Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes

Liu, Kaifeng; Guo, Fangfang; Ma, Yingying; Yu, Xiangyu; Fu, Xueqi; Li, Wannan; Han, Weiwei

doi:10.3390/ijms241914471

Cited by 4 publications

(4 citation statements)

References 51 publications

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“…For trajectory examination, we conducted K-means clustering, utilizing the Cpptraj module within Amber16 [ 61 ]. The MM-PBSA method facilitated the computation of binding free energies, a crucial determinant in the evaluation of protein–protein affinities [ 62 , 63 , 64 ].…”

Section: Methodsmentioning

confidence: 99%

Design of Vif-Derived Peptide Inhibitors with Anti-HIV-1 Activity by Interrupting Vif-CBFβ Interaction

Gai,

Duan,

Wang

et al. 2024

Viruses

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One of the major functions of the accessory protein Vif of human immunodeficiency virus type 1 (HIV-1) is to induce the degradation of APOBEC3 (A3) family proteins by recruiting a Cullin5-ElonginB/C-CBFβ E3 ubiquitin ligase complex to facilitate viral replication. Therefore, the interactions between Vif and the E3 complex proteins are promising targets for the development of novel anti-HIV-1 drugs. Here, peptides are designed for the Vif-CBFβ interaction based on the sequences of Vif mutants with higher affinity for CBFβ screened by a yeast surface display platform. We identified two peptides, VMP-63 and VMP-108, that could reduce the infectivity of HIV-1 produced from A3G-positive cells with IC50 values of 49.4 μM and 55.1 μM, respectively. They protected intracellular A3G from Vif-mediated degradation in HEK293T cells, consequently increasing A3G encapsulation into the progeny virions. The peptides could rapidly enter cells after addition to HEK293T cells and competitively inhibit the binding of Vif to CBFβ. Homology modeling analysis demonstrated the binding advantages of VMP-63 and VMP-108 with CBFβ over their corresponding wild-type peptides. However, only VMP-108 effectively restricted long-term HIV-1 replication and protected A3 functions in non-permissive T lymphocytes. Our findings suggest that competitive Vif-derived peptides targeting the Vif-CBFβ interaction are promising for the development of novel therapeutic strategies for acquired immune deficiency syndrome.

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Section: Methodsmentioning

confidence: 99%

Design of Vif-Derived Peptide Inhibitors with Anti-HIV-1 Activity by Interrupting Vif-CBFβ Interaction

Gai,

Duan,

Wang

et al. 2024

Viruses

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“…Similar to our previous work [72], we employed the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method to investigate the binding affinity between kaempferol and PTP1B. The binding free energy (∆G bind ) is represented by the following formula:…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Mulberry Leaf Compounds and Gut Microbiota in Alzheimer’s Disease and Diabetes: A Study Using Network Pharmacology, Molecular Dynamics Simulation, and Cellular Assays

Bai,

Zhao,

Liu

et al. 2024

IJMS

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Recently, studies have reported a correlation that individuals with diabetes show an increased risk of developing Alzheimer’s disease (AD). Mulberry leaves, serving as both a traditional medicinal herb and a food source, exhibit significant hypoglycemic and antioxidative properties. The flavonoid compounds in mulberry leaf offer therapeutic effects for relieving diabetic symptoms and providing neuroprotection. However, the mechanisms of this effect have not been fully elucidated. This investigation aimed to investigate the combined effects of specific mulberry leaf flavonoids (kaempferol, quercetin, rhamnocitrin, tetramethoxyluteolin, and norartocarpetin) on both type 2 diabetes mellitus (T2DM) and AD. Additionally, the role of the gut microbiota in these two diseases’ treatment was studied. Using network pharmacology, we investigated the potential mechanisms of flavonoids in mulberry leaves, combined with gut microbiota, in combating AD and T2DM. In addition, we identified protein tyrosine phosphatase 1B (PTP1B) as a key target for kaempferol in these two diseases. Molecular docking and molecular dynamics simulations showed that kaempferol has the potential to inhibit PTP1B for indirect treatment of AD, which was proven by measuring the IC50 of kaempferol (279.23 μM). The cell experiment also confirmed the dose-dependent effect of kaempferol on the phosphorylation of total cellular protein in HepG2 cells. This research supports the concept of food–medicine homology and broadens the range of medical treatments for diabetes and AD, highlighting the prospect of integrating traditional herbal remedies with modern medical research.

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“…Changes in Rg and conformation post-binding altered the binding poses. The Solvent Accessible Surface Area (SASA) indicated that T1R2 combined with IGR and T1R3 with GGR had lower SASA, potentially indicating a tighter binding [26,27].…”

Section: Peptides Screening Based On Structurementioning

confidence: 99%

“…Changes in Rg and conformation postbinding altered the binding poses. The Solvent Accessible Surface Area (SASA) indicated that T1R2 combined with IGR and T1R3 with GGR had lower SASA, potentially indicating a tighter binding [26,27]. The MM-PBSA method provided a more accurate prediction of binding energy, as it is based on multiple structure calculations, accounting for dynamic changes during binding.…”

Section: Peptides Screening Based On Structurementioning

confidence: 99%

Integrating Computational and Experimental Methods to Identify Novel Sweet Peptides from Egg and Soy Proteins

Su,

Liu,

Cui

et al. 2024

IJMS

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Sweetness in food delivers a delightful sensory experience, underscoring the crucial role of sweeteners in the food industry. However, the widespread use of sweeteners has sparked health concerns. This underscores the importance of developing and screening natural, health-conscious sweeteners. Our study represents a groundbreaking venture into the discovery of such sweeteners derived from egg and soy proteins. Employing virtual hydrolysis as a novel technique, our research entailed a comprehensive screening process that evaluated biological activity, solubility, and toxicity of the derived compounds. We harnessed cutting-edge machine learning methodologies, specifically the latest graph neural network models, for predicting the sweetness of molecules. Subsequent refinements were made through molecular docking screenings and molecular dynamics simulations. This meticulous research approach culminated in the identification of three promising sweet peptides: DCY(Asp-Cys-Tyr), GGR(Gly-Gly-Arg), and IGR(Ile-Gly-Arg). Their binding affinity with T1R2/T1R3 was lower than −15 kcal/mol. Using an electronic tongue, we verified the taste profiles of these peptides, with IGR emerging as the most favorable in terms of taste with a sweetness value of 19.29 and bitterness value of 1.71. This study not only reveals the potential of these natural peptides as healthier alternatives to traditional sweeteners in food applications but also demonstrates the successful synergy of computational predictions and experimental validations in the realm of flavor science.

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Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes

Cited by 4 publications

References 51 publications

Design of Vif-Derived Peptide Inhibitors with Anti-HIV-1 Activity by Interrupting Vif-CBFβ Interaction

Design of Vif-Derived Peptide Inhibitors with Anti-HIV-1 Activity by Interrupting Vif-CBFβ Interaction

Mulberry Leaf Compounds and Gut Microbiota in Alzheimer’s Disease and Diabetes: A Study Using Network Pharmacology, Molecular Dynamics Simulation, and Cellular Assays

Integrating Computational and Experimental Methods to Identify Novel Sweet Peptides from Egg and Soy Proteins

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