and doxorubicin (Doxo) -10.04 kcal/mol and with peptidase (PDB: 2GTB) piperacillin -7.08; tobramycin -8.54 and Doxo -9.89 kcal/mol. Furthermore, the interaction and stability behavior of the Doxo-protease and Doxo-peptidase complexes were analyzed for a 100-nanosecond (ns) time. Calculated RMSD values observed using molecular dynamics simulation (MDS) were found to be 0.15-0.25 nm, RMSF calculation per residues showed a value near 0.2 nm and Rg values remained approximately 2.25 nm. MM-PBSA analysis of total binding energy calculation of Doxo-protease and Doxo-peptidase complexes are found to be -148.692 and -105.367 kJ/mol, respectively. Moreover, amino acid residue ASP-197 showed the lowest contribution binding energy i.e. -18.1185 kJ/mol, and amino acid residue ASP-187 showed -17.0267 kJ/mol contribution energy. Thus, significant docking interaction and stable dynamicity of Doxo-protease complex with time was suggested that Doxo could be a choice to inhibit potentially the viral proteases that could prevent the entry inside the host cell to control the COVID-19 disease. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Ali H. Alharbi
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Varish Ahmad
- Health Information Technology Department, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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25
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Abidi M, Soheilifard R, Ghasemi RH. Comparison of the unbinding process of RBD-ACE2 complex between SARS-CoV-2 variants (Delta, delta plus, and Lambda): A steered molecular dynamics simulation. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2114599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Mohadese Abidi
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| | - Reza Soheilifard
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
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26
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Ohradanova-Repic A, Skrabana R, Gebetsberger L, Tajti G, Baráth P, Ondrovičová G, Praženicová R, Jantova N, Hrasnova P, Stockinger H, Leksa V. Blockade of TMPRSS2-mediated priming of SARS-CoV-2 by lactoferricin. Front Immunol 2022; 13:958581. [PMID: 36081512 PMCID: PMC9445877 DOI: 10.3389/fimmu.2022.958581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
In addition to vaccines, there is an urgent need for supplemental antiviral therapeutics to dampen the persistent COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The transmembrane protease serine 2 (TMPRSS2), that is responsible for proteolytic priming of the SARS-CoV-2 spike protein, appears as a rational therapeutic target. Accordingly, selective inhibitors of TMPRSS2 represent potential tools for prevention and treatment of COVID-19. Previously, we identified the human milk glycoprotein lactoferrin as a natural inhibitor of plasminogen conversion to plasmin, a serine protease homologous to TMPRSS2. Here, we tested whether lactoferrin and lactoferricin, a biologically active natural peptide produced by pepsin-mediated digestion of lactoferrin, together with synthetic peptides derived from lactoferrin, were able to block TMPRSS2 and SARS-CoV-2 infection. Particularly, we revealed that both lactoferricin and the N-terminal synthetic peptide pLF1 significantly inhibited: i) proteolytic activity of TMPRSS2 and plasmin, ii) proteolytic processing of the SARS-CoV-2 spike protein, and iii) SARS-CoV-2 infection of SARS-CoV-2-permissive cells. Thus, natural and synthetic peptides derived from lactoferrin represent feasible candidates for supporting prevention and treatment of COVID-19.
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Affiliation(s)
- Anna Ohradanova-Repic
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
- *Correspondence: Vladimir Leksa, ; Anna Ohradanova-Repic,
| | - Rostislav Skrabana
- Laboratory of Structural Biology of Neurodegeneration, Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Laura Gebetsberger
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Gabor Tajti
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Peter Baráth
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Gabriela Ondrovičová
- Laboratory of Molecular Immunology, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Romana Praženicová
- Laboratory of Molecular Immunology, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Biochemistry, Comenius University, Bratislava, Slovakia
| | - Nikola Jantova
- Laboratory of Structural Biology of Neurodegeneration, Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Biochemistry, Comenius University, Bratislava, Slovakia
| | - Patricia Hrasnova
- Laboratory of Structural Biology of Neurodegeneration, Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Biochemistry, Comenius University, Bratislava, Slovakia
| | - Hannes Stockinger
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Vladimir Leksa
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
- Laboratory of Molecular Immunology, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
- *Correspondence: Vladimir Leksa, ; Anna Ohradanova-Repic,
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27
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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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28
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Wu H, Liu J, Chen Z, Lin P, Ou W, Wang Z, Xiao W, Chen Y, Cao D. Mechanism and Application of Surface-Charged Ferrite Nanozyme-Based Biosensor toward Colorimetric Detection of l-Cysteine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8266-8279. [PMID: 35749646 DOI: 10.1021/acs.langmuir.2c00657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Peroxidase-like nanozymes with robust catalytic capacity and detection specificity have been proposed as substitutes to natural peroxidases in biochemical sensing. However, the catalytic activity enhancement, detection mechanism, and application of nanozyme-based biosensors toward l-cysteine (l-Cys) detection still remain significant challenges. In this work, a doped ferrite nanozyme with well-defined structure and surface charges is fabricated by a two-step method of continuous flow coprecipitation and high-temperature annealing. The resulted ferrite nanozyme possesses an average size of 54.5 nm and a zeta-potential of 6.45 mV. A high-performance biosensor is manufactured based on the peroxidase-like catalytic feature of the doped ferrite. The ferrite nanozyme can oxidize the 3,3',5,5'-tetramethylbenzidine (TMB) with the assistance of H2O2 because of the instinctive capacity to decompose H2O2 into ·OH. The Michaelis-Menten constants (0.0911 mM for TMB, 0.140 mM for H2O2) of the ferrite nanozyme are significantly smaller than those of horseradish peroxidase. A reliable colorimetric method is established to selectively analyze l-Cys via a facile mixing-and-detecting methodology. The detection limit and linear range are 0.119 μM and 0.2-20 μM, respectively. Taking the merits of the ferrite nanozyme-based biosensors, the l-Cys level in the human serum can be qualitatively detected. It can be anticipated that the surface-charged ferrite nanozyme shows great application prospects in the fields of bioanalytical chemistry and point-of-care testing.
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Affiliation(s)
- Hongjiao Wu
- Guangdong Provincial Key Laboratory on Functional Soft Condensed Matter, Materials and Energy School, Guangdong University of Technology Panyu District, Guangzhou, 510006, China
- Department of Laboratory Medicine, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Jun Liu
- Guangdong Provincial Key Laboratory on Functional Soft Condensed Matter, Materials and Energy School, Guangdong University of Technology Panyu District, Guangzhou, 510006, China
| | - Zhuoyu Chen
- Guangdong Provincial Key Laboratory on Functional Soft Condensed Matter, Materials and Energy School, Guangdong University of Technology Panyu District, Guangzhou, 510006, China
| | - Pengcheng Lin
- Guangdong Provincial Key Laboratory on Functional Soft Condensed Matter, Materials and Energy School, Guangdong University of Technology Panyu District, Guangzhou, 510006, China
| | - Wentao Ou
- Guangdong Provincial Key Laboratory on Functional Soft Condensed Matter, Materials and Energy School, Guangdong University of Technology Panyu District, Guangzhou, 510006, China
| | - Zian Wang
- Guangdong Provincial Key Laboratory on Functional Soft Condensed Matter, Materials and Energy School, Guangdong University of Technology Panyu District, Guangzhou, 510006, China
| | - Wei Xiao
- Department of Laboratory Medicine, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Ying Chen
- Guangdong Provincial Key Laboratory on Functional Soft Condensed Matter, Materials and Energy School, Guangdong University of Technology Panyu District, Guangzhou, 510006, China
| | - Donglin Cao
- Department of Laboratory Medicine, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
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29
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Thakur A, Sharma G, Badavath VN, Jayaprakash V, Merz KM, Blum G, Acevedo O. Primer for Designing Main Protease (M pro) Inhibitors of SARS-CoV-2. J Phys Chem Lett 2022; 13:5776-5786. [PMID: 35726889 PMCID: PMC9235046 DOI: 10.1021/acs.jpclett.2c01193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/13/2022] [Indexed: 05/08/2023]
Abstract
The COVID-19 outbreak has been devastating, with hundreds of millions of infections and millions of deaths reported worldwide. In response, the application of structure-activity relationships (SAR) upon experimentally validated inhibitors of SARS-CoV-2 main protease (Mpro) may provide an avenue for the identification of new lead compounds active against COVID-19. Upon the basis of information gleaned from a combination of reported crystal structures and the docking of experimentally validated inhibitors, four "rules" for designing potent Mpro inhibitors have been proposed. The aim here is to guide medicinal chemists toward the most probable hits and to provide guidance on repurposing available structures as Mpro inhibitors. Experimental examination of our own previously reported inhibitors using the four "rules" identified a potential lead compound, the cathepsin inhibitor GB111-NH2, that was 2.3 times more potent than SARS-CoV-2 Mpro inhibitor N3.
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Affiliation(s)
- Abhishek Thakur
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gaurav Sharma
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Vishnu Nayak Badavath
- School
of Pharmacy & Technology Management, SVKM’s Narsee Monjee Institute of Management Studies (NMIMS), Hyderabad 509301, India
- Department
of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835 215, India
| | - Venkatesan Jayaprakash
- Department
of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835 215, India
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Galia Blum
- Institute
for Drug Research, The Hebrew University
of Jerusalem, Jerusalem, 9112001, Israel
| | - Orlando Acevedo
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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30
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Moghadasi SA, Esler MA, Otsuka Y, Becker JT, Moraes SN, Anderson CB, Chamakuri S, Belica C, Wick C, Harki DA, Young DW, Scampavia L, Spicer TP, Shi K, Aihara H, Brown WL, Harris RS. Gain-of-Signal Assays for Probing Inhibition of SARS-CoV-2 M pro/3CL pro in Living Cells. mBio 2022; 13:e0078422. [PMID: 35471084 PMCID: PMC9239272 DOI: 10.1128/mbio.00784-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
The main protease, Mpro, of SARS-CoV-2 is required to cleave the viral polyprotein into precise functional units for virus replication and pathogenesis. Here, we report quantitative reporters for Mpro function in living cells in which protease inhibition by genetic or chemical methods results in robust signal readouts by fluorescence (enhanced green fluorescent protein [eGFP]) or bioluminescence (firefly luciferase). These gain-of-signal systems are scalable to high-throughput platforms for quantitative discrimination between Mpro mutants and/or inhibitor potencies as evidenced by validation of several reported inhibitors. Additional utility is shown by single Mpro amino acid variants and structural information combining to demonstrate that both inhibitor conformational dynamics and amino acid differences are able to influence inhibitor potency. We further show that a recent variant of concern (Omicron) has an unchanged response to a clinically approved drug, nirmatrelvir, whereas proteases from divergent coronavirus species show differential susceptibility. Together, we demonstrate that these gain-of-signal systems serve as robust, facile, and scalable assays for live cell quantification of Mpro inhibition, which will help expedite the development of next-generation antivirals and enable the rapid testing of emerging variants. IMPORTANCE The main protease, Mpro, of SARS-CoV-2 is an essential viral protein required for the earliest steps of infection. It is therefore an attractive target for antiviral drug development. Here, we report the development and implementation of two complementary cell-based systems for quantification of Mpro inhibition by genetic or chemical approaches. The first is fluorescence based (eGFP), and the second is luminescence based (firefly luciferase). Importantly, both systems rely upon gain-of-signal readouts such that stronger inhibitors yield higher fluorescent or luminescent signal. The high versatility and utility of these systems are demonstrated by characterizing Mpro mutants and natural variants, including Omicron, as well as a panel of existing inhibitors. These systems rapidly, safely, and sensitively identify Mpro variants with altered susceptibilities to inhibition, triage-nonspecific, or off-target molecules and validate bona fide inhibitors, with the most potent thus far being the first-in-class drug nirmatrelvir.
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Affiliation(s)
- Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Morgan A. Esler
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yuka Otsuka
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, Florida, USA
| | - Jordan T. Becker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Constance B. Anderson
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Christopher Belica
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Chloe Wick
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel A. Harki
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Damian W. Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, Florida, USA
| | - Timothy P. Spicer
- Department of Molecular Medicine, Scripps Research, The Scripps Research Molecular Screening Center, Jupiter, Florida, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA
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Cook S, Castillo D, Williams S, Haake C, Murphy B. Serotype I and II Feline Coronavirus Replication and Gene Expression Patterns of Feline Cells-Building a Better Understanding of Serotype I FIPV Biology. Viruses 2022; 14:1356. [PMID: 35891338 PMCID: PMC9320447 DOI: 10.3390/v14071356] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 01/27/2023] Open
Abstract
Feline infectious peritonitis (FIP) is a disease of domestic cats caused by the genetic variant of the feline coronavirus (FCoV) and feline infectious peritonitis virus (FIPV), currently grouped into two serotypes, I and II. Although serotype I FIPV is more prevalent in cats with FIP, serotype II has been more extensively studied in vitro due to the relative ease in propagating this viral serotype in culture systems. As a result, more is known about serotype II FIPV than the more biologically prevalent serotype I. The primary cell receptor for serotype II has been determined, while it remains unknown for serotype I. The recent development of a culture-adapted feline cell line that more effectively propagates serotype I FIPV, FCWF-4 CU, derived from FCWF-4 cells available through the ATCC, offers the potential for an improved understanding of serotype I FIPV biology. To learn more about FIPV receptor biology, we determined targeted gene expression patterns in feline cells variably permissive to replication of serotype I or II FIPV. We utilized normal feline tissues to determine the immunohistochemical expression patterns of two known coronavirus receptors, ACE2 and DC-SIGN. Lastly, we compared the global transcriptomes of the two closely related FCWF-4 cell lines and identified viral transcripts with potential importance for the differential replication kinetics of serotype I FIPV.
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Affiliation(s)
- Sarah Cook
- Graduate Group Integrative Pathobiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Diego Castillo
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA; (D.C.); (S.W.); (B.M.)
| | - Sonyia Williams
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA; (D.C.); (S.W.); (B.M.)
| | - Christine Haake
- School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Brian Murphy
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA; (D.C.); (S.W.); (B.M.)
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SARS-CoV-2 Spike Furin Cleavage Site and S2' Basic Residues Modulate the Entry Process in a Host Cell-Dependent Manner. J Virol 2022; 96:e0047422. [PMID: 35678602 PMCID: PMC9278140 DOI: 10.1128/jvi.00474-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
SARS-CoV-2 spike (S) envelope glycoprotein constitutes the main determinant of virus entry and the target of host immune response, thus being of great interest for antiviral research. It is constituted of S1 and S2 subunits, which are involved in ACE2 receptor binding and fusion between the viral envelope and host cell membrane, respectively. Induction of the fusion process requires S cleavage at the S1-S2 junction and the S2′ site located upstream of the fusion peptide. Interestingly, the SARS-CoV-2 spike harbors a 4-residue insertion at the S1-S2 junction that is absent in its closest relatives and constitutes a polybasic motif recognized by furin-like proteases. In addition, the S2′ site is characterized by the presence of conserved basic residues. Here, we sought to determine the importance of the furin cleavage site (FCS) and the S2′ basic residues for S-mediated entry functions. We determined the impact of mutations introduced at these sites on S processing, fusogenic activity, and its ability to mediate entry in different cellular backgrounds. Strikingly, mutation phenotypes were highly dependent on the host cell background. We confirmed that although the FCS was not absolutely required for virus entry, it contributed to extending the fusogenic potential of S. Cleavage site mutations, as well as inhibition of furin protease activity, affected the cell surface expression of S in a host cell-dependent manner. Finally, inhibition of furin activity differentially affected SARS-CoV-2 virus infectivity in the tested host cells, thereby confirming the host cell-dependent effect of spike processing for the viral life cycle. IMPORTANCE SARS-CoV-2 is responsible for the current global pandemic that has resulted in several million deaths. As the key determinant of virus entry into host cells and the main target of host immune response, the spike glycoprotein constitutes an attractive target for therapeutics development. Entry functions of spike rely on its processing at two sites by host cell proteases. While SARS-CoV-2 spike differs from its closest relatives by the insertion of a basic furin cleavage motif at the first site, it harbors conserved basic residues at the second cleavage site. Characterization of the importance of the basic sequences present at the two cleavage sites revealed that they were influencing spike processing, intracellular localization, induction of fusion, and entry in a host cell-dependent manner. Thus, our results revealed a high heterogeneity in spike sequence requirement for entry functions in the different host cells, in agreement with the high adaptability of the SARS-CoV-2 virus.
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Fava VM, Bourgey M, Nawarathna PM, Orlova M, Cassart P, Vinh DC, Cheng MP, Bourque G, Schurr E, Langlais D. A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19. SCIENCE ADVANCES 2022; 8:eabm2510. [PMID: 35648852 PMCID: PMC9159580 DOI: 10.1126/sciadv.abm2510] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/12/2022] [Indexed: 05/14/2023]
Abstract
Despite the availability of highly efficacious vaccines, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lacks effective drug treatment, which results in a high rate of mortality. To address this therapeutic shortcoming, we applied a systems biology approach to the study of patients hospitalized with severe COVID. We show that, at the time of hospital admission, patients who were equivalent on the clinical ordinal scale displayed significant differential monocyte epigenetic and transcriptomic attributes between those who would survive and those who would succumb to COVID-19. We identified messenger RNA metabolism, RNA splicing, and interferon signaling pathways as key host responses overactivated by patients who would not survive. Those pathways are prime drug targets to reduce mortality of critically ill patients with COVID-19, leading us to identify tacrolimus, zotatifin, and nintedanib as three strong candidates for treatment of severely ill patients at the time of hospital admission.
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Affiliation(s)
- Vinicius M. Fava
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Pubudu M. Nawarathna
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Marianna Orlova
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Pauline Cassart
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Donald C. Vinh
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Infectious Diseases and Division of Medical Microbiology, McGill University Health Center, McGill University, Montreal, QC, Canada
| | - Matthew Pellan Cheng
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Infectious Diseases and Division of Medical Microbiology, McGill University Health Center, McGill University, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - David Langlais
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
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34
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Integrated computational approach towards repurposing of antimalarial drug against SARS-CoV-2 main protease. Struct Chem 2022; 33:1409-1422. [PMID: 35669793 PMCID: PMC9136827 DOI: 10.1007/s11224-022-01916-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/05/2022] [Indexed: 10/25/2022]
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35
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Hussein RK, Khouqeer G, Alkaoud AM, El-Khayatt AM. Probing the Action of Screened Anticancer Triazole–Tetrazole Derivatives Against COVID-19 Using Molecular Docking and DFT Investigations. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221093915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Drugs are continuously being evaluated for novel therapeutic uses. The purpose of this work was to screen anticancer triazole/tetrazole derivatives for effectiveness against the SARS-CoV-2 main protease (Mpro). First, the chemical structures’ activity was derived from conceptual quantum chemical calculations. According to molecular docking analysis, the compounds scored good interactions against SAR-COV-2's Mpro, with binding energies extending from −8.21 to −8.97 kcal/mol. The docked complexes included various bindings with His41 and Cys145, both catalytic residues responsible for cleavage of the SARS-CoV-2 Mpro. Among the 4 studied compounds, TD3 exhibited the highest affinity by achieving the most stable binding energy and lowest value for the inhibition constant. Most striking was that TD3 not only formed strong bonds with the catalytic residues His41 and Cys145, but also captured the residues of the catalytic loop (Cys44 to Pro52), which flank the catalytic dyads in Mpro's active site. As a result, the studied triazole/tetrazole derivatives, notably TD3, must be reviewed as potent drugs that could be repurposed for SARS-CoV-2 treatment.
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Affiliation(s)
- Rageh K. Hussein
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ghada Khouqeer
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ahmed M. Alkaoud
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ahmed M. El-Khayatt
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
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36
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Wang Y, Wu M, Li Y, Yuen HH, He ML. The effects of SARS-CoV-2 infection on modulating innate immunity and strategies of combating inflammatory response for COVID-19 therapy. J Biomed Sci 2022; 29:27. [PMID: 35505345 PMCID: PMC9063252 DOI: 10.1186/s12929-022-00811-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/27/2022] [Indexed: 12/15/2022] Open
Abstract
The global pandemic of COVID-19 has caused huge causality and unquantifiable loss of social wealth. The innate immune response is the first line of defense against SARS-CoV-2 infection. However, strong inflammatory response associated with dysregulation of innate immunity causes severe acute respiratory syndrome (SARS) and death. In this review, we update the current knowledge on how SARS-CoV-2 modulates the host innate immune response for its evasion from host defense and its corresponding pathogenesis caused by cytokine storm. We emphasize Type I interferon response and the strategies of evading innate immune defense used by SARS-CoV-2. We also extensively discuss the cells and their function involved in the innate immune response and inflammatory response, as well as the promises and challenges of drugs targeting excessive inflammation for antiviral treatment. This review would help us to figure out the current challenge questions of SARS-CoV-2 infection on innate immunity and directions for future studies.
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Affiliation(s)
- Yiran Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Yichen Li
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Ho Him Yuen
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China. .,CityU Shenzhen Research Institute, Nanshan, Shenzhen, China.
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Rani P, Kapoor B, Gulati M, Atanasov AG, Alzahrani Q, Gupta R. Antimicrobial peptides: A plausible approach for COVID-19 treatment. Expert Opin Drug Discov 2022; 17:473-487. [PMID: 35255763 PMCID: PMC8935455 DOI: 10.1080/17460441.2022.2050693] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), which emerged as a major public health threat, has affected >400 million people globally leading to >5 million mortalities to date. Treatments of COVID-19 are still to be developed as the available therapeutic approaches are not able to combat the virus causing the disease (severe acute respiratory syndrome coronavirus-2; SARS-CoV-2) satisfactorily. However, antiviral peptides (AVPs) have demonstrated prophylactic and therapeutic effects against many coronaviruses (CoVs). AREAS COVERED This review critically discusses various types of AVPs evaluated for the treatment of COVID-19 along with their mechanisms of action. Furthermore, the peptides inhibiting the entry of the virus by targeting its binding to angiotensin-converting enzyme 2 (ACE2) or integrins, fusion mechanism as well as activation of proteolytic enzymes (cathepsin L, transmembrane serine protease 2 (TMPRSS2), or furin) are also discussed. EXPERT OPINION Although extensively investigated, successful treatment of COVID-19 is still a challenge due to emergence of virus mutants. Antiviral peptides are anticipated to be blockbuster drugs for the management of this serious infection because of their formulation and therapeutic advantages. Although they may act on different pathways, AVPs having a multi-targeted approach are considered to have the upper hand in the management of this infection.
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Affiliation(s)
- Pooja Rani
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Bhupinder Kapoor
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Atanas G. Atanasov
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Magdalenka, Poland
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Qushmua Alzahrani
- Department of Pharmacy/Nursing/Medicine Health and Environment, University of the Region of Joinville (UNIVILLE) volunteer researcher, Joinville, Brazil
| | - Reena Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
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Identification of a dual acting SARS-CoV-2 proteases inhibitor through in silico design and step-by-step biological characterization. Eur J Med Chem 2021; 226:113863. [PMID: 34571172 PMCID: PMC8457654 DOI: 10.1016/j.ejmech.2021.113863] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/12/2022]
Abstract
COVID-19 pandemic, starting from the latest 2019, and caused by SARS-CoV-2 pathogen, led to the hardest health-socio-economic disaster in the last century. Despite the tremendous scientific efforts, mainly focused on the development of vaccines, identification of potent and efficient anti-SARS-CoV-2 therapeutics still represents an unmet need. Remdesivir, an anti-Ebola drug selected from a repurposing campaign, is the only drug approved, so far, for the treatment of the infection. Nevertheless, WHO in later 2020 has recommended against its use in COVID-19. In the present paper, we describe a step-by-step in silico design of a small library of compounds as main protease (Mpro) inhibitors. All the molecules were screened by an enzymatic assay on Mpro and, then, cellular activity was evaluated using Vero cells viral infection model. The cellular screening disclosed compounds 29 and 34 as in-vitro SARS-CoV-2 replication inhibitors at non-toxic concentrations (0.32 < EC50 < 5.98 μM). To rationalize these results, additional in-vitro assays were performed, focusing on papain like protease (PLpro) and spike protein (SP) as potential targets for the synthesized molecules. This pharmacological workflow allowed the identification of compound 29, as a dual acting SARS-CoV-2 proteases inhibitor featuring micromolar inhibitory potency versus Mpro (IC50 = 1.72 μM) and submicromolar potency versus PLpro (IC50 = 0.67 μM), and of compound 34 as a selective SP inhibitor (IC50 = 3.26 μM).
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Thapa K, Verma N, Singh TG, Kaur Grewal A, Kanojia N, Rani L. COVID-19-Associated acute respiratory distress syndrome (CARDS): Mechanistic insights on therapeutic intervention and emerging trends. Int Immunopharmacol 2021; 101:108328. [PMID: 34768236 PMCID: PMC8563344 DOI: 10.1016/j.intimp.2021.108328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023]
Abstract
AIMS The novel Coronavirus disease 2019 (COVID-19) has caused great distress worldwide. Acute respiratory distress syndrome (ARDS) is well familiar but when it happens as part of COVID-19 it has discrete features which are unmanageable. Numerous pharmacological treatments have been evaluated in clinical trials to control the clinical effects of CARDS, but there is no assurance of their effectiveness. MATERIALS AND METHODS A systematic review of the literature of the Medline, Scopus, Bentham, PubMed, and EMBASE (Elsevier) databases was examined to understand the novel therapeutic approaches used in COVID-19-Associated Acute Respiratory Distress Syndrome and their outcomes. KEY FINDINGS Current therapeutic options may not be enough to manage COVID-19-associated ARDS complications in group of patients and therefore, the current review has discussed the pathophysiological mechanism of COVID-19-associated ARDS, potential pharmacological treatment and the emerging molecular drug targets. SIGNIFICANCE The rationale of this review is to talk about the pathophysiology of CARDS, potential pharmacological treatment and the emerging molecular drug targets. Currently accessible treatment focuses on modulating immune responses, rendering antiviral effects, anti-thrombosis or anti-coagulant effects. It is expected that considerable number of studies conducting globally may help to discover effective therapies to decrease mortality and morbidity occurring due to CARDS. Attention should be also given on molecular drug targets that possibly will help to develop efficient cure for COVID-19-associated ARDS.
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Affiliation(s)
- Komal Thapa
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India; Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Nitin Verma
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
| | | | | | - Neha Kanojia
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
| | - Lata Rani
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
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40
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Ghosh S, Das S, Ahmad I, Patel H. In silico validation of anti-viral drugs obtained from marine sources as a potential target against SARS-CoV-2 Mpro. J INDIAN CHEM SOC 2021. [PMCID: PMC8603876 DOI: 10.1016/j.jics.2021.100272] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
COVID-19 caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has threatened the whole world affecting almost 243 million people globally. Originating from China, it has now spread worldwide with USA and India being the two most affected countries which emphasizes the immense potential of the coronaviruses to cause severity in the human population. This study validates the efficacy of some marine antiviral agents to target the viral main protease (Mpro) of SARS-CoV-2 by in silico studies. A total of 14 marine-derived antiviral agents were screened from several databases including PubChem and DrugBank and docked against the crystallised 3D structure of SARS-CoV-2 Mpro. MD simulation of the top two ligands was carried out for 100 ns to validate the protein-ligand stability. Later, their physicochemical, pharmacokinetics, and drug-likeness properties were evaluated and toxicity prediction was performed using eMOLTOX webtool. We found that all the 14 compounds are acting as a good target for Mpro. Among them, avarol and AcDa-1 procured the best docking results with the estimated docking score of −8.05 and −7.74 kcal/mol respectively. MD simulation revealed good conformational stability. The docked conformation was visualised and subsequent ligand-amino acid interactions were analysed. Avarol revealed good pharmacokinetic properties with oral bioavailability. The overall finding suggested that these marine compounds may have the potential to be used for the treatment of COVID-19 to tackle this pandemic.
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Rodal Canales FJ, Pérez-Campos Mayoral L, Hernández-Huerta MT, Sánchez Navarro LM, Matias-Cervantes CA, Martínez Cruz M, Cruz Parada E, Zenteno E, Ramos-Martínez EG, Pérez-Campos Mayoral E, Romero Díaz C, Pérez-Campos E. Interaction of Spike protein and lipid membrane of SARS-CoV-2 with Ursodeoxycholic acid, an in-silico analysis. Sci Rep 2021; 11:22288. [PMID: 34782703 PMCID: PMC8593036 DOI: 10.1038/s41598-021-01705-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/01/2021] [Indexed: 12/18/2022] Open
Abstract
Numerous repositioned drugs have been sought to decrease the severity of SARS-CoV-2 infection. It is known that among its physicochemical properties, Ursodeoxycholic Acid (UDCA) has a reduction in surface tension and cholesterol solubilization, it has also been used to treat cholesterol gallstones and viral hepatitis. In this study, molecular docking was performed with the SARS-CoV-2 Spike protein and UDCA. In order to confirm this interaction, we used Molecular Dynamics (MD) in “SARS-CoV-2 Spike protein-UDCA”. Using another system, we also simulated MD with six UDCA residues around the Spike protein at random, naming this “SARS-CoV-2 Spike protein-6UDCA”. Finally, we evaluated the possible interaction between UDCA and different types of membranes, considering the possible membrane conformation of SARS-CoV-2, this was named “SARS-CoV-2 membrane-UDCA”. In the “SARS-CoV-2 Spike protein-UDCA”, we found that UDCA exhibits affinity towards the central region of the Spike protein structure of − 386.35 kcal/mol, in a region with 3 alpha helices, which comprises residues from K986 to C1032 of each monomer. MD confirmed that UDCA remains attached and occasionally forms hydrogen bonds with residues R995 and T998. In the presence of UDCA, we observed that the distances between residues atoms OG1 and CG2 of T998 in the monomers A, B, and C in the prefusion state do not change and remain at 5.93 ± 0.62 and 7.78 ± 0.51 Å, respectively, compared to the post-fusion state. Next, in “SARS-CoV-2 Spike protein-6UDCA”, the three UDCA showed affinity towards different regions of the Spike protein, but only one of them remained bound to the region between the region's heptad repeat 1 and heptad repeat 2 (HR1 and HR2) for 375 ps of the trajectory. The RMSD of monomer C was the smallest of the three monomers with a value of 2.89 ± 0.32, likewise, the smallest RMSF was also of the monomer C (2.25 ± 056). In addition, in the simulation of “SARS-CoV-2 membrane-UDCA”, UDCA had a higher affinity toward the virion-like membrane; where three of the four residues remained attached once they were close (5 Å, to the centre of mass) to the membrane by 30 ns. However, only one of them remained attached to the plasma-like membrane and this was in a cluster of cholesterol molecules. We have shown that UDCA interacts in two distinct regions of Spike protein sequences. In addition, UDCA tends to stay bound to the membrane, which could potentially reduce the internalization of SARS-CoV-2 in the host cell.
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Affiliation(s)
- Francisco Javier Rodal Canales
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico
| | - Laura Pérez-Campos Mayoral
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico
| | | | - Luis Manuel Sánchez Navarro
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico
| | | | | | - Eli Cruz Parada
- National Technology of Mexico/IT Oaxaca, 68030, Oaxaca, Mexico
| | - Edgar Zenteno
- Faculty of Medicine, National Autonomous University of Mexico, 04360, Mexico City, Mexico
| | | | - Eduardo Pérez-Campos Mayoral
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico
| | - Carlos Romero Díaz
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico.
| | - Eduardo Pérez-Campos
- National Technology of Mexico/IT Oaxaca, 68030, Oaxaca, Mexico. .,Clinical Pathology Laboratory, "Eduardo Pérez Ortega", 68000, Oaxaca, Mexico.
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Li D, Liu X, Zhang L, He J, Chen X, Liu S, Fu J, Fu S, Chen H, Fu J, Cheng J. COVID-19 disease and malignant cancers: The impact for the furin gene expression in susceptibility to SARS-CoV-2. Int J Biol Sci 2021; 17:3954-3967. [PMID: 34671211 PMCID: PMC8495395 DOI: 10.7150/ijbs.63072] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Furin is a proprotein convertase that activates different kinds of regulatory proteins, including SARS-CoV-2 spike protein which contains an additional furin-specific cleavage site. It is essential in predicting cancer patients' susceptibility to SARS-CoV-2 and the disease outcomes due to varying furin expressions in tumor tissues. In this study, we analyzed furin's expression, methylation, mutation rate, functional enrichment, survival rate and COVID-19 outcomes in normal and cancer tissues using online databases, and our IHC. As a result, furin presented with biased expression profiles in normal tissues, showing 12.25-fold higher than ACE2 in the lungs. The furin expression in tumors were significantly increased in ESCA and TGCT, and decreased in DLBC and THYM, indicating furin may play critical mechanistic functions in COVID-19 viral entry into cells in these cancer patients. Line with furin over/downexpression, furin promoter hypo-/hyper-methylation may be the regulatory cause of disease and lead to pathogenesis of ESCA and THYM. Furthermore, presence of FURIN-201 isoform with functional domains (P_proprotein, Peptidase_S8 and S8_pro-domain) is highest in all cancer types in comparison to other isoforms, demonstrating its use in tumorigenesis and SARS-Cov-2 entry into tumor tissues. Furin mutation frequency was highest in UCES, and its mutation might elevate ACE2 expression in LUAD and UCEC, reduce ACE2 expression in COAD, elevate HSPA5 expression in PAAD, and elevate TMPRSS2 expression in BRCA. These results showed that furin mutations mostly increased expression of ACE2, HSPA5, and TMPRSS2 in certain cancers, indicating furin mutations might facilitate COVID-19 cell entry in cancer patients. In addition, high expression of furin was significantly inversely correlated with long overall survival (OS) in LGG and correlated with long OS in COAD and KIRC, indicating that it could be used as a favorable prognostic marker for cancer patients' survival. GO and KEGG demonstrated that furin was mostly enriched in genes for metabolic and biosynthetic processes, retinal dehydrogenase activity, tRNA methyltransferase activity, and genes involving COVID-19, further supporting its role in COVID-19 and cancer metabolism. Moreover, Cordycepin (CD) inhibited furin expression in a dosage dependent manner. Altogether, furin's high expression might not only implies increased susceptibility to SARS-CoV-2 and higher severity of COVID-19 symptoms in cancer patients, but also it highlights the need for cancer treatment and therapy during the COVID-19 pandemic. CD might have a potential to develop an anti-SARS-CoV-2 drug through inhibiting furin expression.
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Affiliation(s)
- Dabing Li
- Basic Medical School, Southwest Medical University, Luzhou 646000, Sichuan Province, China.,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Xiaoyan Liu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Lianmei Zhang
- Department of Pathology, the Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an 223300, Jiangsu Province, China
| | - Jiayue He
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Xianmao Chen
- Basic Medical School, Southwest Medical University, Luzhou 646000, Sichuan Province, China.,Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Shuguang Liu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Shangyi Fu
- School of Medicine, Baylor College of Medicine, Houston 77030, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston 77030, Texas, USA
| | - Hanchun Chen
- Department of Biochemistry, School of Life Sciences, Central South University, Changsha 410013, Hunan Province, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan Province, China.,Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
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Mei J, Zhou Y, Yang X, Zhang F, Liu X, Yu B. Active components in Ephedra sinica stapf disrupt the interaction between ACE2 and SARS-CoV-2 RBD: Potent COVID-19 therapeutic agents. JOURNAL OF ETHNOPHARMACOLOGY 2021; 278:114303. [PMID: 34102269 PMCID: PMC8178536 DOI: 10.1016/j.jep.2021.114303] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 05/20/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ephedra sinica Stapf is a widely used folk medicine in Asia to treat lung diseases, such as cold, cough and asthma. Many efforts have revealed that some traditional Chinese medicine (TCM) prescriptions containing Ephedra sinica could effectively alleviate the symptoms and prevent the fatal deterioration of COVID-19. AIM OF THE STUDY The present study aims to discover active compounds in Ephedra sinica disrupting the interaction between angiotensin-converting enzyme 2 (ACE2) and the SARS-CoV-2 spike protein receptor-binding domain (SARS-CoV-2 RBD) to inhibit SARS-CoV-2 virus infection. MATERIALS AND METHODS The ethanol extracts of Ephedra sinica were prepared. Activity guided isolation of constituents was carried out by measuring the inhibitory activity on ACE2-RBD interaction. The structures of active compounds were identified by HPLC-Q-TOF-MS/MS and NMR. To testify the contribution of main components for the inhibitory activity, different samples were prepared by components knock-out strategy. The mechanism of compounds inhibiting protein-protein interaction (PPI) was explored by competition inhibition assays, surface plasmon resonance (SPR) assays and molecular docking. SARS-CoV-2 S protein-pseudoviruses were used to observe the viropexis effect in cells. RESULTS Ephedra sinica extracts (ESE) could effectively inhibit the interaction between ACE2 and SARS-CoV-2 RBD (IC50 = 95.01 μg/mL). Three active compounds, 4,6-dihydroxyquinoline-2-carboxylic acid, 4-hydroxyquinoline-2-carboxylic acid and 4-hydroxy-6-methoxyquinoline-2-carboxylic acid were identified to inhibit ACE2-RBD interaction (IC50 = 0.58 μM, 0.07 μM and 0.15 μM respectively). And knock-out the three components could eliminate the inhibitory activity of ESE. Molecular docking calculations indicated that the hydrogen bond was the major intermolecular force. Finally, our results also showed that these compounds could inhibit the infectivity of SARS-CoV-2 S protein-pseudoviruses to 293T-ACE2 (IC50 = 0.44-1.09 μM) and Calu-3 cells. CONCLUSION These findings suggested that quinoline-2-carboxylic acids in Ephedra sinica could be considered as potential therapeutic agents for COVID-19. Further, this study provided some justification for the ethnomedicinal use of Ephedra sinica for COVID-19.
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Affiliation(s)
- Jie Mei
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yatong Zhou
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China.
| | - Xinping Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China.
| | - Fan Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China.
| | - Xiufeng Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China; Jiangsu Key Laboratory of TCM Evaluation and Translational Research, China Pharmaceutical University, Nanjing, 211198, China; Research Center for Traceability and Standardization of TCMs, China Pharmaceutical University, Nanjing, 211198, China.
| | - Boyang Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China; Jiangsu Key Laboratory of TCM Evaluation and Translational Research, China Pharmaceutical University, Nanjing, 211198, China; Research Center for Traceability and Standardization of TCMs, China Pharmaceutical University, Nanjing, 211198, China.
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Guzman NA, Guzman DE. Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression. Biomolecules 2021; 11:1443. [PMID: 34680076 PMCID: PMC8533156 DOI: 10.3390/biom11101443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.
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Affiliation(s)
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, USA;
- Division of Hospital Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
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Duman N, ALzaidi Z, Aynekin B, Taskin D, Demirors B, Yildirim A, Sahin IO, Bilgili F, Turanli ET, Beccari T, Bertelli M, Dundar M. COVID-19 vaccine candidates and vaccine development platforms available worldwide. J Pharm Anal 2021; 11:675-682. [PMID: 34540318 PMCID: PMC8437828 DOI: 10.1016/j.jpha.2021.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 09/08/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
The pandemic caused by the worldwide spread of the coronavirus, which first appeared in 2019, has been named coronavirus disease 19 (COVID-19). More than 4.5 million deaths have been recorded due to the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), according to the World Health Organization. COVID-19 Dashboard in September 2021. Apart from the wildtype, other variations have been successfully transmitted early in the outbreak although they were not discovered until March 2020. Modifications in the SARS-CoV-2 genetic material, such as mutation and recombination, have the ability to modify the viral life span, along with transitivity, cellular tropism, and symptom severity. Several processes are involved in introducing novel vaccines to the population, including vaccine manufacturing, preclinical studies, Food and Drug Administration permission or certification, processing, and marketing. COVID-19 vaccine candidates have been developed by a number of public and private groups employing a variety of strategies, such as RNA, DNA, protein, and viral vectored vaccines. This comprehensive review, which included the most subsequent evidence on unique features of SARS-CoV-2 and the associated morbidity and mortality, was carried out using a systematic search of recent online databases in order to generate useful knowledge about the COVID-19 updated versions and their consequences on the disease symptoms and vaccine development. The ongoing vaccine studies all over the world against the COVID-19 epidemic have been reviewed. The effects of different vaccine platforms and new variants on vaccine studies were discussed. The effect of vaccines on existing and novel variants was evaluated.
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Affiliation(s)
- Nilgun Duman
- Department of Medical Genetics, Dragos Hospital Istanbul, Bezmialem Vakif University, Istanbul, 34854, Turkey
| | - Zahraa ALzaidi
- Department of Biotechnology, Faculty of Applied Science, Cukurova University, Adana, 01380, Turkey
| | - Busra Aynekin
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, 38030, Turkey
| | - Duygu Taskin
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, 38030, Turkey
| | - Busra Demirors
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, 38030, Turkey
| | - Abdulbaki Yildirim
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, 38030, Turkey
| | - Izem Olcay Sahin
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, 38030, Turkey
| | - Faik Bilgili
- Department of Economics, Faculty of Economics and Administrative Sciences, Erciyes University, Kayseri, 38030, Turkey
| | - Eda Tahir Turanli
- Department of Molecular Biology and Genetics, Faculty of Science, Acibadem University, 34684, Istanbul, Turkey
| | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123, Italy
| | | | - Munis Dundar
- Department of Medical Genetics, Medical Faculty, Erciyes University, Kayseri, 38030, Turkey
- Corresponding author.
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Khan WH, Hashmi Z, Goel A, Ahmad R, Gupta K, Khan N, Alam I, Ahmed F, Ansari MA. COVID-19 Pandemic and Vaccines Update on Challenges and Resolutions. Front Cell Infect Microbiol 2021; 11:690621. [PMID: 34568087 PMCID: PMC8461057 DOI: 10.3389/fcimb.2021.690621] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022] Open
Abstract
The coronavirus disease (COVID-19) is caused by a positive-stranded RNA virus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), belonging to the Coronaviridae family. This virus originated in Wuhan City, China, and became the cause of a multiwave pandemic that has killed 3.46 million people worldwide as of May 22, 2021. The havoc intensified with the emergence of SARS-CoV-2 variants (B.1.1.7; Alpha, B.1.351; Beta, P.1; Gamma, B.1.617; Delta, B.1.617.2; Delta-plus, B.1.525; Eta, and B.1.429; Epsilon etc.) due to mutations generated during replication. More variants may emerge to cause additional pandemic waves. The most promising approach for combating viruses and their emerging variants lies in prophylactic vaccines. Several vaccine candidates are being developed using various platforms, including nucleic acids, live attenuated virus, inactivated virus, viral vectors, and protein-based subunit vaccines. In this unprecedented time, 12 vaccines against SARS-CoV-2 have been phased in following WHO approval, 184 are in the preclinical stage, and 100 are in the clinical development process. Many of them are directed to elicit neutralizing antibodies against the viral spike protein (S) to inhibit viral entry through the ACE-2 receptor of host cells. Inactivated vaccines, to the contrary, provide a wide range of viral antigens for immune activation. Being an intracellular pathogen, the cytotoxic CD8+ T Cell (CTL) response remains crucial for all viruses, including SARS-CoV-2, and needs to be explored in detail. In this review, we try to describe and compare approved vaccines against SARS-CoV-2 that are currently being distributed either after phase III clinical trials or for emergency use. We discuss immune responses induced by various candidate vaccine formulations; their benefits, potential limitations, and effectiveness against variants; future challenges, such as antibody-dependent enhancement (ADE); and vaccine safety issues and their possible resolutions. Most of the current vaccines developed against SARS-CoV-2 are showing either promising or compromised efficacy against new variants. Multiple antigen-based vaccines (multivariant vaccines) should be developed on different platforms to tackle future variants. Alternatively, recombinant BCG, containing SARS-CoV-2 multiple antigens, as a live attenuated vaccine should be explored for long-term protection. Irrespective of their efficacy, all vaccines are efficient in providing protection from disease severity. We must insist on vaccine compliance for all age groups and work on vaccine hesitancy globally to achieve herd immunity and, eventually, to curb this pandemic.
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Affiliation(s)
- Wajihul Hasan Khan
- Department of Biotechnology, Host Pathogen Interaction and Molecular Immunology Laboratory, Jamia Hamdard, New Delhi, India
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Zohra Hashmi
- Department of Biotechnology, Host Pathogen Interaction and Molecular Immunology Laboratory, Jamia Hamdard, New Delhi, India
| | - Aditya Goel
- Department of Biotechnology, Host Pathogen Interaction and Molecular Immunology Laboratory, Jamia Hamdard, New Delhi, India
| | - Razi Ahmad
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Kanisha Gupta
- Department of Biotechnology, Host Pathogen Interaction and Molecular Immunology Laboratory, Jamia Hamdard, New Delhi, India
| | - Nida Khan
- Department of Biotechnology, Host Pathogen Interaction and Molecular Immunology Laboratory, Jamia Hamdard, New Delhi, India
| | - Iqbal Alam
- Department of Physiology, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi, India
| | - Faheem Ahmed
- Department of Community Medicine, Hamdard Institute of Medical Sciences and Research, New Delhi, India
| | - Mairaj Ahmed Ansari
- Department of Biotechnology, Host Pathogen Interaction and Molecular Immunology Laboratory, Jamia Hamdard, New Delhi, India
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Selvaraj C, Dinesh DC, Krafcikova P, Boura E, Aarthy M, Pravin MA, Singh SK. Structural Understanding of SARS-CoV-2 Drug Targets, Active Site Contour Map Analysis and COVID-19 Therapeutics. Curr Mol Pharmacol 2021; 15:418-433. [PMID: 34488601 DOI: 10.2174/1874467214666210906125959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
The most iconic word of the year 2020 is 'COVID-19', the shortened name for coronavirus disease 2019. The pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is responsible for multiple worldwide lockdowns, an economic crisis, and a substantial increase in hospitalizations for viral pneumonia along with respiratory failure and multiorgan dysfunctions. Recently, the first few vaccines were approved by World Health Organization (WHO) and can eventually save millions of lives. Even though, few emergency use drugs like Remdesivir and several other repurposed drugs, still there is no approved drug for COVID-19. The coronaviral encoded proteins involved in host-cell entry, replication, and host-cell invading mechanism are potentially therapeutic targets. This perspective review provides the molecular overview of SARS-CoV-2 life cycle for summarizing potential drug targets, structural insights, active site contour map analyses of those selected SARS-CoV-2 protein targets for drug discovery, immunology, and pathogenesis.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | | | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Murali Aarthy
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | - Muthuraja Arun Pravin
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
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Kayode AJ, Banji-Onisile FO, Olaniran AO, Okoh AI. An Overview of the Pathogenesis, Transmission, Diagnosis, and Management of Endemic Human Coronaviruses: A Reflection on the Past and Present Episodes and Possible Future Outbreaks. Pathogens 2021; 10:1108. [PMID: 34578140 PMCID: PMC8470645 DOI: 10.3390/pathogens10091108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 01/08/2023] Open
Abstract
The outbreak of the 2019 coronavirus pandemic caught the world by surprise in late 2019 and has held it hostage for months with an increasing number of infections and deaths. Although coronavirus was first discovered in the 1960s and was known to cause respiratory infection in humans, no information was available about the epidemic pattern of the virus until the past two decades. This review addresses the pathogenesis, transmission dynamics, diagnosis, management strategies, the pattern of the past and present events, and the possibility of future outbreaks of the endemic human coronaviruses. Several studies have described bats as presumptive natural reservoirs of coronaviruses. In essence, the identification of a diverse group of similar SARS coronaviruses in bats suggests the possibility of a future epidemic due to severe acute respiratory syndrome (SARS-like) coronaviruses originating from different reservoir hosts. The study also identified a lack of vaccines to prevent human coronavirus infections in humans in the past, however, the recent breakthrough in vaccine discovery and approval for emergency use for the treatment of Severe Acute Respiratory Syndrome Coronavirus 2 is commendable. The high rates of genomic substitution and recombination due to errors in RNA replication and the potential for independent species crossing suggest the chances of an entirely new strain evolving. Therefore, rapid research efforts should be deployed for vaccination to combat the COVID-19 pandemic and prevent a possible future outbreak. More sensitization and enlightenment on the need to adopt good personal hygiene practices, social distancing, and scientific evaluation of existing medications with promising antiviral effects against SARS-CoV-2 is required. In addition, intensive investigations to unravel and validate the possible reservoirs, the intermediate host, as well as insight into the ability of the virus to break the species barrier are needed to prevent future viral spillover and possible outbreaks.
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Affiliation(s)
- Adeoye J. Kayode
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa; or
- Wastewater Coronavirus Surveillance Laboratory, SAMRC Microbial Water Quality Monitoring Center, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
| | - Folasade O. Banji-Onisile
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; (F.O.B.-O.); (A.O.O.)
| | - Ademola O. Olaniran
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; (F.O.B.-O.); (A.O.O.)
| | - Anthony I. Okoh
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa; or
- Wastewater Coronavirus Surveillance Laboratory, SAMRC Microbial Water Quality Monitoring Center, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
- Department of Environmental Health Sciences, College Health Sciences, University of Sharjah, Sharjah 555588, United Arab Emirates
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Mslati H, Gentile F, Perez C, Cherkasov A. Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns. J Chem Inf Model 2021; 61:3771-3788. [PMID: 34313439 PMCID: PMC8340583 DOI: 10.1021/acs.jcim.1c00384] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 01/18/2023]
Abstract
The current COVID-19 pandemic has elicited extensive repurposing efforts (both small and large scale) to rapidly identify COVID-19 treatments among approved drugs. Herein, we provide a literature review of large-scale SARS-CoV-2 antiviral drug repurposing efforts and highlight a marked lack of consistent potency reporting. This variability indicates the importance of standardizing best practices-including the use of relevant cell lines, viral isolates, and validated screening protocols. We further surveyed available biochemical and virtual screening studies against SARS-CoV-2 targets (Spike, ACE2, RdRp, PLpro, and Mpro) and discuss repurposing candidates exhibiting consistent activity across diverse, triaging assays and predictive models. Moreover, we examine repurposed drugs and their efficacy against COVID-19 and the outcomes of representative repurposed drugs in clinical trials. Finally, we propose a drug repurposing pipeline to encourage the implementation of standard methods to fast-track the discovery of candidates and to ensure reproducible results.
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Affiliation(s)
- Hazem Mslati
- Vancouver Prostate Centre, University of
British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6,
Canada
| | - Francesco Gentile
- Vancouver Prostate Centre, University of
British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6,
Canada
| | - Carl Perez
- Vancouver Prostate Centre, University of
British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6,
Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of
British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6,
Canada
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Computational studies reveal Fluorine based quinolines to be potent inhibitors for proteins involved in SARS-CoV-2 assembly. J Fluor Chem 2021; 250:109865. [PMID: 34393265 PMCID: PMC8356738 DOI: 10.1016/j.jfluchem.2021.109865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/18/2022]
Abstract
World is witnessing one of the worst pandemics of this century caused by SARS-CoV-2 virus which has affected millions of individuals. Despite rapid efforts to develop vaccines and drugs for COVID-19, the disease is still not under control. Chloroquine (CQ) and Hydroxychloroquine (HCQ) are two very promising inhibitors which have shown positive effect in combating the disease in preliminary experimental studies, but their use was reduced due to severe side-effects. Here, we performed a theoretical investigation of the same by studying the binding of the molecules with SARS-COV-2 Spike protein, the complex formed by Spike and ACE2 human receptor and a human serine protease TMPRSS2 which aids in cleavage of the Spike protein to initiate the viral activation in the body. Both the molecules had shown very good docking energies in the range of -6kcal/mol. Subsequently, we did a high throughput screening for other potential quinoline candidates which could be used as inhibitors. From the large pool of ligand candidates, we shortlisted the top three ligands (binding energy -8kcal/mol). We tested the stability of the docked complexes by running Molecular Dynamics (MD) simulations where we observed the stability of the quinoline analogues with the Spike-ACE2 and TMPRSS2 nevertheless the quinolines were not stable with the Spike protein alone. Thus, although the inhibitors bond very well with the protein molecules their intrinsic binding affinity depends on the protein dynamics. Moreover, the quinolines were stable when bound to electronegative pockets of Spike-ACE2 or TMPRSS2 but not with Viral Spike protein. We also observed that a Fluoride based compound: 3-[3-(Trifluoromethyl)phenyl]quinoline helps the inhibitor to bind with both Spike-ACE2 and TMPRSS2 with equal probability. The molecular details presented in this study would be very useful for developing quinoline based drugs for COVID-19 treatment.
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