A Perspective with in Silico Medicinal and Computational Methods to A New Schiff Base Molecule

Year 2023, Volume: 23 Issue: 4, 883 - 897, 31.08.2023

Songül Şahin , Necmi Dege

https://doi.org/10.35414/akufemubid.1237445

Cited By: 1

Abstract

In this study, the synthesis and characterization of a new Schiff base molecule, (E)-1-(5-nitro-2-(piperidin-1-yl) phenyl)-N-(4-phenoxyphenyl) methanimine, were aimed. In addition, the molecular surface area, crystalline structure, intermolecular forces, electronic and spectroscopic properties of the molecule were investigated. Docking studies were also performed on the active sites of the main protease (Mpro) of SARS-CoV-2, and the docking result was compared with the efficacy of the native ligand N3 inhibitor. The main findings for the title molecule can be summarized as follows: The space group is P-1 and it crystallizes in the triclinic system. The unit cell consists of two monomeric units (Z=2). There are strong electrophilic attack sites in the molecule, but nucleophilic centers have low efficiency. According to the FMO analysis, the title compound is a soft, kinetically and chemically unstable and highly reactive material. The value of the binding free energy calculated by docking experiments (-9.28 kcal mol-1) is lower than that of the native inhibitor (-7.11 kcal/mol) and thus can be considered as a potential inhibitor candidate for the main protease of SARS-CoV-2.

Keywords

MEP, HOMO-LUMO, SARS-CoV-2, Schiff base

Supporting Institution

None

Project Number

None

Thanks

None

Yeni Bir Schiff Bazı Molekülüne in Siliko Tıbbi ve Hesaplamalı Yöntemlerle Bir Bakış

Abstract

Bu çalışmada yeni bir Schiff bazı molekülünün, (E)-1-(5-nitro-2-(piperidin-1-yl) phenyl)-N-(4-phenoxyphenyl) methanimine, sentezi ve karakterizasyonu amaçlandı. Bunun yanı sıra bu molekülün moleküler yüzey alanı, kristal yapısı, moleküler arası kuvvetleri, elektronik ve spektroskopik özellikleri araştırıldı. Ayrıca SARS-CoV-2 ana proteazının (Mpro) aktif yerleri üzerinde kenetleme deneyleri gerçekleştirildi ve sonuç yerli ligand N3 inhibitörünün etkinliği ile kıyaslandı. Başlık molekülü için ana bulgular aşağıdaki gibi özetlenebilir: Uzay grubu P-1’dir ve triklinik sistemde kristallenir. Birim hücre iki monomerik birimden oluşur. Molekülde güçlü elektrofilik saldırı pozisyonları vardır ama nükleofilik merkezler düşük etkinliktedir. FMO analizine göre, başlık bileşiği yumuşak, kinetik ve kimyasal olarak kararsız ve oldukça reaktif bir malzemedir. Moleküler kenetleme deneylerine göre, bağlanma serbest enerjisinin hesaplanan değeri (-9.28 kcal/mol) yerli inhibitörün değerinden (-7.11 kcal/mol) daha düşüktür ve bu yüzden başlık bileşiği SARS-CoV-2 ana proteazı için potansiyel bir inhibitör adayı olarak düşünülebilir.

Keywords

MEP, HOMO-LUMO, SARS-CoV-2, Schiff bazı

Project Number

None

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