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Journal articles on the topic 'COVID-19 Spike Glycoprotein Drug Designing in Silico'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Aloufi, Bandar Hamad, Mejdi Snoussi, and Abdel Moneim E. Sulieman. "Antiviral Efficacy of Selected Natural Phytochemicals against SARS-CoV-2 Spike Glycoprotein Using Structure-Based Drug Designing." Molecules 27, no. 8 (2022): 2401. http://dx.doi.org/10.3390/molecules27082401.

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SARS-CoV-2 is a highly virulent coronavirus that first surfaced in late 2019 and has since created a pandemic of the acute respiratory sickness known as “coronavirus disease 2019” (COVID-19), posing a threat to human health and public safety. S-RBD is a coronaviral protein that is essential for a coronavirus (CoV) to bind and penetrate into host cells. As a result, it has become a popular pharmacological target. The goal of this study was to find potential candidates for anti-coronavirus disease 2019 (COVID-19) drugs by targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S-R

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2

Prajapat, Rajneesh, Suman Jain, Manish K. Vaishnav, and Sonal Sogani. "In Silico Characterization of Surface Glycoprotein [QHD43416] of Severe Acute Respiratory Syndrome-Coronavirus 2." Chinese Journal of Medical Research 3, no. 2 (2020): 32–36. http://dx.doi.org/10.37515/cjmr.091x.3201.

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The novel coronavirus (SARS-CoV-2) reported from Wuhan, China, that spread rapidly and cause severe acute respiratory syndrome. The disease associated with infection of SARS-CoV-2 that is referred as COVID-19 (Coronavirus Disease 2019). In the present study, the surface glycoprotein [QHD43416] of SARS-CoV-2 was characterized for structure analysis and validation to provide information about its three-dimensional structure by using in silico tools and techniques. The surface glycoprotein [QHD43416] sequence of SARS-CoV-2 was retrieved from NCBI and its PDB file was designed by using phyre2 serv

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3

Umitaibatin, Ramadhita, Azza Hanif Harisna, Muhammad Miftah Jauhar, et al. "Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein." Vaccines 11, no. 2 (2023): 399. http://dx.doi.org/10.3390/vaccines11020399.

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The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population usin

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4

Morebise, Olugbenga, and Sharvari Kulkarni. "Identifying Potential Inhibitors of SARS-CoV-2 from Three Medicinal Plants: An in silico Study." Journal of Advances in Medicine and Medical Research 35, no. 19 (2023): 26–33. http://dx.doi.org/10.9734/jammr/2023/v35i195136.

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Covid-19, caused by SARS-Cov-2, almost brought the world to a standstill due to its transmission from person to person, thereby leading to abrupt changes globally. The virus has utilized different mechanisms to get access into host tissues in order to enact its virulence. One of such is the ligation of its viral spike glycoproteins to the host’s angiotensin converting enzyme-2 (ACE-2) by transmembrane serine protease. Inhibitors of the ACE-2 have been reported to be useful in curtailing the spread of the virus. Medicinal plants have been reported to be used in different communities to fight th

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5

Marhaeny, Honey Dzikri, Aty Widyawaruyanti, Tri Widiandani, Achmad Fuad Hafid, and Tutik Sri Wahyuni. "Phyllanthin and hypophyllanthin, the isolated compounds of Phyllanthus niruri inhibit protein receptor of corona virus (COVID-19) through in silico approach." Journal of Basic and Clinical Physiology and Pharmacology 32, no. 4 (2021): 809–15. http://dx.doi.org/10.1515/jbcpp-2020-0473.

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Abstract Objectives Phyllanthus niruri has been known as an immunomodulator and also reported to possess an antiviral activity against several RNA viruses, such as hepatitis B virus and hepatitis C virus by inhibiting viral entry and replication. Since the current situation of Coronavirus Disease 2019 (COVID-19) which infected among the world and caused severe disease and high morbidity, it urgently needed to find new agents against COVID-19. Therefore, in silico screening against COVID-19 receptors is carried out as an initial stage of drug discovery by evaluating the activity of phyllanthin

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6

Harish, M., C. V. Ranjith, and C. Sethulekshmy Nair. "Effectiveness of Quercetin and Its Derivatives Against SARS CoV2 -In silico Approach." Journal of Experimental Biology and Agricultural Sciences 10, no. 5 (2022): 1003–15. http://dx.doi.org/10.18006/2022.10(5).1003.1015.

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The COVID-19 pandemic that erupted in November 2019 is continuing, with no effective antiviral agent to date. Synthetic antiviral agents have limitations such as a narrow range of therapeutic effectiveness of the activity, toxicity, and resistant viral strains and traditional antiviral medicines at large seem not to have these limitations. Here, some of the existing phytochemicals are cherry-picked for repurposing against the enzyme or protein targets of SARS CoV2, by the principles of structure-based drug design based on molecular docking studies. The most important drug targets of SARS CoV2

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7

Mousavi, Sarah, Shima Zare, Mahmoud Mirzaei, and Awat Feizi. "Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies." Canadian Journal of Infectious Diseases and Medical Microbiology 2022 (September 25, 2022): 1–70. http://dx.doi.org/10.1155/2022/2044282.

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Background. Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods. A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, dru

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8

Umar, Haruna Isiyaku, Ijeoma Akunna Duru, Uchechi Emmanuela Enenebeaku, Lynda Chioma Ngozi Olehi, Christian Ebere Enyoh, and Chidi Edbert Duru. "Inhibitory potentials of ivermectin, nafamostat, and camostat on spike protein and some nonstructural proteins of SARS-CoV-2: Virtual screening approach." Jurnal Teknologi Laboratorium 11, no. 1 (2022): 33–42. http://dx.doi.org/10.29238/teknolabjournal.v11i1.344.

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The search for potent oral drugs either through synthetic routes or by drug repurposing for combating the dreaded covid-19 virus is still ongoing. The coronavirus spike glycoprotein and several other non-structural proteins play crucial roles in the replication and transmission of this virus. Recent research have identified ivermectin, nafamostat, and camostat as promising drug inhibitors of SARS-CoV-2 target proteins. The broad-spectrum inhibitory action of ivermectin, nafamostat, and camostat on the spike glycoprotein and some non-structural proteins of this virus was studied in silico. The

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9

Shah, Mohibullah, Ramsha Yamin, Iqra Ahmad, et al. "In-silico evaluation of natural alkaloids against the main protease and spike glycoprotein as potential therapeutic agents for SARS-CoV-2." PLOS ONE 19, no. 1 (2024): e0294769. http://dx.doi.org/10.1371/journal.pone.0294769.

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Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV-2) is the causative agent of COVID-19 pandemic, which has resulted in global fatalities since late December 2019. Alkaloids play a significant role in drug design for various antiviral diseases, which makes them viable candidates for treating COVID-19. To identify potential antiviral agents, 102 known alkaloids were subjected to docking studies against the two key targets of SARS-CoV-2, namely the spike glycoprotein and main protease. The spike glycoprotein is vital for mediating viral entry into host cells, and main protease plays a cru

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10

Manna, Sounik, Trinath Chowdhury, Santi M. Mandal, and Sujata Maiti Choudhury. "Short Amphiphiles or Micelle Peptides May Help to Fight Against COVID-19." Current Protein & Peptide Science 23, no. 1 (2022): 33–43. http://dx.doi.org/10.2174/1389203723666220127154159.

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Background: COVID-19 is a worldwide threat because of the incessant spread of SARS-CoV-2 which urges the development of suitable antiviral drug to secure our society. Already, a group of peptides have been recommended for SARS-CoV-2, but not yet established. SARS-CoV-2 is an enveloped virus with hydrophobic fusion protein and spike glycoproteins. Methods: Here, we have summarized several reported amphiphilic peptides and their in-silico docking analysis with spike glycoprotein of SARS-CoV-2. Result: The result revealed the complex formation of spike protein and amphiphilic peptides with higher

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11

AHMED, N. ZAHEER, DICKY JOHN DAVIS, NOMAN ANWAR, et al. "In-Silico Evaluation of Tiryaq-E-Wabai, an Unani Formulation for its Potency against SARS-CoV-2 Spike Glycoprotein and Main Protease." Journal of Drug Delivery and Therapeutics 11, no. 4-S (2021): 86–100. http://dx.doi.org/10.22270/jddt.v11i4-s.4993.

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COVID-19 was originated in Wuhan, China, in December 2019 and has been declared a pandemic disease by WHO. The number of infected cases continues unabated and so far, no specific drug approved for targeted therapy. Hence, there is a need for drug discovery from traditional medicine. Tiryaq-e-Wabai is a well-documented formulation in Unani medicine for its wide use as prophylaxis during epidemics of cholera, plague and other earlier epidemic diseases. The objective of the current study is to generate in-silico evidence and evaluate the potency of Tiryaq-e-Wabai against SARS-CoV-2 spike (S) glyc

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12

Ramírez-Salinas, Gema Lizbeth, Marlet Martínez-Archundia, José Correa-Basurto, and Jazmín García-Machorro. "Repositioning of Ligands That Target the Spike Glycoprotein as Potential Drugs for SARS-CoV-2 in an In Silico Study." Molecules 25, no. 23 (2020): 5615. http://dx.doi.org/10.3390/molecules25235615.

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The worldwide health emergency of the SARS-CoV-2 pandemic and the absence of a specific treatment for this new coronavirus have led to the use of computational strategies (drug repositioning) to search for treatments. The aim of this work is to identify FDA (Food and Drug Administration)-approved drugs with the potential for binding to the spike structural glycoprotein at the hinge site, receptor binding motif (RBM), and fusion peptide (FP) using molecular docking simulations. Drugs that bind to amino acids are crucial for conformational changes, receptor recognition, and fusion of the viral m

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13

Geromichalou, Elena G., and George D. Geromichalos. "In Silico Approach for the Evaluation of the Potential Antiviral Activity of Extra Virgin Olive Oil (EVOO) Bioactive Constituents Oleuropein and Oleocanthal on Spike Therapeutic Drug Target of SARS-CoV-2." Molecules 27, no. 21 (2022): 7572. http://dx.doi.org/10.3390/molecules27217572.

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Since there is an urgent need for novel treatments to combat the current coronavirus disease 2019 (COVID-19) pandemic, in silico molecular docking studies were implemented as an attempt to explore the ability of selected bioactive constituents of extra virgin olive oil (EVOO) to act as potent SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antiviral compounds, aiming to explore their ability to interact with SARS-CoV-2 Spike key therapeutic target protein. Our results suggest that EVOO constituents display substantial capacity for binding and interfering with Spike (S) protein, bo

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14

Chukwudozie, Onyeka S., Clive M. Gray, Tawakalt A. Fagbayi, et al. "Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein." PLOS ONE 16, no. 3 (2021): e0248061. http://dx.doi.org/10.1371/journal.pone.0248061.

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Developing an efficacious vaccine for SARS-CoV-2 infection is critical to stemming COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in designing an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers and 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a

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15

Perovic, Vladimir, Sanja Glisic, Milena Veljkovic, Slobodan Paessler, and Veljko Veljkovic. "In Silico Exploration of CD200 as a Therapeutic Target for COVID-19." Microorganisms 12, no. 6 (2024): 1185. http://dx.doi.org/10.3390/microorganisms12061185.

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SARS-CoV-2, the pathogen causing COVID-19, continues to pose a significant threat to public health and has had major economic implications. Developing safe and effective vaccines and therapies offers a path forward for overcoming the COVID-19 pandemic. The presented study, performed by using the informational spectrum method (ISM), representing an electronic biology-based tool for analysis of protein–protein interactions, identified the highly conserved region of spike protein (SP) from SARS-CoV-2 virus, which is essential for recognition and targeting between the virus and its protein interac

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16

Hang, Ta Thi Thu, Do Thi Hong Khanh, and Bui Thanh Tung. "In silico screening of natural antivirals as potential inhibitors of SARS‐CoV‐2 virus." Vietnam Journal of Chemistry 60, no. 2 (2022): 211–22. http://dx.doi.org/10.1002/vjch.202100187.

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AbstractCoronavirus infectious disease 2019 (COVID‐19) is an infectious disease of the human respiratory tract caused by the SARS‐CoV‐2 virus. Spike protein is a class I glycoprotein trimeric TM involved in viral entry and infection. Four major targets to inhibit the SARS‐CoV‐2 virus are spike protein, angiotensin‐converting enzyme 2 (ACE2), main protease and the enzyme RNA‐dependent RNA polymerase (RdRp). In this study, we evaluated the inhibitory potential of natural antiviral compounds against spike protein, ACE2, main protease, RdRp targets by molecular docking and molecular dynamics simul

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17

Santra, Sourav, Sasti Gopal Das, Suman Kumar Halder, et al. "Structure-based assortment of herbal analogues against spike protein to restrict COVID-19 entry through hACE2 receptor: An in-silico approach." Acta Biologica Szegediensis 64, no. 2 (2021): 159–71. http://dx.doi.org/10.14232/abs.2020.2.159-171.

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On-going global pandemic COVID-19 has spread all over the world and has led to more than 1.97 million deaths till date. Natural compounds may be useful to protecting health in this perilous condition. Mechanism of shuttle entry of SARS-COV-2 virus is by interaction with viral spike protein with human angiotensin-converting enzyme-2 (ACE-2) receptor. To explore potential natural therapeutics, 213 important phytochemi-cals of nine medicinal plants Aconitum heterophyllum, Cassia angustifolia, Cymbopogon flexuosus, Cymbopogon martinii, Nux vomica, Phyllanthus urinaria, Swertia chirayita, Justicia

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18

Robinson, Jared, Indrajit Banerjee, and Alexandra Leclézio. "2-Deoxy D-Glucose in COVID-19: Current Research Trends." Journal of College of Medical Sciences-Nepal 18, no. 1 (2022): 80–84. http://dx.doi.org/10.3126/jcmsn.v18i1.37651.

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2-Deoxy D- glucose is a novel drug. It is an analogue of glucose which has innate therapeutic uses due to both its antiviral properties as well as its anti-neoplastic action. The SARS-CoV-2 virus binds to the host cell via the (S2) spike glycoprotein. Once viral entry has been gained into the host cell the virus hijacks the host’s intracellular machinery via 2 factors; 3CLproand NSP15. It has been shown through the use of Toxicity estimation software as well as via Molinspiration that 2-Deoxy D- glucose and its aforementioned isomers can effectively bind with 3CLpro and NSP15 and intern thus i

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19

Kolita, Bhaskor, Dimplly Borah, Pinaki Hazarika, Ely Phukan, and Rashmi Rekha Borah. "Plant-derived Antiviral Compounds as Potential COVID-19 Drug Candidates: In-silico Investigation in Search of SARS-CoV-2 Inhibitors." Trends in Sciences 20, no. 9 (2023): 5529. http://dx.doi.org/10.48048/tis.2023.5529.

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Corona virus disease 2019 (COVID-19) is an infectious disease caused by SARS-CoV-2, a newly discovered pathogenic corona virus that causes respiratory illness in humans and has now become a major challenge for the entire world. Although several vaccines for COVID-19 have been approved to date, lead compounds are still in high demand for the development of more promising or effective drugs and vaccines. According to the literature, antiviral drugs are used to treat COVID-19; thus, the current study is an attempt to screen lead molecules from plant-derived antiviral compounds. In this study, 33

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BR, Bharath, Hrishikesh Damle, Shiban Ganju, and Latha Damle. "In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19." F1000Research 9 (July 1, 2020): 663. http://dx.doi.org/10.12688/f1000research.24143.1.

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Background: Human coronavirus (SARS-CoV-2) is causing a pandemic with significant morbidity and mortality. As no effective novel drugs are available currently, drug repurposing is an alternative intervention strategy. Here we present an in silico drug repurposing study that implements successful concepts of computer-aided drug design (CADD) technology for repurposing known drugs to interfere with viral cellular entry via the spike glycoprotein (SARS-CoV-2-S), which mediates host cell entry via the hACE2 receptor. Methods: A total of 4015 known and approved small molecules were screened for int

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21

Rathan Kumar. "In Silico Identification of Active Phytochemicals against COVID-19 by Targeting the SARS-CoV-2 Spike Glycoprotein Through Molecular Docking: A Drug Repurposing Approach." International Journal for Research in Applied Sciences and Biotechnology 8, no. 2 (2021): 72–87. http://dx.doi.org/10.31033/ijrasb.8.2.10.

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The spread of coronavirus disease (COVID-19) has become one of the most significant pandemics in modern human history, affecting more than 70 million people worldwide. Currently, only a few fda-approved drugs have suggested fighting the infection, in the absence of a specific antiviral treatment. Thus, repurposing the presently available drugs or using plant-based bioactive compounds can be the fastest possible solution. In this study, the computational methodology of molecular docking techniques was performed to screen and identify the viable potent inhibitors against the SARS-CoV-2 spike pro

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Trinath, Chowdhury, Dutta Joyita, M. Mandal Santi, and Roymahapatra Gourisankar. "In silico identification of a potent arsenic based lead drug di-phenyl phenoxy roxarsone against SARS-CoV-2." Journal of Indian Chemical Society Vol. 97, Aug 2020 (2020): 1279–85. https://doi.org/10.5281/zenodo.5656715.

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Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur-721 302, West Bengal, India School of Applied Science and Humanities, Haldia Institute of Technology, Haldia-721 657, West Bengal, India <em>E-mail</em>:grm.chem@gmail.com, gourisankar1978@gmail.com <em>Manuscript received online</em> <em>20 July 2020, accepted 30 July 2020</em> In this article we have tried to address the plausible identification of a novel lead drug molecule against COVID-19. Nine different arsenic (As) based molecules, roxarsone derivatives were designed and optimized for computational analysis t

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23

Bharathi, Muruganantham, Bhagavathi Sundaram Sivamaruthi, Periyanaina Kesika, Subramanian Thangaleela, and Chaiyavat Chaiyasut. "In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein Trimer." Marine Drugs 20, no. 2 (2022): 148. http://dx.doi.org/10.3390/md20020148.

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Omicron is an emerging SARS-CoV-2 variant, evolved from the Indian delta variant B.1.617.2, which is currently infecting worldwide. The spike glycoprotein, an important molecule in the pathogenesis and transmissions of SARS-CoV-2 variants, especially omicron B.1.1.529, shows 37 mutations distributed over the trimeric protein domains. Notably, fifteen of these mutations reside in the receptor-binding domain of the spike glycoprotein, which may alter transmissibility and infectivity. Additionally, the omicron spike evades neutralization more efficiently than the delta spike. Most of the therapeu

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Moradian, Fatemeh, and Havva Mehralitabar. "In Silico Studies of Lactoferrin as an Anti-Cancer, Anti-Viral, and Anti-Bacterial, Bioactive Compound and Disease Diagnostic Marker." Journal of Microbiology and Biotechnology 13, no. 2 (2024): 11. https://doi.org/10.4172/2320-3528.13.2.002.

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Studying the interaction of proteins and genes by current computational methods is effective in new drug design. Considering the special role of Lactoferrin (Lf) identifying its action mechanism is a new gate to the targeted treatment of some diseases. This study aimed to investigate the molecular interaction of Lf with virus spike, the bacterial cell binding receptor, and the proteins involved in apoptosis by in silico research. The docking results showed that the amino acids involved in the interaction between the spike viruses of COVID-19 with the ACE2 receptor were similar to the amino aci

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Haseeb, Muhammad, Afreenish Amir, and Aamer Ikram. "In Silico Analysis of SARS-CoV-2 Spike Proteins of Different Field Variants." Vaccines 11, no. 4 (2023): 736. http://dx.doi.org/10.3390/vaccines11040736.

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Coronaviruses belong to the group of RNA family of viruses that trigger diseases in birds, humans, and mammals, which can cause respiratory tract infections. The COVID-19 pandemic has badly affected every part of the world. Our study aimed to explore the genome of SARS-CoV-2, followed by in silico analysis of its proteins. Different nucleotide and protein variants of SARS-CoV-2 were retrieved from NCBI. Contigs and consensus sequences were developed to identify these variants using SnapGene. Data of the variants that significantly differed from each other was run through Predict Protein softwa

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Trivedi, Gauravi N., Janhavi T. Karlekar, Khushbu Dhimmar, and Hetal kumar Panchal. "FBDD: In-silico STRATEGY TO INHIBIT MPRO ACTIVITY USING DRUGS FROM PREVIOUS OUTBREAKS." Journal of Experimental Biology and Agricultural Sciences 9, no. 4 (2021): 472–80. http://dx.doi.org/10.18006/2021.9(4).472.480.

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Main protease (Mpro) and Spike (S) proteins are said potential drug targets of COVID-19. Pneumonia like respiratory illness caused by SARS-CoV-2 is spreading rapidly due to its replication and transmission rate. Protease is the protein that is involved in both replication and transcription. Since CoV-2 shares, genomic similarity with CoV and MERS-CoV, drugs from previous outbreaks are used as primary treatment of the disease. In-silico drug development strategies are said to be faster and effective than in-vitro with a lesser amount of risk factors. Fragment Based Drug Designing (FBDD), also k

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27

Suručić, Relja, Jelena Radović Selgrad, Tatjana Kundaković-Vasović, et al. "In Silico and In Vitro Studies of Alchemilla viridiflora Rothm—Polyphenols’ Potential for Inhibition of SARS-CoV-2 Internalization." Molecules 27, no. 16 (2022): 5174. http://dx.doi.org/10.3390/molecules27165174.

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Since the outbreak of the COVID-19 pandemic, it has been obvious that virus infection poses a serious threat to human health on a global scale. Certain plants, particularly those rich in polyphenols, have been found to be effective antiviral agents. The effectiveness of Alchemilla viridiflora Rothm. (Rosaceae) methanol extract to prevent contact between virus spike (S)-glycoprotein and angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1) receptors was investigated. In vitro results revealed that the tested samples inhibited 50% of virus-receptor binding interactions in doses of 0.18

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Aqeel, Imra, Abdul Majid, Tahani Jaser Alahmadi, and Areej Althubaity. "In-silico study of approved drugs as potential inhibitors against 3CLpro and other viral proteins of CoVID-19." PLOS One 20, no. 6 (2025): e0325707. https://doi.org/10.1371/journal.pone.0325707.

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The global pandemic, due to the emergence of COVID-19, has created a public health crisis. It has a huge morbidity rate that was never comprehended in the recent decades. Despite numerous efforts, potent antiviral drugs are lacking. Repurposing of drugs presents a low-cost and rapid solution for finding new drugs by exploiting known drugs. In this study, we employed an integrated In-Silico approach using molecular docking and machine learning regression models to explore the potential inhibitors against key proteins of SARS-CoV-2. A library of 5903 drugs from the ZINC database was retrieved an

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Škrbić, Ranko, Maja Travar, Miloš P. Stojiljković, Dragan M. Djuric, and Relja Suručić. "Folic Acid and Leucovorin Have Potential to Prevent SARS-CoV-2-Virus Internalization by Interacting with S-Glycoprotein/Neuropilin-1 Receptor Complex." Molecules 28, no. 5 (2023): 2294. http://dx.doi.org/10.3390/molecules28052294.

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The interaction of the SARS-CoV-2 spike (S) glycoprotein receptor-binding domain with the host-cell ACE2 receptor is a well-known step in virus infection. Neuropilin-1 (NRP-1) is another host factor involved in virus internalization. The interaction between S-glycoprotein and NRP-1 has been identified as a potential COVID-19 treatment target. Herein, the effectiveness of folic acid and leucovorin in preventing contact between S-glycoprotein and NRP-1 receptors was investigated using in silico studies and then confirmed in vitro. The results of a molecular docking study showed that leucovorin a

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Driche, El-Hadj. "In-silico ADMET and molecular docking evaluation of an active cyclopeptide from a Saharan Streptomyces strain with anticancer, anti-HIV, and anti- SARS-CoV-2 activities." Brazilian Journal of Health Review 7, no. 9 (2024): e76165. https://doi.org/10.34119/bjhrv7n9-448.

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The emergence of new SARS-CoV-2 variants, HIV drug resistance, and the persistent burden of breast cancer have created an urgent need to identify new antiviral and anticancer drug candidates. In this investigation, we employed in-silico methods to evaluate the pharmacokinetic proprieties and toxicity, and the inhibitory potential of a cyclic peptide compound produced by a novel Streptomyces strain using target enzymes. In silico analysis of the ADMET profile indicates that the cyclic peptide cyclo(L-pro-L-tyr) has favorable physicochemical properties, good lipophilicity and water solubility, g

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Cahyono, Bambang, Nur Dina Amalina, Meiny Suzery, and Damar Nur Wahyu Bima. "Exploring the Capability of Indonesia Natural Medicine Secondary Metabolite as Potential Inhibitors of SARS-CoV-2 Proteins to Prevent Virulence of COVID-19: In silico and Bioinformatic Approach." Open Access Macedonian Journal of Medical Sciences 9, A (2021): 336–42. http://dx.doi.org/10.3889/oamjms.2021.5945.

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BACKGROUND: SARS-CoV-2 was causing COVID-19 disease resulting in many deaths and being a significant concern in the world today. There is an emergent need to search for possible medications for COVID-19 treatment. The key point to halt SARS-CoV-2 infection through inhibition of the virus-receptor interaction and stimulates the immune system. Utilization of the bioinformatic and in silico molecular docking a number of available medications might be proven to be effective in inhibiting SARS-CoV-2 main drug targets including the SARS-CoV2 spike glycoprotein, the 3CL protease SARS-CoV-2 active tar

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Das, Poonam, Sabuj Sahoo, Sanatan Majhi, Rout George Kerry, Anup Kumar Singh, and Atala Bihari Jena. "Inhibitory Potential of Chitosan Derivatives against Severe Acute Respiratory Syndrome Coronavirus 2: An In Silico Prospective." INNOSC Theranostics and Pharmacological Sciences 5, no. 2 (2023): 32. http://dx.doi.org/10.36922/itps.1077.

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The present work was designed to investigate the antiviral potential of novel monomeric and oligomeric chitosan derivatives through in silico approaches. The goal was to identify potent broad-spectrum antiviral compounds as promising drug candidates against severe acute respiratory syndrome coronavirus 2 and understand their mode of action. Chitosan biopolymer and its derivatives were virtually screened against the spike glycoprotein and human angiotensin-converting enzyme 2 (ACE2) receptor of novel coronavirus-19. Hydroxypropyl trimethyl ammonium chloride chitosan (HTCC), a polymeric chitosan

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Celebi, Alper Tunga, Goksu Uzel, Ece Oylumlu, et al. "Computational Modeling of T Cell Hypersensitivity during Coronavirus Infections Leading to Autoimmunity and Lethality." Computational and Mathematical Methods in Medicine 2022 (March 22, 2022): 1–21. http://dx.doi.org/10.1155/2022/9444502.

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The human angiotensin-converting enzyme 2 (hACE2) receptor is the primary receptor for SARS-CoV-2 infection. However, the presence of alternative receptors such as the transmembrane glycoprotein CD147 has been proposed as a potential route for SARS-CoV-2 infection. The outcomes of SARS-CoV-2 spike protein binding to receptors have been shown to vary among individuals. Additionally, some patients infected with SARS-CoV-2 develop autoimmune responses. Given that CD147 is involved in the hyperactivation of memory T cells resulting in autoimmunity, we investigated the interaction of the SARS-CoV-2

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Obi, E. O., J. A. Yentumi, D. Mbatuegwu, F. Ayobami, and T. Obi. "Generating Novel Small Molecule Drugs for Selected SARS-CoV-2 Proteins: The Medgnosis GenAI Approach." Advances in Multidisciplinary & Scientific Research Journal Publication 10, no. 4 (2024): 7–18. http://dx.doi.org/10.22624/aims/v10n4p1.

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The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in an unprecedented public health crisis. Owing to the novelty of the virus and its high mutability, there are currently limited SARS-CoV-2-specific treatments available despite extensive research that has been performed on the virus. Therefore, rapid development of effective therapies, especially small molecules against SARS-CoV-2, is urgently needed. In this study, we targeted three core structural proteins of the virus, spike glycoprotein, replicase polypr

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Ambrose, Jenifer Mallavarpu, Malathi Kullappan, Shankargouda Patil, et al. "Plant-Derived Antiviral Compounds as Potential Entry Inhibitors against Spike Protein of SARS-CoV-2 Wild-Type and Delta Variant: An Integrative in SilicoApproach." Molecules 27, no. 6 (2022): 1773. http://dx.doi.org/10.3390/molecules27061773.

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The wild-type SARS-CoV-2 has continuously evolved into several variants with increased transmissibility and virulence. The Delta variant which was initially identified in India created a devastating impact throughout the country during the second wave. While the efficacy of the existing vaccines against the latest SARS-CoV-2 variants remains unclear, extensive research is being carried out to develop potential antiviral drugs through approaches like in silico screening and drug-repurposing. This study aimed to conduct the docking-based virtual screening of 50 potential phytochemical compounds

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Bharathi, Muruganantham, Bhagavathi Sundaram Sivamaruthi, Periyanaina Kesika, Subramanian Thangaleela, and Chaiyavat Chaiyasut. "In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer." Applied Sciences 12, no. 2 (2022): 665. http://dx.doi.org/10.3390/app12020665.

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In October 2020, the SARS-CoV-2 B.1.617 lineage was discovered in India. It has since become a prominent variant in several Indian regions and 156 countries, including the United States of America. The lineage B.1.617.2 is termed the delta variant, harboring diverse spike mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD), which may heighten its immune evasion potentiality and cause it to be more transmissible than other variants. As a result, it has sparked substantial scientific investigation into the development of effective vaccinations and anti-viral drugs. Sev

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Dowluru, SVGK Kaladhar. "EFFECTS OF DRUGS ON SPIKE GLYCOPROTEIN OF SARS-COV 2 IN CONTROL OF COVID-2019." March 15, 2020. https://doi.org/10.5281/zenodo.3778288.

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The spike glycoprotein of SARS-CoV 2 is 3849 bp length present from 21536 to 25384 location in genome as per the prediction from FGENESV0 server and is related to mutated SARS genome. The tiny molecular key on SARS-CoV-2 that gives the virus entry into the cell is called a spike protein, or S-protein. The docking results have shown that compounds like Curcumin (Enol form) and Anti-Viral drugs like Ombitasvir with SARS CoV2 has shown best results. Apart with these compounds Curcumin (Keto form), Cholecalciferol (Vitamin D), Ascorbic acid (Vitamin C), 3-isobutyl-1-methylxanthine (in tea), Chloro

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Siddiqui, Falak A., Sharuk L. Khan, Rajendra P. Marathe, and Nitin V. Nemac. "Design, synthesis and in silico studies of novel N-(2-aminophenyl)-2,3-diphenylquinoxaline-6-sulfonamide derivatives targeting receptor-binding domain (RBD) of SARS-CoV-2 Spike Glycoprotein and evaluation as antimicrobial and antimalarial agents." Letters in Drug Design & Discovery 18 (April 27, 2021). http://dx.doi.org/10.2174/1570180818666210427095203.

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Background: Pneumonia induced by a novel coronavirus (SARS-CoV-2) was named as coronavirus disease 2019 (COVID-19). The Receptor-binding domain (RBD) of SARS-CoV-2 Spike Glycoprotein, causes invasion of the virus into the host cell by attaching with human angiotensin-converting enzyme-2 (hACE-2) which leads to further infection. Objectives: The novel N-(2-aminophenyl)-2,3-diphenylquinoxaline-6-sulfonamide derivatives were designed and synthesized to inhibit the RBD of SARS-CoV-2 Spike Glycoprotein by applying molecular docking tools. Methods: The synthesized products was characterized by Infra

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Jafary, Farzaneh, Sepideh Jafari, and Mohamad Reza Ganjalikhany. "In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-021-86380-2.

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AbstractSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a newly-discovered coronavirus and responsible for the spread of coronavirus disease 2019 (COVID-19). SARS-CoV-2 infected millions of people in the world and immediately became a pandemic in March 2020. SARS-CoV-2 belongs to the beta-coronavirus genus of the large family of Coronaviridae. It is now known that its surface spike glycoprotein binds to the angiotensin-converting enzyme-2 (ACE2), which is expressed on the lung epithelial cells, mediates the fusion of the cellular and viral membranes, and facilitates the entry o

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Ferreira da Silva-Júnior, Edeildo, Weslany Souza Rocha, and Peng Zhan. "SARS-CoV-2 Omicron Variant in Medicinal Chemistry Research." Current Topics in Medicinal Chemistry 23 (April 11, 2023). http://dx.doi.org/10.2174/1568026623666230411095417.

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Abstract: The Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and threatens public health and safety. Nowadays, modern society has faced a new challenging problem, the emergence of novel SARS-CoV-2 variants of concern (VOCs). In this context, the Omicron (B.1.1.529) variant, having more than 60 mutations when compared to its ancestral wild-type virus, has infected many individuals around the world. It is rapidly spread person-to-person due to its increased transmissibility. Additionally, it

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Thanh Binh, Nguyen Thi, Nguyen Thi Hai Yen, Dang Kim Thu, Nguyen Thanh Hai, and Bui Thanh Tung. "The Potential of Medicinal Plants and Bioactive Compounds in the Fight Against COVID-19." VNU Journal of Science: Medical and Pharmaceutical Sciences 37, no. 3 (2021). http://dx.doi.org/10.25073/2588-1132/vnumps.4372.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus , is causing a serious worldwide COVID-19 pandemic. The emergence of strains with rapid spread and unpredictable changes is the cause of the increase in morbidity and mortality rates. A number of drugs as well as vaccines are currently being used to relieve symptoms, prevent and treat the disease caused by this virus. However, the number of approved drugs is still very limited due to their effectiveness and side effects. In such a situation, medicinal plants and bioactive compounds are considered a highly valuabl

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"Natural Product Emerging as Potential SARS Spike Glycoproteins-ACE2 Inhibitors to Combat COVID-19 Attributed by In-Silico Investigations." Biointerface Research in Applied Chemistry 11, no. 3 (2020): 10628–39. http://dx.doi.org/10.33263/briac113.1062810639.

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COVID-19 is a pandemic infectious disorder that emerged as a major outbreak for the community and health care system across the globe. Since the currently available drug therapeutics available for COVID-19 are prone to provide symptomatic and supportive relief, which has invited the entire scientist of all over the nations to investigate therapeutic drug candidates accompanied by anti-COVID-19 activity. The recognition of ACE2 mediated entry of SARS-CoV-2 encouraged us to investigate natural products as a potential inhibitor of the SARS spike glycoprotein-Human ACE2 complex. Using the strategy

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Shanmugam, Anusuya, Anbazhagan Venkattappan, and M. Michael Gromiha. "Structure Based Drug Designing Approaches in SARS-CoV-2 Spike Inhibitor Design." Current Topics in Medicinal Chemistry 23 (November 3, 2022). http://dx.doi.org/10.2174/1568026623666221103091658.

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Abstract: The COVID-19 outbreak and the pandemic situation have hastened the research community to design a novel drug and vaccine against its causative organism, the SARS-CoV-2. The spike glycoprotein present on the surface of this pathogenic organism plays an immense role in viral entry and antigenicity. Hence, it is considered an important drug target in COVID-19 drug design. Several three-dimensional crystal structures of this SARS-CoV-2 spike protein have been identified and deposited in the Protein DataBank during the pandemic period. This accelerated the research in computer-aided drug

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Das, Nabarun Chandra, Rajendra Kumar Labala, Ritwik Patra, Asamanja Chattoraj, and Suprabhat Mukherjee. "In silico identification of new anti-SARS-CoV-2 agents from bioactive phytocompounds targeting the viral spike glycoprotein and human TLR4." Letters in Drug Design & Discovery 18 (September 1, 2021). http://dx.doi.org/10.2174/1570180818666210901125519.

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Background: The recent outbreak of novel coronavirus disease (COVID-19) pandemic caused by SARS-CoV-2 has posed a tremendous threat to mankind. The unavailability of a specific drug or vaccine has been the major concern to date. Spike (S) glycoprotein of SARS-CoV-2 plays the most crucial role in the viral infection and immunopathogenesis, and hence this protein appears to be an efficacious target for drug discovery. Objective: Identifying potent bioactive phytocompound that can target viral spike (S) glycoprotein and human TLR4 to reduce immunopathological manifestations of COVID-19. Method: A

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"SARS-COV-2 Spike Glycoprotein as Inhibitory Target for In silico Screening of Natural Compounds." Biointerface Research in Applied Chemistry 11, no. 6 (2021): 14974–85. http://dx.doi.org/10.33263/briac116.1497414985.

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Coronavirus disease (Covid-19) caused by SARS-Cov-2 has raised global health concerns without approved drugs to manage this life-threatening disease. This study aimed to predict the inhibitory potential of quercetin-3-o-rutinoside against SARS-Cov-2 spike glycoprotein. Targeting the SARS-Cov-2 Nucleocapsid spike glycoprotein (pdb id: 6m3m) is gaining importance. In this present study, the relationship between plant-derived natural drug and spike glycoprotein was predicted using in silico computational approach. The results were evaluated according to the glide (Schrodinger) dock score. Among t

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Sharma, Deepak Chand, Kaushal Kishor Mishra, Asheesh Kumar Mishra, Vandita Anand, Anjana Pandey, and Savita Budhwar. "Design of a Multi-epitope Vaccine against Covid-19: An In silico Approach." Current Biotechnology 12 (June 12, 2023). http://dx.doi.org/10.2174/2211550112666230612153430.

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Background: The control of the Covid-19 epidemic depends on designing a novel, effective vaccine against it. Currently, available vaccines cannot provide complete protection against various mutants of Covid-19. Objective: The present investigation aimed to design a new multi-epitope vaccine by using in silico tools. Method: In the present study, the spike-glycoprotein was targeted, desirably stimulating both B and T-cell lymphocytes, providing effective and safe responses in the host immune system. The desired vaccine has been found to possess 448 amino acids of spike glycoprotein. The prognos

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Liu, Xiao-Huan, Ting Cheng, Bao-Yu Liu, Jia Chi, Ting Shu, and Tao Wang. "Structures of the SARS-CoV-2 spike glycoprotein and applications for novel drug development." Frontiers in Pharmacology 13 (August 9, 2022). http://dx.doi.org/10.3389/fphar.2022.955648.

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COVID-19 caused by SARS-CoV-2 has raised a health crisis worldwide. The high morbidity and mortality associated with COVID-19 and the lack of effective drugs or vaccines for SARS-CoV-2 emphasize the urgent need for standard treatment and prophylaxis of COVID-19. The receptor-binding domain (RBD) of the glycosylated spike protein (S protein) is capable of binding to human angiotensin-converting enzyme 2 (hACE2) and initiating membrane fusion and virus entry. Hence, it is rational to inhibit the RBD activity of the S protein by blocking the RBD interaction with hACE2, which makes the glycosylate

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Nath, Lekshmi R., Adithya J, Maneesha Murali, et al. "Identification of Kaempferol as viral entry inhibitor and DL-Arginine as viral replication inhibitor from selected plants of Indian traditional medicine against COVID-19: An in silico guided in vitro approach." Current Computer-Aided Drug Design 19 (January 12, 2023). http://dx.doi.org/10.2174/1573409919666230112123213.

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Background: Indian traditional medicinal plants are known for their great potential in tackling viral diseases. Previously, we reported a systematic review approach of seven plausible traditional Indian medicinal plants against SARS CoV 2. Methods: Molecular docking was conducted with Biovia Discovery Studio. Three binding domains for Spike glycoprotein (PDB IDs: 6LZG, 6M17, 6M0J) and one binding domain of RdRp (PDB ID: 7BTF) were used. Among 100 phytoconstituents listed from seven plants by IMPPAT Database used for virtual screening, the best six compounds were again filtered using Swiss ADME

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Nurhan, Ahmad Dzulfikri, Maria Apriliani Gani, Saipul Maulana, Siswandono Siswandono, Chrismawan Ardianto, and Junaidi Khotib. "Molecular Docking Studies for Protein-Targeted Drug Development in SARS-CoV-2." Letters in Drug Design & Discovery 18 (May 12, 2021). http://dx.doi.org/10.2174/1570180818666210512021619.

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Background: The SARS-CoV-2/COVID-19 infection has resulted in a global pandemic and emergency. Currently, there is no therapeutic agent that has been proven to be effective and selective to deal with this pandemic. Objective: In this study, we explored and screened 401 compounds-related viruses that may inhibit one or more of the three protein targets in SARS-CoV-2 (3CL protease, RdRp, and spike glycoprotein) using in-silico approach. Methods: Lipinski's rule of five was used as an initial screening for these compounds. Ligand preparation was carried out using JChem software and Schrödinger's

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"In silico Investigation of Tridax procumbens Phyto-Constituents Against SARS-CoV-2 Infection." Biointerface Research in Applied Chemistry 11, no. 4 (2021): 12120–48. http://dx.doi.org/10.33263/briac114.1212012148.

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Tridax procumbens is a popular medicinal plant traditionally used for wound healing and bronchial catarrh. In the current study, in silico computational analysis of 22 active phytoconstituents of T. procumbens was performed against SARS-CoV-2. Molecular Docking studies against six key targets of SARS-CoV-2 including PDB ID: 6LU7, a main protease 3CLpro/Mpro; PDB ID: 6NUR, SARS-Coronavirus NSP12 polymerase bound to NSP7 and NSP8 co-factors, PDB ID: 6m71, SARS-Cov-2 RNA-dependent RNA polymerase (RdRp), PDB ID: 6CS2, SARS Spike Glycoprotein - human ACE2 complex a Stabilized variant; PDB ID: 6VXX,

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