Article
Biotechnology & Applied Microbiology
Yilin Hou, Qing Li, Wei He, Mingyue Li, Jiaqi Xue, Xinao Li, Yu Li
Summary: Molecular docking was used to study the biodegradation of fluoroquinolones under different conditions and design derivatives suitable for aerobic, facultative, and anaerobic biodegradation. These derivatives exhibited improved environmental friendliness and biodegradation performance.
BIOCHEMICAL ENGINEERING JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Syeda Abida Ejaz, Mubashir Aziz, Tanveer A. Wani, Hammad M. Al-Kahtani
Summary: This study used a sophisticated molecular docking strategy to target three beta-keto acyl-ACP synthases. Virtual screening of 1000 fluoroquinolone derivatives and ciprofloxacin was conducted, followed by molecular dynamics simulations to confirm the stability and reliability of the generated conformations. Compounds 155813629, 142486676, and 155567217 exhibited potential molecular interactions against FabH, FabB, and FabF, respectively, with docking scores outperforming ciprofloxacin. Molecular dynamics simulations further demonstrated favorable stability patterns of the complexes. Fluoroquinolone derivatives may serve as highly effective and selective inhibitors of the KAS enzyme.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Sunidhi Bhatt, Priyanka Choudhary, Subhankar Chatterjee, Yusuf Akhter
Summary: Fluoroquinolones (FQs) are widely used antimicrobial drugs, but their environmental pollution poses significant concerns for human and environmental health. Previous studies have shown that alkaline laccase (SilA) from Streptomyces ipomoeae can degrade Ciprofloxacin (CIP) and Norfloxacin (NOR), but the molecular mechanism was not well understood. In this study, molecular modeling, docking, and molecular dynamic analysis were used to elucidate the catalytic mechanism of SilA-laccase in the degradation of CIP, NOR, and Ofloxacin (OFL). The results identified a conserved tetrapeptide catalytic motif and a catalytic triad composed of three conserved amino acid residues. MD trajectories revealed that SilA exhibited the highest degradation potential for CIP, followed by NOR and OFL. This study provides insights into the comparative catalytic mechanism of SilA enzyme in the degradation of FQs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Engineering, Environmental
Xixi Li, Wenwen Gu, Bing Chen, Zhiwen Zhu, Baiyu Zhang
Summary: A systematic molecular design, screening, and performance evaluation approach was developed to generate 15 HHCB derivatives with improved functional properties and less environmental impacts. Toxicokinetic analysis narrowed the candidates to four, with Derivative 7 showing the least dermal adsorption potential. Molecular docking and molecular dynamic simulation were used to assess its interaction with other PCPs additives and impacts on human health risks. Further discussions on the environmental fate of Derivative 7 after transformation recognized biotransformation and chlorination as optimum options for mitigation.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Joao Paulo Menezes Spadeto, Matheus P. Freitas, Rodrigo A. Cormanich
Summary: Voltage-gated calcium channel malfunctions can lead to Alzheimer's and cardiovascular disorders, making it a critical protein target for drug development. The study focused on fluorinated DHP compounds as potential new candidates for inhibition of L-type calcium channels, showing higher affinities than commonly used drugs like nifedipine and amlodipine. The research utilized structure-based drug design methods such as homology modeling, molecular docking, and molecular dynamics calculations to investigate the potential of these compounds.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Hatim Soufi, Mohamed Moussaoui, Soukayna Baammi, Mouna Baassi, Mohammed Salah, Rachid Daoud, Achraf El Allali, M. E. Belghiti, Mohammed Moutaabbid, Said Belaaouad
Summary: A quantitative structure-activity relationship (QSAR) model was developed to study the effect of 45 flavonoid derivatives as cholinesterase inhibitors. The model showed that the energy and refractivity of the compounds were the major factors influencing their anti-cholinesterase activity. Molecular docking and dynamics studies confirmed the stability of the designed compound 1 in the active site of the Butyrylcholinesterase (BuChE) protein. ADMET analysis indicated that the designed compounds met the pharmacokinetic and toxicity criteria.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Guangping Li, Le Fu, Qingxiu He, Yong Hu, Xianlong Su, Haibin Liu, Yuanqiang Wang
Summary: This study investigated the role of MNK1 kinase in tumor development through 3D-QSAR analysis and designed 10 new 4-aniline-thieno[2,3-d] pyrimidine derivatives with predicted activities and analyzed ADME properties. Molecular dynamics simulation revealed the crucial amino acids and docking modes at the active site.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Anushka A. Poola, Prithvi S. Prabhu, T. P. Krishna Murthy, Manikanta Murahari, Swati Krishna, Mahesh Samantaray, Amutha Ramaswamy
Summary: Dengue, a viral disease transmitted by the Aedes mosquito, poses a growing public health concern in tropical and subtropical regions. With a lack of specific antiviral treatments available, identifying compounds with antiviral activity against the dengue virus is crucial. The NS2B-NS3 dengue protease plays a vital role in replication and viral assembly, making it a promising target for antiviral drug design.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Chai Xin Yu, Jian Wei Tan, Kamal Rullah, Syahrul Imran, Chau Ling Tham
Summary: This study aims to develop a theoretical background for designing and selecting human beta-tryptase inhibitors through computational studies. The research used 2D-QSAR models, molecular docking, molecular dynamics simulation, MM-GBSA analysis, and structure-based pharmacophore model to study the binding and inhibition of beta-tryptase. The findings provide insight and knowledge for the development of novel chemical compounds with improved inhibition of beta-tryptase.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Ehsan Jahangirian, Jamil Zargan, Hodjattallah Rabbani, Javad Zamani
Summary: Bladder cancer, including muscle invasive and non-muscle invasive types, is a common worldwide cancer. Non-muscle invasive bladder cancer requires more therapy due to its higher recurrence rate and longer, more expensive care. Experimental studies have shown that crude scorpion venom and purified proteins and peptides can suppress cancer metastasis, inhibit cancer growth, stop cell cycle, and induce cell apoptosis. In this research, three novel peptides (P2, P3, P4) were discovered from scorpions and studied for their antimicrobial and anticancer properties. Peptides 2 and 3 showed the highest binding rate and were confirmed to penetrate the membrane of cancer cells and bacterial cells. QSAR analysis suggests that peptides 2 and 3 can act as anti-cancer and antimicrobial peptides.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Sofia D'Souza, S. Balaji, K. Prema
Summary: This study successfully developed new 3CL protease inhibitors using 2D and 3D QSAR models, and validated their inhibitory effects on SARS-CoV through molecular docking and molecular dynamics simulations. The newly designed compounds showed higher interaction energies with active site residues and improved pharmacokinetic properties.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(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
Medicine, Research & Experimental
Mahmoud Ganji, Shohreh Bakhshi, Alireza Shoari, Reza Ahangari Cohan
Summary: This study utilized pharmacophore and QSAR modeling to identify five potential FGFR3 inhibitors for bladder cancer treatment, which showed promising therapeutic properties and low toxicity levels.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Chemistry, Multidisciplinary
Juan Shi, Li-Xia Zhao, Jia-Yu Wang, Tong Ye, Meng Wang, Shuang Gao, Fei Ye, Ying Fu
Summary: This study designed and synthesized novel HPPD inhibitors, verified their activity, and provided valuable reference for the development of new herbicides.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Xi Gu, Ying Wang, Mingxing Wang, Jian Wang, Ning Li
Summary: Molecular modeling methods were utilized to study the structural requirements of a series of Akt1 allosteric inhibitors, resulting in the design of 15 novel compounds. Through molecular docking, 3D-QSAR, and molecular dynamics simulation, key insights were gained for the discovery of potent Akt1 inhibitors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)