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Catalano A, Ceramella J, Iacopetta D, Marra M, Conforti F, Lupi FR, Gabriele D, Borges F, Sinicropi MS. Aloe vera-An Extensive Review Focused on Recent Studies. Foods 2024; 13:2155. [PMID: 38998660 PMCID: PMC11241682 DOI: 10.3390/foods13132155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/16/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024] Open
Abstract
Since ancient times, Aloe vera L. (AV) has attracted scientific interest because of its multiple cosmetic and medicinal properties, attributable to compounds present in leaves and other parts of the plant. The collected literature data show that AV and its products have a beneficial influence on human health, both by topical and oral use, as juice or an extract. Several scientific studies demonstrated the numerous biological activities of AV, including, for instance, antiviral, antimicrobial, antitumor, and antifungal. Moreover, its important antidepressant activity in relation to several diseases, including skin disorders (psoriasis, acne, and so on) and prediabetes, is a growing field of research. This comprehensive review intends to present the most significant and recent studies regarding the plethora of AV's biological activities and an in-depth analysis exploring the component/s responsible for them. Moreover, its morphology and chemical composition are described, along with some studies regarding the single components of AV available in commerce. Finally, valorization studies and a discussion about the metabolism and toxicological aspects of this "Wonder Plant" are reported.
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Affiliation(s)
- Alessia Catalano
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", Via Orabona 4, 70126 Bari, Italy
| | - Jessica Ceramella
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Domenico Iacopetta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Maria Marra
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Filomena Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Francesca R Lupi
- Department of Information, Modeling, Electronics and System Engineering, (D.I.M.E.S.), University of Calabria, Via P. Bucci, Cubo 39C, CS, 87036 Rende, Italy
| | - Domenico Gabriele
- Department of Information, Modeling, Electronics and System Engineering, (D.I.M.E.S.), University of Calabria, Via P. Bucci, Cubo 39C, CS, 87036 Rende, Italy
| | - Fernanda Borges
- CIQUP-IMS-Centro de Investigação em Química da Universidade do Porto, Institute of Molecular Sciences, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
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Ushasree MV, Jia Q, Do SG, Lee EY. New opportunities and perspectives on biosynthesis and bioactivities of secondary metabolites from Aloe vera. Biotechnol Adv 2024; 72:108325. [PMID: 38395206 DOI: 10.1016/j.biotechadv.2024.108325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/10/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Historically, the genus Aloe has been an indispensable part of both traditional and modern medicine. Decades of intensive research have unveiled the major bioactive secondary metabolites of this plant. Recent pandemic outbreaks have revitalized curiosity in aloe metabolites, as they have proven pharmacokinetic profiles and repurposable chemical space. However, the structural complexity of these metabolites has hindered scientific advances in the chemical synthesis of these compounds. Multi-omics research interventions have transformed aloe research by providing insights into the biosynthesis of many of these compounds, for example, aloesone, aloenin, noreugenin, aloin, saponins, and carotenoids. Here, we summarize the biological activities of major aloe secondary metabolites with a focus on their mechanism of action. We also highlight the recent advances in decoding the aloe metabolite biosynthetic pathways and enzymatic machinery linked with these pathways. Proof-of-concept studies on in vitro, whole-cell, and microbial synthesis of aloe compounds have also been briefed. Research initiatives on the structural modification of various aloe metabolites to expand their chemical space and activity are detailed. Further, the technological limitations, patent status, and prospects of aloe secondary metabolites in biomedicine have been discussed.
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Affiliation(s)
- Mrudulakumari Vasudevan Ushasree
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Qi Jia
- Unigen, Inc., 2121 South street suite 400 Tacoma, Washington 98405, USA
| | - Seon Gil Do
- Naturetech, Inc., 29-8, Yongjeong-gil, Chopyeong-myeon, Jincheon-gun, Chungcheongbuk-do 27858, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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Orabi MAA, Alshahrani MM, Sayed AM, Abouelela ME, Shaaban KA, Abdel-Sattar ES. Identification of Potential Leishmania N-Myristoyltransferase Inhibitors from Withania somnifera (L.) Dunal: A Molecular Docking and Molecular Dynamics Investigation. Metabolites 2023; 13:metabo13010093. [PMID: 36677018 PMCID: PMC9861338 DOI: 10.3390/metabo13010093] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Leishmaniasis is a group of infectious diseases caused by Leishmania protozoa. The ineffectiveness, high toxicity, and/or parasite resistance of the currently available antileishmanial drugs has created an urgent need for safe and effective leishmaniasis treatment. Currently, the molecular-docking technique is used to predict the proper conformations of small-molecule ligands and the strength of the contact between a protein and a ligand, and the majority of research for the development of new drugs is centered on this type of prediction. Leishmania N-myristoyltransferase (NMT) has been shown to be a reliable therapeutic target for investigating new anti-leishmanial molecules through this kind of virtual screening. Natural products provide an incredible source of affordable chemical scaffolds that serve in the development of effective drugs. Withania somnifera leaves, roots, and fruits have been shown to contain withanolide and other phytomolecules that are efficient anti-protozoal agents against Malaria, Trypanosoma, and Leishmania spp. Through a review of previously reported compounds from W. somnifera-afforded 35 alkaloid, phenolic, and steroid compounds and 132 withanolides/derivatives, typical of the Withania genus. These compounds were subjected to molecular docking screening and molecular dynamics against L. major NMT. Calycopteretin-3-rutinoside and withanoside IX showed the highest affinity and binding stability to L. major NMT, implying that these compounds could be used as antileishmanial drugs and/or as a scaffold for the design of related parasite NMT inhibitors with markedly enhanced binding affinity.
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Affiliation(s)
- Mohamed A. A. Orabi
- Department of Pharmacognosy, College of Pharmacy, Najran University, Najran 61441, Saudi Arabia
- Correspondence: or ; Tel.: +966-557398835
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Mohamed E. Abouelela
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt
- Center for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Khaled A. Shaaban
- Center for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - El-Shaymaa Abdel-Sattar
- Department of Medical Microbiology and Immunology, Faculty of Pharmacy, South Valley University, Qena 83523, Egypt
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Singh DD, Han I, Choi EH, Yadav DK. A Clinical Update on SARS-CoV-2: Pathology and Development of Potential Inhibitors. Curr Issues Mol Biol 2023; 45:400-433. [PMID: 36661514 PMCID: PMC9857284 DOI: 10.3390/cimb45010028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome) is highly infectious and causes severe acute respiratory distress syndrome (SARD), immune suppression, and multi-organ failure. For SARS-CoV-2, only supportive treatment options are available, such as oxygen supportive therapy, ventilator support, antibiotics for secondary infections, mineral and fluid treatment, and a significant subset of repurposed effective drugs. Viral targeted inhibitors are the most suitable molecules, such as ACE2 (angiotensin-converting enzyme-2) and RBD (receptor-binding domain) protein-based inhibitors, inhibitors of host proteases, inhibitors of viral proteases 3CLpro (3C-like proteinase) and PLpro (papain-like protease), inhibitors of replicative enzymes, inhibitors of viral attachment of SARS-CoV-2 to the ACE2 receptor and TMPRSS2 (transmembrane serine proteinase 2), inhibitors of HR1 (Heptad Repeat 1)-HR2 (Heptad Repeat 2) interaction at the S2 protein of the coronavirus, etc. Targeting the cathepsin L proteinase, peptide analogues, monoclonal antibodies, and protein chimaeras as RBD inhibitors interferes with the spike protein's ability to fuse to the membrane. Targeting the cathepsin L proteinase, peptide analogues, monoclonal antibodies, and protein chimaeras as RBD inhibitors interferes with the spike protein's ability to fuse to the membrane. Even with the tremendous progress made, creating effective drugs remains difficult. To develop COVID-19 treatment alternatives, clinical studies are examining a variety of therapy categories, including antibodies, antivirals, cell-based therapy, repurposed diagnostic medicines, and more. In this article, we discuss recent clinical updates on SARS-CoV-2 infection, clinical characteristics, diagnosis, immunopathology, the new emergence of variant, SARS-CoV-2, various approaches to drug development and treatment options. The development of therapies has been complicated by the global occurrence of many SARS-CoV-2 mutations. Discussion of this manuscript will provide new insight into drug pathophysiology and drug development.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
- Correspondence: (I.H.); (D.K.Y.); Tel.: +82-2-597-0365 (I.H. & D.K.Y.)
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Dharmendra Kumar Yadav
- Department of R&D Center, Arontier Co., Seoul 06735, Republic of Korea
- Correspondence: (I.H.); (D.K.Y.); Tel.: +82-2-597-0365 (I.H. & D.K.Y.)
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5
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Benarous L, Benarous K, Muhammad G, Ali Z. Deep learning application detecting SARS-CoV-2 key enzymes inhibitors. CLUSTER COMPUTING 2023; 26:1169-1180. [PMID: 35874186 PMCID: PMC9295888 DOI: 10.1007/s10586-022-03656-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/28/2022] [Accepted: 06/17/2022] [Indexed: 05/14/2023]
Abstract
The fast spread of the COVID-19 over the world pressured scientists to find its cures. Especially, with the disastrous results, it engendered from human life losses to long-term impacts on infected people's health and the huge financial losses. In addition to the massive efforts made by researchers and medicals on finding safe, smart, fast, and efficient methods to accurately make an early diagnosis of the COVID-19. Some researchers focused on finding drugs to treat the disease and its symptoms, others worked on creating effective vaccines, while several concentrated on finding inhibitors for the key enzymes of the virus, to reduce its spreading and reproduction inside the human body. These enzymes' inhibitors are usually found in aliments, plants, fungi, or even in some drugs. Since these inhibitors slow and halt the replication of the virus in the human body, they can help fight it at an early stage saving the patient from death risk. Moreover, if the human body's immune system gets rid of the virus at the early stage it can be spared from the disastrous sequels it may leave inside the patient's body. Our research aims to find aliments and plants that are rich in these inhibitors. In this paper, we developed a deep learning application that is trained with various aliments, plants, and drugs to detect if a component contains SARS-CoV-2 key inhibitor(s) intending to help them find more sources containing these inhibitors. The application is trained to identify various sources rich in thirteen coronavirus-2 key inhibitors. The sources are currently just aliments, plants, and seeds and the identification is done by their names.
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Affiliation(s)
- Leila Benarous
- LIM Laboratory (Laboratoire d’informatique Et de Mathématique), Department of Computer Science, Faculty of Science, University of Amar Telidji, Laghouat, Algeria
- LISSI-Tinc-NET Laboratory, University of Paris-Est Creteil, 94400 Vitry-sur-Seine, France
| | - Khedidja Benarous
- Science Fundamental Laboratory, Department of Biology, Faculty of Sciences, University of Amar Telidji, Laghouat, Algeria
| | - Ghulam Muhammad
- Department of Computer Engineering, College of Computer and Information Sciences, King Saud University, Riyadh, 11543 Saudi Arabia
| | - Zulfiqar Ali
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ UK
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Daoud I, Mesli F, Melkemi N, Ghalem S, Salah T. Discovery of potential SARS-CoV 3CL protease inhibitors from approved antiviral drugs using: virtual screening, molecular docking, pharmacophore mapping evaluation and dynamics simulation. J Biomol Struct Dyn 2022; 40:12574-12591. [PMID: 34541995 PMCID: PMC8459931 DOI: 10.1080/07391102.2021.1973563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The spread of corona-virus disease 2019 (COVID-19) has been faster than any other corona-viruses that have succeeded in crossing the animal-human barrier. This disease, caused by the severe acute respiratory syndrome corona-virus 2 (SARS-CoV-2/2019-nCoV) posing a serious threat to global public health and local economies. There are three responsible for this disease; SARS-CoV-2, SARS-CoV and MERS-CoV. Whereas our goal is to test the affinity for a new class of compounds obtained from a hybridization of Chloroquine, Amodiaquine and Mefloquine with three targets SARS-CoV-2, SARS-CoV and MERS-CoV, in order to find new compounds as new inhibitors against Covid-19. In this work, we first used: the molecular docking/dynamics methods and ADME properties to study interaction and affinity between eight new compounds against three targets involved in the Covid-19. The results of the docking simulations and dynamics revealed that inhibitor of the malaria (Ligand 87) has an affinity to interact with SARS-CoV-2, SARS-CoV and MERS-CoV targets and they can be good inhibitors for treatment of Covid-19. Moreover, they give best affinity compared to the Remdesivir and Chloroquine and other clinical tests. The Pharmacokinetics was justified by means of lipophilicity and high coefficient of skin permeability. The in silico evaluation of ADME and drug-likeness revealed that L87 has higher absorption in the intestines with good bioavailability. However, an additional in vitro and/or in vivo experimental study should make it possible to verify the theoretical results obtained in silico.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ismail Daoud
- Department of Matter Sciences, University Mohamed Khider, Biskra, Algeria,Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria,Ismail Daoud Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria
| | - Fouzia Mesli
- Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria,CONTACT Fouzia Mesli ;
| | - Nadjib Melkemi
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, Algeria
| | - Said Ghalem
- Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria
| | - Toufik Salah
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, Algeria
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Abdelkarem FM, Nafady AM, Allam AE, Mostafa MAH, Al Haidari RA, Hassan HA, Zaki MEA, Assaf HK, Kamel MR, Zidan SAH, Sayed AM, Shimizu K. A Comprehensive In Silico Study of New Metabolites from Heteroxenia fuscescens with SARS-CoV-2 Inhibitory Activity. Molecules 2022; 27:molecules27217369. [PMID: 36364194 PMCID: PMC9657797 DOI: 10.3390/molecules27217369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 12/02/2022] Open
Abstract
Chemical investigation of the total extract of the Egyptian soft coral Heteroxenia fuscescens, led to the isolation of eight compounds, including two new metabolites, sesquiterpene fusceterpene A (1) and a sterol fuscesterol A (4), along with six known compounds. The structures of 1–8 were elucidated via intensive studies of their 1D, 2D-NMR, and HR-MS analyses, as well as a comparison of their spectral data with those mentioned in the literature. Subsequent comprehensive in-silico-based investigations against almost all viral proteins, including those of the new variants, e.g., Omicron, revealed the most probable target for these isolated compounds, which was found to be Mpro. Additionally, the dynamic modes of interaction of the putatively active compounds were highlighted, depending on 50-ns-long MDS. In conclusion, the structural information provided in the current investigation highlights the antiviral potential of H. fuscescens metabolites with 3β,5α,6β-trihydroxy steroids with different nuclei against SARS-CoV-2, including newly widespread variants.
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Affiliation(s)
- Fahd M. Abdelkarem
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Alaa M. Nafady
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Ahmed E. Allam
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
- Correspondence: (A.E.A.); (M.E.A.Z.)
| | - Mahmoud A. H. Mostafa
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, Taibah University, Al Madinah Al Munawarah 41477, Saudi Arabia
| | - Rwaida A. Al Haidari
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, Taibah University, Al Madinah Al Munawarah 41477, Saudi Arabia
| | - Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag 82524, Egypt
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
- Correspondence: (A.E.A.); (M.E.A.Z.)
| | - Hamdy K. Assaf
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Mohamed R. Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Sabry A. H. Zidan
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Kuniyoshi Shimizu
- Department of Agro-Environmental Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
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Network Pharmacological Analysis of the Red Sea Sponge Hyrtios erectus Extract to Reveal Anticancer Efficacy of Corresponding Loaded Niosomes. Mar Drugs 2022; 20:md20100628. [PMID: 36286452 PMCID: PMC9604794 DOI: 10.3390/md20100628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, the LC-HRMS-assisted chemical profiling of Hyrtios erectus sponge led to the annotation of eleven major compounds (1-11). H. erectus-derived crude extract (HE) was tested in vitro for its antiproliferative activity against three human cancer cell lines, Hep-G2 (human liver cancer cell line), MCF-7 (breast cancer cell line), and Caco-2 (colon cancer cell line), before and after encapsulation within niosomes. Hyrtios erectus extract showed moderate in vitro antiproliferative activities towards the studied cell lines with IC50 values 18.5 ± 0.08, 15.2 ± 0.11, and 13.4 ± 0.12, respectively. The formulated extract-containing niosomes (size 142.3 ± 10.3 nm, PDI 0.279, and zeta potential 22.8 ± 1.6) increased the in vitro antiproliferative activity of the entrapped extract significantly (IC50 8.5 ± 0.04, 4.1 ± 0.07, and 3.4 ± 0.05, respectively). A subsequent computational chemical study was performed to build a sponge-metabolite-targets-cancer diseases network, by focusing on targets that possess anticancer activity toward the three cancer types: breast, colon, and liver. Pubchem, BindingDB, and DisGenet databases were used to build the network. Shinygo and KEGG databases in addition to FunRich software were used for gene ontology and functional analysis. The computational analysis linked the metabolites to 200 genes among which 147 genes related to cancer and only 64 genes are intersected in the three cancer types. The study proved that the co-occurrence of compounds 1, 2, 3, 7, 8, and 10 are the most probable compounds possessing cytotoxic activity due to large number of connections to the intersected cytotoxic genes with edges range from 9-14. The targets possess the anticancer effect through Pathways in cancer, Endocrine resistance and Proteoglycans in cancer as mentioned by KEGG and ShinyGo 7.1 databases. This study introduces niosomes as a promising strategy to promote the cytotoxic potential of H. erectus extract.
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Mousavi S, Zare S, Mirzaei M, Feizi A. Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:2044282. [PMID: 36199815 PMCID: PMC9527439 DOI: 10.1155/2022/2044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, drug development, In silico, In vitro, and In vivo. A narrative synthesis was performed as a qualitative method for the data synthesis of each outcome measure. Results A total of 2168 articles were identified through searching databases. Finally, 315 studies (266 in silico, 34 in vitro, and 15 in vivo) were included. In studies with in silico approach, 98 article study repurposed drug and 91 studies evaluated herbal medicine on COVID-19. Among 260 drugs repurposed by the computational method, the best results were observed with saquinavir (n = 9), ritonavir (n = 8), and lopinavir (n = 6). Main protease (n = 154) following spike glycoprotein (n = 62) and other nonstructural protein of virus (n = 45) was among the most studied targets. Doxycycline, chlorpromazine, azithromycin, heparin, bepridil, and glycyrrhizic acid showed both in silico and in vitro inhibitory effects against SARS-CoV-2. Conclusion The preclinical studies of novel drug design for COVID-19 focused on main protease and spike glycoprotein as targets for antiviral development. From evaluated structures, saquinavir, ritonavir, eucalyptus, Tinospora cordifolia, aloe, green tea, curcumin, pyrazole, and triazole derivatives in in silico studies and doxycycline, chlorpromazine, and heparin from in vitro and human monoclonal antibodies from in vivo studies showed promised results regarding efficacy. It seems that due to the nature of COVID-19 disease, finding some drugs with multitarget antiviral actions and anti-inflammatory potential is valuable and some herbal medicines have this potential.
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Affiliation(s)
- Sarah Mousavi
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shima Zare
- School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahmoud Mirzaei
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Epidemiology and Biostatistics, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
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10
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Derafa W, Aggoun D, Messasma Z, Houchi S, Bouacida S, Ourari A. An unexpected single crystal structure of nickel(II) complex: Spectral, DFT, NLO, magnetic and molecular docking studies. J Mol Struct 2022; 1264:133190. [PMID: 35531369 PMCID: PMC9055260 DOI: 10.1016/j.molstruc.2022.133190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 01/11/2023]
Abstract
This work explores the study of a synthesized nickel complex as a possible inhibitor against the main protease (Mpro) of the recent emerging coronavirus disease (COVID-19). Overall, the template reaction of 3-acetyl-2-hydroxy-6-methyl-4H-pyran-4-one with nickel(II) chloride hexahydrate in N,N-dimethylformamide (DMF) medium leads to the formation of neutral nickel complex. This resulting complex is formulated as [Ni(DHA)2(DMF)2] on the basis of FT-IR, UV-Vis., single-crystal X-ray diffraction analysis, magnetic susceptibility and CV measurements as well as DFT quantum chemical calculations. Its single crystal suggests was found to be surrounded by the both pairs of molecules of DHA and DMF through six oxygen atoms with octahedral coordination sphere. The obtained magnetic susceptibilities are positive and agree with its paramagnetic state. In addition to the experimental investigations, optimized geometry, spectroscopic and electronic properties were also performed using DFT calculation with B3LYP/6-31G(d,p) level of theory. The nonlinear optical (NLO) properties of this complex are again examined. Some suitable quantum descriptors (EHOMO, ELUMO, Energy gap, Global hardness), Milliken atomic charge, Electrophilic potion and Molecular Electrostatic Potential) have been elegantly described. Molecular docking results demonstrated that the docked nickel complex displayed remarkable binding energy with Mpro. Besides, important molecular properties and ADME pharmacokinetic profiles of possible Mpro inhibitors were assessed by in silico prediction.
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Affiliation(s)
- Wassila Derafa
- Laboratory of Electrochemistry, Molecular Engineering and Redox Catalysis, Department of Process Engineering, Faculty of technology, University of Ferhat Abbas, Setif 19000, Algeria,Chemistry Department, College of Science, Jouf University, Sakaka 72388, Saudi Arabia
| | - Djouhra Aggoun
- Laboratory of Electrochemistry, Molecular Engineering and Redox Catalysis, Department of Process Engineering, Faculty of technology, University of Ferhat Abbas, Setif 19000, Algeria,Chemistry Department, Faculty of sciences, University Ferhat Abbas, Setif 19000 Algeria,Corresponding author at: Laboratory of Electrochemistry, Molecular Engineering and Redox Catalysis, Department of Process Engineering, Faculty of technology, University of Ferhat Abbas, Setif 19000, Algeria
| | - Zakia Messasma
- Laboratory of Electrochemistry, Molecular Engineering and Redox Catalysis, Department of Process Engineering, Faculty of technology, University of Ferhat Abbas, Setif 19000, Algeria,Chemistry Department, Faculty of sciences, University Ferhat Abbas, Setif 19000 Algeria
| | - Selma Houchi
- Laboratory of Applied Biochemistry, Faculty of Natural and Life Sciences, University Ferhat Abbas, Setif 19000 Algeria,Department of Biochemistry Faculty of Natural and Life Sciences, University Ferhat Abbas, Setif 19000 Algeria
| | - Sofiane Bouacida
- Department of Sciences of Matter, Faculty of Exact Sciences, Oum El Bouaghi University, 04000, Algeria,Research Unit of Environmental Chemistry and Molecular Structural CHEMS, University of the Mentouri Brothers, Constantine, Algeria
| | - Ali Ourari
- Laboratory of Electrochemistry, Molecular Engineering and Redox Catalysis, Department of Process Engineering, Faculty of technology, University of Ferhat Abbas, Setif 19000, Algeria
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11
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Shaji D, Suzuki R, Yamamoto S, Orihashi D, Kurita N. Natural inhibitors for severe acute respiratory syndrome coronavirus 2 main protease from Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis: molecular docking and ab initio fragment molecular orbital calculations. Struct Chem 2022; 33:1771-1788. [PMID: 35938063 PMCID: PMC9340690 DOI: 10.1007/s11224-022-02021-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022]
Abstract
The novel coronavirus 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly worldwide, and new drug treatments for COVID-19 are urgently required. To find the potential inhibitors against the main protease (Mpro) of SARS-CoV-2, we investigated the inhibitory potential of naturally occurring compounds from the plants Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis, using molecular docking, classical molecular mechanics optimizations, and ab initio fragment molecular orbital (FMO) calculations. Of the 35 compounds that we simulated, feralolide from Aloe vera exhibited the highest binding affinity against Mpro. Therefore, we proposed novel compounds based on the feralolide and investigated their binding properties to Mpro. The FMO results indicated that the introduction of a hydroxyl group into feralolide significantly enhances its binding affinity to Mpro. These results provide useful information for developing potent Mpro inhibitors.
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Affiliation(s)
- Divya Shaji
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Ryo Suzuki
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Daisuke Orihashi
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580 Japan
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12
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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: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [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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13
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Hamed ANE, Abouelela ME, El Zowalaty AE, Badr MM, Abdelkader MSA. Chemical constituents from Carica papaya Linn. leaves as potential cytotoxic, EGFR wt and aromatase (CYP19A) inhibitors; a study supported by molecular docking. RSC Adv 2022; 12:9154-9162. [PMID: 35424860 PMCID: PMC8985094 DOI: 10.1039/d1ra07000b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/14/2022] [Indexed: 12/26/2022] Open
Abstract
The phytochemical investigation of the hydromethanolic extract of Carica papaya Linn. leaves (Caricaceae) resulted in the isolation and characterization of ten compounds, namely; carpaine (1), methyl gallate (2), loliolide (3), rutin (4), clitorin (5), kaempferol-3-O-neohesperidoside (6), isoquercetin (7), nicotiflorin (8) and isorhamnetin-3-O-β-d-glucopyranoside (9). The compounds 2, 3, 5-7 and 9 were isolated for the first time from the genus Carica. An in vitro breast cancer cytotoxicity study was evaluated with an MCF-7 cell line using the MTT assay. Methyl gallate and clitorin demonstrated the most potent cytotoxic activities with an IC50 of 1.11 ± 0.06 and 2.47 ± 0.14 μM, respectively. Moreover, methyl gallate and nicotiflorin exhibited potential EGFRwt kinase inhibition activities with an IC50 of 37.3 ± 1.9 and 41.08 ± 2.1 nM, respectively, compared with the positive control erlotinib (IC50 = 35.94 ± 1.8 nM). On the other hand, clitorin and nicotiflorin displayed the strongest aromatase kinase inhibition activities with an IC50 of 77.41 ± 4.53 and 92.84 ± 5.44 nM, respectively. Clitorin was comparable to the efficacy of the standard drug letrozole (IC50 = 77.72 ± 4.55). Additionally, molecular docking simulations of the isolated compounds to EGFR and human placental aromatase cytochrome P450 (CYP19A1) were evaluated. Methyl gallate linked with the EGFR receptor through hydrogen bonding with a pose score of -4.5287 kcal mol-1 and RMSD value of 1.69 Å. Clitorin showed the strongest interaction with aromatase (CYP19A1) for the breast cancer receptor with a posing score of -14.2074 and RMSD value of 1.56 Å. Compounds (1-3) possessed a good bioavailability score with a 0.55 value.
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Affiliation(s)
- Ashraf N E Hamed
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University Minia 61519 Egypt
| | - Mohamed E Abouelela
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University Assiut-Branch Assiut 71524 Egypt
| | - Ahmed E El Zowalaty
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg 40530 Gothenburg Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg 40530 Gothenburg Sweden
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University 44519 Egypt
| | - Mohamed M Badr
- Department of Biochemistry, Faculty of Pharmacy, Menoufia University Menoufia 32511 Egypt
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14
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Singh DD, Parveen A, Yadav DK. SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines. Front Cell Infect Microbiol 2022; 11:777212. [PMID: 34970509 PMCID: PMC8713083 DOI: 10.3389/fcimb.2021.777212] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/09/2021] [Indexed: 01/14/2023] Open
Abstract
The emergence of SARS-CoV-2 variants may cause resistance at the immunity level against current vaccines. Some emergent new variants have increased transmissibility, infectivity, hospitalization, and mortality. Since the administration of the first SARS-CoV-2 vaccine to a human in March 2020, there is an ongoing global race against SARS-CoV-2 to control the current pandemic situation. Spike (S) glycoprotein of SARS-CoV-2 is the main target for current vaccine development, which can neutralize the infection. Companies and academic institutions have developed vaccines based on the S glycoprotein, as well as its antigenic domains and epitopes, which have been proven effective in generating neutralizing antibodies. The effectiveness of SARS-CoV-2 vaccines and other therapeutics developments are limited by the new emergent variants at the global level. We have discussed the emergent variants of SARS-CoV-2 on the efficacy of developed vaccines. Presently, most of the vaccines have been tremendously effective in severe diseases. However, there are still noteworthy challenges in certifying impartial vaccines; the stories of re-infections are generating more stressful conditions, and this needs further clinical evaluation.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Amna Parveen
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, South Korea
| | - Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, South Korea
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15
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Aminah NS, Abdjan MI, Wardana AP, Kristanti AN, Siswanto I, Rakhman KA, Takaya Y. The dolabellane diterpenes as potential inhibitors of the SARS-CoV-2 main protease: molecular insight of the inhibitory mechanism through computational studies. RSC Adv 2021; 11:39455-39466. [PMID: 35492446 PMCID: PMC9044469 DOI: 10.1039/d1ra07584e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
An investigation has been carried out on natural products from dolabellane derivatives to understand their potential in inhibiting the SARS-CoV-2 main protease (3CLpro) using an in silico approach. Inhibition of the 3CLpro enzyme is a promising target in stopping the replication of the SARS-CoV-2 virus through inhibition of the subsite binding pocket. The redocking process aims to determine the 3CLpro active sites. The redocking requirement showed a good pose with an RMSD value of 1.39 Å. The combination of molecular docking and MD simulation shows the results of DD13 as a candidate which had a good binding affinity (kcal mol-1) to inhibit the 3CLpro enzyme activity. Prediction of binding free energy (kcal mol-1) of DD13 using the Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PB/GBSA) approach shows the results ΔG bind(MM-GBSA): -52.33 ± 0.34 and ΔG bind(MM-PBSA): -43.52 ± 0.42. The key residues responsible for the inhibition mechanism are Hie41, Ser46, Met49, Asn142, Cys145, Hie163, Met165, and Gln189. Additionally, pharmacokinetic prediction recommended that DD13 had promising criteria as a drug candidate. The results demonstrated in this study provide theoretical information to obtain a potential inhibitor against the SARS-CoV-2 main protease.
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Affiliation(s)
- Nanik Siti Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga Indonesia
| | - Muhammad Ikhlas Abdjan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Ph.D. Student of Mathematics and Natural Sciences, Faculty of Science and Technology, Universitas Airlangga Komplek Kampus C UNAIR, Jl. Mulyorejo 60115 Surabaya Indonesia
| | - Andika Pramudya Wardana
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Ph.D. Student of Mathematics and Natural Sciences, Faculty of Science and Technology, Universitas Airlangga Komplek Kampus C UNAIR, Jl. Mulyorejo 60115 Surabaya Indonesia
| | - Alfinda Novi Kristanti
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga Indonesia
| | - Imam Siswanto
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Bioinformatic Laboratory, UCoE Research Center for Bio-Molecule Engineering, Universitas Airlangga Surabaya Indonesia
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16
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Alnusaire TS, Sayed AM, Elmaidomy AH, Al-Sanea MM, Albogami S, Albqmi M, Alowaiesh BF, Mostafa EM, Musa A, Youssif KA, Refaat H, Othman EM, Dandekar T, Alaaeldin E, Ghoneim MM, Abdelmohsen UR. An In Vitro and In Silico Study of the Enhanced Antiproliferative and Pro-Oxidant Potential of Olea europaea L. cv. Arbosana Leaf Extract via Elastic Nanovesicles (Spanlastics). Antioxidants (Basel) 2021; 10:antiox10121860. [PMID: 34942963 PMCID: PMC8698813 DOI: 10.3390/antiox10121860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 12/27/2022] Open
Abstract
The olive tree is a venerable Mediterranean plant and often used in traditional medicine. The main aim of the present study was to evaluate the effect of Olea europaea L. cv. Arbosana leaf extract (OLE) and its encapsulation within a spanlastic dosage form on the improvement of its pro-oxidant and antiproliferative activity against HepG-2, MCF-7, and Caco-2 human cancer cell lines. The LC-HRESIMS-assisted metabolomic profile of OLE putatively annotated 20 major metabolites and showed considerable in vitro antiproliferative activity against HepG-2, MCF-7, and Caco-2 cell lines with IC50 values of 9.2 ± 0.8, 7.1 ± 0.9, and 6.5 ± 0.7 µg/mL, respectively. The encapsulation of OLE within a (spanlastic) nanocarrier system, using a spraying method and Span 40 and Tween 80 (4:1 molar ratio), was successfully carried out (size 41 ± 2.4 nm, zeta potential 13.6 ± 2.5, and EE 61.43 ± 2.03%). OLE showed enhanced thermal stability, and an improved in vitro antiproliferative effect against HepG-2, MCF-7, and Caco-2 (IC50 3.6 ± 0.2, 2.3 ± 0.1, and 1.8 ± 0.1 µg/mL, respectively) in comparison to the unprocessed extract. Both preparations were found to exhibit pro-oxidant potential inside the cancer cells, through the potential inhibitory activity of OLE against glutathione reductase and superoxide dismutase (IC50 1.18 ± 0.12 and 2.33 ± 0.19 µg/mL, respectively). These inhibitory activities were proposed via a comprehensive in silico study to be linked to the presence of certain compounds in OLE. Consequently, we assume that formulating such a herbal extract within a suitable nanocarrier would be a promising improvement of its therapeutic potential.
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Affiliation(s)
- Taghreed S. Alnusaire
- Biology Department, College of Science, Jouf University, Sakaka 72341, Saudi Arabia; (T.S.A.); (B.F.A.)
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt;
| | - Abeer H. Elmaidomy
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt;
| | - Mohammad M. Al-Sanea
- Pharmaceutical Chemistry Department, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
| | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Mha Albqmi
- Chemistry Department, College of Science and Arts, Jouf University, P.O. Box 756 Alqurayyat, Saudi Arabia;
| | - Bassam F. Alowaiesh
- Biology Department, College of Science, Jouf University, Sakaka 72341, Saudi Arabia; (T.S.A.); (B.F.A.)
| | - Ehab M. Mostafa
- Pharmacognosy Department, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo 11371, Egypt
| | - Arafa Musa
- Pharmacognosy Department, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo 11371, Egypt
- Correspondence: (A.M.); (U.R.A.)
| | - Khayrya A. Youssif
- Department of Pharmacognosy, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 11865, Egypt;
| | - Hesham Refaat
- Department of Pharmaceutics, Faculty of Pharmacy, Deraya University, Minia 61111, Egypt; (H.R.); (E.A.)
| | - Eman M. Othman
- Department of Biochemistry, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt;
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany;
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany;
| | - Eman Alaaeldin
- Department of Pharmaceutics, Faculty of Pharmacy, Deraya University, Minia 61111, Egypt; (H.R.); (E.A.)
- Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, Al Maarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia 61111, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
- Correspondence: (A.M.); (U.R.A.)
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17
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Debnath S, Bhaumik S, Sen D, Debnath B. Phytochemicals of Zingiberaceae family exhibit potentiality against SARS-CoV-2 main protease identified by a rational computer-aided drug design. Nat Prod Res 2021; 36:4563-4568. [PMID: 34694165 DOI: 10.1080/14786419.2021.1994563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Coronavirus disease 2019 (COVID-19) has created huge social, economic and human health crises globally. Discovery of specific drugs has become a new challenge to the researcher. Structure-based virtual-screening of our in-house databank containing1102 phytochemicals of Zingiberaceae family was performed with main protease(Mpro), a crucial enzyme of SARS-CoV-2. Rigorous docking and ADME study of top-scored twenty hits resulted from VS was performed. Then 100 ns molecular dynamics followed by MMPBSA binding free energy(ΔGbind) calculation of A280 and KZ133 was also performed. These two hits showed good interactions with crucial amino acid residues of Mpro HIS-41 and CYS-145, excellent ADME properties, fair ΔGbind values (> ‒188.03 kj/mol), and average protein-ligand complex RMSD < apo-protein RMSD. Therefore, the seed extracts of Alpinia blepharocalyx and rhizome extracts Kaempferia angustifolia containing A280 and KZ133, respectively, may be useful against COVID-19 after the proper biological screening. These two novel scaffolds could be exploited as potent SARS-CoV-2-Mpro inhibitors.
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Affiliation(s)
- Sudhan Debnath
- Department of Chemistry, Netaji Subhash Mahavidyalaya, Udaipur, Tripura, India
| | - Samhita Bhaumik
- Department of Chemistry, Women's College, Agartala, Tripura, India
| | - Debanjan Sen
- BCDA College of Pharmacy & Technology, Kolkata, West Bengal, India
| | - Bimal Debnath
- Department of Forestry and Biodiversity, Tripura University, Suryamaninagar, Tripura, India
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18
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Kushwaha PP, Singh AK, Bansal T, Yadav A, Prajapati KS, Shuaib M, Kumar S. Identification of Natural Inhibitors Against SARS-CoV-2 Drugable Targets Using Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Approach. Front Cell Infect Microbiol 2021; 11:730288. [PMID: 34458164 PMCID: PMC8387699 DOI: 10.3389/fcimb.2021.730288] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 02/05/2023] Open
Abstract
The present study explores the SARS-CoV-2 drugable target inhibition efficacy of phytochemicals from Indian medicinal plants using molecular docking, molecular dynamics (MD) simulation, and MM-PBSA analysis. A total of 130 phytochemicals were screened against SARS-CoV-2 Spike (S)-protein, RNA-dependent RNA polymerase (RdRp), and Main protease (Mpro). Result of molecular docking showed that Isoquercetin potentially binds with the active site/protein binding site of the Spike, RdRP, and Mpro targets with a docking score of -8.22, -6.86, and -9.73 kcal/mole, respectively. Further, MS 3, 7-Hydroxyaloin B, 10-Hydroxyaloin A, showed -9.57, -7.07, -8.57 kcal/mole docking score against Spike, RdRP, and Mpro targets respectively. The MD simulation was performed to study the favorable confirmation and energetically stable complex formation ability of Isoquercetin and 10-Hydroxyaloin A phytochemicals in Mpro-unbound/ligand bound/standard inhibitor bound system. The parameters such as RMSD, RMSF, Rg, SASA, Hydrogen-bond formation, energy landscape, principal component analysis showed that the lead phytochemicals form stable and energetically stabilized complex with the target protein. Further, MM-PBSA analysis was performed to compare the Gibbs free energy of the Mpro-ligand bound and standard inhibitor bound complexes. The analysis revealed that the His-41, Cys145, Met49, and Leu27 amino acid residues were majorly responsible for the lower free energy of the complex. Drug likeness and physiochemical properties of the test compounds showed satisfactory results. Taken together, the study concludes that that the Isoquercetin and 10-Hydroxyaloin A phytochemical possess significant efficacy to bind SARS-Cov-2 Mpro active site. The study necessitates further in vitro and in vivo experimental validation of these lead phytochemicals to assess their anti-SARS-CoV-2 potential.
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Affiliation(s)
- Prem Prakash Kushwaha
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Tanya Bansal
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Akansha Yadav
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
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19
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Nalimu F, Oloro J, Kahwa I, Ogwang PE. Review on the phytochemistry and toxicological profiles of Aloe vera and Aloe ferox. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:145. [PMID: 34307697 PMCID: PMC8294304 DOI: 10.1186/s43094-021-00296-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/05/2021] [Indexed: 12/11/2022] Open
Abstract
Background Aloe vera and Aloe ferox have over the years been among the most sought-after Aloe species in the treatment of ailments worldwide. This review provides categorized literature on the phytochemical and scientifically proven toxicological profiles of A. vera and A. ferox to facilitate their exploitation in therapy. Main body of the abstract Original full-text research articles were searched in PubMed, ScienceDirect, Research gate, Google Scholar, and Wiley Online Library using specific phrases. Phenolic acids, flavonoids, tannins, and anthraquinones were the main phytochemical classes present in all the two Aloe species. Most of the phytochemical investigations and toxicity studies have been done on the leaves. Aloe vera and Aloe ferox contain unique phytoconstituents including anthraquinones, flavonoids, tannins, sterols, alkaloids, and volatile oils. Aloe vera hydroalcoholic leaf extract showed a toxic effect on Kabir chicks at the highest doses. The methanolic, aqueous, and supercritical carbon dioxide extracts of A. vera leaf gel were associated with no toxic effects. The aqueous leaf extract of A. ferox is well tolerated for short-term management of ailments but long-term administration may be associated with organ toxicity. Long-term administration of the preparations from A. vera leaves and roots was associated with toxic effects. Short conclusion This review provides beneficial information about the phytochemistry and toxicity of A. vera and A. ferox and their potential in the treatment of COVID-19 which up to date has no definite cure. Clinical trials need to be carried out to clearly understand the toxic effects of these species.
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Affiliation(s)
- Florence Nalimu
- Pharm-Bio Technology and Traditional Medicine Centre of Excellence, Mbarara University of Science and Technology, Mbarara, Uganda.,Department of Pharmaceutical Sciences, Faculty of Medicine, Mbarara University of Science and Technology, P.O. Box 1410, Mbarara, Uganda
| | - Joseph Oloro
- Pharm-Bio Technology and Traditional Medicine Centre of Excellence, Mbarara University of Science and Technology, Mbarara, Uganda.,Department of Pharmacology and Therapeutics, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ivan Kahwa
- Pharm-Bio Technology and Traditional Medicine Centre of Excellence, Mbarara University of Science and Technology, Mbarara, Uganda.,Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Patrick Engeu Ogwang
- Pharm-Bio Technology and Traditional Medicine Centre of Excellence, Mbarara University of Science and Technology, Mbarara, Uganda.,Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
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Allam AE, Amen Y, Ashour A, Assaf HK, Hassan HA, Abdel-Rahman IM, Sayed AM, Shimizu K. In silico study of natural compounds from sesame against COVID-19 by targeting M pro, PL pro and RdRp. RSC Adv 2021; 11:22398-22408. [PMID: 35480825 PMCID: PMC9034212 DOI: 10.1039/d1ra03937g] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 01/18/2023] Open
Abstract
Natural products and traditional medicine products with known safety profiles are a promising source for the discovery of new drug leads. Natural products as sesame were reported to exhibit potential to protect from COVID-19 disease. In our study, the total methanolic extract of Sesamum indicum L. seeds (sesame) were led to isolation of seven known compounds, five lignan; sesamin 1, sesamolin 2, pinoresinol 3, hydroxymatairesinol 6, spicatolignan 7, together with two simple phenolic compounds; ferulic acid 4 and vanillic acid 5. All isolated compounds were evaluated in silico against three important SARS-CoV-2 protein targets; main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp) which possessed crucial role in replication and proliferation of the virus inside the human cell. The results revealed that compound 6 has the high affinity against the three main proteins, specially towards the SARS-CoV-2 Mpro that exceeded the currently used SARS-CoV-2 Mpro inhibitor darunavir as well as, exhibiting a similar binding energy at SARS CoV-2 PLpro when compared with the co-crystallized ligand. This activity continued to include the RdRp as it displayed a comparable docking score with remdesivir. Inferiorly, compounds 1 and 2 showed also similar triple inhibitory effect against the three main proteins while compound 7 exhibited a dual inhibitory effect against SARS CoV-2 PLPro and RdRp. Further molecular dynamic simulation experiments were performed to validate these docking experiments and to calculate their binding free energies (ΔGs). Compounds 1, 2, 3, 6, and 7 showed comparable binding stability inside the active site of each enzyme with ΔG values ranged from -4.9 to -8.8 kcal mol-1. All the compounds were investigated for their ADME and drug likeness properties, which showed acceptable ADME properties and obeying Lipinski's rule of five parameters. It can be concluded that the isolated compounds from sesame lignans could be an alternative source for the development of new natural leads against COVID-19.
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Affiliation(s)
- Ahmed E Allam
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University Assiut 71524 Egypt
| | - Yhiya Amen
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Hamdy K Assaf
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University Assiut 71524 Egypt
| | - Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone New Minia City 61111 Egypt
| | - Islam M Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University New-Minia 61111 Egypt
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University Beni-Suef 62513 Egypt
| | - Kuniyoshi Shimizu
- Department of Agro-Environmental Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka Japan 819-0395
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21
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Elmi A, Mohamed Abdoul-Latif F, Spina R, Dupire F, Philippot S, Marie-France C, Jacobs H, Laurain-Mattar D. Aloe djiboutiensis: Antioxidant Activity, Molecular Networking-Based Approach and In Vivo Toxicity of This Endemic Species in Djibouti. Molecules 2021; 26:3046. [PMID: 34065292 PMCID: PMC8161010 DOI: 10.3390/molecules26103046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
For the first time, the study of the antioxidant activity, the characterization of the phytoconstituants, and the evaluation of in vitro and in vivo toxicity of A. djiboutiensis leave and latex are performed. The antioxidant activity of both latex (ADL) and the methanolic extract of leaves (ADM) is determined using 1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azino-bis 3-ethylbenzothiazoline-6-sulphonic acid (ABTS) scavenging radical methods and ferric reducing/antioxidant power (FRAP) assay. The phytochemical study of latex is done using Liquid Chromatography-Mass Spectrometry (LC-MS/MS) and a molecular networking-based approach. The evaluation of in vivo toxicity is performed on mice by oral gavage with a suspension of ADL. Our results show that weak antioxidant activity of ADL and ADM in opposition to their high polyphenol, 83.01 mg and 46.4 mg expressed in gallic acid equivalent (GAE)/g of dry weight (DW), respectively, and flavonoid contents 13.12 mg and 4.25 mg expressed in quercetin equivalent (QE)/g dry weight (DW), respectively. Using the Global Natural Products Social Molecular Networking (GNPS) website, nine (9) anthraquinones derivatives, ten (10) chromones derivatives, two (2) flavonols/ chromones isomers are annotated in the molecular network. The treated mice do not display abnormalities in their general physical appearance and biochemistry parameters, compared to the controls. Only glucose and calcium levels are slightly higher in male treated mice compared to the vehicles.
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Affiliation(s)
- Abdirahman Elmi
- Université de Lorraine, CNRS, L2CM, 54000 Nancy, France; (A.E.); (R.S.); (F.D.); (S.P.)
- Centre d’Etudes et de Recherche de Djibouti, Medicinal Research Institute, IRM-CERD, Route de l’Aéroport, Haramous B.P. 486, Djibouti City, Djibouti;
| | - Fatouma Mohamed Abdoul-Latif
- Centre d’Etudes et de Recherche de Djibouti, Medicinal Research Institute, IRM-CERD, Route de l’Aéroport, Haramous B.P. 486, Djibouti City, Djibouti;
| | - Rosella Spina
- Université de Lorraine, CNRS, L2CM, 54000 Nancy, France; (A.E.); (R.S.); (F.D.); (S.P.)
| | - François Dupire
- Université de Lorraine, CNRS, L2CM, 54000 Nancy, France; (A.E.); (R.S.); (F.D.); (S.P.)
| | - Stéphanie Philippot
- Université de Lorraine, CNRS, L2CM, 54000 Nancy, France; (A.E.); (R.S.); (F.D.); (S.P.)
| | - Champy Marie-France
- PHENOMIN-ICS, Institut Clinique de la Souris, Université de Strasbourg, 67404 Illkirch, France; (C.M.-F.); (H.J.)
| | - Hugues Jacobs
- PHENOMIN-ICS, Institut Clinique de la Souris, Université de Strasbourg, 67404 Illkirch, France; (C.M.-F.); (H.J.)
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