Article
Biochemistry & Molecular Biology
Anirudh Pratap Singh Raman, Siwat Pongpaiboon, Rohit Bhatia, Kawar Lal Dabodhia, Ajay Kumar, Durgesh Kumar, Pallavi Jain, Mansi Sagar, Prashant Singh, Kamlesh Kumari
Summary: Hyperglycemia is a complex metabolic condition and a major issue in diabetes mellitus. Developing more effective and safer treatments for diabetes is necessary due to its increasing prevalence across the globe. Inhibiting carbohydrate digestion and lowering glucose formation is one way to manage hyperglycemia. This study investigates the inhibition potential of phytochemicals in Ficus carica against pancreatic amylase and salivary amylase using molecular docking and molecular dynamics simulations. The study also uses density functional theory calculations to analyze electron density delocalization and ADME properties of the compounds. Furthermore, a QSAR model is developed based on binding energy and thermodynamic parameters obtained from molecular docking and DFT calculations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Muthumanickam Sankar, K. Langeswaran, Sangavi Jeyachandran, Boomi Pandi
Summary: In this study, computational methods such as pharmacophore modeling, 3DQSAR, molecular docking, DFT, and molecular dynamic simulations were used to identify new, innovative, and effective potential inhibitors against Ebola virus. The results showed promising novel scaffolds with good predictive power and the best binding free energy and docking scores for potential inhibitors were determined through molecular docking and MM-GBSA analysis. Molecular dynamics simulations indicated stable ligand-protein complexes that may improve potent inhibitor development for Ebola viral treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Multidisciplinary
Mouad Lahyaoui, Hafsa El-Idrissi, Taoufiq Saffaj, Bouchaib Ihssane, Nabil Saffaj, Rachid Mamouni, Youssef Kandri Rodi
Summary: In this study, 28 compounds derived from phosphorus-substituted quinoline were investigated for their anti-proliferative activity and binding affinity with proteins related to lung, ovarian, and kidney malignancies. The results suggest that these compounds could be valuable models for the development of more effective anticancer prospects.
ARABIAN JOURNAL OF CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Mourad Stitou, Hamid Toufik, Taoufik Akabli, Fatima Lamchouri
Summary: This paper focuses on the computational study of hPEBP1 and demonstrates the effectiveness of the DFT/B3LYP method in predicting its activity. The results provide valuable insights for predicting the structures of potential anticancer compounds.
JOURNAL OF MOLECULAR MODELING
(2022)
Article
Plant Sciences
Borakha Bura Gohain, Urvashee Gogoi, Aparoop Das, Sanchaita Rajkhowa
Summary: This study established a 2D-QSAR model to predict the activity of potential xanthone derivatives against breast cancer. New molecules were computationally designed and evaluated for their activity and interactions through molecular docking analysis. Among them, Mol 8 exhibited superior binding energy and ADMET properties, making it a promising candidate for designing novel compounds.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Review
Chemistry, Analytical
Zhenjiao Du, Jeffrey Comer, Yonghui Li
Summary: Food-derived bioactive peptides (FBPs) have great potential in agricultural byproduct valorization and high-activity peptide screening, and the introduction of bioinformatics into FBP studies enhances the prospects of this field. This review provides a comprehensive overview of the latest advances in bioinformatics-driven FBPs studies, including the roles of databases, proteolysis simulation, QSAR models, molecular docking, and more. The employment of bioinformatics accelerates the process from identifying FBPs to product development and enhances the long-term development of various industries.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Applied
Lina Cheng, Zhiwei Zhu, Da-Wen Sun
Summary: The study found that the mechanism of enzyme protein denaturation induced by high pressure freezing is complex, with Pressure-Factors playing a dominant role in the denaturation process, while Freezing-Factors can weaken the effect of Pressure-Factors, leading to the enzyme being transformed into a partially folded intermediate state.
Article
Chemistry, Physical
Anirudh Pratap Singh Raman, Shweta Pal, Prashant Singh, Ajay Kumar, Pallavi Jain, Kamlesh Kumari
Summary: This study explores the potential of eutectic mixtures in various disciplines. The authors conducted DFT calculations, molecular docking, and QSAR analysis of designed eutectic mixtures using different equivalent ratios. They determined the melting temperature of the systems or eutectic mixtures theoretically using the Jakob et al. method. The thermodynamic parameters of the eutectic mixtures at room temperature, such as free energy, enthalpy, and other energies, were determined through DFT calculations using Gaussian. The authors also calculated the physiochemical descriptors of various eutectic mixtures based on DFT calculations, and conducted molecular docking to investigate their biological potential in inhibiting the Mpro of SARS-CoV-2.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Md. Oliullah Rafi, Gourab Bhattacharje, Khattab Al-Khafaji, Tugba Taskin-Tok, Md. Almujaddade Alfasane, Amit Kumar Das, Md. Anowar Khasru Parvez, Md. Shahedur Rahman
Summary: This study investigates the use of structural analogues of lopinavir and favipiravir as potential anti-viral drugs against COVID-19. The researchers found that the modified analogues showed favorable binding affinity and druggable properties when interacting with the active site residues of the main protease and RNA-dependent RNA polymerase. Molecular dynamics simulation and MMPBSA analysis confirmed the high binding affinity of one lopinavir analogue towards the main protease. This study presents a new approach to identify leads for novel anti-viral drugs against COVID-19.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biology
Valeria Miranda-Arizmendi, Diana Fimbres-Olivarria, Anselmo Miranda-Baeza, Karla Martinez-Robinson, Agustin Rascon-Chu, Yubia De Anda-Flores, Jaime Lizardi-Mendoza, Mayra A. Mendez-Encinas, Francisco Brown-Bojorquez, Rafael Canett-Romero, Elizabeth Carvajal-Millan
Summary: Algae and microalgae are important sources of bioactive compounds, particularly polysaccharides, which have been reported to have beneficial bioactivities for human health. However, the structure of polysaccharides in microalgae is not well explored. The present study extracted a sulfated polysaccharide (CMSP) from Chaetoceros muelleri and analyzed its structure, physicochemical properties, and bioactivities. The CMSP showed antioxidant activity, low glycemic index, and no cytotoxicity in colon cells.
Review
Agriculture, Multidisciplinary
Abraham Vidal-Limon, Jose E. Aguilar-Toala, Andrea M. Liceaga
Summary: The use of in silico tools, such as molecular docking, to study biological activity of proteins and peptides can sometimes produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) offer a solution to overcome sampling limitations in docking analysis and provide valuable information in deciphering functional mechanisms of proteins and peptides. This review discusses the traditional use of in silico models, like molecular docking, and highlights the importance of MDS in predicting structural and functional dynamics of food proteins and bioactive peptides.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Yongtao Xu, Baoyi Fan, Yunlong Gao, Yifan Chen, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, John Zenghui Zhang, Meiting Wang
Summary: In this study, a 3D-QSAR model was established for tetrahydroquinoline-derivative inhibitors targeting LSD1. The models CoMFA and CoMSIA showed good statistical and predictive properties. Based on the contour maps, seven novel derivatives were designed. Molecular dynamics simulations, binding free energy calculations, and ADME prediction were performed for three compounds and a template molecule. The results suggested that the designed compounds performed better than the template, providing guidance for the design of LSD1 inhibitors.
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
Chemistry, Physical
A. Jeelani, S. Muthu, P. Ramesh
Summary: In this study, the biologically active compound 2,4,6-tri(propan-2-yl)benzenesulfonyl chloride was investigated using a combination of experimental techniques (FT-IR, Raman, UV-Vis, and proton and carbon NMR) and theoretical methods (DFT and TD-DFT). The analysis involved studying the molecular structure, vibrational frequencies, chemical shifts, electrostatic potential, and charge distribution of the compound. The effects of solvent on the compound's properties were also examined, and its potential biological activities, including antidepressant activity, were predicted using QSAR and docking studies.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Zhihao Hu, Qianxia Lin, Haiyun Liu, Tiansheng Zhao, Bowen Yang, Guogang Tu
Summary: A receptor-dependent 4D-QSAR model on hydroxamate-based HDACs inhibitors was studied, with robustness confirmed through cross-validation and randomization. The best model showed high statistical values, suitable for further drug screening and design purposes.
MOLECULAR DIVERSITY
(2022)