Article
Biochemistry & Molecular Biology
Shubham Dhiman, Moumita Saha, Amena Ali, Abuzer Ali, G. D. Gupta, Vivek Asati
Summary: This study investigated the interaction between a series of compounds and HSP90 using pharmacophore models, quantitative structure-activity relationship (QSAR) models, docking, and ZINC screening. The results showed that DHRRR_1 was the most effective pharmacophore model and compound 34 had the strongest interaction with HSP90. Virtual screening identified some potential ZINC compounds with activity against HSP90.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Environmental Sciences
Arkaprava Banerjee, Priyanka De, Vinay Kumar, Supratik Kar, Kunal Roy
Summary: Endocrine Disruptor Chemicals, found in the environment, can disrupt hormone regulation in humans and animals. This study used 2D-QSAR modeling to analyze the structural features of these chemicals in binding to androgen receptors in rats. Hydrophobicity, steroidal nucleus, bulkiness, and hydrogen bond donors contribute to receptor binding affinity, while electron-rich features decrease it. External validation metrics showed better results for predictions using Read-Across-v3.1 tool. q-RASAR, a combination of read-across and QSAR, provided the best quality of external predictions. Pharmaco-phore mapping, molecular docking, and molecular dynamics simulation supported the findings of QSAR/q-RASAR.
Article
Biochemistry & Molecular Biology
Na Zhai, Chenchen Wang, Fengshou Wu, Liwei Xiong, Xiaogang Luo, Xiulian Ju, Genyan Liu
Summary: Xanthine oxidase (XO) is an important target for treating hyperuricemia-associated diseases. Novel 2-substituted 6-oxo-1,6-dihydropyrimidine-5-carboxylic acids (ODCs) have been reported as XO inhibitors (XOIs) with remarkable activities. Through 3D-QSAR, docking, pharmacophore modeling, and MD studies, key interactions between ODCs and XO protein were identified, leading to the discovery of potential hit compounds for the development of novel XOIs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Balaji Wamanrao Matore, Purusottam Banjare, Jagadish Singh, Partha Pratim Roy
Summary: Designing selective drug candidates for structurally similar targets is a challenging task. This study aimed to explore the selectivity modeling of pyridine and pyrimidine scaffold towards highly homologous targets CYP11B1 and CYP11B2 enzymes using computational methods. Molecular docking and QSAR analysis revealed the importance of structural features and functional groups for selectivity and highlighted the differentiating amino acid residues for ligand selectivity. These findings will be useful for designing selective CYP11B1/CYP11B2 inhibitors.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Review
Endocrinology & Metabolism
Asma Sellami, Manon Reau, Matthieu Montes, Nathalie Lagarde
Summary: This article is a review of computational predictions of NR ligands for both therapeutic and toxicological purposes, based on studies published in the last decade. Over 100 articles concerning 14 NR subfamilies were analyzed to identify commonly used computational methods, databases, and limitations.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Chemistry, Physical
Sushanta Bhattacharya, Vivek Asati, Amena Ali, Abuzer Ali, G. D. Gupta
Summary: The study investigated potential compounds for RET inhibition using pharmacophore modeling and 3D-QSAR analysis. Through virtual screening and docking methodologies, four hit compounds with promising docking scores were identified, showing excellent pharmacokinetic profiles. The results may aid researchers in developing novel RET inhibitors with improved therapeutic efficacy for cancer treatment.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Chemistry, Physical
Swati Krishna, T. P. Krishna Murthy, G. Divyashri, Manikanta Murahari, Rohit Shukla, S. Birendra Kumar, Tiratha Raj Singh
Summary: The study designed drugs with anticancer potential by combining features of synthetic drugs and phytochemicals. Effective compounds were screened using ligand-based pharmacophore model and quantitative structure-activity relationship studies. Docking, ADMET, and molecular dynamics simulation studies confirmed the high activity and good stability of the identified compounds.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Kalirajan Rajagopal, Anandarajagopal Kalusalingam, Anubhav Raj Bharathidasan, Aadarsh Sivaprakash, Krutheesh Shanmugam, Monall Sundaramoorthy, Gowramma Byran
Summary: Cancer is a disease characterized by abnormal cell proliferation and can have various effects on human health. In this study, computational simulations were conducted to explore the binding mechanisms of four major analogs against estrogen receptor-alpha for breast cancer targeting. The benzothiophene analog showed the best binding activity and had potential for further research on breast cancer. This study suggests that estrogen receptor-alpha targeted inhibitors derived from benzothiophene derivatives have better potential and lower toxicity compared to existing market drugs.
Article
Biochemistry & Molecular Biology
Milica Radan, Dusan Ruzic, Mirjana Antonijevic, Teodora Djikic, Katarina Nikolic
Summary: This study combined ligand-based and target-based approaches to design novel potent 5-HT2AR antagonists. By conducting molecular dynamic simulations and molecular docking, bioactive conformations of the ligands and different conformations of the 5-HT2AR were obtained, leading to 3D-QSAR modelling and pharmacophore analysis, demonstrating the reliability and predictive power of the created model.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Kriti Kashyap, Rita Kakkar
Summary: Histone deacetylases (HDACs) are important epigenetic regulators closely linked to various diseases. Current therapeutic strategies target multiple HDAC isoforms, but can result in off-target effects, highlighting the need for developing therapies that target specific isoforms. Efforts are being made to identify structural features of receptors and inhibitors to achieve selective inhibition of HDAC isoforms.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Xiaojiao Zheng, Chenchen Wang, Na Zhai, Xiaogang Luo, Genyan Liu, Xiulian Ju
Summary: The study investigated a novel series of imidazo[1,2-a]-pyridine derivatives for their binding modes in the GABA(A) receptor binding pocket using various methods. The results provide important information for the development of novel drugs with antipsychotic activities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Avinash Kumar, Paridhi Agarwal, Ekta Rathi, Suvarna G. Kini
Summary: Human carbonic anhydrase is a type of metalloenzyme that can catalyze the hydration of carbon dioxide. Certain isoforms of this enzyme are highly expressed in the brain during seizure activity, making them potential targets for antiepileptic drugs. Through computational tools, we have identified and studied some potential inhibitors of a specific isoform of carbonic anhydrase.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Medicinal
Giada Righetti, Michele Tonelli, Paola Fossa, Elena Cichero
Summary: The exploration of structure-activity relationship of aR ligands through computational methods provides useful guidelines for the rational design of more selective compounds.
MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Xiaoyang Qu, Lina Dong, Jinyan Zhang, Yubing Si, Binju Wang
Summary: This study incorporates the features extracted from protein-bound waters into machine learning-based scoring functions using the HydraMap method. The results show that this approach consistently improves the performance of the scoring functions, including their scoring, ranking, and docking power.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Lu Huang, Xulong Wu, Xiaoli Fu, Haoxiang Wang, Biao Tang, Yirong Xiao, Caixia Zhou, Zhiqiao Zhao, Yujun Wan, Hui Chen, Zizhong Tang, Huipeng Yao, Zhi Shan, Tongliang Bu
Summary: In this study, a combination of structure-based drug carriers and molecular docking-based virtual screening was used to screen new potential FGFR1 inhibitors, providing a new approach for further research to explore better therapeutic effects in cancer treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Oncology
Bernhard Roither, Chris Oostenbrink, Georg Pfeiler, Heinz Koelbl, Wolfgang Schreiner
Summary: Cancer cells are normally destroyed by killer T cells, but some tumors evade natural clearance by presenting PD-L1 to induce the PD-1 inhibitory receptor. New anticancer drugs, such as nivolumab and pembrolizumab, disrupt this evasion and enable immune destruction of tumors. The drugs deform the CC'-loop of PD-1 in different ways, with pembrolizumab inducing a new conformation not seen before. This research may provide insights for the development of new anti-cancer drugs.
Article
Chemistry, Medicinal
Christoph Oehlknecht, Sonja Katz, Christina Kroess, Bernhard Sprenger, Petra Engele, Rainer Schneider, Chris Oostenbrink
Summary: The article introduces an efficient method for calculating protein binding free energies by combining the one-step perturbation and the third-power fitting approach. Experimental in silico saturation mutagenesis confirms the method's high accuracy in predicting relative free energies of amino acid mutations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemical Research Methods
Yerko Escalona, Drazen Petrov, Chris Oostenbrink
Summary: Soil Organic Matter (SOM) plays a crucial role in biogeochemical processes, but there is still incomplete understanding of its composition and structure. The Vienna Soil-Organic-Matter Modeler generates computer models of SOM using IHSS data and different types of soil, improving chemical and geometric diversity.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Chemistry, Physical
Bettina Lier, Peter Poliak, Philipp Marquetand, Julia Westermayr, Chris Oostenbrink
Summary: Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have greatly advanced computational chemistry, but their partitioning of a system into different regions and treating them with different theories can cause artifacts at the interface. In this study, the buffer region neural network (BuRNN) is introduced as an alternative approach to minimize these artifacts by fully polarizing a buffer region. The interaction between the quantum mechanics (QM) and buffer regions is described by deep neural networks (NNs), resulting in high computational efficiency and quantum chemical accuracy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Erik Breslmayr, Peter Poliak, Alen Pozgajcic, Roman Schindler, Daniel Kracher, Chris Oostenbrink, Roland Ludwig
Summary: Lytic polysaccharide monooxygenases (LPMOs) are enzymes widely found in fungi that catalyze the oxidative degradation of polysaccharides like cellulose. This study investigates the influence of small molecules and ions on the activity and stability of LPMO during catalysis. The findings suggest that fungal metabolic products like oxalic acid and citric acid can both reduce LPMO activity and protect the enzyme from deactivation. The study also reveals the potential role of small, bidentate molecules as physiological effectors to regulate LPMO activity.
Article
Biochemistry & Molecular Biology
Anja Wagner, Edgar Galicia-Andres, Magdalena Teufl, Lukas Gold, Christian Obinger, Peter Sykacek, Chris Oostenbrink, Michael W. Traxlmayr
Summary: By screening a mutated EGFR library, previously unknown activating mutations in EGFR were discovered. These mutations are not only located in the kinase domain of EGFR, but also in other regions, including the extracellular and transmembrane domains.
Article
Chemistry, Medicinal
Oriol Gracia Carmona, Chris Oostenbrink
Summary: One of the most challenging aspects in the molecular simulation of proteins is studying the slowly relaxing processes. State-of-the-art methods rely on performing several short simulations, but capturing these processes is difficult. A recently developed technique called accelerated enveloping distribution sampling (AEDS) can overcome the high-energy-barrier challenge and sample the relevant degrees of freedom accurately. In this study, AEDS is applied to the T4 lysozyme L99A system, showcasing its advantages and challenges. The results demonstrate the potential of AEDS in responding to more intricate molecular events.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Cristina Gonzalez-Fernandez, Christoph Ohlknecht, Matthias Diem, Yerko Escalona, Eugenio Bringas, Gabriel Moncalian, Chris Oostenbrink, Inmaculada Ortiz
Summary: The development of new strategies to combat Gram-negative bacterial infections, particularly those resistant to antibiotics, is crucial due to the global increase in antibiotic resistance. This study focuses on the use of extracorporeal blood cleansing devices with affinity sorbents for capturing bacterial lipopolysaccharide (LPS), which stimulates an exacerbated immune response during infection. Molecular dynamics simulations were conducted to investigate the interaction mechanism between an anti-LPS factor (ALF) isoform 3 from Penaeus monodon (AL3) and lipid A (LA, a component of LPS). The results revealed the binding mechanism and key interacting residues, which can guide the design of LPS-sequestrating molecules for blood detoxification.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Oriol Gracia Carmona, Michael Gillhofer, Lisa Tomasiak, Anita De Ruiter, Chris Oostenbrink
Summary: Determining the presence of water molecules at protein-ligand interfaces is still challenging in free-energy calculations. In this study, the accelerated enveloping distribution sampling (AEDS) method was applied to probe the presence of water molecules in the active site in a fast and straightforward manner. The combination of AEDS with thermodynamic integration (TI) was used to calculate accurate binding free energies in the presence of buried water molecules.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Agronomy
Yerko Escalona, Drazen Petrov, Edgar Galicia-Andres, Chris Oostenbrink
Summary: By using molecular dynamics simulations and creating molecular systems that resemble soil organic matter (SOM), researchers gained a better understanding of SOM. They studied standardized samples of humic substances (HSs) from various sources and analyzed the structure and dynamics to explore the relationship between properties and protonation state of carboxyl groups as well as the influence of ion interactions and pH.
Article
Biochemistry & Molecular Biology
Bettina Motycka, Florian Csarman, Melanie Rupp, Karoline Schnabel, Gabor Nagy, Kwankao Karnpakdee, Stefan Scheiblbrandner, Rupert Tscheliessnig, Chris Oostenbrink, Michal Hammel, Roland Ludwig
Summary: This study investigates the role of two crucial amino acids in cellobiose dehydrogenase (CDH) in the interaction between the dehydrogenase and cytochrome domains, as well as in the interdomain electron transfer. The results suggest that these two residues play an essential role in shaping the domain interaction and facilitating electron transfer.
Article
Chemistry, Medicinal
Mateo Barria-Urenda, Alvaro Ruiz-Fernandez, Carlos Gonzalez, Chris Oostenbrink, Jose Antonio Garate
Summary: This study systematically investigated the adsorption process of amino acids onto graphene through free-energy calculations. A linear correlation was found between the free energy and the change in solvent accessible surface area, which could be used to predict the adsorption free energy of pentapeptides. Graphene oxidation resulted in a loss of favorability for amino acid adsorption.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Oriol Gracia Carmona, Chris Oostenbrink
Summary: Gaussian accelerated molecular dynamics (GaMD) is an enhanced sampling technique that increases the sampling efficiency by adding a biasing potential. This study presents a GROMOS implementation of GaMD with a flexible selective approach, allowing the user to define multiple boosting potentials for different regions. The method is demonstrated on alanine dipeptide and chignolin peptide, and its applicability to studying conformational changes of glycans and glycosylated proteins is explored.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Oriol Gracia Carmona, Majd Lahham, Peter Poliak, Dominic Goj, Eva Friesser, Silvia Wallner, Peter Macheroux, Chris Oostenbrink
Summary: This study investigates the substrate specificity of the FsqB enzyme and discovers the role of tyrosine and aspartate residues in fixing the substrate close to the isoalloxazine ring of the cofactor. The combination of experimental and theoretical approaches helps solve the mystery behind the activity of FsqB enzyme.
JOURNAL OF MOLECULAR RECOGNITION
(2023)
Article
Chemistry, Physical
Yerko Escalona, Nicolas Espinoza, Mateo Barria-Urenda, Chris Oostenbrink, Jose Antonio Garate
Summary: In this study, the influence of polarizable graphene models on the water-graphene interface was systematically investigated. The results show that polarizable graphene affects the orientation of water molecules nearby and reduced the water contact angles.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)