1
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Zheng T, Mitchell JBO, Dobson S. Revisiting the Application of Machine Learning Approaches in Predicting Aqueous Solubility. ACS OMEGA 2024; 9:35209-35222. [PMID: 39157153 PMCID: PMC11325511 DOI: 10.1021/acsomega.4c06163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/20/2024]
Abstract
The solubility of chemical substances in water is a critical parameter in pharmaceutical development, environmental chemistry, agrochemistry, and other fields; however, accurately predicting it remains a challenge. This study aims to evaluate and compare the effectiveness of some of the most popular machine learning modeling methods and molecular featurization techniques in predicting aqueous solubility. Although these methods were not implemented in a competitive environment, some of their performance surpassed previous benchmarks, offering gradual but significant improvements. Our results show that methods based on graph convolution and graph attention mechanisms demonstrated exceptional predictive abilities with high-quality data sets, albeit with a sensitivity to data noise and errors. In contrast, models leveraging molecular descriptors not only provided better interpretability but also showed more resilience when dealing with inherent noise and errors in data. Our analysis of over 4000 molecular descriptors used in various models identified that approximately 800 of these descriptors make a significant contribution to solubility prediction. These insights offer guidance and direction for future developments in solubility prediction.
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Affiliation(s)
- Tianyuan Zheng
- School
of Computer Science, University of St Andrews, St Andrews, Fife KY16 9SX, U.K.
| | - John B. O. Mitchell
- EaStCHEM
School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, U.K.
| | - Simon Dobson
- School
of Computer Science, University of St Andrews, St Andrews, Fife KY16 9SX, U.K.
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2
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Haufe Y, Loser D, Danker T, Nicke A. Symmetrical Bispyridinium Compounds Act as Open Channel Blockers of Cation-Selective Ion Channels. ACS Pharmacol Transl Sci 2024; 7:771-786. [PMID: 38495220 PMCID: PMC10941285 DOI: 10.1021/acsptsci.3c00308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 03/19/2024]
Abstract
Current treatments against organophosphate poisoning (OPP) do not directly address effects mediated by the overstimulation of nicotinic acetylcholine receptors (nAChR). Non-oxime bispyridinium compounds (BPC) promote acetylcholine esterase-independent recovery of organophosphate-induced paralysis. Here, we test the hypothesis that they act by positive modulatory action on nAChRs. Using two-electrode voltage clamp analysis in combination with mutagenesis and molecular docking analysis, the potency and molecular mode of action of a series of nine BPCs was investigated on human α7 and muscle-type nAChRs expressed in Xenopus laevis oocytes. The investigated BPCs inhibited α7 and/or muscle-type nAChRs with IC50 values in the high nanomolar to high micromolar range. Further analysis of the most potent analogues revealed a noncompetitive, voltage-dependent inhibition. Co-application with the α7-selective positive allosteric modulator PNU120596 and generation of α7/5HT3 receptor chimeras excluded direct interaction with the PNU120596 binding site and binding to the extracellular domain of the α7 nAChR, suggesting that they act as open channel blockers (OCBs). Molecular docking supported by mutagenesis localized the BPC binding area in the outer channel vestibule between the extracellular and transmembrane domains. Analysis of BPC action on other cation-selective channels suggests a rather nonspecific inhibition of pentameric cation channels. BPCs have been shown to ameliorate organophosphate-induced paralysis in vitro and in vivo. Our data support molecular action as OCBs at α7 and muscle-type nAChRs and suggest that their positive physiological effects are more complex than anticipated and require further investigation.
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Affiliation(s)
- Yves Haufe
- Walther
Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany
| | - Dominik Loser
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Timm Danker
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Annette Nicke
- Walther
Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany
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3
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Arer V, Kar D. Biochemical exploration of β-lactamase inhibitors. Front Genet 2023; 13:1060736. [PMID: 36733944 PMCID: PMC9888030 DOI: 10.3389/fgene.2022.1060736] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
The alarming rise of microbial resistance to antibiotics has severely limited the efficacy of current treatment options. The prevalence of β-lactamase enzymes is a significant contributor to the emergence of antibiotic resistance. There are four classes of β-lactamases: A, B, C, and D. Class B is the metallo-β-lactamase, while the rest are serine β-lactamases. The clinical use of β-lactamase inhibitors began as an attempt to combat β-lactamase-mediated resistance. Although β-lactamase inhibitors alone are ineffective against bacteria, research has shown that combining inhibitors with antibiotics is a safe and effective treatment that not only prevents β-lactamase formation but also broadens the range of activity. These inhibitors may cause either temporary or permanent inhibition. The development of new β-lactamase inhibitors will be a primary focus of future research. This study discusses recent advances in our knowledge of the biochemistry behind β-lactam breakdown, with special emphasis on the mechanism of inhibitors for β-lactam complexes with β-lactamase. The study also focuses on the pharmacokinetic and pharmacodynamic properties of all inhibitors and then applies them in clinical settings. Our analysis and discussion of the challenges that exist in designing inhibitors might help pharmaceutical researchers address root issues and develop more effective inhibitors.
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4
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Zhu Q, Ge Y, Li W, Ma J. Treating Polarization Effects in Charged and Polar Bio-Molecules Through Variable Electrostatic Parameters. J Chem Theory Comput 2023; 19:396-411. [PMID: 36592097 DOI: 10.1021/acs.jctc.2c01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Polarization plays important roles in charged and hydrogen bonding containing systems. Much effort ranging from the construction of physics-based models to quantum mechanism (QM)-based and machine learning (ML)-assisted models have been devoted to incorporating the polarization effect into the conventional force fields at different levels, such as atomic and coarse grained (CG). The application of polarizable force fields or polarization models was limited by two aspects, namely, computational cost and transferability. Different from physics-based models, no predetermining parameters were required in the QM-based approaches. Taking advantage of both the accuracy of QM calculations and efficiency of molecular mechanism (MM) and ML, polarization effects could be treated more efficiently while maintaining the QM accuracy. The computational cost could be reduced with variable electrostatic parameters, such as the charge, dipole, and electronic dielectric constant with the help of linear scaling fragmentation-based QM calculations and ML models. Polarization and entropy effects on the prediction of partition coefficient of druglike molecules are demonstrated by using both explicit or implicit all-atom molecular dynamics simulations and machine learning-assisted models. Directions and challenges for future development are also envisioned.
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Affiliation(s)
- Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
| | - Yang Ge
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
| | - Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
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5
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Reliable Prediction of Caco-2 Permeability by Supervised Recursive Machine Learning Approaches. Pharmaceutics 2022; 14:pharmaceutics14101998. [PMID: 36297432 PMCID: PMC9610902 DOI: 10.3390/pharmaceutics14101998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
The heterogeneity of the Caco-2 cell line and differences in experimental protocols for permeability assessment using this cell-based method have resulted in the high variability of Caco-2 permeability measurements. These problems have limited the generation of large datasets to develop accurate and applicable regression models. This study presents a QSPR approach developed on the KNIME analytical platform and based on a structurally diverse dataset of over 4900 molecules. Interpretable models were obtained using random forest supervised recursive algorithms for data cleaning and feature selection. The development of a conditional consensus model based on regional and global regression random forest produced models with RMSE values between 0.43–0.51 for all validation sets. The potential applicability of the model as a surrogate for the in vitro Caco-2 assay was demonstrated through blind prediction of 32 drugs recommended by the International Council for the Harmonization of Technical Requirements for Pharmaceuticals (ICH) for validation of in vitro permeability methods. The model was validated for the preliminary estimation of the BCS/BDDCS class. The KNIME workflow developed to automate new drug prediction is freely available. The results suggest that this automated prediction platform is a reliable tool for identifying the most promising compounds with high intestinal permeability during the early stages of drug discovery.
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6
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Zhou M, Yang H, Li H, Gu L, Zhou Y, Li M. The effects of molecular weight and orientation on the membrane permeation and partitioning of polycyclic aromatic hydrocarbons: a computational study. Phys Chem Chem Phys 2022; 24:2158-2166. [PMID: 35005759 DOI: 10.1039/d1cp04777a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Membrane permeation and the partitioning of polycyclic aromatic hydrocarbons (PAHs) are crucial aspects affecting their carcinogenicity and mutagenicity. However, a clear understanding of these processes is still rare due to the difficulty of determining the details experimentally. Here, the interactions between PAHs and lipid bilayers were studied by molecular simulations, mainly to check the influence of molecular weight and orientation. The liposome-water partition coefficient (KLW), transmembrane time (τ), and permeability coefficient (P) of the PAHs were calculated by integrating free energy profiles from umbrella sampling. For selected PAHs, the membrane adsorption is a spontaneous process. The preferred location is near the CC bond and the orientation is related to the molecular structure. The P values of all the PAHs are basically the same order of magnitude, which means that the molecular weight contributes little to the process. As for KLW and τ, they show obvious increases with different molecular weights. Unconstrained simulations showed that a flat orientation on the membrane surface would prevent PAHs from being transported through the membrane. Highly hydrophobic driving forces are not always good for the absorption of PAHs, especially the formation of aggregates. In addition, the orientations and energetic barriers of PAHs near the midplane of the lipid bilayer explain the different transitions of high- and low-weight PAHs. This work provides molecular level details relating to the interactions of PAHs with lipid membranes, with significance for understanding the health effects of PAHs.
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Affiliation(s)
- Mi Zhou
- School of Materials Science & Engineering, Beijing Institute of Technology, Beijing 100081, China.,Institute of Chemical Materials, Chinese Academy of Engineering and Physics, 621900 Mianyang, China.
| | - Hong Yang
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, 621900 Mianyang, China.
| | - Huarong Li
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, 621900 Mianyang, China.
| | - Lingzhi Gu
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, 621900 Mianyang, China.
| | - Yang Zhou
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, 621900 Mianyang, China.
| | - Ming Li
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, 621900 Mianyang, China.
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7
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Faraag AHI, Shafaa MW, Elkholy NS, Abdel-Hafez LJM. Stress impact of liposomes loaded with ciprofloxacin on the expression level of MepA and NorB efflux pumps of methicillin-resistant Staphylococcus aureus. Int Microbiol 2021; 25:427-446. [PMID: 34822035 DOI: 10.1007/s10123-021-00219-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/05/2021] [Accepted: 10/20/2021] [Indexed: 10/19/2022]
Abstract
One mechanism of ciprofloxacin resistance is attributed to chromosomal DNA-encoded efflux pumps such as the MepA and NorB proteins. The goal of this research is to find a way to bypass Staphylococcus aureus' efflux pumps. Because of its high membrane permeability and low association with NorB and MepA efflux proteins, a liposome-encapsulating antibiotic is one of the promising, cost-effective drug carriers and coating mechanisms for overcoming active transport of methicillin-resistant S. aureus (MRSA) multidrug-resistant efflux protein . The calculated "Log Perm RRCK" membrane permeability values of 1,2-distearoyl-sn-glycerol-3-phosphocholine (DSPC) ciprofloxacin liposome-encapsulated (CFL) showed a lower negative value of - 4,652 cm/s and greater membrane permeability than ciprofloxacin free (CPF). The results of RT-qPCR showed that cationic liposomes containing ciprofloxacin in liposome-encapsulated form (CFL) improved CPF antibacterial activity and affinity for negatively charged bacterial cell surface membrane in comparison to free drug and liposome, as it overcame several resistance mechanisms and reduced the expression of efflux pumps. Ciprofloxacin liposome-encapsulated (CFL) is therefore more effective than ciprofloxacin alone. Liposomes can be combined with a variety of drugs that interact with bacterial cell efflux pumps to maintain high sustained levels of antibiotics in bacterial cells.
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Affiliation(s)
| | - Medhat W Shafaa
- Medical Biophysics Division, Physics Department, Faculty of Science, Helwan University, Cairo, Egypt
| | - Nourhan S Elkholy
- Medical Biophysics Division, Physics Department, Faculty of Science, Helwan University, Cairo, Egypt
| | - Lina Jamil M Abdel-Hafez
- Department of Microbiology and Immunology, Faculty of Pharmacy, October 6 University, 6 October City, Giza, Egypt
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8
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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9
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Yang Y, Dong H, Zhou HX. Effects of Cholesterol on the Partitioning of a Drug Molecule in Lipid Bilayers. J Phys Chem B 2021; 125:5338-5345. [PMID: 33984232 DOI: 10.1021/acs.jpcb.1c02436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Drug molecules either bind to membrane-bound targets or permeate through cell membranes to reach intracellular targets, and hence, their membrane partition and permeation are of great importance. Here, we studied the effects of cholesterol on the partition of amantadine, an antiflu drug molecule, into 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayers using molecular dynamics simulations. The membrane partition of amantadine is sensitive to the cholesterol mole fraction (xchol). In the absence of cholesterol, amantadine is stably bound in membranes, but at xchol = 32%, it can escape to the aqueous phase, in agreement with recent experiments. The reduced membrane partition of amantadine at a high cholesterol content is mainly due to the perturbation of the bilayer structure and dynamics. Surrounding lipids stabilize amantadine by having their tails wrapped around the drug molecule, and this ability is compromised when cholesterol is present to increase the order in lipid tails. The atomic details on interactions with lipids and perturbations by cholesterol revealed here provide insight into membrane partition and delivery of drug molecules to their targets.
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Affiliation(s)
- Yuqin Yang
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China.,Institute for Brain Sciences, Nanjing University, 210023 Nanjing, China
| | - Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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10
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Mastering the Gram-negative bacterial barrier - Chemical approaches to increase bacterial bioavailability of antibiotics. Adv Drug Deliv Rev 2021; 172:339-360. [PMID: 33705882 DOI: 10.1016/j.addr.2021.02.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
To win the battle against resistant, pathogenic bacteria, novel classes of anti-infectives and targets are urgently needed. Bacterial uptake, distribution, metabolic and efflux pathways of antibiotics in Gram-negative bacteria determine what we here refer to as bacterial bioavailability. Understanding these mechanisms from a chemical perspective is essential for anti-infective activity and hence, drug discovery as well as drug delivery. A systematic and critical discussion of in bacterio, in vitro and in silico assays reveals that a sufficiently accurate holistic approach is still missing. We expect new findings based on Gram-negative bacterial bioavailability to guide future anti-infective research.
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11
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Sharifian Gh M. Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules. Mol Pharm 2021; 18:2122-2141. [PMID: 33914545 DOI: 10.1021/acs.molpharmaceut.1c00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to measure the passive membrane permeation of drug-like molecules is of fundamental biological and pharmaceutical importance. Of significance, passive diffusion across the cellular membranes plays an effective role in the delivery of many pharmaceutical agents to intracellular targets. Hence, approaches for quantitative measurement of membrane permeability have been the topics of research for decades, resulting in sophisticated biomimetic systems coupled with advanced techniques. In this review, recent developments in experimental approaches along with theoretical models for quantitative and real-time analysis of membrane transport of drug-like molecules through mimetic and living cell membranes are discussed. The focus is on time-resolved fluorescence-based, surface plasmon resonance, and second-harmonic light scattering approaches. The current understanding of how properties of the membrane and permeant affect the permeation process is discussed.
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Affiliation(s)
- Mohammad Sharifian Gh
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States
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12
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Zhu Q, Gu Y, Hu L, Gaudin T, Fan M, Ma J. Shear viscosity prediction of alcohols, hydrocarbons, halogenated, carbonyl, nitrogen-containing, and sulfur compounds using the variable force fields. J Chem Phys 2021; 154:074502. [PMID: 33607909 DOI: 10.1063/5.0038267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Viscosity of organic liquids is an important physical property in applications of printing, pharmaceuticals, oil extracting, engineering, and chemical processes. Experimental measurement is a direct but time-consuming process. Accurately predicting the viscosity with a broad range of chemical diversity is still a great challenge. In this work, a protocol named Variable Force Field (VaFF) was implemented to efficiently vary the force field parameters, especially λvdW, for the van der Waals term for the shear viscosity prediction of 75 organic liquid molecules with viscosity ranging from -9 to 0 in their nature logarithm and containing diverse chemical functional groups, such as alcoholic hydroxyl, carbonyl, and halogenated groups. Feature learning was applied for the viscosity prediction, and the selected features indicated that the hydrogen bonding interactions and the number of atoms and rings play important roles in the property of viscosity. The shear viscosity prediction of alcohols is very difficult owing to the existence of relative strong intermolecular hydrogen bonding interaction as reflected by density functional theory binding energies. From radial and spatial distribution functions of methanol, we found that the van der Waals related parameters λvdW are more crucial to the viscosity prediction than the rotation related parameters, λtor. With the variable λvdW-based all-atom optimized potentials for liquid simulations force field, a great improvement was observed in the viscosity prediction for alcohols. The simplicity and uniformity of VaFF make it an efficient tool for the prediction of viscosity and other related properties in the rational design of materials with the specific properties.
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Affiliation(s)
- Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yuming Gu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Limu Hu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Théophile Gaudin
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Mengting Fan
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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13
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Huo J, Dong H. Gating and regulation of the calcium release-activated calcium channel: Recent progress from experiments and molecular modeling. Biopolymers 2021; 111:e23392. [PMID: 33460071 DOI: 10.1002/bip.23392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 11/08/2022]
Abstract
Calcium release-activated calcium (CRAC) channels are highly calcium ion (Ca2+)-selective channels in the plasma membrane. The transient drop of endoplasmic reticulum Ca2+ level activates its calcium sensor stromal interaction molecule (STIM) and then triggers the gating of the CRAC channel pore unit Orai. This process involves a variety of activities of the immune system. Therefore, understanding how the activation and regulation of the CRAC channel can be accomplished is essential. Here we briefly summarize the recent progress on Orai gating and its regulation by 2-aminoethoxydiphenylborate (2-APB) obtained from structural biology studies, biochemical and electrophysiological measurements, as well as molecular modeling. Indeed, integration between experiments and computations has further deepened our understanding of the channel gating and regulation.
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Affiliation(s)
- Jun Huo
- Kuang Yaming Honors School, Nanjing University, Nanjing, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing, China.,Institute for Brain Sciences, Nanjing University, Nanjing, China
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14
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Skarmoutsos I, Maurin G, Guardia E, Samios J. Hydration Structure and Dynamics of the Favipiravir Antiviral Drug: A Molecular Modelling Approach. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ioannis Skarmoutsos
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Vas. Constantinou 48, GR-116 35, Athens, Greece
| | | | - Elvira Guardia
- Departament de Física, Universitat Politècnica de Catalunya, Campus Nord-Edifici B4-B5, Jordi Girona 1-3, Barcelona E-08034, Spain
| | - Jannis Samios
- Department of Chemistry, Laboratory of Physical Chemistry, National & Kapodistrian University of Athens, Panepistimiopolis 157-71, Athens, Greece
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15
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Gütlein P, Blumberger J, Oberhofer H. An Iterative Fragment Scheme for the ACKS2 Electronic Polarization Model: Application to Molecular Dimers and Chains. J Chem Theory Comput 2020; 16:5723-5735. [PMID: 32701273 DOI: 10.1021/acs.jctc.0c00151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The treatment of electrostatic interactions is a key ingredient in the force field-based simulation of condensed phase systems. Most approaches used fixed, site-specific point charges. Yet, it is now clear that many applications of force fields (FFs) demand more sophisticated treatments, prompting the implementation of charge equilibration methods in polarizable FFs to allow the redistribution of charge within the system. One approach allowing both, charge redistribution and site-specific polarization, while at the same time solving methodological shortcomings of earlier methods, is the first-principles-derived atom-condensed Kohn-Sham density functional theory method approximated to the second order (ACKS2). In this work, we present two fragment approaches to ACKS2, termed f-ACKS2 and a self-consistent version, scf-ACKS2, that treat condensed phase systems as a collection of electronically polarizable molecular fragments. The fragmentation approach to ACKS2 not only leads to a more transferable and less system-specific collection of electronic response parameters but also opens up the method to large condensed phase systems. We validate the accuracies of f-ACKS2 and scf-ACKS2 by comparing polarization energies and induced dipole moments for a number of charged hydrocarbon dimers against DFT reference calculations. Finally, we also apply both fragmented ACKS2 variants to calculate the polarization energy for electron-hole pair separation along a chain of anthracene molecules and find excellent agreement with reference DFT calculations.
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Affiliation(s)
- Patrick Gütlein
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, U.K.,Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse 2 a, D-85748 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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16
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Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J Am Chem Soc 2019; 141:13421-13433. [PMID: 31382734 DOI: 10.1021/jacs.9b04387] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Permeability (Pm) across biological membranes is of fundamental importance and a key factor in drug absorption, distribution, and development. Although the majority of drugs will be charged at some point during oral delivery, our understanding of membrane permeation by charged species is limited. The canonical model assumes that only neutral molecules partition into and passively permeate across membranes, but there is mounting evidence that these processes are also facile for certain charged species. However, it is unknown whether such ionizable permeants dynamically neutralize at the membrane surface or permeate in their charged form. To probe protonation-coupled permeation in atomic detail, we herein apply continuous constant-pH molecular dynamics along with free energy sampling to study the permeation of a weak base propranolol (PPL), and evaluate the impact of including dynamic protonation on Pm. The simulations reveal that PPL dynamically neutralizes at the lipid-tail interface, which dramatically influences the permeation free energy landscape and explains why the conventional model overestimates the assigned intrinsic permeability. We demonstrate how fixed-charge-state simulations can account for this effect, and propose a revised model that better describes pH-coupled partitioning and permeation. Our results demonstrate how dynamic changes in protonation state may play a critical role in the permeation of ionizable molecules, including pharmaceuticals and drug-like molecules, thus requiring a revision of the standard picture.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Chenghan Li
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Gregory A Voth
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Jessica M J Swanson
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
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Abstract
This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal JP, Ren P. Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications. Annu Rev Biophys 2019; 48:371-394. [PMID: 30916997 DOI: 10.1146/annurev-biophys-070317-033349] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Sara Y Cheng
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Brandon D Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA; .,Sorbonne Université, CNRS, Laboratoire de Chimie Theórique, 75252 Paris CEDEX 05, France.,Institut Universitaire de France, 75005 Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
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Zhu Q, Yuan Y, Ma J, Dong H. A Data‐Driven Accelerated Sampling Method for Searching Functional States of Proteins. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of EducationInstitute of Theoretical and Computational Chemistry School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China
- Kuang Yaming Honors SchoolNanjing University Nanjing 210023 P. R. China
| | - Yigao Yuan
- Kuang Yaming Honors SchoolNanjing University Nanjing 210023 P. R. China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of EducationInstitute of Theoretical and Computational Chemistry School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China
| | - Hao Dong
- Kuang Yaming Honors SchoolNanjing University Nanjing 210023 P. R. China
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Badaoui M, Kells A, Molteni C, Dickson CJ, Hornak V, Rosta E. Calculating Kinetic Rates and Membrane Permeability from Biased Simulations. J Phys Chem B 2018; 122:11571-11578. [DOI: 10.1021/acs.jpcb.8b07442] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Magd Badaoui
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| | - Adam Kells
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| | - Carla Molteni
- Department of Physics, King’s College London, WC2R 2LS London, United Kingdom
| | - Callum J. Dickson
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, Massachusetts 02139, United States
| | - Edina Rosta
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
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