Binding interaction of potent HIV-1 NNRTIs, amino-oxy-diarylquinoline with the transport protein using spectroscopic and molecular docking

Patnin, Suwicha; Makarasen, Arthit; Kuno, Mayuso; Deeyohe, Sirinya; Techasakul, Supanna; Chaivisuthangkura, Apinya

doi:10.1016/j.saa.2020.118159

Cited by 11 publications

(8 citation statements)

References 38 publications

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“…The J value was 1.4305 × 10 –16 cm 3 L mol –1 , R 0 was 1.411 nm, r was 2.07 nm, and E is 0.089, respectively. The binding distance of DG–TY is less than 7 nm, and 0.5 R 0 < r < 1.5 R 0 54 . In conclusion, the fluorescence quenching effect of DG on TY was related to the nonradiative energy transfer.…”

Section: Resultsmentioning

confidence: 80%

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Spectroscopic studies and molecular docking on the interaction of delphinidin‐3‐O‐galactoside with tyrosinase

Chen

Shi

Liu

et al. 2021

Biotech and App Biochem

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The inhibitory effects of delphinidin-3-O-galactoside (DG) on the activities of tyrosinase (EC 1.14.18.1) (TY) from the edible Agaricus bisporus mushroom were investigated by enzyme kinetics, multispectroscopic methods, and molecular docking. As a result, DG showed strong inhibition on TY with the IC 50 of 34.14 × 10 -6 mol L -1 . The inhibition mode of DG against TY was mixed type with α values of 5.09. The binding constant K a and related thermodynamic parameters at the three different temperatures showed that the fluorescence quenching of TY by DG was static quenching. Synchronous fluorescence, three-dimensional fluorescence, ultraviolet-visible spectroscopy, and circular dichroism spectroscopies confirmed that the conformation or microenvironment of the TY protein were changed after binding with DG. Molecular docking revealed that DG had strong binding affinity to TY through hydrogen bonding and van der Waals force, and the results were consistent with the fluorescence data. Our findings suggested that DG may be potential TY inhibitor.

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Section: Resultsmentioning

confidence: 80%

“…The binding distance of DG-TY is less than 7 nm, and 0.5R 0 < r < 1.5R 0 . 54 In conclusion, the fluorescence quenching effect of DG on TY was related to the nonradiative energy transfer.…”

Section: Energy Transfer Between Dg and Tymentioning

confidence: 86%

Spectroscopic studies and molecular docking on the interaction of delphinidin‐3‐O‐galactoside with tyrosinase

Chen

Shi

Liu

et al. 2021

Biotech and App Biochem

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“…The excitation wavelength was fixed at 480 nm. The titration data were utilized to evaluate the value of the Stern–Volmer quenching constant ( K SV ) with the help of the following Stern–Volmer equation ,, where F 0 and F refer to the corrected fluorescence intensities of the fluorophore in the absence and presence of quencher molecules (here, rutin and the rutin–Fe(II) complex), [ Q ] is the concentration of the quencher, K SV represents the Stern–Volmer quenching constant, k q is the biomolecular quenching constant, and τ 0 is the average fluorophore lifetime in the absence of the quencher. According to the available literature, the average lifetime (⟨τ 0 ⟩) of BSA is about 5 ns. , …”

Section: Materials and Methodsmentioning

confidence: 99%

Effect of a Metal Ion in Modulating the Binding Interaction of a Dietary Flavonoid with Bovine Serum Albumin and DNA: A Spectroscopic and Theoretical Approach

Sengupta

Pal

Roy

et al. 2022

ACS Food Sci. Technol.

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Plant-derived flavonoids are an excellent option as a potential substitute to synthetic products in food industries, and flavonoid−metal complexes exhibit better functional properties than free flavonoids. Here, an iron(II) complex of rutin, a dietary flavonoid, has been synthesized and characterized. A comparative assessment of the interaction of rutin and its iron(II) complex with the transport protein [bovine serum albumin (BSA)] and deoxyribonucleic acid (DNA) has been performed. The interaction process has been characterized using multispectroscopic techniques and has been further supported by theoretical studies. We have evidenced the alteration in the interacting mode of rutin with BSA upon complexation with Fe(II). Also, rutin interacts with DNA via minor groove binding, while the complex interacts with DNA through a mixed mode involving both groove binding and intercalative binding. Interestingly, the antioxidant activity of the metal complex has been found to be enhanced, and it also provides better protection against UV radiation-induced cell damage than rutin alone.

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“…To analyze the enzyme–small molecule interaction, ONIOM supports accurate molecular docking and has been widely used to study antiviral activity [ 23 , 24 ]. The two-layered ONIOM calculations were managed using the Gaussian 16 program and optimized by DFT at the B3LYP/6-31G(d,p) level and the semi-empirical PM6 method.…”

Section: Methodsmentioning

confidence: 99%

“…The study found that those compounds might interact and bind in a similar area to NNRTIs within the pocket of HIV-1 RT. Moreover, 2-phenylamino-4-phenoxy-quinoline derivatives have shown high cytotoxic activity against some human cancer cells over normal cells and excellent binding interactions with transported proteins [ 24 ]. Because phenylamino-phenoxy-quinoline derivatives are nitrogen-containing compounds with nitrile side chains, similar to current available drugs for SARS-CoV-2, they are considered to be candidate antiviral drugs for SARS-CoV-2 treatment.…”

Section: Introductionmentioning

confidence: 99%

Computational Screening of Phenylamino-Phenoxy-Quinoline Derivatives against the Main Protease of SARS-CoV-2 Using Molecular Docking and the ONIOM Method

et al. 2022

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In the search for new anti-HIV-1 agents, two forms of phenylamino-phenoxy-quinoline derivatives have been synthesized, namely, 2-phenylamino-4-phenoxy-quinoline and 6-phenylamino-4-phenoxy-quinoline. In this study, the binding interactions of phenylamino-phenoxy-quinoline derivatives and six commercially available drugs (hydroxychloroquine, ritonavir, remdesivir, S-217622, N3, and PF-07321332) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) were investigated using molecular docking and the ONIOM method. The molecular docking showed the hydrogen bonding and hydrophobic interactions of all the compounds in the pocket of SARS-CoV-2 main protease (Mpro), which plays an important role for the division and proliferation of the virus into the cell. The binding free energy values between the ligands and Mpro ranged from −7.06 to −10.61 kcal/mol. The molecular docking and ONIOM results suggested that 4-(2′,6′-dimethyl-4′-cyanophenoxy)-2-(4″-cyanophenyl)-aminoquinoline and 4-(4′-cyanophenoxy)-2-(4″-cyanophenyl)-aminoquinoline have low binding energy values and appropriate molecular properties; moreover, both compounds could bind to Mpro via hydrogen bonding and Pi-Pi stacking interactions with amino acid residues, namely, HIS41, GLU166, and GLN192. These amino acids are related to the proteolytic cleavage process of the catalytic triad mechanisms. Therefore, this study provides important information for further studies on synthetic quinoline derivatives as antiviral candidates in the treatment of SARS-CoV-2.

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Binding interaction of potent HIV-1 NNRTIs, amino-oxy-diarylquinoline with the transport protein using spectroscopic and molecular docking

Cited by 11 publications

References 38 publications

Spectroscopic studies and molecular docking on the interaction of delphinidin‐3‐O‐galactoside with tyrosinase

Spectroscopic studies and molecular docking on the interaction of delphinidin‐3‐O‐galactoside with tyrosinase

Effect of a Metal Ion in Modulating the Binding Interaction of a Dietary Flavonoid with Bovine Serum Albumin and DNA: A Spectroscopic and Theoretical Approach

Computational Screening of Phenylamino-Phenoxy-Quinoline Derivatives against the Main Protease of SARS-CoV-2 Using Molecular Docking and the ONIOM Method

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