Article
Biochemistry & Molecular Biology
Mohd Sajid Ali, Mohd Waseem, Naidu Subbarao, Abdullah Nasser Alahamed, Hamad A. Al-Lohedan
Summary: The interaction between lysozyme and cefoperazone was studied using spectroscopic and computational approaches. The UV-visible spectrum showed a change in lysozyme in the presence of cefoperazone, indicating complex formation. Fluorescence spectroscopy suggested a fair interaction via dynamic quenching, with a binding ratio of approximately 1:1. In silico studies revealed that hydrophobic forces played a major role in the interaction, with some involvement of hydrogen bonding and electrostatic interactions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Medicinal
Joel Ricci-Lopez, Sergio A. Aguila, Michael K. Gilson, Carlos A. Brizuela
Summary: The study demonstrates that using machine learning methods to process ensemble docking results can significantly improve the predictive power of structure-based virtual screening.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Said A. H. Vuai, Marcelina M. Ogedjo, Onoka Isaac, Mtabazi G. Sahini, Hulda S. Swai, Daniel M. Shadrack
Summary: This study identified two potent molecules that interact with and inhibit the catalytic reaction of TMPRSS2, preventing viral cell entry to the host's cell. One of the compounds showed similar inhibitory effects to an existing drug by disrupting the hydrogen bond interaction with catalytic triad residues of TMPRSS2.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Medicinal
Rajendra P. Joshi, Katherine J. Schultz, Jesse William Wilson, Agustin Kruel, Rohith Anand Varikoti, Chathuri J. Kombala, Daniel W. Kneller, Stephanie Galanie, Gwyndalyn Phillips, Qiu Zhang, Leighton Coates, Jyothi Parvathareddy, Surekha Surendranathan, Ying Kong, Austin Clyde, Arvind Ramanathan, Colleen B. Jonsson, Kristoffer R. Brandvold, Mowei Zhou, Martha S. Head, Andrey Kovalevsky, Neeraj Kumar
Summary: Researchers have developed a closed-loop artificial intelligence pipeline to design covalent candidates, and identified several potential inhibitors through experimental validation. The utility and effectiveness of the developed method have been demonstrated.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Abel Ujaigbe Egbemhenghe, Olajide Enoch Aderemi, Bamidele Samson Omotara, Faith Iyayi Akhimien, Faith Osaretin Osabuohien, Habeebulah Ajibola Adedapo, Oluwakemi Rita Temionu, Winner Amaka Egejuru, Chinedum Favour Ajala, Meejay Francis Ihunanya, Oluwatosin Oluwafunmilola Oluwafemi, Chinyere Felicia Duncan Onu, Abosede Christiana Ajibare, Christopher Ddamulira, Justin Onyekachukwu Abalum, Olanrewaju Michael Afolayan
Summary: The activity of MDM2 and MDMX proteins is crucial for regulating the p53 tumor suppressor pathway. In certain cancer cells, excessive MDMX can degrade p53, leading to a reduction in its levels. Therefore, the development of small-molecule inhibitors targeting the MDMX-p53 interaction is a promising strategy for cancer therapy. This study employed computational techniques to identify three potential small molecule inhibitors of the MDMX-p53 interaction, and the results showed their stable binding with MDMX and stronger intermolecular hydrogen bond interactions compared to the control.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Wafa Benselama, Wafaa Benchouk
Summary: This study predicted new ciprofloxacin derivatives by using quantum chemical, molecular docking studies and pharmacokinetic properties. The compounds demonstrated good pharmacokinetic profiles. The results of the docking studies showed that one compound exhibited great inhibitory behavior against gram-positive bacteria, another compound showed the best inhibition against gram-negative bacteria, and one compound was a good inhibitor for β-lactamase. Molecular dynamics simulations confirmed the stability of these compounds in the protein binding pocket.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Giovanni Bolcato, Eleonora Cescon, Matteo Pavan, Maicol Bissaro, Davide Bassani, Stephanie Federico, Giampiero Spalluto, Mattia Sturlese, Stefano Moro
Summary: Fragment-based drug discovery (FBDD) has become a consolidated approach in the drug discovery process, with successful applications seen in kinase inhibitors like Vemurafenib. CK1 δ, a protein kinase in the kinase family, has shown promise as a target in the treatment of neurodegenerative diseases such as Alzheimer's, Parkinson's, and ALS.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Sarah Hall-Swan, Didier Devaurs, Mauricio M. Rigo, Dinler A. Antunes, Lydia E. Kavraki, Geancarlo Zanatta
Summary: An unprecedented research effort has been made in response to the COVID-19 pandemic, focusing on crystallographic structures of SARS-CoV-2 proteins and virtual screening for potential drug inhibitors. Addressing receptor flexibility, a computational tool called DINC-COVID has been implemented for ensemble docking with success in identifying alternative binding modes. This work highlights the importance of considering receptor flexibility in docking studies and provides a platform for new inhibitors against SARS-CoV-2 proteins.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Chemistry, Medicinal
Raef Shams, Akihiro Matsukawa, Yukari Ochi, Yoshihiro Ito, Hideyuki Miyatake
Summary: This study reports a novel nonrapalog inhibitor, WRX606, which efficiently inhibits tumor growth without promoting metastasis by forming a ternary complex with mTOR protein. This finding provides important insights for the development of more effective anticancer drugs.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Lara Callea, Laura Bonati, Stefano Motta
Summary: A protocol combining SMD and metadynamics was developed for studying ligand binding processes, providing satisfactory results in identifying preferred entrance pathways and features of bound states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Mrinal Shekhar, Zachary Smith, Markus A. Seeliger, Pratyush Tiwary
Summary: Understanding how mutations cause drug resistance is important. In this study, we demonstrate how molecular dynamics simulations can provide a detailed mechanistic explanation for the differences in drug dissociation pathway caused by a mutation. We found that a point mutation in a protein leads to changes in its flexibility, resulting in a faster drug dissociation pathway. We believe that this approach can efficiently explain resistance mutations that are hard to understand from a structural perspective.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Hai Ping Shao, Tian Hua Wang, Hong Lin Zhai, Ke Xin Bi, Bing Qiang Zhao
Summary: In this study, the interaction mechanisms of two representative peptide inhibitors (11a and PF-07321332) with SARS-CoV-2 main protease (Mpro) were investigated for the first time using molecular dynamics simulation. Fragment-based drug design method was then employed to select fragments from existing SARS-CoV and SARS-CoV-2 inhibitors to replace the original P2 and P3 fragments, resulting in new molecules. Molecular docking, molecular dynamics simulation, and ADMET properties prediction confirmed the excellent activity and physicochemical properties of two molecules (O-74 and N-98), suggesting their potential as new inhibitors for SARS-CoV-2 main protease.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Irini Doytchinova
Summary: Drug design is a complex pharmaceutical science that has transformed into a coherent and well-organized discipline with solid theoretical foundations. Its goal is to discover effective, specific, non-toxic, safe, and well-tolerated drugs. It is one of the most rapidly developing modern sciences, with advancements driven by the application of artificial intelligence.
Article
Biochemistry & Molecular Biology
Juan Shi, Shuang Gao, Jia-Yu Wang, Tong Ye, Ming-Li Yue, Ying Fu, Fei Ye
Summary: This study established a Topomer comparative molecular field analysis model to screen potential HPPD inhibitors. Molecular docking, ADMET prediction, and drug-like properties evaluation were used to verify the activity of the screened compounds. Molecular dynamics simulation was conducted to validate the stability of the potential inhibitors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Pharmacology & Pharmacy
Rui Tian, Yufei Li, Xiaofeng Wang, Jiajun Li, Yingqian Li, Shaosheng Bei, Huashan Li
Summary: This study used computer-aided drug design technology to investigate the potential mechanism and compounds of artemisinin in the treatment of ulcerative colitis. The constructed networks highlighted the importance of GALNT2, BMP7 and TGFBR2 in the disease treatment, providing guidance for future experiments and case studies.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Jung Hsin Lin
Meeting Abstract
Oncology
Jung-Hsin Lin
Article
Immunology
Hsien-Tsung Chiu, Li-Jiuan Shen, Yee-Chun Chen, Jung-Hsin Lin, Chi-Chuan Wang
Article
Multidisciplinary Sciences
Shin-Fu Chen, Nan-Lan Huang, Jung-Hsin Lin, Chyuan-Chuan Wu, Ying-Ren Wang, Yu-Jen Yu, Michael K. Gilson, Nei-Li Chan
NATURE COMMUNICATIONS
(2018)
Meeting Abstract
Biophysics
Dhananjay C. Joshi, Jung-Hsin Lin
BIOPHYSICAL JOURNAL
(2019)
Article
Chemistry, Multidisciplinary
Dhananjay C. Joshi, Jung-Hsin Lin
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Chih-Ta Chen, Li-Zhu Liao, Ching-Hui Lu, Yung-Hsuan Huang, Yu-Kie Lin, Jung-Hsin Lin, Lu-Ping Chow
EXPERIMENTAL AND MOLECULAR MEDICINE
(2020)
Article
Chemistry, Physical
Wei Lim Chong, Visit Vao-soongnern, Piyarat Nimmanpipug, Chatchai Tayapiwatana, Jung-Hsin Lin, Yi-Ling Lin, Hui Yee Chee, Sharifuddin Md Zain, Noorsaadah Abd Rahman, Vannajan Sanghiran Lee
Summary: In this study, designed ankyrin repeat proteins (DARPins) were explored for their potential in mimicking the interactions of antibodies to bind with domain III (DIII) E protein of dengue virus (DENV). Molecular docking, molecular dynamics simulations, and free energy calculations were performed to improve the binding affinity of DARPins for DIII DENV-2. The correlation between global mode shape and binding free energy was observed, providing valuable tools for understanding the structural dynamics and energy contribution in designing DARPins to bind with the E protein of DENV-2.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Dhananjay C. Joshi, Charlie Gosse, Shu-Yu Huang, Jung-Hsin Lin
Summary: This study investigates the interaction between rapamycin and FKBP12 using a multiple-walker umbrella sampling simulation approach. The results show significant differences in the role of hydrogen bonds in different mutant residues, and removing the carboxylate group of D37 strongly destabilizes the association.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Daniel Forster, Jerome Idier, Leo Liberti, Antonio Mucherino, Jung-Hsin Lin, Therese E. Malliavin
Summary: Intrinsically disordered proteins (IDP) are crucial in biological processes and have attracted significant attention in structural biology. In this study, we systematically enumerated protein conformations using the TAiBP approach, and determined the relative populations of these conformations by fitting SAXS curves and Ramachandran probability maps. The variations in gyration radius between phosphorylated and unphosphorylated states were observed.
SCIENTIFIC REPORTS
(2022)
Meeting Abstract
Biophysics
Dhananjay C. Joshi, Jung-Hsin Lin
BIOPHYSICAL JOURNAL
(2020)
Meeting Abstract
Biophysics
Jung-Hsin Lin
BIOPHYSICAL JOURNAL
(2020)
Proceedings Paper
Computer Science, Information Systems
A. Mucherino, J-H Lin
PROCEEDINGS OF THE 2019 FEDERATED CONFERENCE ON COMPUTER SCIENCE AND INFORMATION SYSTEMS (FEDCSIS)
(2019)
Review
Chemistry, Medicinal
Yu-Hsuan Chen, Jung-Hsin Lin
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2017)
Meeting Abstract
Biophysics
Jung-Hsin Lin
BIOPHYSICAL JOURNAL
(2017)