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

Songül Şahin; Necmi Dege

Makale detayları

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

Yazarlar:

Songül Şahin | Necmi Dege

Yayıncı:

Afyon Kocatepe University

Ana Başlıklar:

Fiziksel Kimya (Diğer)

Dergi:

Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi Vol.23 Issue 4, pp.883-897

Belge Tipi:

Makale

Yayın Tarihi:

8/2023

Belge Dili:

İngilizce

Document ID (Org No.):

2001294332

pISSN:

2149-3367

Anahtar kelimeler:

Özet:

 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 Z2. 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 kcalmol and thus can be considered as a potential inhibitor candidate for the main protease of SARS-CoV-2.

 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 Z2. 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 kcalmol and thus can be considered as a potential inhibitor candidate for the main protease of SARS-CoV-2.

 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 Z2. 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 kcalmol and thus can be considered as a potential inhibitor candidate for the main protease of SARS-CoV-2.

 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-1dir 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 kcalmol yerli inhibitörün değerinden -7.11 kcalmol daha düşüktür ve bu yüzden başlık bileşiği SARS-CoV-2 ana proteazı için potansiyel bir inhibitör adayı olarak düşünülebilir.

Makale detayları

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

Yazarlar:

Songül Şahin | Necmi Dege

Yayıncı:

Afyon Kocatepe University

Ana Başlıklar:

Fiziksel Kimya (Diğer)

Dergi:

Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi Vol.23 Issue 4, pp.883-897

Belge Tipi:

Makale

Yayın Tarihi:

8/2023

Belge Dili:

İngilizce

Document ID (Org No.):

2001294332

pISSN:

2149-3367

MEP

HOMO-LUMO

SARS-CoV-2

Schiff baseMEP

HOMO-LUMO

SARS-CoV-2

Schiff bazı

Sayı

Makale detayları

Yazarlar: Songül Şahin | Necmi Dege

Yayıncı: Afyon Kocatepe University

Ana Başlıklar: Fiziksel Kimya (Diğer)

Dergi: Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi Vol.23 Issue 4, pp.883-897

Belge Tipi: Makale

Yayın Tarihi: 8/2023

Belge Dili: İngilizce

Document ID (Org No.): 2001294332

pISSN: 2149-3367

Sayı

Yazarlar:

Songül Şahin | Necmi Dege

Yayıncı:

Afyon Kocatepe University

Ana Başlıklar:

Fiziksel Kimya (Diğer)

Dergi:

Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi Vol.23 Issue 4, pp.883-897

Belge Tipi:

Makale

Yayın Tarihi:

8/2023

Belge Dili:

İngilizce

Document ID (Org No.):

2001294332

pISSN:

2149-3367