Article
Biochemistry & Molecular Biology
Wenkun Zhuo, Zheng Lian, Wenzhe Bai, Yanrong Chen, Huanling Xia
Summary: In this study, 2D and 3D QSAR models were established to predict the anti-tumor activity of dipeptide-alkylated nitrogen-mustard compounds, and a series of new compounds were designed based on the models. The results showed satisfactory performance of both 2D and 3D QSAR models, and the 3D QSAR model successfully predicted compounds with high anti-tumor activity.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Computer Science, Artificial Intelligence
Andrea Mastropietro, Giuseppe Pasculli, Juergen Bajorath
Summary: In drug design, graph neural networks (GNNs) are used to predict compound potency by analyzing graph representations of protein-ligand interactions. The study reveals that GNNs are influenced by ligand memorization during learning and certain GNN architectures prioritize interaction information for predicting high affinities. While GNNs do not comprehensively account for protein-ligand interactions and physical reality, they provide a helpful balance between ligand memorization and learning of interaction patterns.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Materials Science, Multidisciplinary
Ruizhe Xing, Jiayi Yang, Dongguang Zhang, Wei Gong, Taylor V. Neumann, Meixiang Wang, Renliang Huang, Jie Kong, Wei Qi, Michael D. Dickey
Summary: This paper presents printable metallic gels made of an aqueous suspension of copper particles connected by bridges of liquid eutectic gallium indium alloy. The rheology of the conductive solid-liquid-liquid suspension is tuned for 3D printing by adjusting the composition and pH. The printed parts exhibit metallic electrical conductivity without the need for sintering, and drying at elevated temperatures enables shape change for 4D printing. A conductive spider is successfully printed, demonstrating the potential for printing metallic structures under ambient conditions.
Review
Materials Science, Multidisciplinary
Fatemeh Rajabasadi, Lukas Schwarz, Mariana Medina-Sancehz, Oliver G. Schmidt
Summary: Additive manufacturing technologies like 3D printing and two-photon polymerization have advanced micro/nano-fabrication, offering high resolution and reproducibility. Particularly in the field of medical microrobotics, the use of smart materials and complex structures presents new opportunities for innovation and research.
PROGRESS IN MATERIALS SCIENCE
(2021)
Article
Chemistry, Medicinal
Jannis Born, Tien Huynh, Astrid Stroobants, Wendy D. Cornell, Matteo Manica
Summary: The use of reduced active site sequence representation in kinase-ligand binding affinity prediction has shown significantly higher performance compared to using the full primary structure. This trend persists across different models, data sets, and performance metrics, and holds true when predicting pIC(50) for both unseen ligands and kinases.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Environmental Sciences
Bo-Gyeon Cho, Jae-Ho Lee, Hye-In Kim, Se-Ra Jin, Dae Geun Kim, Chul-Woong Cho, Yeoung-Sang Yun
Summary: The production of fruit waste and organic micropollutants is a serious environmental issue. In order to address this problem, citrus fruit peels were used as biosorbents to remove the pollutants. Quantitative structure-adsorption relationship (QSAR) models were established to assess the adsorption capacity, and the models showed good predictability and were validated through experimental data. These models can be used to estimate adsorption affinity for other micropollutants.
ENVIRONMENTAL RESEARCH
(2023)
Review
Chemistry, Multidisciplinary
Annan Chen, Wanying Wang, Zhengyi Mao, Yunhu He, Shiting Chen, Guo Liu, Jin Su, Pei Feng, Yusheng Shi, Chunze Yan, Jian Lu
Summary: Additive manufacturing (AM) has significant advantages in the fabrication of tissue engineering implants. However, many tissue constructs have anisotropic heterogeneous structures, which pose challenges for conventional AM processes. Multimaterial 3D and 4D bioprinting offer a promising solution for constructing multifunctional implants with heterogeneous structures that can better mimic the host microenvironment.
ADVANCED MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Sowmya Andole, Gouthami Thumma, Rajasekhar Reddy Alavala, Kiran Gangarapu
Summary: The present work aimed to develop a Field-based 3D-QSAR model using existing JAK-2 inhibitors. The JAK-STAT pathway is known to be involved in autoimmune diseases and myeloproliferative diseases. A Field-based 3D QSAR model was developed to determine the inhibitory potential of ligands. Virtual screening and molecular docking were performed to validate the results. The study showed the potential for discovering new JAK-2 inhibitors using the developed 3D QSAR model.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Review
Materials Science, Multidisciplinary
Jessica Mauriello, Romain Maury, Yohann Guillaneuf, Didier Gigmes
Summary: Vat photopolymerization is a method that utilizes light-induced polymerization to create targeted structures from liquid photopolymers. Polyurethanes have gained significant attention in the industrial and academic fields due to their various properties. This review article highlights recent progress in printing techniques, resin compositions, and applications of 3D/4D printing using vat photopolymerization of polyurethanes.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
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)
Article
Chemistry, Multidisciplinary
Eoyoon Lee, Sun Hee Choi, Hyung Chul Ham
Summary: This study evaluated the catalytic activity of CoM homo and double-atom catalysts supported on nitrogen-doped graphene for electrochemical water oxidation under alkaline conditions, with the hetero CoCu/N(4)G double-atom catalyst showing the highest OER activity. Theoretical calculations explained the enhanced OER activity by the crucial impact of Cu dopant and changes in the electron structure characteristics.
NANOSCALE ADVANCES
(2022)
Review
Biochemistry & Molecular Biology
Andrzej Bak
Summary: A key question for computational chemists is the preferred ligand geometry that fits into the receptor pocket, with 4D-QSAR schemes offering higher model abstraction for examining multiple molecular conformations, orientations, and representations. The current interest in this method appears to be experiencing a promising revival.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Muhammad Yasir Khalid, Zia Ullah Arif, Reza Noroozi, Mokarram Hossain, Seeram Ramakrishna, Rehan Umer
Summary: Cellulose nanocrystals (CNCs) have shown promising features for various applications due to their biodegradability, non-toxicity, and remarkable mechanical properties. They can be chemically modified to tailor their mechanical characteristics for high-end applications. Additive manufacturing methods, such as 3D/4D printing, offer great advantages in developing CNC-based structures with complex geometries. This review highlights the advancements, challenges, and future directions of additively manufactured CNC-based composites for diverse engineering sectors.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Medicinal
Gonzalo Cerruela-Garcia, Jose Manuel Cuevas-Munoz, Nicolas Garcia-Pedrajas
Summary: Feature selection is crucial in the construction of QSAR models for predicting molecular activity, as it improves the accuracy and interpretability of the models. This study evaluates a new graph-based feature selection approach and demonstrates its effectiveness in molecular activity prediction.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Review
Chemistry, Physical
Shadpour Mallakpour, Farbod Tabesh, Chaudhery Mustansar Hussain
Summary: The advancing technologies of 3D and 4D printing have found widespread applications in various fields, despite some shortcomings that still need to be addressed.
ADVANCES IN COLLOID AND INTERFACE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Prateek Pathak, Vladislav Naumovich, Maria Grishina, Vladimir Potemkin
Summary: The present investigation estimated the electron properties of EGFR proteins-ligand complexes using AlteQ approach and established the relationship between electron properties and pharmacological activity. The study found that the inhibitory activity of EGFR is closely related to intermolecular contacts between protein and ligands.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Vladislav Naumovich, Maria Grishina, Jurica Novak, Prateek Pathak, Vladimir Potemkin, Mohd Shahbaaz, Magda H. Abdellattif
Summary: This study investigates the interaction between human dihydrofolate reductase (hDHFR) and inhibitors, aiming to identify factors that can reduce side effects and enhance drug activity. Through calculation of electronic properties and statistical analysis, the researchers found that changes in volume and electron number correlated with hDHFR inhibition potency. Molecular dynamics simulations were also used to gain deeper insights into the structural inhibition. The AlteQ approach allowed for the quantitative evaluation of factors influencing activity.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Prem Prakash Sharma, Sumit Kumar, Kumar Kaushik, Archana Singh, Indrakant K. Singh, Maria Grishina, Kailash C. Pandey, Pushpendra Singh, Vladimir Potemkin, Poonam, Geeta Singh, Brijesh Rathi
Summary: Plasmepsin V is an essential protease for the survival of the malaria parasite Plasmodium falciparum, with inhibition showing potential as a drug target. Through molecular docking, a new compound has been identified as a potent inhibitor, which warrants further experimental validation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Jurica Novak, Hrvoje Rimac, Shivananda Kandagalla, Prateek Pathak, Vladislav Naumovich, Maria Grishina, Vladimir Potemkin
Summary: The study identified a more favorable allosteric binding site on the SARS-CoV-2 3CL protease, which could be a better target for non-covalent inhibitors to prevent dimerization and activation. The tyrosine kinase inhibitors radotinib and nilotinib, used for leukemia treatment, showed potential binding to this allosteric site, as confirmed by molecular dynamics simulations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Shivananda Kandagalla, Jurica Novak, Sharath Belenahalli Shekarappa, Maria A. Grishina, Vladimir A. Potemkin, Bhimanagoud Kumbar
Summary: Kyasanur forest disease (KFD) is a tick-borne, neglected tropical disease caused by KFD virus (KFDV). This study evaluated the effectiveness of FDA approved drugs and natural compounds against KFDV proteins using in silico drug repurposing method.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Mohd Shahbaaz, Dmitry A. Maslov, Aleksey A. Vatlin, Valery N. Danilenko, Maria Grishina, Alan Christoffels
Summary: In the current era of a pandemic, infections of COVID-19 and Tuberculosis (TB) enhance the detrimental effects of both diseases in suffering individuals. The resistance mechanisms evolving in Mycobacterium tuberculosis are limiting the efficiency of current therapeutic measures and pressurizing the stressed medical infrastructures.
Article
Chemistry, Medicinal
Vladislav Naumovich, Maria Grishina, Vladimir Potemkin
Summary: The aim of this study was to determine the significance of the 3CLpro enzyme of SARS-CoV-2 as a target for COVID-19 and evaluate the accuracy of drug modeling methods. The authors developed a model using the AlteQ approach to assess the reliability of 3CLpro complexes with ligands, which showed high correlation coefficients and can be utilized to determine the reliability of docked 3CLpro complexes with ligands.
FUTURE MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Prateek Pathak, Vikas Kumar, Habibullah Khalilullah, Maria Grishina, HariOm Singh, Amita Verma
Summary: The study demonstrates that debelalactone can protect tissues, alleviate chronic hepatic inflammation and oxidative stress induced by diethyl nitrosamine in Wistar rats. It significantly reduces parameters associated with liver and non-liver functions, and improves body weight of treated animals. Moreover, debelalactone restores antioxidant markers and inflammatory mediators to normal levels, reduces liver tissue abnormalities and inflammation, and inhibits precancerous cells.
Review
Chemistry, Medicinal
Ankit Kumar Singh, Adarsh Kumar, Harshwardhan Singh, Pankaj Sonawane, Harshali Paliwal, Suresh Thareja, Prateek Pathak, Maria Grishina, Mariusz Jaremko, Abdul-Hamid Emwas, Jagat Pal Yadav, Amita Verma, Habibullah Khalilullah, Pradeep Kumar
Summary: Cancer is a complex disease, and the efficacy of conventional anticancer drugs varies. The hybrid approach of combining two drugs into a single molecule shows potential in improving treatment efficacy and reducing drug resistance. Recent research has identified promising hybrid molecules with anticancer properties. This study provides valuable knowledge for researchers working on complex diseases like cancer.
Article
Biochemistry & Molecular Biology
Ashok Kumar Mandal, Samrat Paudel, Anisha Pandey, Parasmani Yadav, Prateek Pathak, Maria Grishina, Mariusz Jaremko, Abdul-Hamid Emwas, Habibullah Khalilullah, Amita Verma
Summary: The study investigated the antioxidant and anticancer activities of Psidium guajava L. essential oil, demonstrating its potential therapeutic value against breast cancer. The bioactive compounds in the oil showed promising properties in inhibiting tumor growth and exhibited drug likeness properties according to ADME analysis, suggesting their potential for novel drug discovery.
Review
Chemistry, Medicinal
Adarsh Kumar, Ankit Kumar Singh, Harshwardhan Singh, Veena Vijayan, Deepak Kumar, Jashwanth Naik, Suresh Thareja, Jagat Pal Yadav, Prateek Pathak, Maria Grishina, Amita Verma, Habibullah Khalilullah, Mariusz Jaremko, Abdul-Hamid Emwas, Pradeep Kumar
Summary: Cancer is a major healthcare challenge worldwide, calling for the development of safer and target-specific anticancer drugs. This study summarizes the use of nitrogen-containing heterocycles in cancer treatment, providing insights into their pharmacological properties and mechanisms of action.
Review
Pharmacology & Pharmacy
Karlie R. Sharma, Christine M. Colvis, Griffih P. Rodgers, Douglas M. Sheeley
Summary: There are many genes within the druggable genome that have not been studied, and the US National Institutes of Health's program provides resources to explore these genes, with the potential for rapid impact on human health.
DRUG DISCOVERY TODAY
(2024)
Review
Pharmacology & Pharmacy
Mohammad Sameer Khan, B. H. Jaswanth Gowda, Waleed H. Almalki, Tanuja Singh, Amirhossein Sahebkar, Prashant Kesharwani
Summary: Mitochondria-specific functional liposomes hold great potential for cancer therapy. This review discusses the association between mitochondria and tumor formation, as well as the advantages of liposomes in delivering drugs to mitochondria.
DRUG DISCOVERY TODAY
(2024)
Review
Pharmacology & Pharmacy
Choong Yong Ung, Cristina Correia, Hu Li, Christopher M. Adams, Jennifer J. Westendorf, Shizhen Zhu
Summary: With increasing human life expectancy, the global medical burden of chronic diseases is growing. Chronic diseases often involve malfunctioning of multiple organs, and understanding the interorgan crosstalk is crucial to understanding the etiology of chronic diseases. Researchers have proposed the locked-state model (LoSM) and cutting-edge systems biology and artificial intelligence strategies to decipher chronic multiorgan locked states. The findings have important clinical implications for improving treatments for chronic diseases.
DRUG DISCOVERY TODAY
(2024)
