Drug Discovery from Natural Products (In-Silico, In-Vitro and In-Vivo)

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 7317

Special Issue Editors


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Guest Editor
1. Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
2. Department of Natural products, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: natural products; cancer; inflammation; biological activities; molecular docking; ADMET
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Guest Editor
UCL School of Pharmacy, 29/39 Brunswick Square, London WC1N 1AX, UK
Interests: computer-aided molecular design; molecular dynamics; docking; in silico screening; structural chemistry; NMR spectroscopy; antimicrobial resistance; multidrug resistance; efflux pump inhibition; antimicrobial peptides; dendrimer design
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The use of In-silico technologies for drug discovery  began in the early 2000s with applications such as predicting ADMET, bacterial mutagenicity,hERG inhibition, molecular docking and in-depth docking simulations. The field has been continuously expanding ever since and the tasks at hand have become more complex and led to development of a wide range of different methods and applications.

Before any molecule enters for drug formulation in the pharmaceutical or clinical trials field, it is mandatory for each molecule to be evaluated not only for its efficacy but also for its safety zone. No wonder, that in-vivo and in-vitro methods provide a very clear image of every molecule’s result but the main hurdle in these two methods are the time consuming, repetation of experiments and economic burdens. To solve this myth, Today,  In-silico technology can be used in every phase of drug discovery and development and are now strategically integrated into the risk assessment process, These methods are  used as a complement to established in-vitro and in-vivo methods, including profiling large libraries of the early stages of drug discovery, predicting off-target effects in the mid-discovery phase, assessing potential mutagenic impurities in development and degradants as part of life-cycle management. As a part of the process, it is necessary to get the robust profile of any molecule and confirm the results of  in-silico studies with in-vitro or in-vivo studies. Hence, research articles covering interesting applications, reviews that focus not only the capability of the medicinal substances In-silico but also have been examined in-vitro or in-vivo against different diseases serious pathogenic microbes will be published.

Sub-topics:

The sub-topics to be covered within the issue should include:

  1. Natural/ synthetic products with effective bioactivities including in-vitro, in-vivo and in-silico studies.
  2. Natural products derived biomolecules in clinical trails
  3. Computational exploration of a biomolecule using chemoinformatics

Dr. Syed Shams ul Hassan
Prof. Dr. Mire Zloh
Guest Editors

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Keywords

  • drug discovery
  • in silico
  • in vitro
  • in vivo
  • biomolecules
  • natural products
  • synthetic products
  • ADMET
  • computational toxicology

Published Papers (3 papers)

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Research

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12 pages, 1237 KiB  
Communication
Analysis and Identification of Bioactive Compounds of Cannabinoids in Silico for Inhibition of SARS-CoV-2 and SARS-CoV
by Chenxiao Chen, Hao Liang, Yanchun Deng, Xiushi Yang, Xiaoming Li and Chunsheng Hou
Biomolecules 2022, 12(12), 1729; https://doi.org/10.3390/biom12121729 - 22 Nov 2022
Cited by 2 | Viewed by 1337
Abstract
Despite the approval of multiple vaccinations in different countries, the majority of the world’s population remains unvaccinated due to discrepancies in vaccine distribution and limited production capacity. The SARS-CoV-2 RBD-ACE2 complex (receptor binding domain that binds to ACE2) could be a suitable target [...] Read more.
Despite the approval of multiple vaccinations in different countries, the majority of the world’s population remains unvaccinated due to discrepancies in vaccine distribution and limited production capacity. The SARS-CoV-2 RBD-ACE2 complex (receptor binding domain that binds to ACE2) could be a suitable target for the development of a vaccine or an inhibitor. Various natural products have been used against SARS-CoV-2. Here, we docked 42 active cannabinoids to the active site of the SARS-CoV-2 and SARS-CoV complex of RBD-ACE2. To ensure the flexibility and stability of the complex produced after docking, the top three ligand molecules with the best overall binding energies were further analyzed through molecular dynamic simulation (MDS). Then, we used the webserver Swissadme program and binding free energy to calculate and estimate the MMPBSA and ADME characteristics. Our results showed that luteolin, CBGVA, and CBNA were the top three molecules that interact with the SARS-CoV-2 RBD-ACE2 complex, while luteolin, stigmasterol, and CBNA had the strongest contact with that SARS-CoV. Our findings show that luteolin may be a potential inhibitor of infections caused by coronavirus-like pathogens such as COVID-19, although further in vivo and in vitro research is required. Full article
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10 pages, 1774 KiB  
Communication
Structure of New Ferroverdins Recruiting Unconventional Ferrous Iron Chelating Agents
by Loïc Martinet, Dominique Baiwir, Gabriel Mazzucchelli and Sébastien Rigali
Biomolecules 2022, 12(6), 752; https://doi.org/10.3390/biom12060752 - 26 May 2022
Cited by 1 | Viewed by 2528
Abstract
Ferroverdins are ferrous iron (Fe2+)-nitrosophenolato complexes produced by a few Streptomyces species as a response to iron overload. Previously, three ferroverdins were identified: ferroverdin A, in which three molecules of p-vinylphenyl-3-nitroso-4-hydroxybenzoate (p-vinylphenyl-3,4-NHBA) are recruited to bind Fe2+ [...] Read more.
Ferroverdins are ferrous iron (Fe2+)-nitrosophenolato complexes produced by a few Streptomyces species as a response to iron overload. Previously, three ferroverdins were identified: ferroverdin A, in which three molecules of p-vinylphenyl-3-nitroso-4-hydroxybenzoate (p-vinylphenyl-3,4-NHBA) are recruited to bind Fe2+, and Ferroverdin B and Ferroverdin C, in which one molecule of p-vinylphenyl-3,4-NHBA is substituted by hydroxy-p-vinylphenyl-3,4-NHBA, and by carboxy-p-vinylphenyl-3,4-NHBA, respectively. These molecules, especially ferroverdin B, are potent inhibitors of the human cholesteryl ester transfer protein (CETP) and therefore candidate hits for the development of drugs that increase the serum concentration of high-density lipoprotein cholesterol, thereby diminishing the risk of atherosclerotic cardiovascular disease. In this work, we used high-resolution mass spectrometry combined with tandem mass spectrometry to identify 43 novel ferroverdins from the cytosol of two Streptomyces lunaelactis species. For 13 of them (designated ferroverdins C2, C3, D, D2, D3, E, F, G, H, CD, DE, DF, and DG), we could elucidate their structure, and for the other 17 new ferroverdins, ambiguity remains for one of the three ligands. p-formylphenyl-3,4-NHBA, p-benzoic acid-3,4-NHBA, 3,4-NHBA, p-phenylpropionate-3,4-NHBA, and p-phenyacetate-3,4-NHBA were identified as new alternative chelators for Fe2+-binding, and two compounds (C3 and D3) are the first reported ferroverdins that do not recruit p-vinylphenyl-3,4-NHBA. Our work thus uncovered putative novel CETP inhibitors or ferroverdins with novel bioactivities. Full article
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Review

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20 pages, 1834 KiB  
Review
Phytochemical Profiling and Bio-Potentiality of Genus Scutellaria: Biomedical Approach
by Muddaser Shah, Sidra Mubin, Syed Shams ul Hassan, Priti Tagde, Obaid Ullah, Md. Habibur Rahman, Ahmed Al-Harrasi, Najeeb Ur Rehman and Waheed Murad
Biomolecules 2022, 12(7), 936; https://doi.org/10.3390/biom12070936 - 04 Jul 2022
Cited by 11 | Viewed by 2345
Abstract
Scutellaria (Lamiaceae) comprises over 360 species. Based on its morphological structure of calyx, also known as Skullcap, it is herbaceous by habit and cosmopolitan by habitat. The species of Scutellaria are widely used in local communities as a natural remedy. The genus contributed [...] Read more.
Scutellaria (Lamiaceae) comprises over 360 species. Based on its morphological structure of calyx, also known as Skullcap, it is herbaceous by habit and cosmopolitan by habitat. The species of Scutellaria are widely used in local communities as a natural remedy. The genus contributed over three hundred bioactive compounds mainly represented by flavonoids and phenols, chemical ingredients which serve as potential candidates for the therapy of various biological activities. Thus, the current review is an attempt to highlight the biological significance and its correlation to various isolated bioactive ingredients including flavonoids, terpenoids, phenols, alkaloids, and steroids. However, flavonoids were the dominant group observed. The findings of the Scutellaria reveal that due to its affluent basis of numerous chemical ingredients it has a diverse range of pharmacological potentials, such as antimicrobial, antioxidant, antifeedant, enzyme inhibition, anti-inflammatory, and analgesic significance. Currently, various bioactive ingredients have been investigated for various biological activities from the genus Scutellaria in vitro and in vivo. Furthermore, these data help us to highlight its biomedical application and to isolate the responsible compounds to produce innovative medications as an alternative to synthetic drugs. Full article
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