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Rahman MM, Islam MR, Akash S, Mim SA, Rahaman MS, Emran TB, Akkol EK, Sharma R, Alhumaydhi FA, Sweilam SH, Hossain ME, Ray TK, Sultana S, Ahmed M, Sobarzo-Sánchez E, Wilairatana P. In silico investigation and potential therapeutic approaches of natural products for COVID-19: Computer-aided drug design perspective. Front Cell Infect Microbiol 2022; 12:929430. [PMID: 36072227 PMCID: PMC9441699 DOI: 10.3389/fcimb.2022.929430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/03/2022] [Indexed: 12/07/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a substantial number of deaths around the world, making it a serious and pressing public health hazard. Phytochemicals could thus provide a rich source of potent and safer anti-SARS-CoV-2 drugs. The absence of approved treatments or vaccinations continues to be an issue, forcing the creation of new medicines. Computer-aided drug design has helped to speed up the drug research and development process by decreasing costs and time. Natural compounds like terpenoids, alkaloids, polyphenols, and flavonoid derivatives have a perfect impact against viral replication and facilitate future studies in novel drug discovery. This would be more effective if collaboration took place between governments, researchers, clinicians, and traditional medicine practitioners’ safe and effective therapeutic research. Through a computational approach, this study aims to contribute to the development of effective treatment methods by examining the mechanisms relating to the binding and subsequent inhibition of SARS-CoV-2 ribonucleic acid (RNA)-dependent RNA polymerase (RdRp). The in silico method has also been employed to determine the most effective drug among the mentioned compound and their aquatic, nonaquatic, and pharmacokinetics’ data have been analyzed. The highest binding energy has been reported -11.4 kcal/mol against SARS-CoV-2 main protease (7MBG) in L05. Besides, all the ligands are non-carcinogenic, excluding L04, and have good water solubility and no AMES toxicity. The discovery of preclinical drug candidate molecules and the structural elucidation of pharmacological therapeutic targets have expedited both structure-based and ligand-based drug design. This review article will assist physicians and researchers in realizing the enormous potential of computer-aided drug design in the design and discovery of therapeutic molecules, and hence in the treatment of deadly diseases.
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Affiliation(s)
- Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Sadia Afsana Mim
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md. Saidur Rahaman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
- *Correspondence: Eduardo Sobarzo-Sánchez, ; Talha Bin Emran, ; Polrat Wilairatana,
| | - Esra Küpeli Akkol
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara, Turkey
| | - Rohit Sharma
- Department of Rasashastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Sherouk Hussein Sweilam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Egyptian Russian University, Badr City, Egypt
| | - Md. Emon Hossain
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Tanmay Kumar Ray
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Sharifa Sultana
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Muniruddin Ahmed
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Eduardo Sobarzo-Sánchez
- Instituto de Investigación y Postgrado, Facultad de Ciencias de la Salud, Universidad Central de Chile, Santiago, Chile
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
- *Correspondence: Eduardo Sobarzo-Sánchez, ; Talha Bin Emran, ; Polrat Wilairatana,
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- *Correspondence: Eduardo Sobarzo-Sánchez, ; Talha Bin Emran, ; Polrat Wilairatana,
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Luo L, Yang J, Wang C, Wu J, Li Y, Zhang X, Li H, Zhang H, Zhou Y, Lu A, Chen S. Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1123-1145. [PMID: 34705221 PMCID: PMC8548270 DOI: 10.1007/s11427-020-1959-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
As coronavirus disease 2019 (COVID-19) threatens human health globally, infectious disorders have become one of the most challenging problem for the medical community. Natural products (NP) have been a prolific source of antimicrobial agents with widely divergent structures and a range vast biological activities. A dataset comprising 618 articles, including 646 NP-based compounds from 672 species of natural sources with biological activities against 21 infectious pathogens from five categories, was assembled through manual selection of published articles. These data were used to identify 268 NP-based compounds classified into ten groups, which were used for network pharmacology analysis to capture the most promising lead-compounds such as agelasine D, dicumarol, dihydroartemisinin and pyridomycin. The distribution of maximum Tanimoto scores indicated that compounds which inhibited parasites exhibited low diversity, whereas the chemistries inhibiting bacteria, fungi, and viruses showed more structural diversity. A total of 331 species of medicinal plants with compounds exhibiting antimicrobial activities were selected to classify the family sources. The family Asteraceae possesses various compounds against C. neoformans, the family Anacardiaceae has compounds against Salmonella typhi, the family Cucurbitacea against the human immunodeficiency virus (HIV), and the family Ancistrocladaceae against Plasmodium. This review summarizes currently available data on NP-based antimicrobials against refractory infections to provide information for further discovery of drugs and synthetic strategies for anti-infectious agents.
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Affiliation(s)
- Lu Luo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Cheng Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100006, China
| | - Jie Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yafang Li
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xu Zhang
- weMED Health, Houston, 77054, USA
| | - Hui Li
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Zhang
- Akupunktur Akademiet, Aabyhoej, Aarhus, 8230, Denmark
| | - Yumei Zhou
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 518033, China
| | - Aiping Lu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Omer SE, Ibrahim TM, Krar OA, Ali AM, Makki AA, Ibraheem W, Alzain AA. Drug repurposing for SARS-CoV-2 main protease: Molecular docking and molecular dynamics investigations. Biochem Biophys Rep 2022; 29:101225. [PMID: 35128086 PMCID: PMC8801302 DOI: 10.1016/j.bbrep.2022.101225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/23/2022] Open
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Tuli HS, Sood S, Kaur J, Kumar P, Seth P, Punia S, Yadav P, Sharma AK, Aggarwal D, Sak K. Mechanistic insight into anti-COVID-19 drugs: recent trends and advancements. 3 Biotech 2021; 11:110. [PMID: 33552835 PMCID: PMC7851641 DOI: 10.1007/s13205-021-02644-8] [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: 09/25/2020] [Accepted: 01/03/2021] [Indexed: 12/27/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has been established now to be a deadly disease afflicting the whole world with worst consequences on healthcare, economy and day-to-day life activities. Being a communicable disease, which is highly pathogenic in humans, causing cough, throat infection, breathing problems, high fever, muscle pain, and may lead to death in some cases especially those having other comorbid conditions such as heart or kidney problems, and diabetes. Finding an appropriate drug and vaccine candidate against coronavirus disease (COVID-19) remains an ultimate and immediate goal for the global scientific community. Based on previous studies in the literature on SARS-CoV infection, there are a number of drugs that may inhibit the replication of SARS-CoV-2 and its infection. Such drugs comprise of inhibitors of Angiotensin-Converting Enzyme 2 (ACE2), transmembrane Serine Protease 2 (TMPRSS2), nonstructural protein 3C-like protease, nonstructural RNA-dependent RNA polymerase (RdRp) and many more. The antiviral drugs such as chloroquine and hydroxychloroquine, lopinavir and ritonavir as inhibitors for HIV protease, nucleotide analogue remdesivir, and broad-spectrum antiviral drugs are available to treat the SARS-CoV-2-infected patients. Therefore, this review article is planned to gain insight into the mechanism for blocking the entry of SARS-CoV-2, its validation, other inhibition mechanisms, and development of therapeutic drugs and vaccines against SARS-CoV-2.
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Affiliation(s)
- Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed To Be University), Mullana, Ambala, 133207 India
| | - Shivani Sood
- Department of Biotechnology, Mukand Lal National College, Yamuna Nagar, Haryana India
| | - Jagjit Kaur
- Graduate School of Biomedical Engineering, ARC Centre of Excellence in Nanoscale Biophotonics (CNBP), Faculty of Engineering, The University of New South Wales, Sydney, 2052 Australia
| | - Pawan Kumar
- Institute of Plant Sciences, Agricultural Research Organisation (ARO), The Volcani Center, 7505101 Rishon LeZion, Israel
| | - Prachi Seth
- Department of Biotechnology, Mukand Lal National College, Yamuna Nagar, Haryana India
| | - Sandeep Punia
- Department of Biotechnology, Multani Mal Modi College, Patiala, India
| | - Priya Yadav
- Department of Biotechnology, Maharishi Markandeshwar (Deemed To Be University), Mullana, Ambala, 133207 India
| | - Anil Kumar Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed To Be University), Mullana, Ambala, 133207 India
| | - Diwakar Aggarwal
- Department of Biotechnology, Maharishi Markandeshwar (Deemed To Be University), Mullana, Ambala, 133207 India
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Rameshkumar MR, Indu P, Arunagirinathan N, Venkatadri B, El-Serehy HA, Ahmad A. Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study. Saudi J Biol Sci 2021; 28:448-458. [PMID: 33110386 PMCID: PMC7581406 DOI: 10.1016/j.sjbs.2020.10.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/17/2020] [Accepted: 10/18/2020] [Indexed: 02/06/2023] Open
Abstract
An outbreak of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has been recognized as a global health concern. Since, no specific antiviral drug is proven effective for treatment against COVID-19, identification of new therapeutics is an urgent need. In this study, flavonoid compounds were analyzed for its inhibitory potential against important protein targets of SARS-CoV-2 using computational approaches. Virtual docking was performed for screening of flavonoid compounds retrieved from PubChem against the main protease of SARS-CoV-2 using COVID-19 docking server. The cut off of dock score was set to >-9 kcal/mol and screened compounds were individually docked against main protease, RNA-dependent RNA polymerase, and spike proteins using AutoDock 4.1 software. Finally, lead flavonoid compounds were subjected to ADMET analysis. A total of 458 flavonoid compounds were virtually screened against main protease target and 36 compounds were selected based on the interaction energy value >-9 kcal/mol. Furthermore, these compounds were individually docked against protein targets and top 10 lead compounds were identified. Among the lead compounds, agathisflavone showed highest binding energy value of -8.4 kcal/mol against main protease, Albireodelphin showed highest dock score of -9.8 kcal/mol and -11.2 kcal/mol against RdRp, and spike proteins, respectively. Based on the high dock score and ADMET properties, top 5 lead molecules such as Albireodelphin, Apigenin 7-(6″-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6″-O-malonate were identified as potent inhibitors against main protease, RdRp, and spike protein targets of SARS-CoV-2. These all compounds are having non-carcinogenic and non-mutagenic properties. This study finding suggests that the screened compounds include Albireodelphin, Apigenin 7-(6″-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6″-O-malonate could be the potent inhibitors of SARS-CoV-2 targets.
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Affiliation(s)
| | - Purushothaman Indu
- Department of Microbiology and Biotechnology, Presidency College (Autonomous), Affiliated to University of Madras, Chennai, India
| | - Narasingam Arunagirinathan
- Department of Microbiology and Biotechnology, Presidency College (Autonomous), Affiliated to University of Madras, Chennai, India
- Central Research Laboratory, Meenakshi Academy of Higher Research and Education (Deemed to be University), Chennai, India
| | - Babu Venkatadri
- Department of Plant Biology and Biotechnology, Loyola College (Autonomous), Affiliated to University of Madras, Chennai, India
| | - Hamed A. El-Serehy
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ajaz Ahmad
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Attia YA, Alagawany MM, Farag MR, Alkhatib FM, Khafaga AF, Abdel-Moneim AME, Asiry KA, Mesalam NM, Shafi ME, Al-Harthi MA, Abd El-Hack ME. Phytogenic Products and Phytochemicals as a Candidate Strategy to Improve Tolerance to Coronavirus. Front Vet Sci 2020; 7:573159. [PMID: 33195565 PMCID: PMC7606864 DOI: 10.3389/fvets.2020.573159] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/09/2020] [Indexed: 12/28/2022] Open
Abstract
Coronaviruses are the causative agents of many infectious diseases in human and animals. These included severe acute respiratory syndrome (SARS), avian infectious bronchitis (IBV) in poultry, Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19) in humans. These results had considerable death burdens and negative influences on social-economic life. Since the appearance of the outbreak of the COVID-19 pandemic, continuous investigations have been carried out by researchers to find active compounds, mainly from plants, as natural sources, that could inhibit or stop the proliferation of the causative agent of COVID-19 (SARS-CoV-2). The most common symptoms caused by infections with COVID-19 can include cough, fever, and sore throat. Nevertheless, there is a shortage of active antiviral compounds for treating different strains of coronavirus. Herbal medicine is a class of medication that originates from nature and is aimed at decreasing the use of preservatives, excipients, or other additives and, consequently, lesser side effects. The rapid spread of COVID-19 infection besides the lack of knowledge about any treatments and the growing concern of the public from the virus directed us toward writing this review article in an aim to provide alternatives to the allopathic medicine use. There is a wealth of chemical diversity in the naturally existing compounds, including their antiviral activities, which may encourage their utilization as therapeutics against viral infections, including coronaviruses. The majority of publications on the herbal remedies of coronavirus, MERS, or SARS focused primarily on the use of polar compounds. These substances displayed encouraging inhibitory influences on coronavirus in humans. These include psoralidin, scutellarein, silvestrol, tryptanthrin, caffeic acid, quercetin, myricetin, saikosaponin B2, griffithsin (lectins), and isobavachalcone. Some other agents like lycorine may be useful, if the antiviral activity is obtained by concentrations below the toxic plasma levels. According to the available literatures, the most promising inhibitors of coronaviruses are polyphenolic compounds, which are small molecules with conjugated fused ring structures.
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Affiliation(s)
- Youssef A. Attia
- Agriculture Department, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- The Strategic Center to Kingdom Vision Realization, King Abdulaziz University, Jeddah, Saudi Arabia
- Animal and Poultry Production Department, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
| | - Mahmoud M. Alagawany
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Mayada R. Farag
- Forensic Medicine and Toxicology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Fatmah M. Alkhatib
- Chemistry Department, Faculty of Applied Science, UmmAl-Qura University, Makkah, Saudi Arabia
| | - Asmaa F. Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina, Egypt
| | | | - Khalid A. Asiry
- Agriculture Department, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noura M. Mesalam
- Biological Application Department, Nuclear Research Center, Atomic Energy Authority, Abu-Zaabal, Egypt
| | - Manal E. Shafi
- Department of Biological Sciences, Zoology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed A. Al-Harthi
- Agriculture Department, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Derosa G, Maffioli P, D'Angelo A, Di Pierro F. A role for quercetin in coronavirus disease 2019 (COVID-19). Phytother Res 2020; 35:1230-1236. [PMID: 33034398 PMCID: PMC7675685 DOI: 10.1002/ptr.6887] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/05/2020] [Accepted: 09/13/2020] [Indexed: 01/04/2023]
Abstract
Several months ago, an outbreak of pneumonia of unknown aetiology was detected in Wuhan City (China) and the aetiological agent of the atypical pneumonia was isolated by the Chinese authorities as novel coronavirus (2019‐nCoV or SARS‐CoV‐2). The WHO announced this new disease was to be known as “COVID‐19.” When looking for new antiviral compounds, knowledge of the main viral proteins is fundamental. The major druggable targets of SARS‐CoV‐2 include 3‐chymotrypsin‐like protease (3CLpro), papain‐like protease (PLpro), RNA‐dependent RNA polymerase, and spike (S) protein. Quercetin inhibits 3CLpro and PLpro with a docking binding energy corresponding to −6.25 and −4.62 kcal/mol, respectively. Quercetin has a theoretical, but significant, capability to interfere with SARS‐CoV‐2 replication, with the results showing this to be the fifth best compound out of 18 candidates. On the basis of the clinical COVID‐19 manifestations, the multifaceted aspect of quercetin as both antiinflammatory and thrombin‐inhibitory actions, should be taken into consideration.
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Affiliation(s)
- Giuseppe Derosa
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy.,Laboratory of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Pamela Maffioli
- Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Angela D'Angelo
- Laboratory of Molecular Medicine, University of Pavia, Pavia, Italy
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Mathpal S, Joshi T, Sharma P, Joshi T, Pundir H, Pande V, Chandra S. A dynamic simulation study of FDA drug from zinc database against COVID-19 main protease receptor. J Biomol Struct Dyn 2020; 40:1084-1100. [PMID: 32940134 PMCID: PMC7544932 DOI: 10.1080/07391102.2020.1821785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The sudden outbreak of COVID-19 has been responsible for several deaths across the globe. Due to its high contagious nature, it spreads from one human to another very quickly. Now it becomes a global public health threat with no approved treatments. In silico techniques can accelerate the drug development process. Our research aimed to identify the novel drugs for inhibition of Main protease (Mpro) enzyme of COVID-19 by performing in silico approach. In this context, a library consisting of 3180 FDA-approved drugs from ‘the ZINC database’ was used to identify novel drug candidates against ‘the Mpro’ of SARS-CoV-2. Initially, the top 10 drugs out of 3180 drugs were selected by molecular docking according to their binding score. Among 10 selected drugs; seven drugs that showed binding with Mpro enzyme residue Glu166 were subjected to100 ns Molecular dynamics (MD) simulation. Out of seven compounds, four namely, ZINC03831201, ZINC08101052, ZINC01482077, and ZINC03830817 were found significant based on MD simulation results. Furthermore, RMSD, RMSF, RG, SASA, PCA, MMPBSA (for last 40 ns) were calculated for the 100 ns trajectory period. Currently, the world needs potent drugs in a short period and this work suggests that these four drugs could be used as novel drugs against COVID-19 and it also provides new lead compounds for further in vitro, in vivo, and ongoing clinical studies against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Shalini Mathpal
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India
| | - Tanuja Joshi
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India.,Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India (Formerly Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India)
| | - Hemlata Pundir
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India.,Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India (Formerly Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India)
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9
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Bhatt K, Maheshwari DK. Insights into zinc-sensing metalloregulator 'Zur' deciphering mechanism of zinc transportation in Bacillus spp. by modeling, simulation and molecular docking. J Biomol Struct Dyn 2020; 40:764-779. [PMID: 32924811 DOI: 10.1080/07391102.2020.1818625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To comprehend the molecular mechanism of zinc transportation by bacteria tends to be a very complicated and time-consuming method. To date, fragmented and scanty studies are available about the mechanism of zinc transportation at molecular level. So, the present study scrutinizes in silico pathways of zinc fractions transportation, specifically in Bacillus spp. stimulating dynamic performance of zinc. For this, the constructed model reveals Zur to be the prime regulatory transport protein maintaining bacterial survivability at fluctuation in zinc concentrations, thereby attaining zinc homeostasis. Topology for hub nodes displays appropriate evidence of the molecular basis of bacterial zinc imports and exports. Further, the molecular docking reveals interaction of Zur protein with the zinc ligands (ZnCO3 and ZnSO4). By validation of binding affinity, binding energy and docking score via Autodock Vina and X-Score, the ZnSO4 compound was found to possess excellent stability in the active pocket site of Zur, stating Zur-ZnSO4 complex to be the most potential. Owing to which, the Zur-ZnSO4 complex was selected and subjected to molecular dynamics simulation, revealing RMSD, RG, RMSF, SASA and interaction energy for 20 ns trajectory period. Henceforth,the study provides novel insight into revealing the unrecognized Zur protein pathway, assisting zinc transportation, besides retaining best interaction with ZnSO4 ligand. This is the first system biology where molecular docking and molecular dynamics simulation-based investigation decipher the role of Zur transport protein system and interaction of its amino acids with zinc ligands in a simpler and economical form via in silico techniques.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kalpana Bhatt
- Department of Botany and Microbiology, Gurukula Kangri University, Haridwar, Uttarakhand, India
| | - Dinesh Kumar Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri University, Haridwar, Uttarakhand, India
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Hosseini-Zare MS, Thilagavathi R, Selvam C. Targeting severe acute respiratory syndrome-coronavirus (SARS-CoV-1) with structurally diverse inhibitors: a comprehensive review. RSC Adv 2020; 10:28287-28299. [PMID: 35519094 PMCID: PMC9055768 DOI: 10.1039/d0ra04395h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses, which were discovered in 1968, can lead to some human viral disorders, like severe acute respiratory syndrome (SARS), Middle East respiratory syndrome-related (MERS), and, recently, coronavirus disease 2019 (COVID-19). The coronavirus that leads to COVID-19 is rapidly spreading all over the world and is the reason for the deaths of thousands of people. Recent research has revealed that there is about 80% sequence homology between the coronaviruses that cause SARS and COVID-19. Considering this fact, we decided to collect the maximum available information on targets, structures, and inhibitors reported so far for SARS-CoV-1 that could be useful for researchers who work on closely related COVID-19. There are vital proteases, like papain-like protease 2 (PL2pro) and 3C-like protease (3CLpro), or main protease (Mpro), that are involved in and are essential for the replication of SARS coronavirus and so are valuable targets for the treatment of patients affected by this type of virus. SARS-CoV-1 NTPase/helicase plays an important role in the release of several non-structural proteins (nsps), so it is another essential target relating to the viral life cycle. In this paper, we provide extensive information about diverse molecules with anti-SARS activity. In addition to traditional medicinal chemistry outcomes, HTS, virtual screening efforts, and structural insights for better understanding inhibitors and SARS-CoV-1 target complexes are also discussed. This study covers a wide range of anti-SARS agents, particularly SARS-CoV-1 inhibitors, and provides new insights into drug design for the deadly SARS-CoV-2 virus.
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Affiliation(s)
- Maryam S Hosseini-Zare
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University Houston TX-77004 USA +1-713-313-7552
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education Coimbatore India
| | - Chelliah Selvam
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University Houston TX-77004 USA +1-713-313-7552
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11
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Fuzimoto AD, Isidoro C. The antiviral and coronavirus-host protein pathways inhibiting properties of herbs and natural compounds - Additional weapons in the fight against the COVID-19 pandemic? J Tradit Complement Med 2020; 10:405-419. [PMID: 32691005 PMCID: PMC7260130 DOI: 10.1016/j.jtcme.2020.05.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
Introduction As of March 11th, 2020, the World Health Organization declared the COVID-19 outbreak a pandemic. Articles published after the SARS-CoV-1 (2002) epidemic suggest that the use of an herbal-drug integrative medical approach could have contributed to a lower fatality rate and a more rapid response in controlling the outbreak. Methods Pubmed was searched for articles that investigated the antiviral properties and mechanisms of action of herbs or natural compounds against the SARS-coronavirus (CoV). Results Forty-three (43) relevant papers were located. A general count rendered 450+ herbs and natural compounds with antiviral properties against the SARS-CoV and related viruses. From the 43 articles, thirty-one (31) uncovered the mechanisms of action of the natural substances able to oppose the coronavirus. Discussion A series of herbs and natural compounds demonstrated moderate to strong antiviral activity. Research on many herbs-natural compounds also showed potent and significant inhibition of CoV-host protein pathways responsible for different phases of viral replication specifically targeting 3CLPRO, PLPRO, RdRp, helicase protein, S protein, N protein, 3a protein, Cathepsin L, Nsp1, Nsp3c, and ORF7a, and the S protein/ACE-2 interaction. Conclusion The herbs-natural compounds with antiviral activity and that caused inhibition/blockade of the CoV-host protein pathways are potential therapeutic candidates. The homology between the SARS-CoV-1 and SARS-CoV-2 is around 80%. Thus, effective herbs-compounds for the former would likely be beneficial for the latter also depending on target protein similarities between the viruses. Here we provide the mechanistic bases supporting an integrative approach that includes natural compounds to fight coronavirus infections.
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Affiliation(s)
| | - Ciro Isidoro
- Dipartimento di Scienze della Salute, Università "A. Avogadro", Novara, Italy
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Mani JS, Johnson JB, Steel JC, Broszczak DA, Neilsen PM, Walsh KB, Naiker M. Natural product-derived phytochemicals as potential agents against coronaviruses: A review. Virus Res 2020; 284:197989. [PMID: 32360300 PMCID: PMC7190535 DOI: 10.1016/j.virusres.2020.197989] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022]
Abstract
Coronaviruses are responsible for a growing economic, social and mortality burden, as the causative agent of diseases such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), avian infectious bronchitis virus (IBV) and COVID-19. However, there is a lack of effective antiviral agents for many coronavirus strains. Naturally existing compounds provide a wealth of chemical diversity, including antiviral activity, and thus may have utility as therapeutic agents against coronaviral infections. The PubMed database was searched for papers including the keywords coronavirus, SARS or MERS, as well as traditional medicine, herbal, remedy or plants, with 55 primary research articles identified. The overwhelming majority of publications focussed on polar compounds. Compounds that show promise for the inhibition of coronavirus in humans include scutellarein, silvestrol, tryptanthrin, saikosaponin B2, quercetin, myricetin, caffeic acid, psoralidin, isobavachalcone, and lectins such as griffithsin. Other compounds such as lycorine may be suitable if a therapeutic level of antiviral activity can be achieved without exceeding toxic plasma concentrations. It was noted that the most promising small molecules identified as coronavirus inhibitors contained a conjugated fused ring structure with the majority being classified as being polyphenols.
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Affiliation(s)
- Janice S Mani
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Joel B Johnson
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Jason C Steel
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Daniel A Broszczak
- Institute of Health & Biomedical Innovation (Q-Block), Queensland University of Technology, Kelvin Grove Campus, QLD, Australia
| | - Paul M Neilsen
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Kerry B Walsh
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia
| | - Mani Naiker
- School of Health, Medical and Applied Sciences, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia; Centre for Indigenous Health Equity Research, CQUniversity, Bruce Hwy, North Rockhampton, QLD, Australia.
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Kandeel M, Al-Nazawi M. Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sci 2020; 251:117627. [PMID: 32251634 PMCID: PMC7194560 DOI: 10.1016/j.lfs.2020.117627] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
Abstract
Aims In December 2019, the Coronavirus disease-2019 (COVID-19) virus has emerged in Wuhan, China. In this research, the first resolved COVID-19 crystal structure (main protease) was targeted in a virtual screening study by of FDA approved drugs dataset. In addition, a knowledge gap in relations of COVID-19 with the previously known fatal Coronaviruses (CoVs) epidemics, SARS and MERS CoVs, was covered by investigation of sequence statistics and phylogenetics. Materials and methods Molecular modeling, virtual screening, docking, sequence comparison statistics and phylogenetics of the COVID-19 main protease were investigated. Key findings COVID-19 Mpro formed a phylogenetic group with SARS CoV that was distant from MERS CoV. The identity% was 96.061 and 51.61 for COVID-19/SARS and COVID-19/MERS CoV sequence comparisons, respectively. The top 20 drugs in the virtual screening studies comprised a broad-spectrum antiviral (ribavirin), anti-hepatitis B virus (telbivudine), two vitamins (vitamin B12 and nicotinamide) and other miscellaneous systemically acting drugs. Of special interest, ribavirin had been used in treating cases of SARS CoV. Significance The present study provided a comprehensive targeting of the first resolved COVID+19 structure of Mpro and found a suitable save drugs for repurposing against the viral Mpro. Ribavirin, telbivudine, vitamin B12 and nicotinamide can be combined and used for COVID treatment. This initiative relocates already marketed and approved safe drugs for potential use in COVID-treatment.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, 31982, Al-ahsa, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh 33516, Egypt.
| | - Mohammed Al-Nazawi
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, 31982, Al-ahsa, Saudi Arabia
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14
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In silico screening of Chinese herbal medicines with the potential to directly inhibit 2019 novel coronavirus. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2020; 18:152-158. [PMID: 32113846 PMCID: PMC7102521 DOI: 10.1016/j.joim.2020.02.005] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 12/13/2022]
Abstract
Objective In this study we execute a rational screen to identify Chinese medical herbs that are commonly used in treating viral respiratory infections and also contain compounds that might directly inhibit 2019 novel coronavirus (2019-nCoV), an ongoing novel coronavirus that causes pneumonia. Methods There were two main steps in the screening process. In the first step we conducted a literature search for natural compounds that had been biologically confirmed as against sever acute respiratory syndrome coronavirus or Middle East respiratory syndrome coronavirus. Resulting compounds were cross-checked for listing in the Traditional Chinese Medicine Systems Pharmacology Database. Compounds meeting both requirements were subjected to absorption, distribution, metabolism and excretion (ADME) evaluation to verify that oral administration would be effective. Next, a docking analysis was used to test whether the compound had the potential for direct 2019-nCoV protein interaction. In the second step we searched Chinese herbal databases to identify plants containing the selected compounds. Plants containing 2 or more of the compounds identified in our screen were then checked against the catalogue for classic herbal usage. Finally, network pharmacology analysis was used to predict the general in vivo effects of each selected herb. Results Of the natural compounds screened, 13 that exist in traditional Chinese medicines were also found to have potential anti-2019-nCoV activity. Further, 125 Chinese herbs were found to contain 2 or more of these 13 compounds. Of these 125 herbs, 26 are classically catalogued as treating viral respiratory infections. Network pharmacology analysis predicted that the general in vivo roles of these 26 herbal plants were related to regulating viral infection, immune/inflammation reactions and hypoxia response. Conclusion Chinese herbal treatments classically used for treating viral respiratory infection might contain direct anti-2019-nCoV compounds.
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Pereira F, Latino DARS, Gaudêncio SP. QSAR-assisted virtual screening of lead-like molecules from marine and microbial natural sources for antitumor and antibiotic drug discovery. Molecules 2015; 20:4848-73. [PMID: 25789820 PMCID: PMC6272462 DOI: 10.3390/molecules20034848] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 02/27/2015] [Accepted: 03/04/2015] [Indexed: 11/17/2022] Open
Abstract
A Quantitative Structure-Activity Relationship (QSAR) approach for classification was used for the prediction of compounds as active/inactive relatively to overall biological activity, antitumor and antibiotic activities using a data set of 1746 compounds from PubChem with empirical CDK descriptors and semi-empirical quantum-chemical descriptors. A data set of 183 active pharmaceutical ingredients was additionally used for the external validation of the best models. The best classification models for antibiotic and antitumor activities were used to screen a data set of marine and microbial natural products from the AntiMarin database-25 and four lead compounds for antibiotic and antitumor drug design were proposed, respectively. The present work enables the presentation of a new set of possible lead like bioactive compounds and corroborates the results of our previous investigations. By other side it is shown the usefulness of quantum-chemical descriptors in the discrimination of biologically active and inactive compounds. None of the compounds suggested by our approach have assigned non-antibiotic and non-antitumor activities in the AntiMarin database and almost all were lately reported as being active in the literature.
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Affiliation(s)
- Florbela Pereira
- Centro de Química Fina e Biotecnologia (CQFB)/LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Campus Caparica, Caparica 2829-516, Portugal.
| | - Diogo A R S Latino
- Centro de Química Fina e Biotecnologia (CQFB)/LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Campus Caparica, Caparica 2829-516, Portugal.
- Centro de Ciências Moleculares e Materiais (CCMM), Departamento de Química e Bioquímica, Faculdade de Ciências, Universida Lisboa, Campo Grande, Lisboa 1749-016, Portugal.
| | - Susana P Gaudêncio
- Centro de Química Fina e Biotecnologia (CQFB)/LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Campus Caparica, Caparica 2829-516, Portugal.
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16
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Pereira F, Latino DARS, Gaudêncio SP. A chemoinformatics approach to the discovery of lead-like molecules from marine and microbial sources en route to antitumor and antibiotic drugs. Mar Drugs 2014; 12:757-78. [PMID: 24473174 PMCID: PMC3944514 DOI: 10.3390/md12020757] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/16/2013] [Accepted: 01/16/2014] [Indexed: 12/01/2022] Open
Abstract
The comprehensive information of small molecules and their biological activities in the PubChem database allows chemoinformatic researchers to access and make use of large-scale biological activity data to improve the precision of drug profiling. A Quantitative Structure-Activity Relationship approach, for classification, was used for the prediction of active/inactive compounds relatively to overall biological activity, antitumor and antibiotic activities using a data set of 1804 compounds from PubChem. Using the best classification models for antibiotic and antitumor activities a data set of marine and microbial natural products from the AntiMarin database were screened-57 and 16 new lead compounds for antibiotic and antitumor drug design were proposed, respectively. All compounds proposed by our approach are classified as non-antibiotic and non-antitumor compounds in the AntiMarin database. Recently several of the lead-like compounds proposed by us were reported as being active in the literature.
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Affiliation(s)
- Florbela Pereira
- CQFB (Centro de Química Fina e Biotecnologia)/REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Campus Caparica, Caparica 2829-516, Portugal.
| | - Diogo A R S Latino
- CQFB (Centro de Química Fina e Biotecnologia)/REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Campus Caparica, Caparica 2829-516, Portugal.
| | - Susana P Gaudêncio
- CQFB (Centro de Química Fina e Biotecnologia)/REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa Campus Caparica, Caparica 2829-516, Portugal.
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17
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Harvey AL, Clark RL, Mackay SP, Johnston BF. Current strategies for drug discovery through natural products. Expert Opin Drug Discov 2010; 5:559-68. [PMID: 22823167 DOI: 10.1517/17460441.2010.488263] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE TO THE FIELD Natural products are the most consistently successful source of drug leads, both historically and currently. Despite this, the use of natural products in industrial drug discovery has fallen out of favour. Natural products are likely to continue to be sources of new commercially viable drug leads because the chemical novelty associated with natural products is higher than that of any other source: this is particularly important when searching for lead molecules against newly discovered targets for which there are no known small molecule leads. Areas to be covered: Current drug discovery strategies involving natural products are described in three sections: developments from traditionally used medicines, random testing of natural compounds on biological assays and use of virtual screening techniques with structures of natural products. WHAT THE READER WILL GAIN The reader will gain an insight into the potential for natural products in current drug discovery paradigms, particularly in the value of using natural products in virtual screening approaches. TAKE HOME MESSAGE Drug discovery would be enriched if fuller use was made of the chemistry of natural products.
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Affiliation(s)
- Alan L Harvey
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 27 Taylor Street, Glasgow G4 0NR, UK +44 141 553 4155 ; +44 141 552 8376 ;
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18
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Rodríguez-Terol A, Caraballo M, Palma D, Santos-Ramos B, Molina T, Desongles T, Aguilar A. Calidad estructural de las bases de datos de interacciones. FARMACIA HOSPITALARIA 2009. [DOI: 10.1016/s1130-6343(09)71155-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Rodríguez-Terol A, Caraballo M, Palma D, Santos-Ramos B, Molina T, Desongles T, Aguilar A. Quality of interaction database management systems. ACTA ACUST UNITED AC 2009. [PMCID: PMC7148979 DOI: 10.1016/s2173-5085(09)70079-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Objective To identify drug interaction databases (DID) and assess the quality of their structures. Method A search was made of the literature for DID and a series of exclusion and structural quality criteria were defined (at least 4 quality criteria: classification according to severity, classification according to level of evidence, bibliographical reference data, description of clinical management, and 11 criteria used for weighting). The level of compliance of every DID with the criteria defined was analysed, together with the level of compliance of each criteria in each DID. Results A total of 54 DID were identified, 30 of which complied with exclusion criteria and 15 of which did not meet the minimum criteria. The rest of the criteria were evaluated in 9 DID: Botplus and Medinteract (100%), SEFH Guide, Lexi-interact and Medscape (89%), Hansten (83%), Micromedex and Stockley (78%), Drug Interactions Facts (68%). Ninety-two percent of the DID describe the mechanism of action, 87% classify the information according to the active ingredient, 75% do not state they have any conflict of interest, classify according to level of severity, have electronic format, and are easy to search. A total of 67% are specific DID, 62% are classified according to level of evidence, contain bibliographical references, and describe clinical management. Conclusions A third of the DID comply with the minimum criteria. Differences were observed in the level and compliance criteria among Spanish and foreign DID. Some of the main DID used as references in the bibliography have significant structural defects: no web presentation, no multi-check function and others.
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20
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Rollinger JM, Stuppner H, Langer T. Virtual screening for the discovery of bioactive natural products. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2008; 65:211, 213-49. [PMID: 18084917 PMCID: PMC7124045 DOI: 10.1007/978-3-7643-8117-2_6] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this survey the impact of the virtual screening concept is discussed in the field of drug discovery from nature. Confronted by a steadily increasing number of secondary metabolites and a growing number of molecular targets relevant in the therapy of human disorders, the huge amount of information needs to be handled. Virtual screening filtering experiments already showed great promise for dealing with large libraries of potential bioactive molecules. It can be utilized for browsing databases for molecules fitting either an established pharmacophore model or a three dimensional (3D) structure of a macromolecular target. However, for the discovery of natural lead candidates the application of this in silico tool has so far almost been neglected. There are several reasons for that. One concerns the scarce availability of natural product (NP) 3D databases in contrast to synthetic libraries; another reason is the problematic compatibility of NPs with modern robotized high throughput screening (HTS) technologies. Further arguments deal with the incalculable availability of pure natural compounds and their often too complex chemistry. Thus research in this field is time-consuming, highly complex, expensive and ineffective. Nevertheless, naturally derived compounds are among the most favorable source of drug candidates. A more rational and economic search for new lead structures from nature must therefore be a priority in order to overcome these problems. Here we demonstrate some basic principles, requirements and limitations of virtual screening strategies and support their applicability in NP research with already performed studies. A sensible exploitation of the molecular diversity of secondary metabolites however asks for virtual screening concepts that are interfaced with well-established strategies from classical pharmacognosy that are used in an effort to maximize their efficacy in drug discovery. Such integrated virtual screening workflows are outlined here and shall help to motivate NP researchers to dare a step towards this powerful in silico tool.
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Affiliation(s)
- Judith M Rollinger
- Institute of Pharmacy/Pharmacognosy, Leopold-Franzens University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
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Yang CW, Yang YN, Liang PH, Chen CM, Chen WL, Chang HY, Chao YS, Lee SJ. Novel small-molecule inhibitors of transmissible gastroenteritis virus. Antimicrob Agents Chemother 2007; 51:3924-31. [PMID: 17709464 PMCID: PMC2151441 DOI: 10.1128/aac.00408-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We used swine testicle (ST) cells infected with transmissible gastroenteritis virus (TGEV) and an indirect immunofluorescent assay with antibodies against TGEV spike and nucleocapsid proteins to screen small-molecule compounds that inhibit TGEV replication. Analogues of initial hits were collected and subjected to a 3CL protease (3CL(pro)) inhibition assay with recombinant 3CL(pro) and a fluorogenic peptide substrate. A series of benzothiazolium compounds were found to have inhibitory activity against TGEV 3CL(pro) and to exert anti-TGEV activities in terms of viral protein and RNA replication in TGEV-infected ST cells, with consequent protection of TGEV-infected ST cells from cytopathic effect by blocking the activation of caspase-3.
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Affiliation(s)
- Cheng-Wei Yang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institute, 35, Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, Republic of China
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Saxena AK, Prathipati P. Collection and preparation of molecular databases for virtual screening. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2006; 17:371-92. [PMID: 16920660 DOI: 10.1080/10629360600884462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Drug discovery and development research is undergoing a paradigm shift from a linear and sequential nature of the various steps involved in the drug discovery process of the past to the more parallel approach of the present, due to a lack of sufficient correlation between activities estimated by in vitro and in vivo assays. This is attributed to the non-drug-likeness of the lead molecules, which has often been detected at advanced drug development stages. Thus a striking aspect of this paradigm shift has been early/parallel in silico prioritization of drug-like molecular databases (also database pre-processing), in addition to prioritizing compounds with high affinity and selectivity for a protein target. In view of this, a drug-like database useful for virtual screening has been created by prioritizing molecules from 36 catalog suppliers, using our recently derived binary QSAR based drug-likeness model as a filter. The performance of this model was assessed by a comparative evaluation with respect to commonly used filters implemented by the ZINC database. Since the model was derived considering all the limitations that have plagued the existing rules and models, it performs better than the existing filters and thus the molecules prioritized by this filter represent a better subset of drug-like compounds. The application of this model on exhaustive subsets of 4,972,123 molecules, many of which have passed the ZINC database filters for drug-likeness, led to a further prioritization of 2,920,551 drug-like molecules. This database may have a great potential for in silico virtual screening for discovering molecules, which may survive the later stages of the drug development research.
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Affiliation(s)
- A K Saxena
- Central Drug Research Institute (CDRI), Chattar Manzil Palace, India.
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Martina E, Stiefl N, Degel B, Schulz F, Breuning A, Schiller M, Vicik R, Baumann K, Ziebuhr J, Schirmeister T. Screening of electrophilic compounds yields an aziridinyl peptide as new active-site directed SARS-CoV main protease inhibitor. Bioorg Med Chem Lett 2005; 15:5365-9. [PMID: 16216498 PMCID: PMC7127417 DOI: 10.1016/j.bmcl.2005.09.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 08/30/2005] [Accepted: 09/06/2005] [Indexed: 11/26/2022]
Abstract
The coronavirus main protease, M(pro), is considered a major target for drugs suitable to combat coronavirus infections including the severe acute respiratory syndrome (SARS). In this study, comprehensive HPLC- and FRET-substrate-based screenings of various electrophilic compounds were performed to identify potential M(pro) inhibitors. The data revealed that the coronaviral main protease is inhibited by aziridine- and oxirane-2-carboxylates. Among the trans-configured aziridine-2,3-dicarboxylates the Gly-Gly-containing peptide 2c was found to be the most potent inhibitor.
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Affiliation(s)
- Erika Martina
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Nikolaus Stiefl
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Björn Degel
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Franziska Schulz
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Alexander Breuning
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Markus Schiller
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Radim Vicik
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Knut Baumann
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - John Ziebuhr
- Institute of Virology and Immunology, Versbacher Street 7, D-97078 Würzburg, University of Würzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
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