1
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Ghosh D, Biswas A, Radhakrishna M. Advanced computational approaches to understand protein aggregation. BIOPHYSICS REVIEWS 2024; 5:021302. [PMID: 38681860 PMCID: PMC11045254 DOI: 10.1063/5.0180691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Protein aggregation is a widespread phenomenon implicated in debilitating diseases like Alzheimer's, Parkinson's, and cataracts, presenting complex hurdles for the field of molecular biology. In this review, we explore the evolving realm of computational methods and bioinformatics tools that have revolutionized our comprehension of protein aggregation. Beginning with a discussion of the multifaceted challenges associated with understanding this process and emphasizing the critical need for precise predictive tools, we highlight how computational techniques have become indispensable for understanding protein aggregation. We focus on molecular simulations, notably molecular dynamics (MD) simulations, spanning from atomistic to coarse-grained levels, which have emerged as pivotal tools in unraveling the complex dynamics governing protein aggregation in diseases such as cataracts, Alzheimer's, and Parkinson's. MD simulations provide microscopic insights into protein interactions and the subtleties of aggregation pathways, with advanced techniques like replica exchange molecular dynamics, Metadynamics (MetaD), and umbrella sampling enhancing our understanding by probing intricate energy landscapes and transition states. We delve into specific applications of MD simulations, elucidating the chaperone mechanism underlying cataract formation using Markov state modeling and the intricate pathways and interactions driving the toxic aggregate formation in Alzheimer's and Parkinson's disease. Transitioning we highlight how computational techniques, including bioinformatics, sequence analysis, structural data, machine learning algorithms, and artificial intelligence have become indispensable for predicting protein aggregation propensity and locating aggregation-prone regions within protein sequences. Throughout our exploration, we underscore the symbiotic relationship between computational approaches and empirical data, which has paved the way for potential therapeutic strategies against protein aggregation-related diseases. In conclusion, this review offers a comprehensive overview of advanced computational methodologies and bioinformatics tools that have catalyzed breakthroughs in unraveling the molecular basis of protein aggregation, with significant implications for clinical interventions, standing at the intersection of computational biology and experimental research.
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Affiliation(s)
- Deepshikha Ghosh
- Department of Biological Sciences and Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Anushka Biswas
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
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2
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Chen M, Jiang X, Zhang L, Chen X, Wen Y, Gu Z, Li X, Zheng M. The emergence of machine learning force fields in drug design. Med Res Rev 2024; 44:1147-1182. [PMID: 38173298 DOI: 10.1002/med.22008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
In the field of molecular simulation for drug design, traditional molecular mechanic force fields and quantum chemical theories have been instrumental but limited in terms of scalability and computational efficiency. To overcome these limitations, machine learning force fields (MLFFs) have emerged as a powerful tool capable of balancing accuracy with efficiency. MLFFs rely on the relationship between molecular structures and potential energy, bypassing the need for a preconceived notion of interaction representations. Their accuracy depends on the machine learning models used, and the quality and volume of training data sets. With recent advances in equivariant neural networks and high-quality datasets, MLFFs have significantly improved their performance. This review explores MLFFs, emphasizing their potential in drug design. It elucidates MLFF principles, provides development and validation guidelines, and highlights successful MLFF implementations. It also addresses potential challenges in developing and applying MLFFs. The review concludes by illuminating the path ahead for MLFFs, outlining the challenges to be overcome and the opportunities to be harnessed. This inspires researchers to embrace MLFFs in their investigations as a new tool to perform molecular simulations in drug design.
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Affiliation(s)
- Mingan Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Xinyu Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Lehan Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxu Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Yiming Wen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Zhiyong Gu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
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3
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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024; 59:20-68. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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4
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Krupa MA, Krupa P. Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking. Methods Mol Biol 2024; 2780:27-41. [PMID: 38987462 DOI: 10.1007/978-1-0716-3985-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Docking methods can be used to predict the orientations of two or more molecules with respect of each other using a plethora of various algorithms, which can be based on the physics of interactions or can use information from databases and templates. The usability of these approaches depends on the type and size of the molecules, whose relative orientation will be estimated. The two most important limitations are (i) the computational cost of the prediction and (ii) the availability of the structural information for similar complexes. In general, if there is enough information about similar systems, knowledge-based and template-based methods can significantly reduce the computational cost while providing high accuracy of the prediction. However, if the information about the system topology and interactions between its partners is scarce, physics-based methods are more reliable or even the only choice. In this chapter, knowledge-, template-, and physics-based methods will be compared and briefly discussed providing examples of their usability with a special emphasis on physics-based protein-protein, protein-peptide, and protein-fullerene docking in the UNRES coarse-grained model.
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Affiliation(s)
- Magdalena A Krupa
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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5
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Domingo L, Djukic M, Johnson C, Borondo F. Binding affinity predictions with hybrid quantum-classical convolutional neural networks. Sci Rep 2023; 13:17951. [PMID: 37864075 PMCID: PMC10589342 DOI: 10.1038/s41598-023-45269-y] [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: 08/07/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023] Open
Abstract
Central in drug design is the identification of biomolecules that uniquely and robustly bind to a target protein, while minimizing their interactions with others. Accordingly, precise binding affinity prediction, enabling the accurate selection of suitable candidates from an extensive pool of potential compounds, can greatly reduce the expenses associated to practical experimental protocols. In this respect, recent advances revealed that deep learning methods show superior performance compared to other traditional computational methods, especially with the advent of large datasets. These methods, however, are complex and very time-intensive, thus representing an important clear bottleneck for their development and practical application. In this context, the emerging realm of quantum machine learning holds promise for enhancing numerous classical machine learning algorithms. In this work, we take one step forward and present a hybrid quantum-classical convolutional neural network, which is able to reduce by 20% the complexity of the classical counterpart while still maintaining optimal performance in the predictions. Additionally, this results in a significant cost and time savings of up to 40% in the training stage, which means a substantial speed-up of the drug design process.
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Affiliation(s)
- L Domingo
- Grupo de Sistemas Complejos, Universidad Politécnica de Madrid, 28035, Madrid, Spain.
- Instituto de Ciencias Matemáticas (ICMAT), Campus de Cantoblanco UAM, Nicolás Cabrera, 13-15, 28049, Madrid, Spain.
- Departamento de Química, Universidad Autónoma de Madrid, 28049, Cantoblanco, Madrid, Spain.
- Ingenii Inc., New York, USA.
| | | | | | - F Borondo
- Departamento de Química, Universidad Autónoma de Madrid, 28049, Cantoblanco, Madrid, Spain
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6
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Sheik Ismail Z, Worth R, Mosebi S, Sayed Y. HIV Protease Hinge Region Insertions at Codon 38 Affect Enzyme Kinetics, Conformational Stability and Dynamics. Protein J 2023; 42:490-501. [PMID: 37421557 PMCID: PMC10480237 DOI: 10.1007/s10930-023-10132-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
HIV-1 protease is essential for the production of mature, infectious virions and is a major target in antiretroviral therapy. We successfully purified a HIV-1 subtype C variant, L38↑N↑L- 4, containing an insertion of asparagine and leucine at position 38 without the four background mutations - K20R, E35D, R57K, V82I using a modified purification protocol. Isothermal titration calorimetry indicated that 50% of the variant protease sample was in the active conformation compared to 62% of the wild type protease. The secondary structure composition of the variant protease was unaffected by the double insertion. The specific activity and kcat values of the variant protease were approximately 50% lower than the wild type protease values. The variant protease also exhibited a 1.6-fold increase in kcat/KM when compared to the wild type protease. Differential scanning calorimetry showed a 5 °C increase in Tm of the variant protease, indicating the variant was more stable than the wild type. Molecular dynamics simulations indicated the variant was more stable and compact than the wild type protease. A 3-4% increase in the flexibility of the hinge regions of the variant protease was observed. In addition, increased flexibility of the flaps, cantilever and fulcrum regions of the variant protease B chain was observed. The variant protease sampled only the closed flap conformation indicating a potential mechanism for drug resistance. The present study highlights the direct impact of a double amino acid insertion in hinge region on enzyme kinetics, conformational stability and dynamics of an HIV-1 subtype C variant protease.
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Affiliation(s)
- Zaahida Sheik Ismail
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Roland Worth
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Salerwe Mosebi
- College of Agriculture & Environmental Sciences, School of Agriculture and Life Sciences, Department of Life and Consumer Sciences, UNISA, Pretoria, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa.
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7
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Oliveira MP, Hünenberger PH. Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization. J Chem Theory Comput 2023; 19:2048-2063. [PMID: 36920838 PMCID: PMC10100539 DOI: 10.1021/acs.jctc.2c01170] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
We recently introduced the CombiFF scheme [Oliveira et al., J. Chem. Theory Comput. 2020, 16, 7525], an approach for the automated refinement of force-field parameters against experimental condensed-phase data for large compound families. Using this scheme, once the time-consuming task of target-data selection and curation has been performed, the force-field optimization itself is both straightforward and fast. As a result, CombiFF provides an ideal framework for evaluating the influence of functional-form decisions on the accuracy of a force field at an optimal level of parametrization. We already used this approach to assess the effect of using an all-atom representation compared to united-atom representations in the force field [Oliveira et al., J. Chem. Theory Comput. 2022, 18, 6757]. Here, CombiFF is applied to assess the effect of three Lennard-Jones combination rules, geometric-mean (GM), Lorentz-Berthelot (LB), or Waldman-Hagler (WH), on the simulated properties of organic liquids. The comparison is performed in terms of the experimental liquid density ρliq, vaporization enthalpy ΔHvap, surface-tension coefficient γ, static relative dielectric permittivity ϵ, and self-diffusion coefficient D. The calibrations of the three force-field variants are carried out independently against 2044 experimental values for ρliq, and ΔHvap concerning 1516 compounds. The resulting root-mean-square deviations from experiment are 30.0, 26.9, and 36.7 kg m-3 for ρliq and 2.8, 2.8, and 2.9 kJ mol-1 for ΔHvap, when applying the GM, LB, and WH combination rules, respectively. In terms of these (and the other) properties, the three combination rules perform comparatively well, with the GM and LB results being more similar to each other and slightly more accurate compared to experiment. In contrast, the use of distinct combination rules for the parameter calibration and property calculation leads to much larger errors.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
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8
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Zhao S, Cieplak P, Duan Y, Luo R. Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model. J Chem Theory Comput 2023; 19:924-941. [PMID: 36696564 PMCID: PMC10152989 DOI: 10.1021/acs.jctc.2c01048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Accuracy and transferability are the two highly desirable properties of molecular mechanical force fields. Compared with the extensively used point-charge additive force fields that apply fixed atom-centered point partial charges to model electrostatic interactions, polarizable force fields are thought to have the advantage of modeling the atomic polarization effects. Previous works have demonstrated the accuracy of the recently developed polarizable Gaussian multipole (pGM) models. In this work, we assessed the transferability of the electrostatic parameters of the pGM models with (pGM-perm) and without (pGM-ind) atomic permanent dipoles in terms of reproducing the electrostatic potentials surrounding molecules/oligomers absent from electrostatic parameterizations. Encouragingly, both the pGM-perm and pGM-ind models show significantly improved transferability than the additive model in the tests (1) from water monomer to water oligomer clusters; (2) across different conformations of amino acid dipeptides and tetrapeptides; (3) from amino acid tetrapeptides to longer polypeptides; and (4) from nucleobase monomers to Watson-Crick base pair dimers and tetramers. Furthermore, we demonstrated that the double-conformation fittings using amino acid tetrapeptides in the αR and β conformations can result in good transferability not only across different tetrapeptide conformations but also from tetrapeptides to polypeptides with lengths ranging from 1 to 20 repetitive residues for both the pGM-ind and pGM-perm models. In addition, the observation that the pGM-ind model has significantly better accuracy and transferability than the point-charge additive model, even though they have an identical number of parameters, strongly suggest the importance of intramolecular polarization effects. In summary, this and previous works together show that the pGM models possess both accuracy and transferability, which are expected to serve as foundations for the development of next-generation polarizable force fields for modeling various polarization-sensitive biological systems and processes.
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Affiliation(s)
- Shiji Zhao
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
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9
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Guseva DV, Glagolev MK, Lazutin AA, Vasilevskaya VV. Revealing Structural and Physical Properties of Polylactide: What Simulation Can Do beyond the Experimental Methods. POLYM REV 2023. [DOI: 10.1080/15583724.2023.2174136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- D. V. Guseva
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - M. K. Glagolev
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - A. A. Lazutin
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - V. V. Vasilevskaya
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
- Chemistry Department, M. V. Lomonosov Moscow State University, Moscow, Russia
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10
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Tavares CA, Santos TMR, da Cunha EFF, Ramalho TC. Molecular Dynamics-Assisted Interaction of Vanadium Complex-AMPK: From Force Field Development to Biological Application for Alzheimer's Treatment. J Phys Chem B 2023; 127:495-504. [PMID: 36603208 DOI: 10.1021/acs.jpcb.2c07147] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A large part of the world's population is affected by Alzheimer's disease (AD) and diabetes mellitus type 2, which cause both social and economic impacts. These two conditions are associated with one protein, AMPK. Studies have shown that vanadium complexes, such as bis(N',N'-dimethylbiguanidato)-oxovanadium(IV), VO(metf)2·H2O, are potential agents against AD. A crucial step in drug design studies is obtaining information about the structure and interaction of these complexes with the biological targets involved in the process through molecular dynamics (MD) simulations. However, MD simulations depend on the choice of a good force field that could present reliable results. Moreover, general force fields are not efficient for describing the properties of metal complexes, and a VO(metf)2·H2O-specific force field does not yet exist; thus, the proper development of a parameter set is necessary. Furthermore, this investigation is essential and relevant given the importance for both the scientific community and the population that is affected by this neurodegenerative disease. Therefore, the present work aims to develop and validate the AMBER force field parameters for VO(metf)2·H2O since the literature lacks such information on metal complexes and investigate through classical molecular dynamics the interactions made by the complex with the protein. The proposed force field proved to be effective for describing the vanadium complex (VC), supported by different analyses and validations. Moreover, it had a great performance when compared to the general AMBER force field. Beyond that, MD findings provided an in-depth perspective of vanadium complex-protein interactions that should be taken into consideration in future studies.
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Affiliation(s)
- Camila A Tavares
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras37200-000, MG, Brazil
| | - Taináh M R Santos
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras37200-000, MG, Brazil
| | - Elaine F F da Cunha
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras37200-000, MG, Brazil
| | - Teodorico C Ramalho
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras37200-000, MG, Brazil.,Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové500 03, Czech Republic
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11
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Shahbabaei M, Tang T. Molecular modeling of thin-film nanocomposite membranes for reverse osmosis water desalination. Phys Chem Chem Phys 2022; 24:29298-29327. [PMID: 36453147 DOI: 10.1039/d2cp03839k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The scarcity of freshwater resources is a major global challenge causedby population and economic growth. Water desalination using a reverse osmosis (RO) membrane is a promising technology to supply potable water from seawater and brackish water. The advancement of RO desalination highly depends on new membrane materials. Currently, the RO technology mainly relies on polyamide thin-film composite (TFC) membranes, which suffer from several drawbacks (e.g., low water permeability, permeability-selectivity tradeoff, and low fouling resistance) that hamper their real-world applications. Nanoscale fillers with specific characteristics can be used to improve the properties of TFC membranes. Embedding nanofillers into TFC membranes using interfacial polymerization allows the creation of thin-film nanocomposite (TFNC) membranes, and has become an emerging strategy in the fabrication of high-performance membranes for advanced RO water desalination. To achieve optimal design, it is indispensable to search for reliable methods that can provide fast and accurate predictions of the structural and transport properties of the TFNC membranes. However, molecular understanding of permeability-selectivity characteristics of nanofillers remains limited, partially due to the challenges in experimentally exploring microscopic behaviors of water and salt ions in confinement. Molecular modeling and simulations can fill this gap by generating molecular-level insights into the effects of nanofillers' characteristics (e.g., shape, size, surface chemistry, and density) on water permeability and ion selectivity. In this review, we summarize molecular simulations of a diverse range of nanofillers including nanotubes (carbon nanotubes, boron nitride nanotubes, and aquaporin-mimicking nanochannels) and nanosheets (graphene, graphene oxide, boron nitride sheets, molybdenum disulfide, metal and covalent organic frameworks) for water desalination applications. These simulations reveal that water permeability and salt rejection, as the major factors determining the desalination performance of TFNC membranes, significantly depend on the size, topology, density, and chemical modifications of the nanofillers. Identifying their influences and the physicochemical processes behind, via molecular modeling, is expected to yield important insights for the fabrication and optimization of the next generation high-performance TFNC membranes for RO water desalination.
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Affiliation(s)
- Majid Shahbabaei
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada.
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada.
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12
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D’Amore L, Hahn DF, Dotson DL, Horton JT, Anwar J, Craig I, Fox T, Gobbi A, Lakkaraju SK, Lucas X, Meier K, Mobley DL, Narayanan A, Schindler CE, Swope WC, in ’t Veld PJ, Wagner J, Xue B, Tresadern G. Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. J Chem Inf Model 2022; 62:6094-6104. [PMID: 36433835 PMCID: PMC9873353 DOI: 10.1021/acs.jcim.2c01185] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small-molecule force field. In this report, industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4, and SMIRNOFF99Frosst. We analyzed force-field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.
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Affiliation(s)
- Lorenzo D’Amore
- Computational Chemistry, Janssen R&D, C/ Jarama 75A, 45007 Toledo, Spain
| | - David F. Hahn
- Computational Chemistry, Janssen R&D, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - David L. Dotson
- The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, USA
| | - Joshua T. Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jamshed Anwar
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, UK
| | - Ian Craig
- Molecular Modeling & Drug Discovery, BASF SE, 67056 Ludwigshafen, Germany
| | - Thomas Fox
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach/Riss, Germany
| | - Alberto Gobbi
- Genentech, Inc., 1 DNA Way, South San Francisco, California, 94080, USA
| | | | - Xavier Lucas
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Katharina Meier
- Computational Life Science Technology Functions, Crop Science, R&D, Bayer AG, 40789 Monheim, Germany
| | - David L. Mobley
- Departments of Pharmaceutical Sciences and Chemistry, University of California 92617, Irvine, USA
| | - Arjun Narayanan
- Data and Computational Sciences, Vertex Pharmaceuticals, 50 Northern Ave, Boston, MA 02210, USA
| | | | - William C. Swope
- Genentech, Inc., 1 DNA Way, South San Francisco, California, 94080, USA
| | | | - Jeffrey Wagner
- The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California, 95616, USA,Chemistry Department, The University of California at Irvine, Irvine, California, 92617, USA
| | - Bai Xue
- XtalPi Inc. Floor 3, International Biomedical Innovation Park II, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, Guangdong, 518040 China
| | - Gary Tresadern
- Computational Chemistry, Janssen R&D, Turnhoutseweg 30, Beerse B-2340, Belgium
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13
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Borišek J, Aupič J, Magistrato A. Establishing the catalytic and regulatory mechanism of
RNA
‐based machineries. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jure Borišek
- Theory Department National Institute of Chemistry Ljubljana Slovenia
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14
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Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρliq and vaporization enthalpies ΔHvap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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15
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Zhao S, Wei H, Cieplak P, Duan Y, Luo R. Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model. J Chem Theory Comput 2022; 18:6172-6188. [PMID: 36094401 PMCID: PMC10152986 DOI: 10.1021/acs.jctc.2c00710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A key advantage of polarizable force fields is their ability to model the atomic polarization effects that play key roles in the atomic many-body interactions. In this work, we assessed the accuracy of the recently developed polarizable Gaussian Multipole (pGM) models in reproducing quantum mechanical (QM) interaction energies, many-body interaction energies, as well as the nonadditive and additive contributions to the many-body interactions for peptide main-chain hydrogen-bonding conformers, using glycine dipeptide oligomers as the model systems. Two types of pGM models were considered, including that with (pGM-perm) and without (pGM-ind) permanent atomic dipoles. The performances of the pGM models were compared with several widely used force fields, including two polarizable (Amoeba13 and ff12pol) and three additive (ff19SB, ff15ipq, and ff03) force fields. Encouragingly, the pGM models outperform all other force fields in terms of reproducing QM interaction energies, many-body interaction energies, as well as the nonadditive and additive contributions to the many-body interactions, as measured by the root-mean-square errors (RMSEs) and mean absolute errors (MAEs). Furthermore, we tested the robustness of the pGM models against polarizability parameterization errors by employing alternative polarizabilities that are either scaled or obtained from other force fields. The results show that the pGM models with alternative polarizabilities exhibit improved accuracy in reproducing QM many-body interaction energies as well as the nonadditive and additive contributions compared with other polarizable force fields, suggesting that the pGM models are robust against the errors in polarizability parameterizations. This work shows that the pGM models are capable of accurately modeling polarization effects and have the potential to serve as templates for developing next-generation polarizable force fields for modeling various biological systems.
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Affiliation(s)
- Shiji Zhao
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Haixin Wei
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
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16
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Wang G, Bai Y, Cui J, Zong Z, Gao Y, Zheng Z. Computer-Aided Drug Design Boosts RAS Inhibitor Discovery. Molecules 2022; 27:molecules27175710. [PMID: 36080477 PMCID: PMC9457765 DOI: 10.3390/molecules27175710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/13/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
The Rat Sarcoma (RAS) family (NRAS, HRAS, and KRAS) is endowed with GTPase activity to regulate various signaling pathways in ubiquitous animal cells. As proto-oncogenes, RAS mutations can maintain activation, leading to the growth and proliferation of abnormal cells and the development of a variety of human cancers. For the fight against tumors, the discovery of RAS-targeted drugs is of high significance. On the one hand, the structural properties of the RAS protein make it difficult to find inhibitors specifically targeted to it. On the other hand, targeting other molecules in the RAS signaling pathway often leads to severe tissue toxicities due to the lack of disease specificity. However, computer-aided drug design (CADD) can help solve the above problems. As an interdisciplinary approach that combines computational biology with medicinal chemistry, CADD has brought a variety of advances and numerous benefits to drug design, such as the rapid identification of new targets and discovery of new drugs. Based on an overview of RAS features and the history of inhibitor discovery, this review provides insight into the application of mainstream CADD methods to RAS drug design.
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Affiliation(s)
- Ge Wang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Yuhao Bai
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Jiarui Cui
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Zirui Zong
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Yuan Gao
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Zhen Zheng
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Correspondence:
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17
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Ricci E, Minelli M, De Angelis MG. Modelling Sorption and Transport of Gases in Polymeric Membranes across Different Scales: A Review. MEMBRANES 2022; 12:membranes12090857. [PMID: 36135877 PMCID: PMC9502097 DOI: 10.3390/membranes12090857] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 06/02/2023]
Abstract
Professor Giulio C. Sarti has provided outstanding contributions to the modelling of fluid sorption and transport in polymeric materials, with a special eye on industrial applications such as membrane separation, due to his Chemical Engineering background. He was the co-creator of innovative theories such as the Non-Equilibrium Theory for Glassy Polymers (NET-GP), a flexible tool to estimate the solubility of pure and mixed fluids in a wide range of polymers, and of the Standard Transport Model (STM) for estimating membrane permeability and selectivity. In this review, inspired by his rigorous and original approach to representing membrane fundamentals, we provide an overview of the most significant and up-to-date modeling tools available to estimate the main properties governing polymeric membranes in fluid separation, namely solubility and diffusivity. The paper is not meant to be comprehensive, but it focuses on those contributions that are most relevant or that show the potential to be relevant in the future. We do not restrict our view to the field of macroscopic modelling, which was the main playground of professor Sarti, but also devote our attention to Molecular and Multiscale Hierarchical Modeling. This work proposes a critical evaluation of the different approaches considered, along with their limitations and potentiality.
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Affiliation(s)
- Eleonora Ricci
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy
| | - Matteo Minelli
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy
| | - Maria Grazia De Angelis
- Institute for Materials and Processes, School of Engineering, University of Edinburgh, Edinburgh EH9 3FB, UK
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18
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Rieder SR, Ries B, Schaller K, Champion C, Barros EP, Hünenberger PH, Riniker S. Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. J Chem Inf Model 2022; 62:3043-3056. [PMID: 35675713 PMCID: PMC9241072 DOI: 10.1021/acs.jcim.2c00383] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Free-energy differences
between pairs of end-states can be estimated
based on molecular dynamics (MD) simulations using standard pathway-dependent
methods such as thermodynamic integration (TI), free-energy perturbation,
or Bennett’s acceptance ratio. Replica-exchange enveloping
distribution sampling (RE-EDS), on the other hand, allows for the
sampling of multiple end-states in a single simulation without the
specification of any pathways. In this work, we use the RE-EDS method
as implemented in GROMOS together with generalized AMBER force-field
(GAFF) topologies, converted to a GROMOS-compatible format with a
newly developed GROMOS++ program amber2gromos, to
compute relative hydration free energies for a series of benzene derivatives.
The results obtained with RE-EDS are compared to the experimental
data as well as calculated values from the literature. In addition,
the estimated free-energy differences in water and in vacuum are compared
to values from TI calculations carried out with GROMACS. The hydration
free energies obtained using RE-EDS for multiple molecules are found
to be in good agreement with both the experimental data and the results
calculated using other free-energy methods. While all considered free-energy
methods delivered accurate results, the RE-EDS calculations required
the least amount of total simulation time. This work serves as a validation
for the use of GAFF topologies with the GROMOS simulation package
and the RE-EDS approach. Furthermore, the performance of RE-EDS for
a large set of 28 end-states is assessed with promising results.
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Affiliation(s)
- Salomé R Rieder
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Benjamin Ries
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Kay Schaller
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Candide Champion
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Emilia P Barros
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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19
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Gupta MK, Panwar V, Mahapatra RP. Computational analysis of mechanical behavior and potential energy of thermoresponsive copper-tantalum nanoalloy. J Mol Model 2022; 28:187. [PMID: 35695979 DOI: 10.1007/s00894-022-05183-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/03/2022] [Indexed: 10/18/2022]
Abstract
Temperature, strain rate, and defects are important considerations in determining the mechanical properties of materials. The mechanical properties of nanocrystalline copper-tantalum (Cu-Ta) alloy are investigated using classical molecular dynamics simulation approach in which embedded atom method of potential with periodic boundary conditions in all directions has been adopted. Numerical simulation has been performed to predict the mechanical properties of nanocrystalline copper-tantalum alloy. The virtual tensile test has been conducted at a fixed strain rate and increasing temperature where the discreet change in temperature from 50 to 1600 K has been used as a controlling parameter. The strain rate is fixed in the direction of the principal crystallographic planes and has not been affected by the change in temperature. The mechanical properties of the Cu-Ta nanocrystalline alloy such as yield strength, ultimate strength, and Young's modulus are observed. Further, simulations are carried out to analyze the vacancy formation energy with vacancy concentration and potential energy response at discrete temperatures. Nanocrystalline Cu-Ta alloy is observed to be more susceptible to failure at high temperatures. Particularly at 300 K, the strength of nanocrystalline Cu-Ta is 6 GPa which decreases to 4 GPa at 1200 K.
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Affiliation(s)
- Mahesh Kumar Gupta
- Department of Mechanical Engineering, SRM Institute of Science and Technology, Delhi-NCR Campus, Modinagar, Ghaziabad, UP, 201204, India
| | - Vinay Panwar
- Mechanical Engineering Department, Netaji Subhas University of Technology, Dwarka, New Delhi, 110078, India.
| | - R P Mahapatra
- Department of Computer Science & Engineering, SRM Institute of Science and Technology, Delhi-NCR Campus, Modinagar, Ghaziabad, UP, 201204, India
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20
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Zimmermann MT. Molecular Modeling is an Enabling Approach to Complement and Enhance Channelopathy Research. Compr Physiol 2022; 12:3141-3166. [PMID: 35578963 DOI: 10.1002/cphy.c190047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hundreds of human membrane proteins form channels that transport necessary ions and compounds, including drugs and metabolites, yet details of their normal function or how function is altered by genetic variants to cause diseases are often unknown. Without this knowledge, researchers are less equipped to develop approaches to diagnose and treat channelopathies. High-resolution computational approaches such as molecular modeling enable researchers to investigate channelopathy protein function, facilitate detailed hypothesis generation, and produce data that is difficult to gather experimentally. Molecular modeling can be tailored to each physiologic context that a protein may act within, some of which may currently be difficult or impossible to assay experimentally. Because many genomic variants are observed in channelopathy proteins from high-throughput sequencing studies, methods with mechanistic value are needed to interpret their effects. The eminent field of structural bioinformatics integrates techniques from multiple disciplines including molecular modeling, computational chemistry, biophysics, and biochemistry, to develop mechanistic hypotheses and enhance the information available for understanding function. Molecular modeling and simulation access 3D and time-dependent information, not currently predictable from sequence. Thus, molecular modeling is valuable for increasing the resolution with which the natural function of protein channels can be investigated, and for interpreting how genomic variants alter them to produce physiologic changes that manifest as channelopathies. © 2022 American Physiological Society. Compr Physiol 12:3141-3166, 2022.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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21
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Kulkarni PU, Shah H, Vyas VK. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery. Mini Rev Med Chem 2021; 22:1096-1107. [PMID: 34620049 DOI: 10.2174/1389557521666211007115250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 11/22/2022]
Abstract
Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.
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Affiliation(s)
- Prajakta U Kulkarni
- School of Pharmacy, ITM (SLS) Baroda University, Vadodara 391510, Gujarat. India
| | - Harshil Shah
- Department of Pharmaceutical Chemistry, Sardar Patel College of Pharmacy, Bakrol, Anand 388315, Gujarat. India
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat. India
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22
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P. Oliveira M, Hünenberger PH. Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds. Phys Chem Chem Phys 2021; 23:17774-17793. [PMID: 34350931 PMCID: PMC8386690 DOI: 10.1039/d1cp02001c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/30/2021] [Indexed: 12/04/2022]
Abstract
The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumeration. One peculiarity of this approach is that it relies on an electronegativity-equalization scheme to account for induction effects within molecules, with values of the atomic hardness and electronegativity as electrostatic parameters, rather than the partial charges themselves. In a previous article [M. P. Oliveira, M. Andrey, S. R. Rieder, L. Kern, D. F. Hahn, S. Riniker, B. A. C. Horta and P. H. Hünenberger, J. Chem. Theory. Comput. 2020, 16, 7525], CombiFF was introduced and applied to calibrate a GROMOS-compatible united-atom force field for the saturated acyclic (halo-)alkane family. Here, this scheme is employed for the construction of a corresponding force field for saturated acyclic compounds encompassing eight common chemical functional groups involving oxygen and/or nitrogen atoms, namely: ether, aldehyde, ketone, ester, alcohol, carboxylic acid, amine, and amide. Monofunctional as well as homo-polyfunctional compounds are considered. A total of 1712 experimental liquid densities ρliq and vaporization enthalpies ΔHvap concerning 1175 molecules are used for the calibration (339 molecules) and validation (836 molecules) of the 102 non-bonded interaction parameters of the force field. Using initial parameter values based on the GROMOS 2016H66 parameter set, convergence is reached after five iterations. Given access to one processor per simulated system, this operation only requires a few days of wall-clock computing time. After optimization, the root-mean-square deviations from experiment are 29.9 (22.4) kg m-3 for ρliq and 4.1 (5.5) kJ mol-1 for ΔHvap for the calibration (validation) set. Thus, a very good level of agreement with experiment is achieved in terms of these two properties, although the errors are inhomogeneously distributed across the different chemical functional groups.
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Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 5503
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 5503
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23
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Westermayr J, Marquetand P. Machine Learning for Electronically Excited States of Molecules. Chem Rev 2021; 121:9873-9926. [PMID: 33211478 PMCID: PMC8391943 DOI: 10.1021/acs.chemrev.0c00749] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.
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Affiliation(s)
- Julia Westermayr
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Data
Science @ Uni Vienna, University of Vienna, Währinger Strasse 29, 1090 Vienna, Austria
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24
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Unke O, Chmiela S, Sauceda HE, Gastegger M, Poltavsky I, Schütt KT, Tkatchenko A, Müller KR. Machine Learning Force Fields. Chem Rev 2021; 121:10142-10186. [PMID: 33705118 PMCID: PMC8391964 DOI: 10.1021/acs.chemrev.0c01111] [Citation(s) in RCA: 397] [Impact Index Per Article: 132.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/27/2022]
Abstract
In recent years, the use of machine learning (ML) in computational chemistry has enabled numerous advances previously out of reach due to the computational complexity of traditional electronic-structure methods. One of the most promising applications is the construction of ML-based force fields (FFs), with the aim to narrow the gap between the accuracy of ab initio methods and the efficiency of classical FFs. The key idea is to learn the statistical relation between chemical structure and potential energy without relying on a preconceived notion of fixed chemical bonds or knowledge about the relevant interactions. Such universal ML approximations are in principle only limited by the quality and quantity of the reference data used to train them. This review gives an overview of applications of ML-FFs and the chemical insights that can be obtained from them. The core concepts underlying ML-FFs are described in detail, and a step-by-step guide for constructing and testing them from scratch is given. The text concludes with a discussion of the challenges that remain to be overcome by the next generation of ML-FFs.
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Affiliation(s)
- Oliver
T. Unke
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- DFG
Cluster of Excellence “Unifying Systems in Catalysis”
(UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
| | - Stefan Chmiela
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Huziel E. Sauceda
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- BASLEARN,
BASF-TU Joint Lab, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Michael Gastegger
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- DFG
Cluster of Excellence “Unifying Systems in Catalysis”
(UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
- BASLEARN,
BASF-TU Joint Lab, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Igor Poltavsky
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Kristof T. Schütt
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Alexandre Tkatchenko
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Klaus-Robert Müller
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- BIFOLD−Berlin
Institute for the Foundations of Learning and Data, Berlin, Germany
- Department
of Artificial Intelligence, Korea University, Anam-dong, Seongbuk-gu, Seoul 02841, Korea
- Max Planck
Institute for Informatics, Stuhlsatzenhausweg, 66123 Saarbrücken, Germany
- Google
Research, Brain Team, Berlin, Germany
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25
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Ebenso EE, Verma C, Olasunkanmi LO, Akpan ED, Verma DK, Lgaz H, Guo L, Kaya S, Quraishi MA. Molecular modelling of compounds used for corrosion inhibition studies: a review. Phys Chem Chem Phys 2021; 23:19987-20027. [PMID: 34254097 DOI: 10.1039/d1cp00244a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular modelling of organic compounds using computational software has emerged as a powerful approach for theoretical determination of the corrosion inhibition potential of organic compounds. Some of the common techniques involved in the theoretical studies of corrosion inhibition potential and mechanisms include density functional theory (DFT), molecular dynamics (MD) and Monte Carlo (MC) simulations, and artificial neural network (ANN) and quantitative structure-activity relationship (QSAR) modeling. Using computational modelling, the chemical reactivity and corrosion inhibition activities of organic compounds can be explained. The modelling can be regarded as a time-saving and eco-friendly approach for screening organic compounds for corrosion inhibition potential before their wet laboratory synthesis would be carried out. Another advantage of computational modelling is that molecular sites responsible for interactions with metallic surfaces (active sites or adsorption sites) and the orientation of organic compounds can be easily predicted. Using different theoretical descriptors/parameters, the inhibition effectiveness and nature of the metal-inhibitor interactions can also be predicted. The present review article is a collection of major advancements in the field of computational modelling for the design and testing of the corrosion inhibition effectiveness of organic corrosion inhibitors.
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Affiliation(s)
- Eno E Ebenso
- Institute for Nanotechnology and Water Sustainability, College of Science, Engineering and Technology, University of South Africa, Johannesburg, South Africa.
| | - Chandrabhan Verma
- Interdisciplinary Research Center for Advanced Materials, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia
| | - Lukman O Olasunkanmi
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife 220005, Nigeria
| | - Ekemini D Akpan
- Material Science Innovation and Modelling Research Focus Area, Faculty of Natural and Agricultural Sciences, North-West University (Mafikeng Campus) Private Bag X2046, Mmabatho 2735, South Africa
| | - Dakeshwar Kumar Verma
- Department of Chemistry, Govt. Digvijay Autonomous Postgraduate College, Rajnandgaon, Chhattisgarh 491441, India
| | - Hassane Lgaz
- Department of Crop Science, College of Sanghur Life Science, Konkuk University, Seoul 05029, South Korea
| | - Lei Guo
- School of Materials and Chemical Engineering, Tongren University, Tongren, 554300, China
| | - Savas Kaya
- Faculty of Science, Department of Chemistry, Cumhuriyet University, 58140, Sivas, Turkey
| | - M A Quraishi
- Interdisciplinary Research Center for Advanced Materials, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia
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26
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Hong SJ, Chun H, Lee J, Kim BH, Seo MH, Kang J, Han B. First-Principles-Based Machine-Learning Molecular Dynamics for Crystalline Polymers with van der Waals Interactions. J Phys Chem Lett 2021; 12:6000-6006. [PMID: 34165310 DOI: 10.1021/acs.jpclett.1c01140] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Machine-learning (ML) techniques have drawn an ever-increasing focus as they enable high-throughput screening and multiscale prediction of material properties. Especially, ML force fields (FFs) of quantum mechanical accuracy are expected to play a central role for the purpose. The construction of ML-FFs for polymers is, however, still in its infancy due to the formidable configurational space of its composing atoms. Here, we demonstrate the effective development of ML-FFs using kernel functions and a Gaussian process for an organic polymer, polytetrafluoroethylene (PTFE), with a data set acquired by first-principles calculations and ab initio molecular dynamics (AIMD) simulations. Even though the training data set is sampled only with short PTFE chains, structures of longer chains optimized by our ML-FF show an excellent consistency with density functional theory calculations. Furthermore, when integrated with molecular dynamics simulations, the ML-FF successfully describes various physical properties of a PTFE bundle, such as a density, melting temperature, coefficient of thermal expansion, and Young's modulus.
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Affiliation(s)
- Sung Jun Hong
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hoje Chun
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jehyun Lee
- Platform Technology Laboratory, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Byung-Hyun Kim
- Platform Technology Laboratory, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Min Ho Seo
- Fuel Cell Research & Demonstration Center, Future Energy Research Division, Korea Institute of Energy Research, Buan-gun 56322, Republic of Korea
| | - Joonhee Kang
- Platform Technology Laboratory, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Byungchan Han
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
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27
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Chakraborty A, Schmahl S, Asmis KR. Isomer-Specific Vibrational Spectroscopy of Microhydrated Lithium Dichloride Anions: Spectral Fingerprint of Solvent-Shared Ion Pairs. Chemphyschem 2021; 22:1036-1041. [PMID: 33783947 PMCID: PMC8252531 DOI: 10.1002/cphc.202100170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/28/2021] [Indexed: 12/21/2022]
Abstract
The vibrational spectroscopy of lithium dichloride anions microhydrated with one to three water molecules, [LiCl2 (H2 O)1-3 ]- , is studied in the OH stretching region (3800-2800 cm-1 ) using isomer-specific IR/IR double-resonance population labelling experiments. The spectroscopic fingerprints of individual isomers can only be unambiguously assigned after anharmonic effects are considered, but then yield molecular level insight into the onset of salt dissolution in these gas phase model systems. Based on the extent of the observed frequency shifts ΔνOH of the hydrogen-bonded OH stretching oscillators solvent-shared ion pair motifs (<3200 cm-1 ) can be distinguished from intact-core structures (>3200 cm-1 ). The characteristic fingerprint of a water molecule trapped directly in-between two ions of opposite charge provides an alternative route to evaluate the extent of ion pairing in aqueous electrolyte solutions.
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Affiliation(s)
- Arghya Chakraborty
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103, Leipzig, Germany
| | - Sonja Schmahl
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103, Leipzig, Germany
| | - Knut R Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103, Leipzig, Germany
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28
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Computational Drug Repurposing Resources and Approaches for Discovering Novel Antifungal Drugs against Candida albicans N-Myristoyl Transferase. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is a yeast that is an opportunistic fungal pathogen and also identified as ubiquitous polymorphic species that is mainly linked with major fungal infections in humans, particularly in the immunocompromised patients including transplant recipients, chemotherapy patients, HIV-infected patients as well as in low-birth-weight infants. Systemic Candida infections have a high mortality rate of around 29 to 76%. For reducing its infection, limited drugs are existing such as caspofungin, fluconazole, terbinafine, and amphotericin B, etc. which contain unlikable side effects and also toxic. This review intends to utilize advanced bioinformatics technologies such as Molecular docking, Scaffold hopping, Virtual screening, Pharmacophore modeling, Molecular dynamics (MD) simulation for the development of potentially new drug candidates with a drug-repurpose approach against Candida albicans within a limited time frame and also cost reductive.
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29
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Bodo E. Modelling biocompatible ionic liquids based on organic acids and amino acids: challenges for computational models and future perspectives. Org Biomol Chem 2021; 19:4002-4013. [PMID: 33978045 DOI: 10.1039/d1ob00011j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this short review I shall highlight the basic principle and the difficulties that arise in attempting the computational modeling of seemingly simple systems which hide an unexpected complexity. Biocompatible ionic liquids which are based on the coupling of organic or amino acid anions with metabolic cations such as cholinium are the target of this review. These substances have been the subject of intense research activities in the last few years and have attracted the attention of computational chemists. I shall show that the computational description of these substances is far from trivial and requires the use of sophisticated techniques in order to account for a surprisingly rich chemistry that is due to several phenomena such as polarization, charge transfer, proton transfer equilibria and tautomerization reactions.
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Affiliation(s)
- Enrico Bodo
- Chemistry Department, University of Rome "La Sapienza", P. A. Moro 5, 00185 Rome, Italy.
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30
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Banerjee T, Samanta A. Chemical computational approaches for optimization of effective surfactants in enhanced oil recovery. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2020-0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Abstract
The surfactant flooding becomes an attractive method among several Enhanced Oil Recovery (EOR) processes to improve the recovery of residual oil left behind in the reservoir after secondary oil recovery process. The designing of a new effective surfactant is a comparatively complex and often time consuming process as well as cost-effective due to its dependency on the crude oil and reservoir properties. An alternative chemical computational approach is focused in this article to optimize the performance of effective surfactant system for EOR. The molecular dynamics (MD), dissipative particle dynamics (DPD) and density functional theory (DFT) simulations are mostly used chemical computational approaches to study the behaviour in multiple phase systems like surfactant/oil/brine. This article highlighted a review on the impact of surfactant head group structure on oil/water interfacial property like interfacial tensions, interface formation energy, interfacial thickness by MD simulation. The effect of entropy in micelle formation has also discussed through MD simulation. The polarity, dipole moment, charge distribution and molecular structure optimization have been illustrated by DFT. A relatively new coarse-grained method, DPD is also emphasized the phase behaviour of surfactant/oil/brine as well as polymer-surfactant complex system.
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Affiliation(s)
- Tandrima Banerjee
- Department of Chemical Sciences , Indian Institute of Science Education and Research (IISER) Kolkata , West Bengal 741246 , India
| | - Abhijit Samanta
- School of Engineering and Applied Sciences , The Neotia University , Sarisha , West Bengal 743368 , India
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31
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Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
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32
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Puentes PR, Henao MC, Torres CE, Gómez SC, Gómez LA, Burgos JC, Arbeláez P, Osma JF, Muñoz-Camargo C, Reyes LH, Cruz JC. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics (Basel) 2020; 9:E854. [PMID: 33265897 PMCID: PMC7759991 DOI: 10.3390/antibiotics9120854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.
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Affiliation(s)
- Paola Ruiz Puentes
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - María C. Henao
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carlos E. Torres
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Saúl C. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Laura A. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Juan C. Burgos
- Chemical Engineering Program, Universidad de Cartagena, Cartagena 130015, Colombia;
| | - Pablo Arbeláez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Johann F. Osma
- Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carolina Muñoz-Camargo
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Luis H. Reyes
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Juan C. Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide 5005, Australia
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33
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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34
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Kashefolgheta S, Oliveira MP, Rieder SR, Horta BAC, Acree WE, Hünenberger PH. Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies. J Chem Theory Comput 2020; 16:7556-7580. [DOI: 10.1021/acs.jctc.0c00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - William E. Acree
- Department of Chemistry, University of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76203, United States
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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35
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Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology 2020; 30:516-527. [PMID: 32080710 PMCID: PMC8179626 DOI: 10.1093/glycob/cwaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/15/2022] Open
Abstract
Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
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36
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Wei W, Champion C, Barigye SJ, Liu Z, Labute P, Moitessier N. Use of Extended-Hückel Descriptors for Rapid and Accurate Predictions of Conjugated Torsional Energy Barriers. J Chem Inf Model 2020; 60:3534-3545. [DOI: 10.1021/acs.jcim.0c00440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wanlei Wei
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Candide Champion
- Chemical Computing Group Incorporation, 1010 Sherbrooke St. W., Montreal H3A 2R7, Québec, Canada
| | - Stephen J. Barigye
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Zhaomin Liu
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Paul Labute
- Chemical Computing Group Incorporation, 1010 Sherbrooke St. W., Montreal H3A 2R7, Québec, Canada
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
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37
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Jafarpour R, Fatemi F, Eidi A, Mehrnejad F. Effect of the Met148Leu mutation on the structure and dynamics of the rusticyanin protein from Acidithiobacillus sp. FJ2. J Biomol Struct Dyn 2020; 39:4122-4132. [PMID: 32462978 DOI: 10.1080/07391102.2020.1775119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The rusticyanin protein, a blue monomeric copper protein type-1, is one of the main components in the iron-electron transfer chain of the Acidithiobacillus ferrooxidans, and is the product of the rus gene expression. Herein, first the bacterial DNA of Acidithiobacillus sp. FJ2 was extracted. Then, the rus gene sequence and the sequence amino acid rusticyanin protein were determined. The Met148Leu mutation increased the oxidase activity of the rusticyanin protein, thereby enhancing the efficiency of the bioleaching process by bacteria Acidithiobacillus ferroxidans. Met148Leu mutation was created in the rusticyanin protein, then molecular dynamics (MD) simulations and structural analysis were performed. The MD analysis of the wild-type and mutant protein demonstrated a slight instability in the mutant protein and significant instability in the active site of the mutant protein. The usefulness of this study is the genetic manipulation of the native Acidithiobacillus sp. FJ2 bacterium, which can boost the bioleaching efficiency of the bacterium to some extent, and investigating its effects on the structure of a mutant protein using computational methods.
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Affiliation(s)
- Roghayeh Jafarpour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faezeh Fatemi
- Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Akram Eidi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
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38
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Nelson TR, White AJ, Bjorgaard JA, Sifain AE, Zhang Y, Nebgen B, Fernandez-Alberti S, Mozyrsky D, Roitberg AE, Tretiak S. Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials. Chem Rev 2020; 120:2215-2287. [PMID: 32040312 DOI: 10.1021/acs.chemrev.9b00447] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Optically active molecular materials, such as organic conjugated polymers and biological systems, are characterized by strong coupling between electronic and vibrational degrees of freedom. Typically, simulations must go beyond the Born-Oppenheimer approximation to account for non-adiabatic coupling between excited states. Indeed, non-adiabatic dynamics is commonly associated with exciton dynamics and photophysics involving charge and energy transfer, as well as exciton dissociation and charge recombination. Understanding the photoinduced dynamics in such materials is vital to providing an accurate description of exciton formation, evolution, and decay. This interdisciplinary field has matured significantly over the past decades. Formulation of new theoretical frameworks, development of more efficient and accurate computational algorithms, and evolution of high-performance computer hardware has extended these simulations to very large molecular systems with hundreds of atoms, including numerous studies of organic semiconductors and biomolecules. In this Review, we will describe recent theoretical advances including treatment of electronic decoherence in surface-hopping methods, the role of solvent effects, trivial unavoided crossings, analysis of data based on transition densities, and efficient computational implementations of these numerical methods. We also emphasize newly developed semiclassical approaches, based on the Gaussian approximation, which retain phase and width information to account for significant decoherence and interference effects while maintaining the high efficiency of surface-hopping approaches. The above developments have been employed to successfully describe photophysics in a variety of molecular materials.
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Affiliation(s)
- Tammie R Nelson
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Alexander J White
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Josiah A Bjorgaard
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Andrew E Sifain
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States.,U.S. Army Research Laboratory , Aberdeen Proving Ground , Maryland 21005 , United States
| | - Yu Zhang
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Benjamin Nebgen
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | | | - Dmitry Mozyrsky
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Adrian E Roitberg
- Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Sergei Tretiak
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
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39
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Kubincová A, Riniker S, Hünenberger PH. Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff. Phys Chem Chem Phys 2020; 22:26419-26437. [DOI: 10.1039/d0cp03835k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Shifting and switching schemes are developed to enable strict energy conservation in molecular dynamics simulations relying on reaction-field electrostatic (as well as Lennard-Jones) interactions with an atom-based cutoff truncation.
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Affiliation(s)
| | - Sereina Riniker
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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40
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Quantum mechanics/molecular mechanics multiscale modeling of biomolecules. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2020. [DOI: 10.1016/bs.apoc.2020.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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41
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Plazinski W, Plazinska A, Brzyska A. Efficient sampling of high-energy states by machine learning force fields. Phys Chem Chem Phys 2020; 22:14364-14374. [DOI: 10.1039/d0cp01399d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A method extending the range of applicability of machine-learning force fields is proposed. It relies on biased subsampling of the high-energy states described by the predefined coordinate(s).
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Affiliation(s)
- Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences
- 30-239 Krakow
- Poland
| | - Anita Plazinska
- Department of Biopharmacy
- Medical University of Lublin Chodźki 4a
- 20-093 Lublin
- Poland
| | - Agnieszka Brzyska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences
- 30-239 Krakow
- Poland
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42
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Orellana L. Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier. Front Mol Biosci 2019; 6:117. [PMID: 31750315 PMCID: PMC6848229 DOI: 10.3389/fmolb.2019.00117] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/14/2019] [Indexed: 12/16/2022] Open
Abstract
Large-scale conformational changes are essential to link protein structures with their function at the cell and organism scale, but have been elusive both experimentally and computationally. Over the past few years developments in cryo-electron microscopy and crystallography techniques have started to reveal multiple snapshots of increasingly large and flexible systems, deemed impossible only short time ago. As structural information accumulates, theoretical methods become central to understand how different conformers interconvert to mediate biological function. Here we briefly survey current in silico methods to tackle large conformational changes, reviewing recent examples of cross-validation of experiments and computational predictions, which show how the integration of different scale simulations with biological information is already starting to break the barriers between the in silico, in vitro, and in vivo worlds, shedding new light onto complex biological problems inaccessible so far.
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Affiliation(s)
- Laura Orellana
- Institutionen för Biokemi och Biofysik, Stockholms Universitet, Stockholm, Sweden.,Science for Life Laboratory, Solna, Sweden
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43
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Deplazes E, Chin YKY, King GF, Mancera RL. The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides. Proteins 2019; 88:485-502. [PMID: 31589791 DOI: 10.1002/prot.25828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/04/2023]
Abstract
The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.
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Affiliation(s)
- Evelyne Deplazes
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
| | - Yanni K-Y Chin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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44
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Kumi RO, Issahaku AR, Soremekun OS, Agoni C, Olotu FA, Soliman MES. From the Explored to the Unexplored: Computer-Tailored Drug Design Attempts in the Discovery of Selective Caspase Inhibitors. Comb Chem High Throughput Screen 2019; 22:432-444. [PMID: 31560284 DOI: 10.2174/1386207322666190927143026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/19/2019] [Accepted: 08/01/2019] [Indexed: 01/09/2023]
Abstract
The pathophysiological roles of caspases have made them attractive targets in the treatment and amelioration of neurologic diseases. In normal conditions, the expression of caspases is regulated in the brain, while at the onset of neurodegeneration, such as in Alzheimer's disease, they are typically overexpressed. Till date, several therapeutic efforts that include the use of small endogenous binders have been put forward to curtail dysfunctionalities that drive aberrant death in neuronal cells. Caspases are highly homologous, both in structure and in sequence, which leaves us with the question: is it possible to specifically and individually target caspases, while multiple therapeutic attempts to achieve selective targeting have failed! Based on antecedent events, the use of Computer-Aided Drug Design (CADD) methods has significantly contributed to the design of small molecule inhibitors, especially with selective target ability and reduced off-target therapeutic effects. Interestingly, we found out that there still exists an enormous room for the integration of structure/ligand-based drug design techniques towards the development of highly specific reversible and irreversible caspase inhibitors. Therefore, in this review, we highlight drug discovery approaches that have been directed towards caspase inhibition in addition to an insightful focus on applicable CADD techniques for achieving selective targeting in caspase research.
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Affiliation(s)
- Ransford O Kumi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Abdul R Issahaku
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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45
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Chiba S, Okuno Y, Honma T, Ikeguchi M. Force-field parametrization based on radial and energy distribution functions. J Comput Chem 2019; 40:2577-2585. [PMID: 31343749 PMCID: PMC6790663 DOI: 10.1002/jcc.26035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
We propose a novel force‐field‐parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher‐level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Shuntaro Chiba
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Cluster for Science and Technology Hub, 6-3-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Yasushi Okuno
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Graduate School of Medicine, Kyoto University, Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Teruki Honma
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mitsunori Ikeguchi
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
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46
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Dayhoff GW, Rogers DM. Hydration and Dispersion Forces in Hydroxypropylcellulose Phase Behavior. J Phys Chem B 2019; 123:4976-4985. [PMID: 31082228 DOI: 10.1021/acs.jpcb.9b01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many-body polarization and hydration forces can strongly affect the equilibrium structure and energetics of mixed phases. Accurately reproducing both forces presents a challenge to force field models because it requires balancing hydrogen bonding at short range with many-body orientational order and dispersive attraction at long range. This work reports the first comparison of experimental measurements of the pressure-area isotherm for hydroxypropylcellulose (HPC) against molecular dynamics results with four different force field models-united-atom, all-atom (OPLS and CHARMM), and Drude oscillator models. All force fields exhibit the experimentally determined, exponentially shaped repulsive force at short range. Above a critical temperature of about 40 °C and a lattice spacing of around 14 Å, HPC experiments show a reversible, heat-induced polymer aggregation into an ordered phase driven by loss of water. The nonpolarizable force fields do not display the critical point and instead show biphasic behavior at all temperatures tested. This indicates net attractive forces at intermediate lattice spacings. In contrast, the Drude polarizable force field shows positive osmotic pressure and a single, homogeneous phase over all temperatures and spacings tested. Analysis of structural data from our simulations provides several clues to help interpret these findings. Although all force fields show similar water-water hydrogen bond numbers in the mixed phase, the polarizable model predicts that water-HPC hydrogen bonds are much more favorable than HPC-HPC hydrogen bonds when polymers are dispersed. At high density, water is driven out and replaced by HPC-HPC hydrogen bonds. The polarizable force field shows that both effects have a stronger dependence on polymer density than any of the nonpolarizable models. Our observations support the conclusion that hydration forces are coupled to the polymer coordination number by local, structural waters and that long-range dispersive attraction is overestimated by pairwise additive models.
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Affiliation(s)
- Guy W Dayhoff
- Department of Chemistry , University of South Florida , Tampa 33620 , United States
| | - David M Rogers
- Department of Chemistry , University of South Florida , Tampa 33620 , United States
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47
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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48
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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49
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Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward Learned Chemical Perception of Force Field Typing Rules. J Chem Theory Comput 2019; 15:402-423. [PMID: 30512951 PMCID: PMC6467725 DOI: 10.1021/acs.jctc.8b00821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanics force fields define how the energy and forces in a molecular system are computed from its atomic positions, thus enabling the study of such systems through computational methods like molecular dynamics and Monte Carlo simulations. Despite progress toward automated force field parametrization, considerable human expertise is required to develop or extend force fields. In particular, human input has long been required to define atom types, which encode chemically unique environments that determine which parameters will be assigned. However, relying on humans to establish atom types is suboptimal. Human-created atom types are often developed without statistical justification, leading to over- or under-fitting of data. Human-created types are also difficult to extend in a systematic and consistent manner when new chemistries must be modeled or new data becomes available. Finally, human effort is not scalable when force fields must be generated for new (bio)polymers, compound classes, or materials. To remedy these deficiencies, our long-term goal is to replace human specification of atom types with an automated approach, based on rigorous statistics and driven by experimental and/or quantum chemical reference data. In this work, we describe novel methods that automate the discovery of appropriate chemical perception: SMARTY allows for the creation of atom types, while SMIRKY goes further by automating the creation of fragment (nonbonded, bonds, angles, and torsions) types. These approaches enable the creation of move sets in atom or fragment type space, which are used within a Monte Carlo optimization approach. We demonstrate the power of these new methods by automating the rediscovery of human defined atom types (SMARTY) or fragment types (SMIRKY) in existing small molecule force fields. We assess these approaches using several molecular data sets, including one which covers a diverse subset of the DrugBank database.
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Affiliation(s)
- Camila Zanette
- Department of Pharmaceutical Sciences, University of California, Irvine
| | | | | | - Josh Fass
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
| | - Michael R. Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - David L. Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine
- Department of Chemistry, University of California, Irvine
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50
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Dawes R, Quintas‐Sánchez E. THE CONSTRUCTION OF AB INITIO‐BASED POTENTIAL ENERGY SURFACES. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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