Identification of Novel SARS-CoV-2 Inhibitors: A Structure-Based Virtual Screening Approach

Aissouq, Abdellah El; Chedadi, Oussama; Bouachrine, Mohammed; Ouammou, Abdelkrim

doi:10.1155/2021/1901484

Cited by 26 publications

(14 citation statements)

References 24 publications

(24 reference statements)

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“…Moreover, the link between the medication concentration in the human body and the degree of drug removal is defined as clearance. 81,82 Basically, a lower clearance index value indicates greater drug persistence in the body. 83 The results in Table 9 demonstrate that all studied molecules present low clearance index values, indicating the high persistence of these molecules in the body.…”

Section: Adme and Toxicity Resultsmentioning

confidence: 99%

Computational study of quinoline-based thiadiazole compounds as potential antileishmanial inhibitors

et al. 2022

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Section: Adme and Toxicity Resultsmentioning

confidence: 99%

Computational study of quinoline-based thiadiazole compounds as potential antileishmanial inhibitors

et al. 2022

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“…Ile 189, on the other hand, has a pi-sigma-type interaction, while amino acids Glu 188, Leu 144, Ala 141, Thr 138, Val 154, Gln 157, Thr 40, and Ile 285 have van der Waals-type interaction. Thus, binding orientations with ligands structurally related to binding sites can present a variety of interactions, including hydrophobic interactions (pi-sigma, alkyl, and pi-alkyl) as well as van der Waals-type interactions, and interactions of this type are characterized by being weaker compared to the other bonds represented here (Kleshchonok and Tkatchenko, 2018;Ranjbar et al, 2020;El Aissouq et al, 2021).…”

Section: Discussion Tunnel Analysismentioning

confidence: 99%

In Silico Evaluation of Enzymatic Tunnels in the Biotransformation of α-Tocopherol Esters

Azevedo

Silva

Lima

et al. 2022

Front. Bioeng. Biotechnol.

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Motivation: α-Tocopherol is a molecule obtained primarily from plant sources that are important for the pharmaceutical and cosmetics industry. However, this component has some limitations such as sensitivity to oxygen, presence of light, and high temperatures. For this molecule to become more widely used, it is important to carry out a structural modification so that there is better stability and thus it can carry out its activities. To carry out this structural modification, some modifications are carried out, including the application of biotransformation using enzymes as biocatalysts. Thus, the application of a computational tool that helps in understanding the transport mechanisms of molecules in the tunnels present in the enzymatic structures is of fundamental importance because it promotes a computational screening facilitating bench applications.Objective: The aim of this work was to perform a computational analysis of the biotransformation of α-tocopherol into tocopherol esters, observing the tunnels present in the enzymatic structures as well as the energies which correspond to the transport of molecules.Method: To carry out this work, 9 lipases from different organisms were selected; their structures were analyzed by identifying the tunnels (quantity, conformation, and possibility of transport) and later the calculations of substrate transport for the biotransformation reaction in the identified tunnels were carried out. Additionally, the transport of the product obtained in the reaction through the tunnels was also carried out.Results: In this work, the quantity of existing tunnels in the morphological conformational characteristics in the lipases was verified. Thus, the enzymes with fewer tunnels were RML (3 tunnels), LBC and RNL (4 tunnels), PBLL (5 tunnels), CALB (6 tunnels), HLG (7 tunnels), and LCR and LTL (8 tunnels) and followed by the enzyme LPP with the largest number of tunnels (39 tunnels). However, the enzyme that was most likely to transport substrates in terms of α-tocopherol biotransformation (in relation to the Emax and Ea energies of ligands and products) was CALB, as it obtains conformational and transport characteristics of molecules with a particularity. The most conditions of transport analysis were α-tocopherol tunnel 3 (Emax: −4.6 kcal/mol; Ea: 1.1 kcal/mol), vinyl acetate tunnel 1 (Emax: −2.4 kcal/mol; Ea: 0.1 kcal/mol), and tocopherol acetate tunnel 2 (Emax: −3.7 kcal/mol; Ea: 2 kcal/mol).

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“…Năng lượng liên kết được dự đoán thấp nhất là của Pyranoamentoflavone với mức năng lượng -11,6 kcal/mol. Đây là mức năng lượng rất thấp, thấp hơn năng lượng liên kết của một số nghiên cứu trước đó với đối tượng hợp chất từ biển [18] (−9,87), từ các thuốc được chấp thuận bởi FDA [19] (−8,7).…”

Section: Sàng Lọc Các Hợp Chất Tự Nhiên Có Khả Năng Gắn Kết Với Prote...unclassified

Xác Định Chất Ức Chế Tiềm Năng Mpro Của Sars-Cov-2 Từ Cơ Sở Dữ Liệu Các Hợp Chất Có Nguồn Gốc Thảo Mộc Việt Nam Bằng Cách Sàng Lọc Ảo

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2021

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Nghiên cứu nhằm sàng lọc các hợp chất có nguồn gốc từ thảo mộc có khả năng kháng protein SARS-CoV-2 Mpro - là protein có vai trò quan trọng trong việc nhân lên của virus SARS-CoV-2. Thư viện gồm 320 hợp chất có nguồn gốc từ 121 loài thảo dược được sàng lọc thông qua năng lượng liên kết, thuộc tính dược độc học và tương tác phân tử bằng các công cụ tin sinh học. Ba hợp chất tiềm năng nhất là Pyranoamentoflavone, Celastrol, Pomolic acid thể hiện ái lực cao với Mpro, đáp ứng năm quy tắc Lipinski và tương tác phân tử tốt với protein mục tiêu. Các phát hiện cho thấy rằng, các hợp chất được xác định có thể đóng vai trò là các chất dẫn tiềm năng hoạt động như chất ức chế COVID-19 Mpro, đáng được đánh giá và phát triển thêm.

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Identification of Novel SARS-CoV-2 Inhibitors: A Structure-Based Virtual Screening Approach

Cited by 26 publications

References 24 publications

Computational study of quinoline-based thiadiazole compounds as potential antileishmanial inhibitors

Computational study of quinoline-based thiadiazole compounds as potential antileishmanial inhibitors

In Silico Evaluation of Enzymatic Tunnels in the Biotransformation of α-Tocopherol Esters

Xác Định Chất Ức Chế Tiềm Năng Mpro Của Sars-Cov-2 Từ Cơ Sở Dữ Liệu Các Hợp Chất Có Nguồn Gốc Thảo Mộc Việt Nam Bằng Cách Sàng Lọc Ảo

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