1
|
Daniell H, Nair SK, Guan H, Guo Y, Kulchar RJ, Torres MDT, Shahed-Al-Mahmud M, Wakade G, Liu YM, Marques AD, Graham-Wooten J, Zhou W, Wang P, Molugu SK, de Araujo WR, de la Fuente-Nunez C, Ma C, Short WR, Tebas P, Margulies KB, Bushman FD, Mante FK, Ricciardi RP, Collman RG, Wolff MS. Debulking different Corona (SARS-CoV-2 delta, omicron, OC43) and Influenza (H1N1, H3N2) virus strains by plant viral trap proteins in chewing gums to decrease infection and transmission. Biomaterials 2022; 288:121671. [PMID: 35953331 PMCID: PMC9290430 DOI: 10.1016/j.biomaterials.2022.121671] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 12/13/2022]
Abstract
Because oral transmission of SARS-CoV-2 is 3-5 orders of magnitude higher than nasal transmission, we investigated debulking of oral viruses using viral trap proteins (CTB-ACE2, FRIL) expressed in plant cells, delivered through the chewing gum. In omicron nasopharyngeal (NP) samples, the microbubble count (based on N-antigen) was significantly reduced by 20 μg of FRIL (p < 0.0001) and 0.925 μg of CTB-ACE2 (p = 0.0001). Among 20 delta or omicron NP samples, 17 had virus load reduced below the detection level of spike protein in the RAPID assay, after incubation with the CTB-ACE2 gum powder. A dose-dependent 50% plaque reduction with 50-100 ng FRIL or 600-800 μg FRIL gum against Influenza strains H1N1, H3N2, and Coronavirus HCoV-OC43 was observed with both purified FRIL, lablab bean powder or gum. In electron micrographs, large/densely packed clumps of overlapping influenza particles and FRIL protein were observed. Chewing simulator studies revealed that CTB-ACE2 release was time/dose-dependent and release was linear up to 20 min chewing. Phase I/II placebo-controlled, double-blinded clinical trial (IND 154897) is in progress to evaluate viral load in saliva before or after chewing CTB-ACE2/placebo gum. Collectively, this study advances the concept of chewing gum to deliver proteins to debulk oral viruses and decrease infection/transmission.
Collapse
Affiliation(s)
- Henry Daniell
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Smruti K Nair
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hancheng Guan
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yuwei Guo
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rachel J Kulchar
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marcelo D T Torres
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Md Shahed-Al-Mahmud
- Genomics Research Center, Taiwan Academy of Sciences, 128 Academia Rd. Section 2, Nangang District, Taipei, 11529, Taiwan
| | - Geetanjali Wakade
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yo-Min Liu
- Genomics Research Center, Taiwan Academy of Sciences, 128 Academia Rd. Section 2, Nangang District, Taipei, 11529, Taiwan
| | - Andrew D Marques
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jevon Graham-Wooten
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wan Zhou
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ping Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sudheer K Molugu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William R de Araujo
- Institute of Chemistry, State University of Campinas - UNICAMP, Campinas, Sao Paulo, 13083-970, Brazil
| | | | - Che Ma
- Genomics Research Center, Taiwan Academy of Sciences, 128 Academia Rd. Section 2, Nangang District, Taipei, 11529, Taiwan
| | - William R Short
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Pablo Tebas
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kenneth B Margulies
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Frederic D Bushman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Francis K Mante
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert P Ricciardi
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ronald G Collman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mark S Wolff
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| |
Collapse
|
2
|
Skariyachan S. Scope of computational biology and bioinformatics towards the discovery of potential therapeutic agents against viral diseases. Future Virol 2022. [DOI: 10.2217/fvl-2021-0281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tweetable abstract Computational biology and bioinformatics resources provide a cutting-edge platform for the screening and development of novel therapeutic agents against probable targets of emerging viral diseases.
Collapse
Affiliation(s)
- Sinosh Skariyachan
- Department of Microbiology, St Pius X College, Rajapuram, Kasaragod, Kerala, 671532, India
| |
Collapse
|
3
|
Zarei O, Kleine-Weber H, Hoffmann M, Hamzeh-Mivehroud M. Development and evaluation of peptidomimetic compounds against SARS-CoV-2 spike protein: an in silico and in vitro study. Mol Inform 2022; 41:e2100231. [PMID: 35068079 PMCID: PMC9015386 DOI: 10.1002/minf.202100231] [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: 01/12/2022] [Accepted: 01/16/2022] [Indexed: 11/08/2022]
Abstract
Background: Coronavirus disease 2019 (COVID‐19) as global pandemic disease has been adversely affecting public health and social life with considerable loss of human life worldwide. Therefore, there is an urgent need for developing novel therapeutics to combat COVID‐19. The causative agent of COVID‐19 is SARS‐CoV‐2 which targets human angiotensin converting enzyme 2 (ACE2) as cellular receptor via its spike (S) protein. In this context, interfering with the binding of SARS‐CoV‐2 S protein to target molecules could provide a promising strategy to find novel therapeutic agents against SARS‐CoV‐2. The purpose of the current study was to identify potential peptidomimetics against S protein with a combination of structure‐based virtual screening methods and in vitro assays. Methods: The candidates were inspected in terms of ADME properties, drug‐likeness, as well as toxicity profiles. Additionally, molecular docking and dynamics simulations were performed to predict binding of the studied ligands to spike protein. Results: Biological evaluation of the compounds revealed that PM2 molecule exhibits some antiviral activity. Conclusion: In summary, this study highlights the importance of combining in silico and in vitro techniques in order to identify antiviral compound to tackle COVID‐19 and presents a new scaffold that may be structurally optimized for improved antiviral activity.
Collapse
Affiliation(s)
- Omid Zarei
- Kurdistan University of Medical Sciences, IRAN (THE ISLAMIC REPUBLIC OF)
| | | | - Markus Hoffmann
- German Primate Centre Leibniz Institute for Primate Research, GERMANY
| | | |
Collapse
|
4
|
Cai C, Xu L, Fang J, Dai Z, Wu Q, Liu X, Wang Q, Fang J, Liu AL, Du GH. In Silico Prediction and Bioactivity Evaluation of Chemical Ingredients Against Influenza A Virus From Isatis tinctoria L. Front Pharmacol 2021; 12:755396. [PMID: 34950027 PMCID: PMC8689007 DOI: 10.3389/fphar.2021.755396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/09/2021] [Indexed: 01/11/2023] Open
Abstract
Influenza A virus (IAV) is one of the major causes of seasonal endemic diseases and unpredictable periodic pandemics. Due to the high mutation rate and drug resistance, it poses a persistent threat and challenge to public health. Isatis tinctoria L. (Banlangen, BLG), a traditional herbal medicine widely used in Asian countries, has been reported to possess strong efficacy on respiratory viruses, including IAV. However, its effective anti-IAV components and the mechanism of actions (MOAs) are not yet fully elucidated. In this study, we first summarized the chemical components and corresponding contents in BLG according to current available chemical analysis literature. We then presented a network-based in silico framework for identifying potential drug candidates against IAV from BLG. A total of 269 components in BLG were initially screened by drug-likeness and ADME (absorption, distribution, metabolism, and excretion) evaluation. Thereafter, network predictive models were built via the integration of compound–target networks and influenza virus–host proteins. We highlighted 23 compounds that possessed high potential as anti-influenza virus agents. Through experimental evaluation, six compounds, namely, eupatorin, dinatin, linarin, tryptanthrin, indirubin, and acacetin, exhibited good inhibitory activity against wild-type H1N1 and H3N2. Particularly, they also exerted significant effects on drug-resistant strains. Finally, we explored the anti-IAV MOAs of BLG and showcased the potential biological pathways by systems pharmacology analysis. In conclusion, this work provides important information on BLG regarding its use in the development of anti-IAV drugs, and the network-based prediction framework proposed here also offers a powerfulful strategy for the in silico identification of novel drug candidates from complex components of herbal medicine.
Collapse
Affiliation(s)
- Chuipu Cai
- Division of Data Intelligence, Department of Computer Science, Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, College of Engineering, Shantou University, Shantou, China.,Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lvjie Xu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junfeng Fang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhao Dai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qihui Wu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoyi Liu
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiansong Fang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ai-Lin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guan-Hua Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
5
|
Mathew S, Taleb S, Eid AH, Althani AA, Yassine HM. In silico virtual screening of lead compounds for major antigenic sites in respiratory syncytial virus fusion protein. EMERGENT MATERIALS 2021; 5:295-305. [PMID: 33969268 PMCID: PMC8090912 DOI: 10.1007/s42247-021-00213-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Human respiratory syncytial virus (RSV) is a leading ubiquitous respiratory pathogen in newborn infants, young children, and the elderly, with no vaccine available to date. The viral fusion glycoprotein (RSV F) plays an essential role in the infection process, and it is a primary target of neutralizing antibodies, making it an attractive site for vaccine development. With this in view, there is a persistent need to identify selective antiviral drugs against RSV, targeting the major antigenic sites on the F protein. We aimed to conduct a robust in silico high-throughput drug screening of one million compounds to explore potential inhibitors that bind the major antigenic site Ø and site II on RSV F protein, which are the main target of neutralizing antibodies (NAb). We utilized the three-dimensional crystallographic structure of both antigenic site Ø on pre-F and antigenic II on post-F to screen for potential anti-RSV inhibitors. A library of one million small compounds was docked to explore lead binders in the major antigenic sites by using virtual lab bench CLC Drug Discovery. We also performed Quantitative Structure-Activity and Relationship (QSAR) for the lead best binders known for their antiviral activity. Among one million tested ligands, seven ligands (PubChem ID: 3714418, 24787350, 49828911, 24802036, 79824892, 49726463, and 3139884) were identified as the best binders to neutralizing epitopes site Ø and four ligands (PubChem ID: 865999, 17505357, 24802036, and 24285058) to neutralizing epitopes site II, respectively. These binders exhibited significant interactions with neutralizing epitopes on RSV F, with an average of six H bonds, docking energy of - 15.43 Kcal·mol-1, and minimum interaction energy of - 7.45 Kcal·mol-1. Using in silico virtual screening, we identified potential RSV inhibitors that bind two major antigenic sites on the RSV F protein. Using structure-based design and combination-based drug therapy, identified molecules could be modified to generate the next generation anti-RSV drugs. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s42247-021-00213-6.
Collapse
Affiliation(s)
- Shilu Mathew
- Biomedical Research Center, Qatar University, Doha, 2713 Qatar
| | - Sara Taleb
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Asmaa A. Althani
- Biomedical Research Center, Qatar University, Doha, 2713 Qatar
- College of Health Sciences, Qatar University, Doha, 2713 Qatar
| | - Hadi M. Yassine
- Biomedical Research Center, Qatar University, Doha, 2713 Qatar
- College of Health Sciences, Qatar University, Doha, 2713 Qatar
| |
Collapse
|
6
|
Mirza AZ, Shamshad H, Osra FA, Habeebullah TM, Morad M. An overview of viruses discovered over the last decades and drug development for the current pandemic. Eur J Pharmacol 2021; 890:173746. [PMID: 33221318 PMCID: PMC8711773 DOI: 10.1016/j.ejphar.2020.173746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 01/06/2023]
Abstract
Since the discovery of the yellow fever virus in 1901, thus far, two hundred nineteen viral species are recognized as human pathogens. Each year, the number of viruses causing infections in humans increases, triggering epidemics and pandemics, such as the current COVID-19 pandemic. Pointing to bats as the natural host, in 2019, a genome highly identical to a bat coronavirus (COVID-19) spread all over the world, and the World Health Organization (WHO) officially confirmed it as a pandemic. The virus mainly spreads through the respiratory tract, uses angiotensin-converting enzyme 2 (ACE2) as a receptor, and is characterized by symptoms of fever, cough, and fatigue. Antivirals and vaccines have provided improvements in some cases, but the discovery of a new and diverse variety of viruses with outbreaks has posed a challenge in timely treatments for medical scientists. Currently, few specific antiviral strategies are being used, and many of the effective antiviral drugs and reported active molecules are under vital exploration. In this review, with the details of viral diseases, we summarize the current attempts in drug development, epidemiology, and the latest treatments and scientific advancements to combat the COVID-19 epidemic. Moreover, we discuss ways to reduce epidemics and pandemics in the near future.
Collapse
Affiliation(s)
- Agha Zeeshan Mirza
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Hina Shamshad
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, University of Karachi, Karachi, 75270, Pakistan
| | | | - Turki M Habeebullah
- Department of Environment and Health Research, Custodian of Two Holy Mosques Institute for Hajj and Umrah Research, Umm-Al-Qura University, Makkah, Saudi Arabia
| | - Moataz Morad
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| |
Collapse
|
7
|
Mahal A, Duan M, Zinad DS, Mohapatra RK, Obaidullah AJ, Wei X, Pradhan MK, Das D, Kandi V, Zinad HS, Zhu Q. Recent progress in chemical approaches for the development of novel neuraminidase inhibitors. RSC Adv 2021; 11:1804-1840. [PMID: 35424082 PMCID: PMC8693540 DOI: 10.1039/d0ra07283d] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/22/2020] [Indexed: 12/28/2022] Open
Abstract
Influenza virus is the main cause of an infectious disease called influenza affecting the respiratory system including the throat, nose and lungs. Neuraminidase inhibitors are reagents used to block the enzyme called neuraminidase to prevent the influenza infection from spreading. Neuraminidase inhibitors are widely used in the treatment of influenza infection, but still there is a need to develop more potent agents for the more effective treatment of influenza. Complications of the influenza disease lead to death, and one of these complications is drug resistance; hence, there is an urgent need to develop more effective agents. This review focuses on the recent advances in chemical synthesis pathways used for the development of new neuraminidase agents along with the medicinal aspects of chemically modified molecules, including the structure-activity relationship, which provides further rational designs of more active small molecules.
Collapse
Affiliation(s)
- Ahmed Mahal
- Department of Medical Biochemical Analysis, College of Health Technology, Cihan University-Erbil Erbil Kurdistan Region Iraq
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, Chinese Academy of Sciences South China Botanical Garden Guangzhou 510650 People's Republic of China
- Guangzhou HC Pharmaceutical Co., Ltd Guangzhou 510663 People's Republic of China
| | - Meitao Duan
- School of Traditional Chinese Medicine, Southern Medical University Guangzhou 510515 People's Republic of China
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics Guangzhou 510515 People's Republic of China
| | - Dhafer S Zinad
- Applied Science Department, University of Technology Baghdad 10001 Iraq
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering Keonjhar Odisha 758002 India
| | - Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh 11451 Saudi Arabia
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh 11451 Saudi Arabia
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, Chinese Academy of Sciences South China Botanical Garden Guangzhou 510650 People's Republic of China
| | - Manoj K Pradhan
- Department of Chemistry, Government College of Engineering Keonjhar Odisha 758002 India
| | - Debadutta Das
- Department of Chemistry, Sukanti Degree College Subarnapur Odisha 767017 India
| | - Venkataramana Kandi
- Department of Microbiology, Prathima Institute of Medical Sciences Karimnagar Telangana India
| | - Hany S Zinad
- Biosciences Institute, Faculty of Medical Science, Newcastle University NE2 4HH Newcastle upon Tyne UK
- Iraq Natural History Museum and Research Centre (INHM), University of Baghdad Baghdad Iraq
| | - Quanhong Zhu
- School of Traditional Chinese Medicine, Southern Medical University Guangzhou 510515 People's Republic of China
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics Guangzhou 510515 People's Republic of China
| |
Collapse
|
8
|
Nagarajan N, Yapp EKY, Le NQK, Yeh HY. In silico screening of sugar alcohol compounds to inhibit viral matrix protein VP40 of Ebola virus. Mol Biol Rep 2019; 46:3315-3324. [PMID: 30982214 DOI: 10.1007/s11033-019-04792-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/28/2019] [Indexed: 12/11/2022]
Abstract
Ebola virus is a virulent pathogen that causes highly lethal hemorrhagic fever in human and non-human species. The rapid growth of this virus infection has made the scenario increasingly complicated to control the disease. Receptor viral matrix protein (VP40) is highly responsible for the replication and budding of progeny virus. The binding of RNA to VP40 could be the crucial factor for the successful lifecycle of the Ebola virus. In this study, we aimed to identify the potential drug that could inhibit VP40. Sugar alcohols were enrich with antiviral properties used to inhibit VP40. Virtual screening analysis was perform for the 48 sugar alcohol compounds, of which the following three compounds show the best binding affinity: Sorbitol, Mannitol and Galactitol. To understand the perfect binding orientation and the strength of non-bonded interactions, individual molecular docking studies were perform for the best hits. Further molecular dynamics studies were conduct to analyze the efficacy between the protein-ligand complexes and it was identify that Sorbitol obtains the highest efficacy. The best-screened compounds obtained drug-like property and were less toxic, which could be use as a potential lead compound to develop anti-Ebola drugs.
Collapse
Affiliation(s)
- Nagasundaram Nagarajan
- School of Humanities, Nanyang Technological University, 14 Nanyang Dr, Singapore, 637332, Singapore.
| | - Edward K Y Yapp
- Singapore Institute of Manufacturing Technology, 2 Fusionopolis Way, Singapore, 138634, Singapore
| | - Nguyen Quoc Khanh Le
- School of Humanities, Nanyang Technological University, 14 Nanyang Dr, Singapore, 637332, Singapore
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, 14 Nanyang Dr, Singapore, 637332, Singapore.
| |
Collapse
|