Article
Biochemistry & Molecular Biology
Hao-Chun Chuang, Ming-Fang Liu, Hsin-Yi Wu, Ying-Ta Wu, Ting-Jen Rachel Cheng, Jim-Min Fang
Summary: A benzophenone-containing salicylanilide compound was synthesized and used as a photoaffinity probe to identify the binding site of Acinetobacter baumannii penicillin-binding protein. Molecular docking experiments suggested that the binding site is a hydrophobic pocket that can disrupt the growth of peptidoglycan chain.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Food Science & Technology
Rui Chang, Zhilei Zhou, Yong Dong, Yuezheng Xu, Zhongwei Ji, Shuangping Liu, Jian Mao
Summary: This study analyzed the umami peptides in huangjiu using various methods and techniques. A total of 4158 peptides were identified through peptidomics, and six novel umami peptides and five umami-enhancing peptides were filtered. Computational approaches were used to investigate the structure-activity relationship, and key residues and active sites were found to potentially influence taste differences in the identified peptides.
Article
Chemistry, Analytical
Somaye Cheraghi, Pelin Senel, Burcu Dogan Topal, Soykan Agar, Mahsa Majidian, Mine Yurtsever, Esen Bellur Atici, Aysegul Golcu, Sibel A. Ozkan
Summary: In this study, the interaction mechanism between Eltrombopag and DNA was investigated using voltammetry, spectroscopic techniques, and viscosity measurements. A DNA-based biosensor and nano-biosensor were developed to detect the binding of DNA and Eltrombopag. Experimental results showed that Eltrombopag strongly interacts with dsDNA, as evidenced by the reduction of dGuo and dAdo oxidation signals in the presence of the drug. UV absorption, fluorescence emission spectroscopy, and viscosity measurements were used to further characterize the binding mode of the drug. Molecular docking and molecular dynamics simulations revealed that Eltrombopag binds to DNA through intercalation.
Article
Biochemistry & Molecular Biology
Elaine Yang, Weiming Bu, Antonio Suma, Vincenzo Carnevale, Kimberly C. Grasty, Patrick J. Loll, Kellie Woll, Natarajan Bhanu, Benjamin A. Garcia, Roderic G. Eckenhoff, Manuel Covarrubias
Summary: This study utilized PAL technique and MD simulation to uncover the mechanism through which propofol inhibits Nay channel function by promoting activation-coupled inactivation, while also providing direct insights into the structural basis of propofol modulation of Nay channels.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Juntamanee Jewboonchu, Jirakrit Saetang, Dennapa Saeloh, Thanyaluck Siriyong, Thanyada Rungrotmongkol, Supayang Piyawan Voravuthikunchai, Varomyalin Tipmanee
Summary: The study revealed the mechanism of action of conessine against Pseudomonas aeruginosa's efflux pump, including its impact on glycine loop flexibility and binding site in the efflux pump. This could serve as a key for designing and developing novel EPIs against multidrug-resistant P. aeruginosa.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
G. Jeyanthi, C. Gnana Sambandam
Summary: The optimized geometry and vibrational wave numbers of Benzoguanamine (BG) normal modes were investigated using Gaussian'09 at B1B95/6-31 G (d) level. The study elucidated the structural and spectral analysis of the compound, as well as molecular docking with target proteins to confirm biological activity and drug likeness influences.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Daniel Pushparaju Yeggoni, Shreya Dubey, Yusuf Zamal Mohammad, Aparna Rachamallu, Rajagopal Subramanyam
Summary: The study investigated the interaction between the phytochemical stigmasterol and human serum albumin under physiological conditions, revealing anti-inflammatory and anti-cancer properties of stigmasterol. Stigmasterol bound to a specific subdomain of HSA, altering the protein's secondary structure. Molecular docking and dynamic simulation further supported the binding mechanism between HSA and stigmasterol.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Bilge Bicak
Summary: The aim of this study is to investigate the molecular structure and interactions of the antihypertensive peptide Val-Trp using molecular mechanical, quantum mechanical, and spectroscopic methods. The peptide's structure was optimized and analyzed, and its interactions with ACE, AT1R, and Renin were studied through molecular docking and molecular dynamics simulation. The ADME analysis provided valuable information about the feasibility of Val-Trp as an antihypertensive drug.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Multidisciplinary Sciences
Abbeha Malik, Muhammad Nasir Iqbal, Sidrah Ashraf, Muhammad Saleem Khan, Samar Shahzadi, Muhammad Farhan Shafique, Zureesha Sajid, Muhammad Sajid, Sheikh Arslan Sehgal
Summary: A study found that the deficiency of calcium regulatory protein (CaM) leads to dysfunction of the cGMP signaling pathway, which is associated with various diseases. Through high-throughput virtual screening and comparative molecular docking, two compounds with strong binding affinity to eNOS were identified, which may be helpful in designing therapeutic targets against eNOS.
Article
Infectious Diseases
Faizul Azam
Summary: Teicoplanin, a glycopeptide antibiotic, has shown promising therapeutic efficacy against COVID-19 in vitro. This study utilized molecular modeling techniques to investigate its interaction with various COVID-19 drug targets, with the N-terminal domain of the nucleocapsid protein displaying the strongest affinity. Molecular dynamics simulations and MM-GBSA computations revealed stable binding energies between teicoplanin and the nucleocapsid protein, suggesting its potential as a therapeutic agent for SARS-CoV-2 infection. Additional studies are needed to confirm its clinical use in COVID-19 management.
Article
Biochemistry & Molecular Biology
Mohd Amir, Saleem Javed
Summary: This study evaluated the binding relationship between TPT and HSA, and found that the interaction between TPT and HSA triggered a static fluorescence quenching process. TPT preferred binding to site III of HSA, inducing conformational changes and reducing alpha-helical content. Additionally, TPT enhanced protein stability in the temperature range of 20 to 90 degrees C. The findings provide a clear picture of the impacts of TPT on HSA interaction.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Yue Wang, Ruiwei Ye, Liming Fan, Xin Zhao, Linxue Li, Hao Zheng, Yan Qiu, Xiuxia He, Yiming Lu
Summary: The study demonstrates that an anti-tumor necrosis factor-alpha (TNF-α) peptide, SN1-13, has anti-inflammatory activity by inhibiting TNF-α-induced cytotoxicity and blocking TNF-α-triggered signaling pathways. Molecular docking analysis also suggests that SN1-13 can disrupt the binding between TNF-α and its receptors, TNFR1 and TNFR2. These findings indicate that SN1-13 has potential as a therapeutic peptide for TNF-α-mediated inflammatory diseases.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Food Science & Technology
Weijia Li, Haoming Li, Jia Li, Jia Xu, Li Fang, Chunlei Liu, Dan Wu, Weihong Min
Summary: This study explored the relationship between the digestion of walnut peptide (<3 kDa) and its antioxidant activity, focusing on the inhibitory effect of DPP-IV on the antioxidant peptide KGHLFPN. The results showed that after simulated gastrointestinal digestion, the antioxidant capacity of the peptides was enhanced, while their tertiary structures became weaker and secondary structures became random coiled. The study also found that the antioxidant walnut peptide KGHLFPN exhibited good DPP-IV inhibitory activity, and the optimal time for oral absorption of KGHLFPN in vivo was found to be 4-8 hours. Therefore, walnut protein hydrolysate (<3 kDa) can be used as an antioxidant precursor, and walnut peptides have the potential to serve as food-derived antioxidants.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Chemistry, Medicinal
Daniela Pagnozzi, Nicolino Pala, Grazia Biosa, Roberto Dallocchio, Alessandro Dessi, Pankaj Kumar Singh, Dominga Rogolino, Anna Di Fiore, Giuseppina De Simone, Claudiu T. Supuran, Mario Sechi
Summary: The letter describes the application of experimental and computational techniques to study the interactions between human carbonic anhydrases and sulfonamide inhibitors. A series of affinity-labeled carbonic anhydrase inhibitors containing sulfonamido photoprobes was designed and synthesized, and a photoaffinity labeling method followed by mass spectrometry analysis was applied to elucidate the inhibitor binding site. Comparisons with X-ray crystallography and molecular dynamics simulation data were made to fully understand the protein/inhibitor complex stabilization.
ACS MEDICINAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Sameh S. Elhady, Reda F. A. Abdelhameed, Mayada M. El-Ayouty, Amany K. Ibrahim, Eman S. Habib, Mohamed S. Elgawish, Hashim A. Hassanean, Martin K. Safo, Mohamed S. Nafie, Safwat A. Ahmed
Summary: Isolates from Thymelaea hirsuta were identified and a new triflavanone compound was isolated, showing remarkable cytotoxicity against breast cancer cells by inducing apoptosis.