Article
Chemistry, Physical
Valery Lutsyk, Pawel Wolski, Wojciech Plazinski
Summary: This article presents a coarse-grained force field dedicated to glucopyranose-based carbohydrates, compatible with the Martini force field. The new model successfully displays spontaneous formation of aggregates with experimentally identified features and accurately identifies binding pockets in carbohydrate-binding proteins.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Yangyang Zhang, Donghui Liu, Yiyang Zhang, Yachong Guo, Wenfei Li, Fabrice Thalmann
Summary: This article describes a coarse-grained model of POPC and DOPC lipid peroxides and discusses their predicted structure and the influence of hydration. In addition, electron and neutron scattering length density profiles of the simulated bilayers are provided.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Stephan Thaler, Maximilian Stupp, Julija Zavadlav
Summary: Neural network potentials are a natural choice for coarse-grained models, but they suffer from finite data effects when trained bottom-up via force matching. In this work, the authors demonstrate that relative entropy training is more data efficient and improves free energy surfaces and sensitivity to prior potentials. The findings support the use of training objectives beyond force matching for improving the accuracy and reliability of coarse-grained neural network potentials.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Fabian Grunewald, Mats H. Punt, Elizabeth E. Jefferys, Petteri A. Vainikka, Melanie Koenig, Valtteri Virtanen, Travis A. Meyer, Weria Pezeshkian, Adam J. Gormley, Maarit Karonen, Mark S. P. Sansom, Paulo C. T. Souza, Siewert J. Marrink
Summary: The study develops a consistent strategy to accurately parametrize carbohydrate molecules within the framework of Martini 3 model and demonstrates the validity and transferability of this approach through various test cases.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Diego Ugarte La Torre, Shoji Takada
Summary: A lipid-protein interaction model was developed for coarse-grained molecular dynamics simulations, showing good agreement with experimental results and prior knowledge. This model has been implemented in the publicly available software, CafeMol.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Xukai Jiang, Yuliang Sun, Kai Yang, Bing Yuan, Tony Velkov, Lushan Wang, Jian Li
Summary: The study developed an asymmetric outer membrane (OM) model and used molecular dynamics simulations to investigate the interaction dynamics of lipopolysaccharide (LPS)-containing OM with the polymyxins. It was discovered that polymyxin molecules penetrated the OM core sugar region but were trapped before entering the lipid A region due to a major free energy barrier at the LPS inner core and lipid A interface. Calcium ions were found to inhibit the penetration of polymyxins into the hydrophobic region of the OM by mediating cross-linking interactions between LPS molecules.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Physical
Aditi Khot, Brett M. Savoie
Summary: Coarse-grained molecular dynamics (CGMD) simulations address critical lengthscales and timescales in chemical and material applications. The development of black-box CGMD methodologies similar to density functional theory for electronic structure is still lacking. Machine learning (ML)-based CGMD potentials show promise in simplifying model development, but they have yet to outperform physics-based CGMD methods. In this study, λ-learning models are explored to combine the advantages of both approaches. The λ-models outperform ML-only CGMD models and provide essentially free gains in reproducing atomistic properties. However, neither the λ-learning models nor the ML-only models significantly outperform elementary pairwise models in reproducing atomistic properties due to the large irreducible force errors associated with coarse-graining.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Gaurav Mitra, Chuan Chang, Angus McMullen, Daniela Puchall, Jasna Brujic, Glen M. Hocky
Summary: Colloidal particles with mobile binding molecules allow for spontaneous control over the number of droplet-droplet bonds by tuning the concentration of binders. A coarse-grained molecular dynamics model was used to study the self-assembly of these systems and explore how the valence of assembled structures can be controlled through the kinetics of binding and unbinding. This model provides insights into the molecular features governing valence control and can guide programmable design in experiments.
Article
Biochemistry & Molecular Biology
Ritika Gupta, Jyoti Kumari, Soumya Pati, Shailja Singh, Manasi Mishra, Sajal K. Ghosh
Summary: The study investigates the interaction of protein KB1 with different phospholipids at the air-water interface, showing that the electrostatic nature plays a crucial role in determining the initial driving force for protein recognition and attachment to a cellular membrane. The protein induces changes in lipid monolayers, affecting their phase behavior and elastic properties, with the long ranged electrostatic force as the key factor for KB1 to recognize and attach to the membrane before penetrating into the hydrophobic core.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Mechanics
Fernando F. Grinstein, Juan A. Saenz, Massimo Germano
Summary: The study revisits coarse-grained simulation strategies for turbulent material mixing involving shock-driven turbulence, using newly available LMC-xRAGE hydrodynamics. Improved simulated mixing and turbulence levels on coarser grids were achieved, with the more accurate models requiring less resolution and resulting in grid-coarsening savings for mixing prediction.
Article
Biochemistry & Molecular Biology
Nikhil Agrawal, Adam A. Skelton, Emilio Parisini
Summary: Alzheimer's disease, characterized by the misfolding and aggregation of amyloid-beta (A beta) peptides, remains poorly understood in terms of its molecular mechanism of interaction with cell membranes. In this study, simulations were conducted to investigate the interaction between A beta 1-40 fibrils and different bilayers composed of DPPC and cholesterol. The results show the involvement of hydrophobic amino acid clusters, lysine residues, and C-terminal hydrophobic residues in the binding process. Furthermore, the data suggest that the binding affinity of A beta 1-40 fibrils to the membrane increases with the presence of cholesterol. These findings provide insights into potential target regions for the development of inhibitors against A beta oligomer/fibril-membrane interaction.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Physical
Khayrul Islam, Meghdad Razizadeh, Yaling Liu
Summary: In recent years, extracellular vesicles have emerged as promising carriers for next-generation drug delivery platforms. This study developed a systematic algorithm to simulate nanopore formation and predict drug loading during extracellular vesicle squeezing. The effects of various squeezing test parameters on pore formation and drug loading efficiency were analyzed, and a phase diagram was provided as a design guide. This method can be used to optimize nanofluidic device configuration and flow setup for desired drug loading into extracellular vesicles.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Kai Steffen Stroh, Paulo C. T. Souza, Luca Monticelli, Herre Jelger Risselada
Summary: This study utilizes mixed-variable particle swarm optimization to automatically parameterize molecules within the Martini 3 coarse-grained force field, matching both structural and thermodynamic data. The approach optimizes both bonded and nonbonded interactions while maintaining the search efficiency of vector guided particle swarm optimization methods. Additionally, noise-mitigation strategies are explored for matching the phase-transition temperatures of lipid membranes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Michael R. DeLyser, W. G. Noid
Summary: Investigated a new class of one-body potentials called square gradient (SG) potentials that can improve the accuracy and transferability of coarse-grained (CG) models. These SG potentials can tune interfacial properties and enhance the performance of various models.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Enrico Skoruppa, Aderik Voorspoels, Jocelyne Vreede, Enrico Carlon
Summary: Investigations on the influence of nonlocal couplings on DNA torsional and bending elasticities revealed strong off-site couplings for tilt-tilt and twist-twist, while they were weaker in the roll-roll case. Analysis indicated that off-site interactions generate a length-scale-dependent elasticity in DNA models. Simulation-generated data predicted significant length-scale-dependent effect on torsional fluctuations, but only a modest effect on bending fluctuations, consistent with experimental observations probing DNA mechanics.
Article
Biochemistry & Molecular Biology
Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Julianna Olah, Jon Mujika, James R. Ketudat-Cairns, Supa Hannongbua, Jitrayut Jitonnom
Summary: Using QM/MM method, simulations were conducted to understand the dynamics, catalytic mechanism, and electrostatic influence of the active site of GH43 endo-arabinanase, supporting the proposed single-displacement mechanism and identifying potential mutation targets.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Patchreenart Saparpakorn, Aunlika Chimprasit, Theerawat Jantarat, Supa Hannongbua
Summary: This study investigates the binding of rilpivirine in FIV RT and uses virtual screening to search for new candidates from mushrooms. Cordyceamide A and B from cordyceps were found to be possible to bind with FIV RT, supported by previous reports. Molecular dynamics simulations and quantum chemical calculations confirmed their binding capabilities, with cordyceamide A showing better binding free energies than rilpivirine. The study highlights the potential of these interactions for FIV drug development.
MOLECULAR SIMULATION
(2022)
Article
Biochemistry & Molecular Biology
Siriluk Ratanabunyong, Supaphorn Seetaha, Supa Hannongbua, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Atchara Paemanee, Kiattawee Choowongkomon
Summary: This research identified the KY44 aptamer as a potential inhibitor of both wildtype and mutant forms of HIV-RT. The aptamer showed low cytotoxicity and inhibited pseudo-HIV particle infection.
Article
Chemistry, Medicinal
Chayanin Hanwarinroj, Nareudon Phusi, Bundit Kamsri, Pharit Kamsri, Auradee Punkvang, Sombat Ketrat, Patchreenart Saparpakorn, Supa Hannongbua, Khomson Suttisintong, Prasat Kittakoop, James Spencer, Adrian J. Mulholland, Pornpan Pungpo
Summary: This study used in silico screening approaches to discover four novel InhA inhibitors with potential activity against Mycobacterium tuberculosis. The binding interactions and binding energy of the candidate compounds were investigated using molecular mechanics calculations. These compounds showed suitable physicochemical, pharmacokinetic, and antibacterial properties, making them promising hit compounds for further experimental studies.
FUTURE MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Inorganic & Nuclear
Zhong Zheng, Ze-Lin Zhu, Cheuk-Lam Ho, Shek-Man Yiu, Chun-Sing Lee, Songwut Suramitr, Supa Hannongbua, Yun Chi
Summary: A series of multi-dentate coordinated chelates LnH2, [Ir(Kappa 4-Ln)(mu-Cl)]2, and Ir(Kappa 4-Ln)(thd) with different coordination modes have been successfully designed and synthesized. The structures and properties of these complexes were investigated.
INORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sasipha Seetin, Patchreenart Saparpakorn, Jarunee Vanichtanankul, Danoo Vitsupakorn, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan, Supa Hannongbua
Summary: This study investigated the interactions of a series of compounds with Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) and human DHFR enzymes using various methods. The analysis of key interactions provided a general scheme for designing selective inhibitors for PfDHFR.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Phujinn Honorio, Supa Hannongbua, Patchreenart Saparpakorn
Summary: This study investigated the key binding interactions of hybrid donepezils for the treatment of Alzheimer's disease (AD) using molecular docking, molecular dynamics simulations, and quantum chemical calculations. The results revealed the important interactions between the hybrid donepezils and key residues in the binding pocket of acetylcholinesterase (AChE). The modification of the scaffolds and HOMO-LUMO predictions provided insights into the electron transfer and adaptation in the binding pocket. The bioavailability, drug-likeness, and pharmacokinetics predictions confirmed the suitability of the hybrid donepezils for AD drug development.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Multidisciplinary Sciences
Wei Lim Chong, Patchareenart Saparpakorn, Chak Sangma, Vannajan Sanghiran Lee, Supa Hannongbua
Summary: The SARS-CoV-2 virus is continuously evolving and mutating, resulting in many of the mutated variants resisting therapeutic monoclonal antibodies (mAbs). Efforts are being made to find mAb with broader neutralization coverage while maintaining neutralizing ability. In this study, the binding affinity of mAb MW06 and its cocktail formulation with MW05 for the SARS-CoV-2 virus receptor binding domain (RBD) was investigated using molecular dynamics simulations (MDs). The combination of MDs and ENM techniques provided simplicity in analyzing the interactions between mAbs and RBD.
Article
Integrative & Complementary Medicine
Viwan Jarerattanachat, Chompunuch Boonarkart, Supa Hannongbua, Prasert Auewarakul, Ruchuta Ardkhean
Summary: This study identified Isoquercitrin, a compound found in Ginseng and Notoginseng, as a potential inhibitor of Dengue NS5 protein. Isoquercitrin showed significant antiviral activity against Dengue virus by reducing viral RNA and protein synthesis with low cell toxicity.
JOURNAL OF TRADITIONAL AND COMPLEMENTARY MEDICINE
(2023)
Article
Chemistry, Medicinal
Bundit Kamsri, Bongkochawan Pakamwong, Paptawan Thongdee, Naruedon Phusi, Pharit Kamsri, Auradee Punkvang, Sombat Ketrat, Patchreenart Saparpakorn, Supa Hannongbua, Jidapa Sangswan, Khomson Suttisintong, Sanya Sureram, Prasat Kittakoop, Poonpilas Hongmanee, Pitak Santanirand, Jiraporn Leanpolchareanchai, Kirsty E. Goudar, James Spencer, Adrian J. Mulholland, Pornpan Pungpo
Summary: Mutations in DNA gyrase confer resistance to fluoroquinolones, second-line antibiotics for Mycobacterium tuberculosis infections. Identification of new agents that inhibit M. tuberculosis DNA gyrase ATPase activity is one strategy to overcome this. Compound R3-13, derived from bioisosteric designs, is a promising ATPase inhibitor against M. tuberculosis DNA gyrase. Additional screening using R3-13 as a template identified seven more ATPase inhibitors, with compound 1 showing the highest potency and noncytotoxicity to Caco-2 cells. Molecular dynamics simulations suggest that compound 1 binds to the ATP binding pocket in M. tuberculosis DNA gyrase GyrB subunit, making it a potential scaffold for further optimization.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Pavinee Prapassornwattana, Supa Hannongbua, Patchreenart Saparpakorn
Summary: This study reported the inhibitory activity of a benzene sulfonamide derivative against Coxsackievirus B3. By using molecular dynamics simulations and density functional theory, the key interactions between the compound and the viral capsid were investigated, and the differences in inhibitory activity against different mutants were explained. These findings are important for the development of drugs against CVB3.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Supaphorn Seetaha, Nuntaporn Kamonsutthipaijit, Maho Yagi-Utsumi, Yanaka Seako, Takumi Yamaguchi, Supa Hannongbua, Koichi Kato, Kiattawee Choowongkomon
Summary: This study characterized the structure and monomer forms of HIV-1 RT using biophysical techniques, and found that the unliganded monomers have different conformations compared to the complexes. Small-angle X-ray scattering experiments confirmed the binding of p66(W401A) and p51(W401A) with inhibitors.
Article
Chemistry, Multidisciplinary
Kewalin Posansee, Monrudee Liangruksa, Teerasit Termsaithong, Patchreenart Saparpakorn, Supa Hannongbua, Teeraphan Laomettachit, Thana Sutthibutpong
Summary: A deep learning model supported by principal component analysis and structural methods was used to search for an alternative mTOR inhibitor from mushrooms. Through filtering and molecular docking calculations, a potential candidate with therapeutic value was identified.
Article
Biochemical Research Methods
Malinee Promkatkaew, Pornthip Boonsri, Songwut Suramitr, Thitinun Karpkird, Peter Wolschann, Supa Hannongbua
Summary: This study investigated the host-guest interaction between methoxy cinnamic acid derivatives and cyclodextrins using density functional theory (DFT) and timedependent DFT (TD-DFT) calculations. The results revealed that intermolecular hydrogen bonds are the main driving force of this interaction. In addition, UV-vis absorption spectra analysis showed that one particular orientation is the most stable and similar to the parent MCA in terms of absorption in both UVB and UVA regions. These findings provide valuable insights into the host-guest interaction and stability improvement of UV-filter compounds.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Pharmacology & Pharmacy
Suriyan Thengyai, Yuewei Guo, Khanit Suwanborirux, Heinz Berner, Helmut Spreitzer, Peter Wolschann, Supa Hannongbua, Anuchit Plubrukarn
Summary: A series of scalarane sesterterpenes were synthesized using heteronemin (1) as the primary precursor. QSAR models based on 2D-QSAR and CoMFA approaches were built using a total of 22 antitubercular scalaranes obtained from natural sources and synthesis. The models indicated the significance of substitutions near C-12 and C-16 of the scalaranes.
SCIENTIA PHARMACEUTICA
(2022)