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N Hegde V, J S S, B S C, Benedict Leoma M, N K L. Structural, computational and in silico studies of 4-bromo-3-flurobenzonitrile as anti-Alzheimer and anti-Parkinson agents. J Biomol Struct Dyn 2024; 42:4619-4643. [PMID: 37418246 DOI: 10.1080/07391102.2023.2226755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 05/29/2023] [Indexed: 07/08/2023]
Abstract
A novel dimer of the 4-bromo-3-fluorobenzonitrile was crystallized and studied using a spectroscopic method such as the scanning electron microscope method. The computational simulations substantiated the structural analysis findings. The Hirshfeld surface analysis has been performed for visualizing, exploring and quantifying the intra and inter-molecular interactions that stabilize the crystal packing of the compound. The NBO and QTAIM analyses were applied to study the nature and origin of the attractive forces involved in the crystal structure. Further, the pharmacokinetic properties of the compound were evaluated, indicating good brain-blood barrier and central nervous system penetration capability. Hence, in silico studies was carried out to explore the binding pattern of the titled compound against acetylcholinesterase and butyrylcholinesterase, and tumor necrosis factor-alpha converting enzyme proteins using molecular docking and molecular dynamics simulations approach. Further, the titled compound is compared with standard drugs through molecular docking studies. The in silico studies finally predicts that the compound under investigation may act as a good inhibitor for treating Alzheimer's disease and further in vitro and in vivo studies may provide its therapeutic potential.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Shyambhargav J S
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | - Chethan B S
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | | | - Lokanath N K
- Department of Studies in Physics, University of Mysore, Mysuru, India
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Noce A, Marrone G, Di Lauro M, Vita C, Montalto G, Giorgino G, Chiaramonte C, D’Agostini C, Bernardini S, Pieri M. Potential Anti-Inflammatory and Anti-Fatigue Effects of an Oral Food Supplement in Long COVID Patients. Pharmaceuticals (Basel) 2024; 17:463. [PMID: 38675423 PMCID: PMC11053797 DOI: 10.3390/ph17040463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Long coronavirus disease (COVID) syndrome leads to chronic inflammatory state onset that can have a multisystem impact and compromise organ function. Moreover, long COVID syndrome is often characterized by the presence of chronic fatigue, which affects subjects' daily activities and worsens their quality of life. The aim of our double-blind, placebo-controlled randomized trial (protocol code RS 150.21, approved on 4 November 2021) was to evaluate the beneficial effects of the consumption of 2 cps/day, for two months, of an oral food supplement (OFS), based on Echinacea angustifolia, rosehip, propolis, royal jelly and zinc, in long COVID patients, compared to a two-month placebo period. The OFS's vitamin C content was equal to 22.17 mg/g (8.87 mg/capsule). The OFS's total polyphenol content was 43.98 mg/g gallic acid equivalents. At the end of the in vivo study, we highlighted a significant decrease in the inflammatory parameters in the OFS period, compared to the placebo period (neutrophil-to-lymphocyte ratio, p = 0.0455; monocyte to-lymphocyte ratio, p = 0.0005; C-reactive protein, p = 0.0145). Our study also highlighted a significant increase in vitamin D serum values (p = 0.0005) and, at the same time, an improvement in patients' life quality and a reduction in fatigue, monitored by the fatigue severity scale. This study showed the OFS's beneficial effects on the inflammatory state, fatigue and quality of life in long COVID patients.
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Affiliation(s)
- Annalisa Noce
- UOSD Nephrology and Dialysis, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Giulia Marrone
- UOSD Nephrology and Dialysis, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Manuela Di Lauro
- UOSD Nephrology and Dialysis, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Chiara Vita
- QuMAP-PIN, University Center “Città di Prato” Educational and Scientific Services for the University of Florence, 59100 Prato, Italy
| | - Giulia Montalto
- School of Specialization in Nephrology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gloria Giorgino
- School of Specialization in Nephrology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Carlo Chiaramonte
- Department of Statistics, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Cartesio D’Agostini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Laboratory of Clinical Microbiology, Policlinico Tor Vergata, 00133 Rome, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Department of Laboratory Medicine, Tor Vergata University Hospital, 00133 Rome, Italy
| | - Massimo Pieri
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Department of Laboratory Medicine, Tor Vergata University Hospital, 00133 Rome, Italy
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Alotaibi F, Aba Alkhayl FF, Foudah AI, Azhar Kamal M, Moglad EH, Khan S, Rehman ZU, Warsi MK, Jawaid T, Alam A. Investigating the effects of four medicinal plants against dengue virus through QSAR modeling and molecular dynamics studies. J Biomol Struct Dyn 2024:1-18. [PMID: 38197579 DOI: 10.1080/07391102.2024.2301744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/28/2023] [Indexed: 01/11/2024]
Abstract
The Dengue virus (DENV) has been increasingly recognized as a prevalent viral pathogen responsible for global transmission of infection. It has been established that DENV's NS5 methyltransferase (MTase) controls viral replication. As a result, NS5 MTase is considered a potentially useful drug target for DENV. In this study, the two phases of virtual screening were conducted using the ML-based QSAR model and molecular docking to identify potential compounds against NS5 of DENV. Four medicinal plants [Aloe vera, Cannabis sativa (Hemp), Ocimum sanctum (Holy Basil; Tulsi), and Zingiber officinale (Ginger)] that showed anti-viral properties were selected for sourcing the phytochemicals and screening them against NS5. Additionally, re-docking at higher exhaustiveness and interaction analysis were performed which resulted in the identification of the top four hits (135398658, 5281675, 119394, and 969516) which showed comparable results with the control Sinefungin (SFG). Post molecular dynamics simulation, 135398658 showed the lowest RMSD (0.4-0.5 nm) and the maximum number of hydrogen bonds (eight hydrogen bonds) after the control while 5281675 and 969516 showed comparable hydrogen bonds to the control. These compounds showed direct interactions with the catalytic site residues GLU111 and ASP131, in addition to this these compounds showed stable complex formation as depicted by principal component analysis and free energy landscape. 135398658 showed lower total binding free energy (ΔGTotal = -36.56 kcal/mol) than the control, while 5281675 had comparable values to the control (ΔGTotal = -34.1 kcal/mol). Overall, the purpose of this study was to identify phytochemicals that inhibit NS5 function, that could be further tested experimentally to treat dengue virus (DENV).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faisal Alotaibi
- Department of Pharmacy Practice, College of Pharmacy, Shaqra University, Al-Dawadmi, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ahmed I Foudah
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Ehssan H Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- Department of Microbiology and Parasitology, Medicinal and Aromatic Plants Research Institute, National Center for Research, Khartoum, Sudan
| | - Shamshir Khan
- Department of Pharmacognosy & Pharmaceutical Chemistry, College of Dentistry and Pharmacy, Buraydah Private Colleges, Buraydah, Saudi Arabia
| | - Zia Ur Rehman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohiuddin Khan Warsi
- Department of Biological Sciences, Faculty of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Talha Jawaid
- Department of Pharmacology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Aftab Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Shah AA, Kumar N, Mohinder Singh Bedi P, Akhtar S. Molecular modeling, dynamic simulation, and metabolic reactivity studies of quinazoline derivatives to investigate their anti-angiogenic potential by targeting wild EGFR wt and mutant EGFR T790M receptor tyrosine kinases. J Biomol Struct Dyn 2023:1-23. [PMID: 37921704 DOI: 10.1080/07391102.2023.2274974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Non-small cell lung cancer, head and neck cancer, glioblastoma, and various other cancer types often demonstrate persistent elevation in EGFR tyrosine kinase activity due to acquired mutations in its kinase domain. Any alteration in the EGFR is responsible for triggering the upregulation of tumor angiogenic pathways, such as the PI3k-AKT-mTOR pathway, MAPK-ERK pathway and PLC-Ƴ pathway, which are critically involved in promoting tumor angiogenesis in cancer cells. The emergence of frequently occurring EGFR kinase domain mutations (L858R/T790M/C797S) that confer resistance to approved therapeutic agents has presented a significant challenge for researchers aiming to develop effective and well-tolerated treatments against tumor angiogenesis. In this study, we directed our efforts towards the rational design and development of novel quinazoline derivatives with the potential to act as antagonists against both wild-type and mutant EGFR. Our approach encompasing the application of advanced drug design strategies, including structure-based virtual screening, molecular docking, molecular dynamics, metabolic reactivity and cardiotoxicity prediction studies led to the identification of two prominent lead compounds: QU648, for EGFRwt inhibition and QU351, for EGFRmt antagonism. The computed binding energies of selected leads and their molecular dynamics simulations exhibited enhanced conformational stability of QU648 and QU351 when compared to standard drugs Erlotinib and Afatinib. Notably, the lead compounds also demonstrated promising pharmacokinetic properties, metabolic reactivity, and cardiotoxicity profiles. Collectively, the outcomes of our study provide compelling evidence supporting the potential of QU648 and QU351 as prominent anti-angiogenic agents, effectively inhibiting EGFR activity across various cancer types harboring diverse EGFR mutations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Nitish Kumar
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | | | - Salman Akhtar
- Department of Bioengineering, Integral University, Lucknow, India
- Novel Global Community Educational Foundation, Hebersham, Australia
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Kaboudi N, Krüger N, Hamzeh-Mivehroud M. Development of novel ligands against SARS-CoV-2 M pro enzyme: an in silico and in vitro Study. Mol Inform 2023; 42:e202300120. [PMID: 37590494 DOI: 10.1002/minf.202300120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/22/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Despite tremendous efforts made by scientific community during the outbreak of COVID-19 pandemic, this disease still remains as a public health concern. Although different types of vaccines were globally used to reduce the mortality, emergence of new variants of SARS-CoV-2 is a challenging issue in COVID-19 pharmacotherapy. In this context, target therapy of SARS-CoV-2 by small ligands is a promising strategy. METHODS In this investigation, we applied ligand-based virtual screening for finding novel molecules based on nirmatrelvir structure. Various criteria including drug-likeness, ADME, and toxicity properties were applied for filtering the compounds. The selected candidate molecules were subjected to molecular docking and dynamics simulation for predicting the binding mode and binding free energy, respectively. Then the molecules were experimentally evaluated in terms of antiviral activity against SARS-CoV-2 and toxicity assessment. RESULTS The results demonstrated that the identified compounds showed inhibitory activity towards SARS-CoV-2 Mpro . CONCLUSION In summary, the introduced compounds may provide novel scaffold for further structural modification and optimization with improved anti SARS-CoV-2 Mpro activity.
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Affiliation(s)
- Navid Kaboudi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nadine Krüger
- Platform Infection Models, German Primate Center-Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Rafiq A, Jabeen T, Aslam S, Ahmad M, Ashfaq UA, Mohsin NUA, Zaki MEA, Al-Hussain SA. A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products. Molecules 2023; 28:4860. [PMID: 37375415 DOI: 10.3390/molecules28124860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The ongoing COVID-19 pandemic has resulted in a global panic because of its continual evolution and recurring spikes. This serious malignancy is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak, millions of people have been affected from December 2019 till now, which has led to a great surge in finding treatments. Despite trying to handle the pandemic with the repurposing of some drugs, such as chloroquine, hydroxychloroquine, remdesivir, lopinavir, ivermectin, etc., against COVID-19, the SARS-CoV-2 virus continues its out-of-control spread. There is a dire need to identify a new regimen of natural products to combat the deadly viral disease. This article deals with the literature reports to date of natural products showing inhibitory activity towards SARS-CoV-2 through different approaches, such as in vivo, in vitro, and in silico studies. Natural compounds targeting the proteins of SARS-CoV-2-the main protease (Mpro), papain-like protease (PLpro), spike proteins, RNA-dependent RNA polymerase (RdRp), endoribonuclease, exoribonuclease, helicase, nucleocapsid, methyltransferase, adeno diphosphate (ADP) phosphatase, other nonstructural proteins, and envelope proteins-were extracted mainly from plants, and some were isolated from bacteria, algae, fungi, and a few marine organisms.
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Affiliation(s)
- Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Tooba Jabeen
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Noor Ul Amin Mohsin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
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Bavaro DF, Diella L, Belati A, Metrangolo G, De Santis L, Spada V, Camporeale M, Dargenio A, Brindicci G, Balena F, Fiordelisi D, Signorile F, Loseto G, Pasciolla C, Minoia C, Attolico I, Perrone T, Simone S, Rendina M, Giovine N, Di Gennaro F, Musto P, Guarini A, Di Leo A, Gesualdo L, Dell'Aera M, Saracino A. Efficacy of Remdesivir and Neutralizing Monoclonal Antibodies in Monotherapy or Combination Therapy in Reducing the Risk of Disease Progression in Elderly or Immunocompromised Hosts Hospitalized for COVID-19: A Single Center Retrospective Study. Viruses 2023; 15:v15051199. [PMID: 37243285 DOI: 10.3390/v15051199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
INTRODUCTION Remdesivir (REM) and monoclonal antibodies (mAbs) could alleviate severe COVID-19 in at-risk outpatients. However, data on their use in hospitalized patients, particularly in elderly or immunocompromised hosts, are lacking. METHODS All consecutive patients hospitalized with COVID-19 at our unit from 1 July 2021 to 15 March 2022 were retrospectively enrolled. The primary outcome was the progression to severe COVID-19 (P/F < 200). Descriptive statistics, a Cox univariate-multivariate model, and an inverse probability treatment-weighted (IPTW) analysis were performed. RESULTS Overall, 331 subjects were included; their median (q1-q3) age was 71 (51-80) years, and they were males in 52% of the cases. Of them, 78 (23%) developed severe COVID-19. All-cause in-hospital mortality was 14%; it was higher in those with disease progression (36% vs. 7%, p < 0.001). REM and mAbs resulted in a 7% (95%CI = 3-11%) and 14% (95%CI = 3-25%) reduction in the risk of severe COVID-19, respectively, after adjusting the analysis with the IPTW. In addition, by evaluating only immunocompromised hosts, the combination of REM and mAbs was associated with a significantly lower incidence of severe COVID-19 (aHR = 0.06, 95%CI = 0.02-0.77) when compared with monotherapy. CONCLUSIONS REM and mAbs may reduce the risk of COVID-19 progression in hospitalized patients. Importantly, in immunocompromised hosts, the combination of mAbs and REM may be beneficial.
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Affiliation(s)
- Davide Fiore Bavaro
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Lucia Diella
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Alessandra Belati
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Giuliana Metrangolo
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Laura De Santis
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Vito Spada
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Michele Camporeale
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Angelo Dargenio
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Gaetano Brindicci
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Flavia Balena
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Deborah Fiordelisi
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Fabio Signorile
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Giacomo Loseto
- Hematology Unit, IRCCS Istituto Tumori "Giovanni Paolo II", 70124 Bari, Italy
| | - Crescenza Pasciolla
- Hematology Unit, IRCCS Istituto Tumori "Giovanni Paolo II", 70124 Bari, Italy
| | - Carla Minoia
- Hematology Unit, IRCCS Istituto Tumori "Giovanni Paolo II", 70124 Bari, Italy
| | - Immacolata Attolico
- Unit of Hematology and Stem Cell Transplantation, AOUC Policlinic, 70124 Bari, Italy
| | - Tommasina Perrone
- Unit of Hematology and Stem Cell Transplantation, AOUC Policlinic, 70124 Bari, Italy
| | - Simona Simone
- Nephrology Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
| | - Maria Rendina
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy
| | - Nicoletta Giovine
- Hospital Pharmacy Department, University Hospital of Bari, 70124 Bari, Italy
| | - Francesco Di Gennaro
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Pellegrino Musto
- Unit of Hematology and Stem Cell Transplantation, AOUC Policlinic, 70124 Bari, Italy
- Department of Precision and Regenerative Medicine and Ionian Area University of Bari and Unit of Hematology and Stem Cell Transplantation, AOUC Policlinico, 70124 Bari, Italy
| | - Attilio Guarini
- Hematology Unit, IRCCS Istituto Tumori "Giovanni Paolo II", 70124 Bari, Italy
| | - Alfredo Di Leo
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy
| | - Loreto Gesualdo
- Nephrology Dialysis and Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, 70124 Bari, Italy
| | - Maria Dell'Aera
- Hospital Pharmacy Department, University Hospital of Bari, 70124 Bari, Italy
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
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Rabaan AA, Halwani MA, Aljeldah M, Al Shammari BR, Garout M, Aldali J, Alawfi A, Alshengeti A, Alsulaiman AM, Alsayyah A. Exploration of potent antiviral phytomedicines from Lauraceae family plants against SARS-CoV-2 RNA-dependent RNA polymerase. J Biomol Struct Dyn 2023; 41:15085-15105. [PMID: 36883874 DOI: 10.1080/07391102.2023.2186720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
RNA-dependent RNA polymerase, also known as RdRp, is a possible therapeutic target that could be used to suppress the proliferation of RNA viruses such as SARS-CoV-2. This protein has two major functional sites (a) catalytic and (b) substrate entry, which regulate the natural substrate entry and its corresponding interaction with the protein. In this study, a computational drug design pipeline was applied to investigate potential inhibitors against SARS-CoV-2 RdRp from Lauraceae plants, and five top hits were selected based on the docked score (< -7 kcal/mol). The docking study suggested that the Glochidioboside had a minimum binding score of -7.8 kcal/mol. This compound showed total five hydrogen bonds while two of them were with catalytic residues Asp618 and Asp760. However, another compound, Sitogluside showed a binding score of -7.3 kcal/mol with four hydrogen bonds targeting three functional residues (Arg555, Ser759, and Asp760). Later, 100 ns explicit solvent molecular dynamics (MD) simulation was performed to evaluate the stability of the protein-ligand docked system. These compounds translocated their positions from the catalytic site to the substrate entry site, as observed in the MD simulation trajectory. However, translocation did not affect the binding strength of these compounds, and they retained the strong binding affinity (ΔG < -11.5 kcal/mol), estimated using the MM/GBSA method. In general, the findings of this study indicated the potential therapeutic compounds that may be used targeting SARS-CoV-2 RdRp. However, these compounds still need to be validated by experimentation in order to determine their inhibitory function.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Basim R Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Jehad Aldali
- Pathology Organization, Imam Mohammed Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah, Saudi Arabia
| | | | - Ahmed Alsayyah
- Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Bajrai LH, El-Kafrawy SA, Hassan AM, Tolah AM, Alnahas RS, Sohrab SS, Rehan M, Azhar EI. In vitro screening of anti-viral and virucidal effects against SARS-CoV-2 by Hypericum perforatum and Echinacea. Sci Rep 2022; 12:21723. [PMID: 36522420 PMCID: PMC9754313 DOI: 10.1038/s41598-022-26157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Hypericum perforatum and Echinacea are reported to have antiviral activities against several viral infections. In this study, H. perforatum (St. John's Wort) and Echinacea were tested in vitro using Vero E6 cells for their anti-viral effects against the newly identified Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) through its infectious cycle from 0 to 48 h post infection. The hypericin of H. perforatum and the different parts (roots, seeds, aerial) of two types of Echinacea species (Echinacea purpurea and Echinacea angustifolia) were tested for their anti-viral activities to measure the inhibition of viral load using quantitative real-time polymerase chain reaction (qRT-PCR) on cell culture assay. Interestingly, the H. perforatum-Echinacea mixture (1:1 ratio) of H. perforatum and Echinacea was tested as well on SARS-CoV-2 and showed crucial anti-viral activity competing H. perforatum then Echinacea effects as anti-viral treatment. Therefore, the results H. perforatum and Echinacea species, applied in this study showed significant anti-viral and virucidal effects in the following order of potency: H. perforatum, H. perforatum-Echinacea mixture, and Echinacea on SARS-CoV-2 infectious cycle. Additionally, molecular simulation analysis of the compounds with essential proteins (Mpro and RdRp) of the SARS-CoV-2 revealed the most potent bioactive compounds such as Echinacin, Echinacoside, Cyanin, Cyanidin 3-(6''-alonylglucoside, Quercetin-3-O-glucuronide, Proanthocyanidins, Rutin, Kaempferol-3-O-rutinoside, and Quercetin-3-O-xyloside. Thus, based on the outcome of this study, it is demanding the setup of clinical trial with specific therapeutic protocol.
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Affiliation(s)
- Leena Hussein Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sherif Ali El-Kafrawy
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Mohamed Hassan
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Majdi Tolah
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabig, Saudi Arabia
| | - Rabie Saleh Alnahas
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
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10
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Bora H, Kamle M, Hassan H, Al-Emam A, Chopra S, Kirtipal N, Bharadwaj S, Kumar P. Exploration of Potent Antiviral Phytomedicines from Lauraceae Family Plants against SARS-CoV-2 Main Protease. Viruses 2022; 14. [PMID: 36560787 DOI: 10.3390/v14122783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
A new Coronaviridae strain, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), emerged from Wuhan city of China and caused one of the substantial global health calamities in December 2019. Even though several vaccines and drugs have been developed worldwide since COVID-19, a cost-effective drug with the least side effects is still unavailable. Currently, plant-derived compounds are mostly preferred to develop antiviral therapeutics due to its less toxicity, easy access, and cost-effective characteristics. Therefore, in this study, 124 phytochemical compounds from plants of Lauraceae family with medicinal properties were virtually screened against SARS-CoV-2 Mpro. Identification of four phytomolecules, i.e., cassameridine, laetanine, litseferine and cassythicine, with docking scores -9.3, -8.8, -8.6, and -8.6 kcal/mol, respectively, were undertaken by virtual screening, and molecular docking. Furthermore, the molecular dynamic simulation and essential dynamics analysis have contributed in understanding the stability and inhibitory effect of these selected compounds. These phytomolecules can be considered for further in vitro and in vivo experimental study to develop anti-SARS-CoV-2 therapeutics targeting the main protease (Mpro).
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11
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Lopes SM, de Medeiros HIR, Scotti MT, Scotti L. Natural Products Against COVID-19 Inflammation: A Mini-Review. Comb Chem High Throughput Screen 2022; 25:2358-2369. [PMID: 35088662 DOI: 10.2174/1386207325666220128114547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/03/2021] [Accepted: 11/18/2021] [Indexed: 01/27/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is a virus whose genetic material is positive single-stranded RNA, being responsible for coronavirus disease 2019 (COVID- 19), an infection that compromises the lungs and consequently the respiratory capacity of the infected individual, according to the WHO in November 2021, 249,743,428 cases were confirmed, of which 5,047,652 individuals died due to complications resulting from the infection caused by SARSCOV- 2. As the infection progresses, the individual may experience loss of smell and taste, as well as breathing difficulties, severe respiratory failure, multiple organ failure, and death. Due to this new epidemiological agent in March 2020 it was announced by the director general of the World Health Organization (WHO) a pandemic status, and with that, many research groups are looking for new therapeutic alternatives through synthetic and natural bioactives. This research is a literature review of some in silico studies involving natural products against COVID-19 inflammation published in 2020 and 2021. Work like this presents relevant information to the scientific community, boosting future research and encouraging the use of natural products for the search for new antivirals against COVID-19.
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Affiliation(s)
- Simone Mendes Lopes
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Herbert Igor Rodrigues de Medeiros
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil.,Lauro Wanderley University Hospital (HULW), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
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12
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Agrawal S, Pathak E, Mishra R, Mishra V, Parveen A, Mishra SK, Byadgi PS, Dubey SK, Chaudhary AK, Singh V, Chaurasia RN, Atri N. Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host. Comput Biol Med 2022; 149:106049. [PMID: 36103744 PMCID: PMC9452420 DOI: 10.1016/j.compbiomed.2022.106049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections generate approximately one million virions per day, and the majority of available antivirals are ineffective against it due to the virus's inherent genetic mutability. This necessitates the investigation of concurrent inhibition of multiple SARS-CoV-2 targets. We show that fortunellin (acacetin 7-O-neohesperidoside), a phytochemical, is a promising candidate for preventing and treating coronavirus disease (COVID-19) by targeting multiple key viral target proteins. Fortunellin supports protective immunity while inhibiting pro-inflammatory cytokines and apoptosis pathways and protecting against tissue damage. Fortunellin is a phytochemical found in Gojihwadi kwath, an Indian traditional Ayurvedic formulation with an antiviral activity that is effective in COVID-19 patients. The mechanistic action of its antiviral activity, however, is unknown. The current study comprehensively evaluates the potential therapeutic mechanisms of fortunellin in preventing and treating COVID-19. We have used molecular docking, molecular dynamics simulations, free-energy calculations, host target mining of fortunellin, gene ontology enrichment, pathway analyses, and protein-protein interaction analysis. We discovered that fortunellin reliably binds to key targets that are necessary for viral replication, growth, invasion, and infectivity including Nucleocapsid (N-CTD) (-54.62 kcal/mol), Replicase-monomer at NSP-8 binding site (-34.48 kcal/mol), Replicase-dimer interface (-31.29 kcal/mol), Helicase (-30.02 kcal/mol), Papain-like-protease (-28.12 kcal/mol), 2'-O-methyltransferase (-23.17 kcal/mol), Main-protease (-21.63 kcal/mol), Replicase-monomer at dimer interface (-22.04 kcal/mol), RNA-dependent-RNA-polymerase (-19.98 kcal/mol), Nucleocapsid-NTD (-16.92 kcal/mol), and Endoribonuclease (-16.81 kcal/mol). Furthermore, we identify and evaluate the potential human targets of fortunellin and its effect on the SARS-CoV-2 infected tissues, including normal-human-bronchial-epithelium (NHBE) and lung cells and organoids such as pancreatic, colon, liver, and cornea using a network pharmacology approach. Thus, our findings indicate that fortunellin has a dual role; multi-target antiviral activities against SARS-CoV-2 and immunomodulatory capabilities against the host.
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Affiliation(s)
- Shivangi Agrawal
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | - Ekta Pathak
- Institute of Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Rajeev Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India.
| | - Vibha Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | - Afifa Parveen
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | | | | | - Sushil Kumar Dubey
- Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, India
| | | | | | | | - Neelam Atri
- Department of Botany, MMV, Banaras Hindu University, India
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13
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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14
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Yadav P, El-Kafrawy SA, El-Day MM, Alghafari WT, Faizo AA, Jha SK, Dwivedi VD, Azhar EI. Discovery of Small Molecules from Echinacea angustifolia Targeting RNA-Dependent RNA Polymerase of Japanese Encephalitis Virus. Life (Basel) 2022; 12:life12070952. [PMID: 35888042 PMCID: PMC9324244 DOI: 10.3390/life12070952] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 05/28/2023] Open
Abstract
The Japanese encephalitis virus (JEV), a mosquito-borne flavivirus that causes viral encephalitis leading to neural damage, is a major threat in most Asian countries. The RNA-dependent RNA polymerase (RdRp) present in the viral genome is the key component for genome replication, making it an attractive target for antiviral drug development. In this study, the natural products from Echinacea angustifolia were retrieved for structure-based virtual screening against JEV-RdRp. The top six compounds (Echinacoside, Echinacin, Rutin, Cynaroside, Quercetagetin 7-glucoside, and Kaempferol-3-glucoside) were obtained based on the highest negative docking score, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and molecular interaction. The computational analysis of these selected compounds against the co-crystallized ligands, i.e., ATP and GTP, were performed. Further, 100 ns molecular dynamic simulation and post-free binding energy calculation of all the selected compounds complexed with JEV-RdRP were performed to check the stability of the complexes. The obtained results showed considerable stability and intermolecular interaction with native ligand-binding site residues of JEV-RdRp. Hence, selected natural compounds are admissible inhibitors of JEV-RdRp protein and can be considered for future antiviral drug development studies.
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Affiliation(s)
- Pardeep Yadav
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida 201310, India; (P.Y.); (S.K.J.)
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India
| | - Sherif A. El-Kafrawy
- Special Infectious Agents Unit-BSL-3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (S.A.E.-K.); (M.M.E.-D.); (W.T.A.); (A.A.F.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Mai M. El-Day
- Special Infectious Agents Unit-BSL-3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (S.A.E.-K.); (M.M.E.-D.); (W.T.A.); (A.A.F.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Wejdan T. Alghafari
- Special Infectious Agents Unit-BSL-3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (S.A.E.-K.); (M.M.E.-D.); (W.T.A.); (A.A.F.)
- Clinical Nutrition Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Arwa A. Faizo
- Special Infectious Agents Unit-BSL-3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (S.A.E.-K.); (M.M.E.-D.); (W.T.A.); (A.A.F.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida 201310, India; (P.Y.); (S.K.J.)
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali 140413, India
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun 248007, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India
- Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
| | - Esam I. Azhar
- Special Infectious Agents Unit-BSL-3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (S.A.E.-K.); (M.M.E.-D.); (W.T.A.); (A.A.F.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
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15
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Bharadwaj KK, Ahmad I, Pati S, Ghosh A, Sarkar T, Rabha B, Patel H, Baishya D, Edinur HA, Abdul Kari Z, Ahmad Mohd Zain MR, Wan Rosli WI. Potent Bioactive Compounds From Seaweed Waste to Combat Cancer Through Bioinformatics Investigation. Front Nutr 2022; 9:889276. [PMID: 35529456 PMCID: PMC9075044 DOI: 10.3389/fnut.2022.889276] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 12/25/2022] Open
Abstract
The seaweed industries generate considerable amounts of waste that must be appropriately managed. This biomass from marine waste is a rich source of high-value bioactive compounds. Thus, this waste can be adequately utilized by recovering the compounds for therapeutic purposes. Histone deacetylases (HDACs) are key epigenetic regulators established as one of the most promising targets for cancer chemotherapy. In the present study, our objective is to find the HDAC 2 inhibitor. We performed top-down in silico methodologies to identify potential HDAC 2 inhibitors by screening compounds from edible seaweed waste. One hundred ninety-three (n = 193) compounds from edible seaweeds were initially screened and filtered with drug-likeness properties using SwissADME. After that, the filtered compounds were followed to further evaluate their binding potential with HDAC 2 protein by using Glide high throughput virtual screening (HTVS), standard precision (SP), extra precision (XP), and quantum polarized ligand docking (QPLD). One compound with higher negative binding energy was selected, and to validate the binding mode and stability of the complex, molecular dynamics (MD) simulations using Desmond were performed. The complex-binding free energy calculation was performed using molecular mechanics-generalized born surface area (MM-GBSA) calculation. Post-MD simulation analyses such as PCA, DCCM, and free energy landscape were also evaluated. The quantum mechanical and electronic properties of the potential bioactive compounds were assessed using the density functional theory (DFT) study. These findings support the use of marine resources like edible seaweed waste for cancer drug development by using its bioactive compounds. The obtained results encourage further in vitro and in vivo research. Our in silico findings show that the compound has a high binding affinity for the catalytic site of the HDAC 2 protein and has drug-likeness properties, and can be utilized in drug development against cancer.
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Affiliation(s)
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Siddhartha Pati
- NatNov Bioscience Private Limited, Balasore, India
- Skills Innovation & Academic Network (SIAN) Institute-Association for Biodiversity Conservation and Research, Balasore, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Govt. of West Bengal, Malda, India
| | - Bijuli Rabha
- Department of Bioengineering and Technology, Gauhati University, Guwahati, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Gauhati University, Guwahati, India
- *Correspondence: Debabrat Baishya
| | - Hisham Atan Edinur
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Zulhisyam Abdul Kari
- Department of Agricultural Sciences, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Kelantan, Malaysia
| | - Muhammad Rajaei Ahmad Mohd Zain
- Department of Orthopaedics, School of Medical Sciences, Universiti Sains Malaysia, Kubang, Malaysia
- Muhammad Rajaei Ahmad Mohd Zain
| | - Wan Ishak Wan Rosli
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
- Nutrition Programme, School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
- Wan Ishak Wan Rosli
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16
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Antonopoulou I, Sapountzaki E, Rova U, Christakopoulos P. Inhibition of the main protease of SARS-CoV-2 (M pro) by repurposing/designing drug-like substances and utilizing nature's toolbox of bioactive compounds. Comput Struct Biotechnol J 2022; 20:1306-1344. [PMID: 35308802 PMCID: PMC8920478 DOI: 10.1016/j.csbj.2022.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
The emergence of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in a long pandemic, with numerous cases and victims worldwide and enormous consequences on social and economic life. Although vaccinations have proceeded and provide a valuable shield against the virus, the approved drugs are limited and it is crucial that further ways to combat infection are developed, that can also act against potential mutations. The main protease (Mpro) of the virus is an appealing target for the development of inhibitors, due to its importance in the viral life cycle and its high conservation among different coronaviruses. Several compounds have shown inhibitory potential against Mpro, both in silico and in vitro, with few of them also having entered clinical trials. These candidates include: known drugs that have been repurposed, molecules specifically designed based on the natural substrate of the protease or on structural moieties that have shown high binding affinity to the protease active site, as well as naturally derived compounds, either isolated or in plant extracts. The aim of this work is to collectively present the results of research regarding Mpro inhibitors to date, focusing on the function of the compounds founded by in silico simulations and further explored by in vitro and in vivo assays. Creating an extended portfolio of promising compounds that may block viral replication by inhibiting Mpro and by understanding involved structure-activity relationships, could provide a basis for the development of effective solutions against SARS-CoV-2 and future related outbreaks.
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Affiliation(s)
| | | | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
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17
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Brogi S, Quimque MT, Notarte KI, Africa JG, Hernandez JB, Tan SM, Calderone V, Macabeo AP. Virtual Combinatorial Library Screening of Quinadoline B Derivatives against SARS-CoV-2 RNA-Dependent RNA Polymerase. Computation 2022; 10:7. [DOI: 10.3390/computation10010007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The unprecedented global health threat of SARS-CoV-2 has sparked a continued interest in discovering novel anti-COVID-19 agents. To this end, we present here a computer-based protocol for identifying potential compounds targeting RNA-dependent RNA polymerase (RdRp). Starting from our previous study wherein, using a virtual screening campaign, we identified a fumiquinazolinone alkaloid quinadoline B (Q3), an antiviral fungal metabolite with significant activity against SARS-CoV-2 RdRp, we applied in silico combinatorial methodologies for generating and screening a library of anti-SARS-CoV-2 candidates with strong in silico affinity for RdRp. For this study, the quinadoline pharmacophore was subjected to structural iteration, obtaining a Q3-focused library of over 900,000 unique structures. This chemical library was explored to identify binders of RdRp with greater affinity with respect to the starting compound Q3. Coupling this approach with the evaluation of physchem profile, we found 26 compounds with significant affinities for the RdRp binding site. Moreover, top-ranked compounds were submitted to molecular dynamics to evaluate the stability of the systems during a selected time, and to deeply investigate the binding mode of the most promising derivatives. Among the generated structures, five compounds, obtained by inserting nucleotide-like scaffolds (1, 2, and 5), heterocyclic thiazolyl benzamide moiety (compound 3), and a peptide residue (compound 4), exhibited enhanced binding affinity for SARS-CoV-2 RdRp, deserving further investigation as possible antiviral agents. Remarkably, the presented in silico procedure provides a useful computational procedure for hit-to-lead optimization, having implications in anti-SARS-CoV-2 drug discovery and in general in the drug optimization process.
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Tolah AM, Altayeb LM, Alandijany TA, Dwivedi VD, El-Kafrawy SA, Azhar EI. Computational and In Vitro Experimental Investigations Reveal Anti-Viral Activity of Licorice and Glycyrrhizin against Severe Acute Respiratory Syndrome Coronavirus 2. Pharmaceuticals (Basel) 2021; 14:1216. [PMID: 34959616 PMCID: PMC8703534 DOI: 10.3390/ph14121216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Without effective antivirals, the COVID-19 pandemic will likely continue to substantially affect public health. Medicinal plants and phytochemicals are attractive therapeutic options, particularly those targeting viral proteins essential for replication cycle. Herein, a total 179 phytochemicals of licorice (Glycyrrhiza glabra) were screened and scrutinized against the SARS-CoV-2 main protease (Mpro) with considerable binding affinities in the range of -9.831 to -2.710 kcal/mol. The top 10 compounds with the best docking scores, licuraside, glucoliquiritin apioside, 7,3'-Dihydroxy-5'-methoxyisoflavone, licuroside, kanzonol R, neoisoliquiritin, licochalcone-A, formononetin, isomucronulatol, and licoricone, were redocked using AutoDock Vina, yielding -8.7 to -7.3 kcal/mol binding energy against Glycyrrhizin (-8.0 kcal/mol) as a reference ligand. Four compounds, licuraside, glucoliquiritin apioside, 7,3'-Dihydroxy-5'-methoxyisoflavone, and licuroside, with glycyrrhizin (reference ligand) were considered for the 100 ns MD simulation and post-simulation analysis which support the stability of docked bioactive compounds with viral protein. In vitro studies demonstrated robust anti-SARS-CoV-2 activity of licorice and glycyrrhizin under different treatment protocols (simulations treatment with viral infection, post-infection treatment, and pre-treatment), suggesting multiple mechanisms for action. Although both compounds inhibited SARS-CoV-2 replication, the half-maximal inhibitory concentration (IC50) of glycyrrhizin was substantially lower than licorice. This study supports proceeding with in vivo experimentation and clinical trials and highlights licorice and glycyrrhizin as potential therapeutics for COVID-19.
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Affiliation(s)
- Ahmed M. Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, P.O. Box 21911, Rabigh 344, Saudi Arabia
| | - Lamya M. Altayeb
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
| | - Thamir A. Alandijany
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and System Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India;
| | - Sherif A. El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Lin Z, Teng C, Ni L, Zhang Z, Lu X, Lou J, Wang L, Wang Y, Chen W, Zhang X, Lin Z. Echinacoside Upregulates Sirt1 to Suppress Endoplasmic Reticulum Stress and Inhibit Extracellular Matrix Degradation In Vitro and Ameliorates Osteoarthritis In Vivo. Oxid Med Cell Longev 2021; 2021:3137066. [PMID: 34777682 DOI: 10.1155/2021/3137066] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/08/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022]
Abstract
Background Osteoarthritis (OA) is a progressive illness that destroys cartilage. Oxidative stress is a major contributor of OA, while endoplasmic reticulum (ER) stress is the key cellular damage under oxidative stress in chondrocytes. Echinacoside (ECH) is the main extract and active substance of Cistanche, with potent antioxidative stress (OS) properties, and currently under clinical trials in China. However, its function in OA is yet to be determined. Purpose We aimed to explore the specific role of ECH in the occurrence and development of OA and its underlying mechanism in vivo and in vitro. Methods After the mice were anesthetized, the bilateral medial knee joint meniscus resection was performed to establish the DMM model. TBHP was used to induce oxidative stress to establish the OA model in chondrocytes in vitro. Western blot and RT-PCR were used to evaluate the level of ER stress-related biomarkers such as p-PERK/PERK, GRP78, ATF4, p-eIF2α/eIF2α, and CHOP and apoptosis-related proteins such as BAX, Bcl-2, and cleaved caspase-3. Meanwhile, we used SO staining, immunofluorescence, and immunohistochemical staining to evaluate the pharmacological effects of ECH in mice in vivo. Results We demonstrated the effectiveness of ECH in suppressing ER stress and restoring ECM metabolism in vitro. In particular, ECH was shown to suppress tert-Butyl hydroperoxide- (TBHP-) induced OS and subsequently lower the levels of p-PERK/PERK, GRP78, ATF4, p-eIF2α/eIF2α, and CHOP in vitro. Simultaneously, ECH reduced MMP13 and ADAMTS5 levels and promoted Aggrecan and Collagen II levels, suggesting ECM degradation suppression. Moreover, we showed that ECH mediates its cellular effects via upregulation of Sirt1. Lastly, we confirmed that ECH can protect against OA in mouse OA models. Conclusion In summary, our findings indicate that ECH can inhibit ER stress and ECM degradation by upregulating Sirt1 in mouse chondrocytes treated with TBHP. It can also prevent OA development in vivo.
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Lundstrom K, Aljabali AAA. COVID-19 in 2021. Viruses 2021; 13:2098. [PMID: 34696528 PMCID: PMC8539425 DOI: 10.3390/v13102098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022] Open
Abstract
The Special Issue on Vaccines and Therapeutics against Coronaviruses, which was launched in early 2021, has attracted the scientific community at large, and more than 20 manuscripts have been accepted for publication.[...].
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Affiliation(s)
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
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