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Combinatorial, Computational and High Throughput Screening for Bioactive/Lead Finding from Nature/Synthesis

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Natural Products Chemistry".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 3971

Special Issue Editor


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Guest Editor
Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Campus Nueva Granada, Cajicá 250247, Colombia
Interests: natural product chemistry (isolation and structure elucidation); secondary/specialized metabolism; metabolic profiling; molecular modelling; docking and dynamics; bioorganic and medicinal chemistry; anti-parasitic, anti-cancer; anti-fungal; anti-inflammatory bioactive compounds
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Special Issue Information

Dear Colleagues,

High throughput screening has been considered since last century as a meaningful strategy for the discovery of bioactives from different sources and to enhance the finding of leads that become clinical candidates as effective therapies in different problems/disorders/diseases. In this sense, combinatorial chemistry was firstly employed in those purposes, due to their remarkable influence on the expansion of the available chemical space (very interrelated to the widening of biological target space) through generation of a large sets of structurally-related substances from different synthetic procedures. Computer-aided design and in-silico protocols/approaches have been also considered as a high throughput screening and they were rapidly used to improve, filtrate and/or depurate the lead/hit finding with high efficieny/efficacy. In contrast, the chemical space had been modestly assisted by compounds from natural sources (e.g., plants, animals, microorganisms, among others) due to the low throughput of traditional/conventional practices. However, this fact has been currently improving as a result of the several recent advances in analytical methods/techniques and the technological development and innovation of different analytical instruments (often hyphenated) for naturally-occurring bioactives identification. Thus, the consequently evolution of innovative combinatorial chemistry, bio and chemoinformatics, chemometrics (e.g., metabolomics and related approaches), the efforts to improve the quality of screening methods to increase throughput, the developing of in-vitro bioassays that truly emulate biological processes and the target identification in the omics age, has led to the regularly discovery of more leads and more targets. Based on these facts, this Special Issue aims to collect some of the latest advances, techniques, approaches, methods, outcome and reviews on topics related to finding/identification of bioactives/hits/leads from natural sources and/or through synthetic procedures using combinatorial, computational, chemometrics and/or other high throughput approaches.

Prof. Dr. Ericsson Coy-Barrera
Guest Editor

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Keywords

  • Bioactives, leads, hits
  • High throughput screening
  • Combinatorial approaches
  • Computational, bio and chemoinformatics approaches
  • Chemometrics and metabolomics
  • Hyphenated techniques
  • In-vitro assays
  • Targets and screening approaches

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Published Papers (1 paper)

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Research

16 pages, 10061 KiB  
Article
In Silico Molecular Studies of Antiophidic Properties of the Amazonian Tree Cordia nodosa Lam.
by Carmen X. Luzuriaga-Quichimbo, José Blanco-Salas, Luz María Muñoz-Centeno, Rafael Peláez, Carlos E. Cerón-Martínez and Trinidad Ruiz-Téllez
Molecules 2019, 24(22), 4160; https://doi.org/10.3390/molecules24224160 - 16 Nov 2019
Cited by 2 | Viewed by 3455
Abstract
We carried out surveys on the use of Cordia nodosa Lam. in the jungles of Bobonaza (Ecuador). We documented this knowledge to prevent its loss under the Framework of the Convention on Biological Diversity and the Nagoya Protocol. We conducted bibliographic research and [...] Read more.
We carried out surveys on the use of Cordia nodosa Lam. in the jungles of Bobonaza (Ecuador). We documented this knowledge to prevent its loss under the Framework of the Convention on Biological Diversity and the Nagoya Protocol. We conducted bibliographic research and identified quercetrin as a significant bioactive molecule. We studied its in silico biological activity. The selected methodology was virtual docking experiments with the proteins responsible for the venomous action of snakes. The molecular structures of quercetrin and 21 selected toxins underwent corresponding tests with SwissDock and Chimera software. The results point to support its antiophidic use. They show reasonable geometries and a binding free energy of −7 to −10.03 kcal/mol. The most favorable values were obtained for the venom of the Asian snake Naja atra (5Z2G, −10.03 kcal/mol). Good results were also obtained from the venom of the Latin American Bothrops pirajai (3CYL, −9.71 kcal/mol) and that of Ecuadorian Bothrops asper snakes (5TFV, −9.47 kcal/mol) and Bothrops atrox (5TS5, −9.49 kcal/mol). In the 5Z2G and 5TS5 L-amino acid oxidases, quercetrin binds in a pocket adjacent to the FAD cofactor, while in the myotoxic homologues of PLA2, 3CYL and 5TFV, it joins in the hydrophobic channel formed when oligomerizing, in the first one similar to α-tocopherol. This study presents a case demonstration of the potential of bioinformatic tools in the validation process of ethnobotanical phytopharmaceuticals and how in silico methods are becoming increasingly useful for sustainable drug discovery. Full article
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