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Abu-Mahfouz A, Ali M, Elfiky A. Anti-breast cancer drugs targeting cell-surface glucose-regulated protein 78: a drug repositioning in silico study. J Biomol Struct Dyn 2023; 41:7794-7808. [PMID: 36129131 DOI: 10.1080/07391102.2022.2125076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/10/2022] [Indexed: 10/14/2022]
Abstract
Breast cancer (BC) is prevalent worldwide and is a leading cause of death among women. However, cell-surface glucose-regulated protein 78 (cs-GRP78) is overexpressed in several types of cancer and during pathogen infections. This study examines two well-known BC drugs approved by the FDA as BC treatments to GRP78. The first type consists of inhibitors of cyclin-based kinases 4/6, including abemaciclib, palbociclib, ribociclib, and dinaciclib. In addition, tunicamycin, and doxorubicin, which are among the most effective anticancer drugs for early and late-stage BC, are tested against GRP78. As (-)-epiGallocatechin gallate inhibits GRP78, it is also being evaluated (used as positive control). Thus, using molecular dynamics simulation approaches, this study aims to examine the advantages of targeting GRP78, which represents a promising cancer therapy regime. In light of recent advances in computational drug response prediction models, this study aimed to examine the benefits of GRP78 targeting, which represents a promising cancer therapy regime, by utilizing combined molecular docking and molecular dynamics simulation approaches. The simulated protein (50 ns) was docked with the drugs, then a second round of dynamics simulation was performed for 100 ns. After that, the binding free energies were calculated from 30 to 100 ns for each complex during the simulation period. These findings demonstrate the efficacy of abemaciclib, ribociclib, and tunicamycin in binding to the nucleotide-binding domain of the GRP78, paving the way for elucidating the mode of interactions between these drugs and cancer (and other stressed) cells that overexpress GRP78.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alaa Abu-Mahfouz
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Maha Ali
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Abdo Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
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2
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Elfiky AA, Ibrahim IM, Elgohary AM. SARS-CoV-2 Delta Variant is Recognized Through GRP78 Host-Cell Surface Receptor, In Silico Perspective. Int J Pept Res Ther 2022; 28:146. [PMID: 36034049 PMCID: PMC9395890 DOI: 10.1007/s10989-022-10450-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2022] [Indexed: 12/30/2022]
Abstract
Different SARS-CoV-2 new variants emerged and spread during the past few months, sparking infections and death counts. The new variant B.1.617 (delta variant) sparked in India in the past few months, causing the highest records. The B.1.617 variant of SARS-CoV-2 has the double mutations E484Q and L452R on its spike Receptor Binding Domain (RBD). The first mutation is like the reported South African and the Brazilian variants (501.V2 and B.1.1.248). This mutation lies in the region C480-C488, which we predicted before to be recognized by the host-cell receptor; Glucose Regulated Protein 78 (GRP78). In the current study, we test the binding affinity of the host-cell receptor GRP78 to the delta variant spike RBD using molecular docking and molecular dynamics simulations of up to 100 ns. Additionally, the ACE2-RBD is tested by protein–protein docking. The results reveal equal average binding affinities of the GRP78 against wildtype and delta variant spikes. This supports our previous predictions of the contribution of GRP78 in SARS-CoV-2 spike recognition as an auxiliary route for entry.
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Affiliation(s)
- Abdo A. Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Ibrahim M. Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Alaa M. Elgohary
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
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Elshemey WM, Elfiky AA, Ibrahim IM, Elgohary AM. Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective. Comput Biol Med 2022; 145:105478. [PMID: 35421790 PMCID: PMC8988443 DOI: 10.1016/j.compbiomed.2022.105478] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
Finding a potent inhibitor to the pandemic SARS-CoV-2 is indispensable nowadays. Currently, in-silico methods work as expeditious investigators to screen drugs for possible repurposing or design new ones. Targeting one of the possible SARS-CoV-2 attachment and entry receptors, Glucose-regulated protein 78 (GRP78), is an approach of major interest. Recently, GRP78 was reported as a recognized representative in recognition of the latest variants of SARS-CoV-2. In this work, molecular docking and molecular dynamics simulations were performed on the host cell receptor GRP78. With its many terpenoid compounds, Chaga mushroom was tested as a potential therapeutic against the SARS-CoV-2 receptor, GRP78. Results revealed low binding energies (high affinities) toward the GRP78 substrate-binding domain β (SBDβ) of Chaga mushroom terpenoids. Even the highly specific cyclic peptide Pep42, which selectively targeted GRP78 over cancer cells in vivo, showed lower binding affinity against GRP78 SBDβ compared to the binding affinities of terpenoids. These are auspicious results that need to be tested experimentally. Intriguingly, terpenoids work as a double sword as they can be used to interfere with VUI 202,012/01, 501.V2, and B.1.1.248 variants of SARS-CoV-2 spike recognition.
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Affiliation(s)
- Wael M. Elshemey
- Physics Department, Faculty of Science, Islamic University of Madinah, Madinah, Saudi Arabia,Corresponding author
| | - Abdo A. Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Ibrahim M. Ibrahim
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Alaa M. Elgohary
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
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Fu YS, Ho WY, Kang N, Tsai MJ, Wu J, Huang L, Weng CF. Pharmaceutical Prospects of Curcuminoids for the Remedy of COVID-19: Truth or Myth. Front Pharmacol 2022; 13:863082. [PMID: 35496320 PMCID: PMC9047796 DOI: 10.3389/fphar.2022.863082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/01/2022] [Indexed: 01/09/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus, and has rapidly spread worldwide as a pandemic. The vaccines, repurposed drugs, and specific treatments have led to a surge of novel therapies and guidelines nowadays; however, the epidemic of COVID-19 is not yet fully combated and is still in a vital crisis. In repositioning drugs, natural products are gaining attention because of the large therapeutic window and potent antiviral, immunomodulatory, anti-inflammatory, and antioxidant properties. Of note, the predominant curcumoid extracted from turmeric (Curcuma longa L.) including phenolic curcumin influences multiple signaling pathways and has demonstrated to possess anti-inflammatory, antioxidant, antimicrobial, hypoglycemic, wound healing, chemopreventive, chemosensitizing, and radiosensitizing spectrums. In this review, all pieces of current information related to curcumin-used for the treatment and prevention of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through in vitro, in vivo, and in silico studies, clinical trials, and new formulation designs are retrieved to re-evaluate the applications based on the pharmaceutical efficacy of clinical therapy and to provide deep insights into knowledge and strategy about the curcumin's role as an immune booster, inflammatory modulator, and therapeutic agent against COVID-19. Moreover, this study will also afford a favorable application or approach with evidence based on the drug discovery and development, pharmacology, functional foods, and nutraceuticals for effectively fighting the COVID-19 pandemic.
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Affiliation(s)
- Yaw-Syan Fu
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China,Department of Basic Medical Science, Institute of Respiratory Disease, Xiamen Medical College, Xiamen, China
| | - Wan-Yi Ho
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ning Kang
- Department of Otorhinolaryngology, the Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - May-Jywan Tsai
- Department of Neurosurgery, Neurological Institute, Neurological Institute, Taipei, Taiwan
| | - Jingyi Wu
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China
| | - Liyue Huang
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China
| | - Ching-Feng Weng
- Department of Basic Medical Science, Anatomy and Functional Physiology Section, Xiamen Medical College, Xiamen, China,Department of Basic Medical Science, Institute of Respiratory Disease, Xiamen Medical College, Xiamen, China,*Correspondence: Ching-Feng Weng, ,
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Gusev E, Sarapultsev A, Solomatina L, Chereshnev V. SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19. Int J Mol Sci 2022; 23:1716. [PMID: 35163638 PMCID: PMC8835786 DOI: 10.3390/ijms23031716] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
The review aims to consolidate research findings on the molecular mechanisms and virulence and pathogenicity characteristics of coronavirus disease (COVID-19) causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and their relevance to four typical stages in the development of acute viral infection. These four stages are invasion; primary blockade of antiviral innate immunity; engagement of the virus's protection mechanisms against the factors of adaptive immunity; and acute, long-term complications of COVID-19. The invasion stage entails the recognition of the spike protein (S) of SARS-CoV-2 target cell receptors, namely, the main receptor (angiotensin-converting enzyme 2, ACE2), its coreceptors, and potential alternative receptors. The presence of a diverse repertoire of receptors allows SARS-CoV-2 to infect various types of cells, including those not expressing ACE2. During the second stage, the majority of the polyfunctional structural, non-structural, and extra proteins SARS-CoV-2 synthesizes in infected cells are involved in the primary blockage of antiviral innate immunity. A high degree of redundancy and systemic action characterizing these pathogenic factors allows SARS-CoV-2 to overcome antiviral mechanisms at the initial stages of invasion. The third stage includes passive and active protection of the virus from factors of adaptive immunity, overcoming of the barrier function at the focus of inflammation, and generalization of SARS-CoV-2 in the body. The fourth stage is associated with the deployment of variants of acute and long-term complications of COVID-19. SARS-CoV-2's ability to induce autoimmune and autoinflammatory pathways of tissue invasion and development of both immunosuppressive and hyperergic mechanisms of systemic inflammation is critical at this stage of infection.
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Affiliation(s)
- Evgenii Gusev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Alexey Sarapultsev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080 Chelyabinsk, Russia
| | - Liliya Solomatina
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Valeriy Chereshnev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
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Elgohary AM, Elfiky AA, Barakat K. GRP78: A possible relationship of COVID-19 and the mucormycosis; in silico perspective. Comput Biol Med 2021; 139:104956. [PMID: 34695683 PMCID: PMC8536376 DOI: 10.1016/j.compbiomed.2021.104956] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 10/25/2022]
Abstract
Mucormycosis is a severe fungal infection reported in many cancer survivors, diabetic and immune-suppressed patients during organ transplants. A vast spark in the reported COVID-19 cases is noticed in India during the second wave in May 2021, when Mucormycosis is declared an epidemic. Despite being a rare disease, the mortality rate associated with Mucormycosis is more than 40%. Spore coat proteins (CotH) are essential proteins in many pathogenic bacteria and fungi. CotH3 was reported as the vital protein required for fungal virulence in Mucormycosis. We previously reported the involvement of the host cell-surface receptor GRP78 in SARS-CoV-2 spike recognition. Additionally, GRP78 is known to be the virulence factor during Mucormycosis. Using state-of-the-art structural bioinformatics and molecular modeling tools, we predicted the GRP78 binding site to the Rhizopus delemar CotH3 protein. Our findings pave the way toward rationally designing small molecule inhibitors targeting the GRP78 and its counter proteins in both pathogenic viral (SARS-CoV-2 spike) and fungal (R. delemar CotH3) diseases.
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Affiliation(s)
- Alaa M Elgohary
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
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Abosheasha MA, El-Gowily AH, Elfiky AA. Potential antiviral properties of antiplatelet agents against SARS-CoV-2 infection: an in silico perspective. J Thromb Thrombolysis 2021; 53:273-281. [PMID: 34510337 PMCID: PMC8435103 DOI: 10.1007/s11239-021-02558-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 12/14/2022]
Abstract
SARS-CoV-2 represents the causative agent of the current pandemic (COVID-19). The drug repurposing technique is used to search for possible drugs that can bind to SARS-CoV-2 proteins and inhibit viral replication. In this study, the FDA-approved antiplatelets are tested against the main protease and spike proteins of SARS-CoV-2 using in silico methods. Molecular docking and molecular dynamics simulation are used in the current study. The results suggest the effectiveness of vorapaxar, ticagrelor, cilostazol, cangrelor, and prasugrel in binding the main protease (Mpro) of SARS-CoV-2. At the same time, vorapaxar, ticagrelor, and cilostazol are the best binders of the spike protein. Therefore, these compounds could be successful candidates against COVID-19 that need to be tested experimentally.
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Affiliation(s)
- Mohammed A Abosheasha
- Cellular Genetics Laboratory, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Afnan H El-Gowily
- Department of Chemistry, Biochemistry Division, Faculty of Science, Tanta University, Tanta, Egypt.,Department of Organ and Cell Physiology, Juntendo University, Tokyo, Japan
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.
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