1
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Takaba K, Friedman AJ, Cavender CE, Behara PK, Pulido I, Henry MM, MacDermott-Opeskin H, Iacovella CR, Nagle AM, Payne AM, Shirts MR, Mobley DL, Chodera JD, Wang Y. Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chem Sci 2024; 15:12861-12878. [PMID: 39148808 PMCID: PMC11322960 DOI: 10.1039/d4sc00690a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/17/2024] [Indexed: 08/17/2024] Open
Abstract
The development of reliable and extensible molecular mechanics (MM) force fields-fast, empirical models characterizing the potential energy surface of molecular systems-is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1 M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides and folded proteins, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest.
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Affiliation(s)
- Kenichiro Takaba
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Pharmaceuticals Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation Shizuoka 410-2321 Japan
| | - Anika J Friedman
- Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA
| | - Chapin E Cavender
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Pavan Kumar Behara
- Center for Neurotherapeutics, Department of Pathology and Laboratory Medicine, University of California Irvine CA 92697 USA
| | - Iván Pulido
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Michael M Henry
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | | | - Christopher R Iacovella
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Arnav M Nagle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Department of Bioengineering, University of California, Berkeley Berkeley CA 94720 USA
| | - Alexander Matthew Payne
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center New York 10065 USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California Irvine California 92697 USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York University New York NY 10004 USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
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2
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Lam CK, Fung LY, Wang Y. Orientation and Membrane Partition Free Energy of PeT-Based Voltage-Sensitive Dyes from Molecular Simulations. J Phys Chem B 2024; 128:2734-2744. [PMID: 38459942 PMCID: PMC10961725 DOI: 10.1021/acs.jpcb.3c08090] [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] [Received: 12/11/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/11/2024]
Abstract
Voltage measurement via small-molecule fluorescent indicators is a valuable approach in deciphering complex dynamics in electrically excitable cells. However, our understanding of various physicochemical properties governing the performance of fluorescent voltage sensors based on the photoinduced electron transfer (PeT) mechanism remains incomplete. Here, through extensive molecular dynamics and free energy calculations, we systematically examine the orientation and membrane partition of three PeT-based voltage-sensing VoltageFluor (VF) dyes in different lipid environment. We show that the symmetry of the molecular scaffold and the net charge of the hydrophilic headgroup of a given VF dye dominate its orientation and membrane partition, respectively. Our work provides a mechanistic understanding of the physical properties contributing to the voltage sensitivity, signal-to-noise ratio, as well as membrane distribution of VF dyes and sheds light onto rational design principles of PeT-based fluorescent probes in general.
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Affiliation(s)
- Chun Kei Lam
- Department of Physics, The
Chinese University
of Hong Kong, Shatin, Hong Kong SAR, China
| | - Lap Yan Fung
- Department of Physics, The
Chinese University
of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yi Wang
- Department of Physics, The
Chinese University
of Hong Kong, Shatin, Hong Kong SAR, China
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3
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Kang C, Shoji A, Chipot C, Sun R. Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs. J Chem Inf Model 2024; 64:933-943. [PMID: 38206804 DOI: 10.1021/acs.jcim.3c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Over the last two decades, numerous molecular dynamics (MD) simulation-based investigations have attempted to predict the membrane permeability to small-molecule drugs as indicators of their bioavailability, a majority of which utilize the inhomogeneous solubility diffusion (ISD) model. However, MD-based membrane permeability is routinely 3-4 orders of magnitude larger than the values measured with the intestinal perfusion technique. There have been contentious discussions on the sources of the large discrepancies, and the two indisputable, potentially dominant ones are the fixed protonation state of the permeant and the neglect of the unstirred water layer (UWL). Employing six small-molecule drugs of different biopharmaceutical classification system classes, the current MD study relies on the ISD model but introduces the (de)protonation of the permeant by characterizing the permeation free energy of both neutral and charged states. In addition, the role of the UWL as a potential resistance against permeation is explored. The new MD protocol closely mimics the nature of small-molecule permeation and yields estimates that agree well with in vivo intestinal permeability.
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Affiliation(s)
- Christopher Kang
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Alyson Shoji
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex 54506, France
- Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Rui Sun
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
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4
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Kabedev A, Bergström CAS, Larsson P. Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison. J Comput Aided Mol Des 2023; 38:5. [PMID: 38103089 PMCID: PMC10725378 DOI: 10.1007/s10822-023-00541-1] [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: 09/06/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Theoretical predictions of the solubilizing capacity of micelles and vesicles present in intestinal fluid are important for the development of new delivery techniques and bioavailability improvement. A balance between accuracy and computational cost is a key factor for an extensive study of numerous compounds in diverse environments. In this study, we aimed to determine an optimal molecular dynamics (MD) protocol to evaluate small-molecule interactions with micelles composed of bile salts and phospholipids. MD simulations were used to produce free energy profiles for three drug molecules (danazol, probucol, and prednisolone) and one surfactant molecule (sodium caprate) as a function of the distance from the colloid center of mass. To address the challenges associated with such tasks, we compared different simulation setups, including freely assembled colloids versus pre-organized spherical micelles, full free energy profiles versus only a few points of interest, and a coarse-grained model versus an all-atom model. Our findings demonstrate that combining these techniques is advantageous for achieving optimal performance and accuracy when evaluating the solubilization capacity of micelles. All-atom (AA) and coarse-grained (CG) umbrella sampling (US) simulations and point-wise free energy (FE) calculations were compared to their efficiency to computationally analyze the solubilization of active pharmaceutical ingredients in intestinal fluid colloids.
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Affiliation(s)
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
- Swedish Drug Delivery Center, Uppsala University, Uppsala, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden.
- Swedish Drug Delivery Center, Uppsala University, Uppsala, Sweden.
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5
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Pandey P, MacKerell AD. Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. J Chem Inf Model 2023; 63:5903-5915. [PMID: 37682640 PMCID: PMC10603762 DOI: 10.1021/acs.jcim.3c00514] [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: 09/10/2023]
Abstract
Membrane permeability of drug molecules plays a significant role in the development of new therapeutic agents. Accordingly, methods to predict the passive permeability of drug candidates during a medicinal chemistry campaign offer the potential to accelerate the drug design process. In this work, we combine the physics-based site identification by ligand competitive saturation (SILCS) method and data-driven artificial intelligence (AI) to create a high-throughput predictive model for the passive permeability of druglike molecules. In this study, we present a comparative analysis of four regression models to predict membrane permeabilities of small druglike molecules; of the tested models, Random Forest was the most predictive yielding an R2 of 0.81 for the independent data set. The input feature vector used to train the developed prediction model includes absolute free energy profiles of ligands through a POPC-cholesterol bilayer based on ligand grid free energy (LGFE) profiles obtained from the SILCS approach. The use of the membrane free energy profiles from SILCS offers information on the physical forces contributing to ligand permeability, while the use of AI yields a more predictive model trained on experimental PAMPA permeability data for a collection of 229 molecules. This combination allows for rapid estimations of ligand permeability at a level of accuracy beyond currently available predictive models while offering insights into the contributions of the functional groups in the ligands to the permeability barrier, thereby offering quantitative information to facilitate rational ligand design.
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Affiliation(s)
- Poonam Pandey
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
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6
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Chipot C. Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice? J Chem Inf Model 2023; 63:4533-4544. [PMID: 37449868 DOI: 10.1021/acs.jcim.3c00686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Predicting from first-principles the rate of passive permeation of small molecules across the biological membrane represents a promising strategy for screening lead compounds upstream in the drug-discovery and development pipeline. One popular avenue for the estimation of permeation rates rests on computer simulations in conjunction with the inhomogeneous solubility-diffusion model, which requires the determination of the free-energy change and position-dependent diffusivity of the substrate along the translocation pathway through the lipid bilayer. In this Perspective, we will clarify the physical meaning of the membrane permeability inferred from such computer simulations, and how theoretical predictions actually relate to what is commonly measured experimentally. We will also examine why these calculations remain both technically challenging and overly computationally expensive, which has hitherto precluded their routine use in nonacademic settings. We finally synopsize possible research directions to meet these challenges, increase the predictive power of physics-based rates of passive permeation, and, by ricochet, improve their practical usefulness.
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Affiliation(s)
- Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n◦7019, Université de Lorraine, 54500 Vandœuvre-lès-Nancy cedex, France
- Beckman Institute for Advanced Science and Technology, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
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7
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Benmameri M, Chantemargue B, Humeau A, Trouillas P, Fabre G. MemCross: Accelerated Weight Histogram method to assess membrane permeability. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184120. [PMID: 36669638 DOI: 10.1016/j.bbamem.2023.184120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
Passive permeation events across biological membranes are determining steps in the pharmacokinetics of xenobiotics. To reach an accurate and rapid prediction of membrane permeation coefficients of drugs is a complex challenge, which can efficiently support drug discovery. Such predictions are indeed highly valuable as they may guide the selection of potential leads with optimum bioavailabilities prior to synthesis. Theoretical models exist to predict these coefficients. Many of them are based on molecular dynamics (MD) simulations, which allow calculation of permeation coefficients through the evaluation of both the potential of mean force (PMF) and the diffusivity profiles. However, these simulations still require intensive computational efforts, and novel methodologies should be developed and benchmarked. Free energy perturbation (FEP) method was recently shown to estimate PMF with a significantly reduced computational cost compared to the adaptive biasing force method. This benchmarking was achieved with small molecules, namely short-chain alcohols. Here, we show that to estimate the PMF of bulkier, drug-like xenobiotics, conformational sampling is a critical issue. To reach a sufficient sampling with FEP calculations requires a relatively long time-scale, which can lower the benefits related to the computational gain. In the present work, the Accelerated Weight Histogram (AWH) method was employed for the first time in all-atom membrane models. The AWH-based protocol, named MemCross, appears affordable to estimate PMF profiles of a series of drug-like xenobiotics, compared to other enhanced sampling methods. The continuous exploration of the crossing pathway by MemCross also allows modeling subdiffusion by computing fractional diffusivity profiles. The method is also versatile as its input parameters are largely insensitive to the molecule properties. It also ensures a detailed description of the molecule orientations along the permeation pathway, picturing all intermolecular interactions at an atomic resolution. Here, MemCross was applied on a series of 12 xenobiotics, including four weak acids, and a coherent structure-activity relationship was established.
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Affiliation(s)
| | | | | | - Patrick Trouillas
- INSERM, UMR 1248, F-87000 Limoges, France; CATRIN RCPTM, 779 00 Olomouc, Holice, Czech Republic
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8
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Yuan T, Hu J, Zhu X, Yin H, Yin J. Oxidative stress-mediated up-regulation of ABC transporters in lung cancer cells. J Biochem Mol Toxicol 2022; 36:e23095. [PMID: 35478211 DOI: 10.1002/jbt.23095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 11/12/2022]
Abstract
This paper aimed to evaluate the role of oxidative stress in the regulation of ABC transporters in human lung cancer (A549) cells facing substrate (doxorubicin, DOX) and non-substrate (ethanol, ETH and hydrogen peroxide, HP) chemicals. After 24-h treatment, all the chemicals caused significant cytotoxicity as reflected by the reduction in cell viability and the increase in reactive oxygen species (ROS) levels. Depending on the rescuing effects of ROS scavenger including glutathione (GSH) and Vitamin C (VC), the toxicity dependence on oxidative stress were found to be HP>ETH>DOX. Addition of transporter inhibitors significantly enhanced the ROS levels and death-inducing effects of chemicals, indicating the universal detoxification function of ABC transporters. At moderate ROS levels (about 3-4 folds of control levels, caused by 10 μM DOX, 400 mM ETH, and 400 μM HP), all the three chemicals induced the gene expressions and activities of ABC transporters, but these values decreased at too high ROS levels (8.36 folds of control levels) caused by HP at LC50 (800 μM). Such induction could be attenuated by GSH and KCZ, and was completely abolished by 50 μM KCZ, indicating an important role of oxidative stress and pregnane X receptor (PXR) in the induction of ABC transporters. After all, this paper revealed a critical role of oxidative stress in the modulation of ABC transporters by either substrate or non-substrate chemicals during 24-h treatment. Such information should be beneficial for overcoming ABC transporter-mediated multidrug resistance (MDR). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tongkuo Yuan
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, Jiangsu, 215163, PR China.,CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, PR China.,Jinan Guo Ke Medical Technology Development Co., Ltd, Jinan, 250001, PR China
| | - Jia Hu
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Xiaoming Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau SAR, China
| | - Huancai Yin
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, Jiangsu, 215163, PR China.,CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, PR China.,Jinan Guo Ke Medical Technology Development Co., Ltd, Jinan, 250001, PR China
| | - Jian Yin
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, Jiangsu, 215163, PR China.,CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, PR China.,Jinan Guo Ke Medical Technology Development Co., Ltd, Jinan, 250001, PR China
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9
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Zhang S, Thompson JP, Xia J, Bogetti AT, York F, Skillman AG, Chong LT, LeBard DN. Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories. J Chem Inf Model 2022; 62:1891-1904. [PMID: 35421313 PMCID: PMC9044451 DOI: 10.1021/acs.jcim.1c01540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Passive permeability
of a drug-like molecule is a critical property
assayed early in a drug discovery campaign that informs a medicinal
chemist how well a compound can traverse biological membranes, such
as gastrointestinal epithelial or restrictive organ barriers, so it
can perform a specific therapeutic function. However, the challenge
that remains is the development of a method, experimental or computational,
which can both determine the permeation rate and provide mechanistic
insights into the transport process to help with the rational design
of any given molecule. Typically, one of the following three methods
are used to measure the membrane permeability: (1) experimental permeation
assays acting on either artificial or natural membranes; (2) quantitative
structure–permeability relationship models that rely on experimental
values of permeability or related pharmacokinetic properties of a
range of molecules to infer those for new molecules; and (3) estimation
of permeability from the Smoluchowski equation, where free energy
and diffusion profiles along the membrane normal are taken as input
from large-scale molecular dynamics simulations. While all these methods
provide estimates of permeation coefficients, they provide very little
information for guiding rational drug design. In this study, we employ
a highly parallelizable weighted ensemble (WE) path sampling strategy,
empowered by cloud computing techniques, to generate unbiased permeation
pathways and permeability coefficients for a set of drug-like molecules
across a neat 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine
membrane bilayer. Our WE method predicts permeability coefficients
that compare well to experimental values from an MDCK-LE cell line
and PAMPA assays for a set of drug-like amines of varying size, shape,
and flexibility. Our method also yields a series of continuous permeation
pathways weighted and ranked by their associated probabilities. Taken
together, the ensemble of reactive permeation pathways, along with
the estimate of the permeability coefficient, provides a clearer picture
of the microscopic underpinnings of small-molecule membrane permeation.
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Affiliation(s)
- She Zhang
- OpenEye Scientific, Santa Fe, New Mexico 87508, United States
| | - Jeff P Thompson
- OpenEye Scientific, Santa Fe, New Mexico 87508, United States
| | - Junchao Xia
- OpenEye Scientific, Santa Fe, New Mexico 87508, United States
| | - Anthony T Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Forrest York
- OpenEye Scientific, Santa Fe, New Mexico 87508, United States
| | | | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - David N LeBard
- OpenEye Scientific, Santa Fe, New Mexico 87508, United States
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10
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Miao M, Shao X, Cai W. Conformational Change from U- to I-Shape of Ion Transporters Facilitates K + Transport across Lipid Bilayers. J Phys Chem B 2022; 126:1520-1528. [PMID: 35142530 DOI: 10.1021/acs.jpcb.1c09423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated, at the atomic level, the ion-fishing mechanism underlying the ion transport across membranes mediated by an artificial ion transporter composed of a hydroxyl-rich cholesterol group, a flexible alkyl chain, and a crown ether. Our results show that the transporter can spontaneously insert into the membrane and switch between the folded (U-shaped) and extended (I-shaped) conformations. The free-energy profile associated with the conformational transition indicates that compared with the U-shaped conformation of the transporter, the I-shaped one is thermodynamically more favorable. Furthermore, the free-energy profiles describing the ion translocation reveal that the transporter capturing the ion in U-shape on one side of the membrane and releasing it in I-shape on the other side constitutes a key way for the highly efficient transport of K+ ions. We present herewith a rigorous and rational framework to decipher the detailed ion-fishing mechanism of transmembrane ion transport with exceptionally high activity.
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Affiliation(s)
- Mengyao Miao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
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11
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Jorgensen C, Ulmschneider MB, Searson PC. Atomistic Model of Solute Transport across the Blood-Brain Barrier. ACS OMEGA 2022; 7:1100-1112. [PMID: 35036773 PMCID: PMC8757349 DOI: 10.1021/acsomega.1c05679] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
The blood-brain barrier remains a major roadblock to the delivery of drugs to the brain. While in vitro and in vivo measurements of permeability are widely used to predict brain penetration, very little is known about the mechanisms of passive transport. Detailed insight into interactions between solutes and cell membranes could provide new insight into drug design and screening. Here, we perform unbiased atomistic MD simulations to visualize translocation of a library of 24 solutes across a lipid bilayer representative of brain microvascular endothelial cells. A temperature bias is used to achieve steady state of all solutes, including those with low permeability. Based on free-energy surface profiles, we show that the solutes can be classified into three groups that describe distinct mechanisms of transport across the bilayer. Simulations down to 310 K for solutes with fast permeability were used to justify the extrapolation of values at 310 K from higher temperatures. Comparison of permeabilities at 310 K to experimental values obtained from in vitro transwell measurements and in situ brain perfusion revealed that permeabilities obtained from simulations vary from close to the experimental values to more than 3 orders of magnitude faster. The magnitude of the difference was dependent on the group defined by free-energy surface profiles. Overall, these results show that MD simulations can provide new insight into the mechanistic details of brain penetration and provide a new approach for drug discovery.
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Affiliation(s)
- Christian Jorgensen
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Peter C. Searson
- Institute
for Nanobiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
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12
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Bohinc K, Špadina M, Reščič J, Shimokawa N, Spada S. Influence of Charge Lipid Head Group Structures on Electric Double Layer Properties. J Chem Theory Comput 2021; 18:448-460. [PMID: 34937343 PMCID: PMC8757465 DOI: 10.1021/acs.jctc.1c00800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this study we
derived a model for a multicomponent lipid monolayer
in contact with an aqueous solution by means of a generalized classical
density functional theory and Monte Carlo simulations. Some of the
important biological lipid systems were studied as monolayers composed
of head groups with different shapes and charge distributions. Starting
from the free energy of the system, which includes the electrostatic
interactions, additional internal degrees of freedom are included
as positional and orientational entropic contributions to the free
energy functional. The calculus of variation was used to derive Euler–Lagrange
equations, which were solved numerically by the finite element method.
The theory and Monte Carlo simulations predict that there are mainly
two distinct regions of the electric double layer: (1) the interfacial
region, with thickness less than or equal to the length of the fully
stretched conformation of the lipid head group, and (2) the outside
region, which follows the usual screening of the interface. In the
interfacial region, the electric double layer is strongly perturbed,
and electrostatic profiles and ion distributions have functionality
distinct to classical mean-field theories. Based purely on Coulomb
interactions, the theory suggests that the dominant effect on the
lipid head group conformation is from the charge density of the interface
and the structured lipid mole fraction in the monolayer, rather than
the salt concentration in the system.
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Affiliation(s)
- Klemen Bohinc
- Faculty of Health Sciences, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Mario Špadina
- Faculty of Health Sciences, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jurij Reščič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Naofumi Shimokawa
- Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Simone Spada
- National Institute of Oceanography and Applied Geophysics - OGS, 34010 Trieste, Italy
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13
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Shoji A, Kang C, Fujioka K, Rose JP, Sun R. Assessing the Intestinal Permeability of Small Molecule Drugs via Diffusion Motion on a Multidimensional Free Energy Surface. J Chem Theory Comput 2021; 18:503-515. [PMID: 34851637 DOI: 10.1021/acs.jctc.1c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A protocol that accurately assesses the intestinal permeability of small molecule compounds plays an essential role in decreasing the cost and time in inventing a new drug. This manuscript presents a novel computational method to study the passive permeation of small molecule drugs based on the inhomogeneous solubility-diffusion model. The multidimensional free energy surface of the drug transiting through a lipid bilayer is computed with transition-tempered metadynamics that accurately captures the mechanisms of passive permeation. The permeability is computed by following the diffusion motion of the drug molecules along the minimal free energy path found on the multidimensional free energy surface. This computational method is assessed by studying the permeability of five small molecule drugs (ketoprofen, naproxen, metoprolol, propranolol, and salicylic acid). The results demonstrate a remarkable agreement between the computed permeabilities and those measured with the intestinal assay. The in silico method reported in this manuscript also reproduces the permeability measured from the intestinal assay (in vivo) better than the cell-based assays (e.g., PAMPA and Caco-2) do. In addition, the multidimensional free energy surface reveals the interplay between the structure of the small molecule and its permeability, shedding light on strategies of drug optimization.
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Affiliation(s)
- Alyson Shoji
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Christopher Kang
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Kazuumi Fujioka
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - John P Rose
- DDCS, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Rui Sun
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
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14
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Chen M. Collective variable-based enhanced sampling and machine learning. THE EUROPEAN PHYSICAL JOURNAL. B 2021; 94:211. [PMID: 34697536 PMCID: PMC8527828 DOI: 10.1140/epjb/s10051-021-00220-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/03/2021] [Indexed: 05/14/2023]
Abstract
ABSTRACT Collective variable-based enhanced sampling methods have been widely used to study thermodynamic properties of complex systems. Efficiency and accuracy of these enhanced sampling methods are affected by two factors: constructing appropriate collective variables for enhanced sampling and generating accurate free energy surfaces. Recently, many machine learning techniques have been developed to improve the quality of collective variables and the accuracy of free energy surfaces. Although machine learning has achieved great successes in improving enhanced sampling methods, there are still many challenges and open questions. In this perspective, we shall review recent developments on integrating machine learning techniques and collective variable-based enhanced sampling approaches. We also discuss challenges and future research directions including generating kinetic information, exploring high-dimensional free energy surfaces, and efficiently sampling all-atom configurations. GRAPHIC ABSTRACT
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Affiliation(s)
- Ming Chen
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 USA
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15
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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16
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Aydin F, Durumeric AEP, da Hora GCA, Nguyen JDM, Oh MI, Swanson JMJ. Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables. J Chem Phys 2021; 155:045101. [PMID: 34340389 DOI: 10.1063/5.0055489] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Understanding the permeation of biomolecules through cellular membranes is critical for many biotechnological applications, including targeted drug delivery, pathogen detection, and the development of new antibiotics. To this end, computer simulations are routinely used to probe the underlying mechanisms of membrane permeation. Despite great progress and continued development, permeation simulations of realistic systems (e.g., more complex drug molecules or biologics through heterogeneous membranes) remain extremely challenging if not intractable. In this work, we combine molecular dynamics simulations with transition-tempered metadynamics and techniques from the variational approach to conformational dynamics to study the permeation mechanism of a drug molecule, trimethoprim, through a multicomponent membrane. We show that collective variables (CVs) obtained from an unsupervised machine learning algorithm called time-structure based Independent Component Analysis (tICA) improve performance and substantially accelerate convergence of permeation potential of mean force (PMF) calculations. The addition of cholesterol to the lipid bilayer is shown to increase both the width and height of the free energy barrier due to a condensing effect (lower area per lipid) and increase bilayer thickness. Additionally, the tICA CVs reveal a subtle effect of cholesterol increasing the resistance to permeation in the lipid head group region, which is not observed when canonical CVs are used. We conclude that the use of tICA CVs can enable more efficient PMF calculations with additional insight into the permeation mechanism.
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Affiliation(s)
- Fikret Aydin
- Quantum Simulation Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | | | - Gabriel C A da Hora
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - John D M Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Myong In Oh
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
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17
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Teo RD, Tieleman DP. Modulation of Phospholipid Bilayer Properties by Simvastatin. J Phys Chem B 2021; 125:8406-8418. [PMID: 34296883 DOI: 10.1021/acs.jpcb.1c03359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Simvastatin (Zocor) is one of the most prescribed drugs for reducing high cholesterol. Although simvastatin is ingested in its inactive lactone form, it is converted to its active dihydroxyheptanoate form by carboxylesterases in the liver. The dihydroxyheptanoate form can also be converted back to its original lactone form. Unfortunately, some of the side effects associated with the intake of simvastatin and other lipophilic statins at higher doses include statin-associated myopathy (SAM) and, in more severe cases, kidney failure. While the cause of SAM is unknown, it is hypothesized that these side effects are dependent on the localization of statins in lipid bilayers and their impact on bilayer properties. In this work, we carry out all-atom molecular dynamics simulations on both the lactone and dihydroxyheptanoate forms of simvastatin (termed "SN" and "SA", respectively) with a pure 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer and a POPC/cholesterol (30 mol %) binary mixture as membrane models. Additional simulations were carried out with multiple simvastatin molecules to mimic in vitro conditions that produced pleiotropic effects. Both SN and SA spontaneously diffused into the lipid bilayer, and a longer simulation time of 4 μs was needed for the complete incorporation of multiple SAs into the bilayer. By constructing potential mean force and electron density profiles, we find that SN localizes deeper within the hydrophobic interior of the bilayer and that SA has a greater tendency to form hydrogen-bonding interactions with neighboring water molecules and lipid headgroups. For the pure POPC bilayer, both SN and SA increase membrane order, while membrane fluidity increases for the POPC/cholesterol bilayer.
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Affiliation(s)
- Ruijie D Teo
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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18
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Casalini T. Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations. J Control Release 2021; 332:390-417. [PMID: 33675875 DOI: 10.1016/j.jconrel.2021.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
Abstract
The use of methods at molecular scale for the discovery of new potential active ligands, as well as previously unknown binding sites for target proteins, is now an established reality. Literature offers many successful stories of active compounds developed starting from insights obtained in silico and approved by Food and Drug Administration (FDA). One of the most famous examples is raltegravir, a HIV integrase inhibitor, which was developed after the discovery of a previously unknown transient binding area thanks to molecular dynamics simulations. Molecular simulations have the potential to also improve the design and engineering of drug delivery devices, which are still largely based on fundamental conservation equations. Although they can highlight the dominant release mechanism and quantitatively link the release rate to design parameters (size, drug loading, et cetera), their spatial resolution does not allow to fully capture how phenomena at molecular scale influence system behavior. In this scenario, the "computational microscope" offered by simulations at atomic scale can shed light on the impact of molecular interactions on crucial parameters such as release rate and the response of the drug delivery device to external stimuli, providing insights that are difficult or impossible to obtain experimentally. Moreover, the new paradigm brought by nanomedicine further underlined the importance of such computational microscope to study the interactions between nanoparticles and biological components with an unprecedented level of detail. Such knowledge is a fundamental pillar to perform device engineering and to achieve efficient and safe formulations. After a brief theoretical background, this review aims at discussing the potential of molecular simulations for the rational design of drug delivery systems.
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Affiliation(s)
- Tommaso Casalini
- Department of Chemistry and Applied Bioscience, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zürich 8093, Switzerland; Polymer Engineering Laboratory, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via la Santa 1, Lugano 6962, Switzerland.
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19
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Chan C, Du S, Dong Y, Cheng X. Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems. Curr Top Med Chem 2021; 21:92-114. [PMID: 33243123 PMCID: PMC8191596 DOI: 10.2174/1568026620666201126162945] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023]
Abstract
Lipid nanoparticles (LNPs) have been widely applied in drug and gene delivery. More than twenty years ago, DoxilTM was the first LNPs-based drug approved by the US Food and Drug Administration (FDA). Since then, with decades of research and development, more and more LNP-based therapeutics have been used to treat diverse diseases, which often offer the benefits of reduced toxicity and/or enhanced efficacy compared to the active ingredients alone. Here, we provide a review of recent advances in the development of efficient and robust LNPs for drug/gene delivery. We emphasize the importance of rationally combining experimental and computational approaches, especially those providing multiscale structural and functional information of LNPs, to the design of novel and powerful LNP-based delivery systems.
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Affiliation(s)
- Chun Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Shi Du
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Yizhou Dong
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Engineering; The Center for Clinical and Translational Science; The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute; Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
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20
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Kazarinov KD, Shchelkonogov VA, Baranova OA, Chekanov AV, Solovieva EU, Fedin AI. The Effect of Microwave Radiation on Cell Sensitivity to Monohydric Alcohols in Platelet-Rich Plasma. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s000635092006007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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21
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Casalini T, Rosolen A, Henriques CYH, Perale G. Permeation of Biopolymers Across the Cell Membrane: A Computational Comparative Study on Polylactic Acid and Polyhydroxyalkanoate. Front Bioeng Biotechnol 2020; 8:718. [PMID: 32714910 PMCID: PMC7344160 DOI: 10.3389/fbioe.2020.00718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 06/08/2020] [Indexed: 11/23/2022] Open
Abstract
Polymeric nanoparticles, which by virtue of their size (1-1000 nm) are able to penetrate even into cells, are attracting increasing interest in the emerging field of nanomedicine, as devices for, e.g., drugs or vaccines delivery. Because of the involved dimensional scale in the nanoparticle/cell membrane interactions, modeling approaches at molecular level are the natural choice in order to understand the impact of nanoparticle formulation on cellular uptake mechanisms. In this work, the passive permeation across cell membrane of oligomers made of two employed polymers in the biomedical field [poly-D,L-lactic acid (PDLA) and poly(3-hydroxydecanoate) (P3HD)] is investigated at fundamental atomic scale through molecular dynamics simulations. The free energy profile related to membrane crossing is computed adopting umbrella sampling. Passive permeation is also investigated using a coarse-grained model with MARTINI force field, adopting well-tempered metadynamics. Simulation results showed that P3HD permeation is favored with respect to PDLA by virtue of its higher hydrophobicity. The free energy profiles obtained at full atomistic and coarse-grained scale are in good agreement each for P3HD, while only a qualitative agreement was obtained for PDLA. Results suggest that a reparameterization of non-bonded interactions of the adopted MARTINI beads for the oligomer is needed in order to obtain a better agreement with more accurate simulations at atomic scale.
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Affiliation(s)
- Tommaso Casalini
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
| | - Amanda Rosolen
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
| | - Carolina Yumi Hosoda Henriques
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
| | - Giuseppe Perale
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Vienna, Austria
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22
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Tang PK, Chakraborty K, Hu W, Kang M, Loverde SM. Interaction of Camptothecin with Model Cellular Membranes. J Chem Theory Comput 2020; 16:3373-3384. [PMID: 32126167 DOI: 10.1021/acs.jctc.9b00541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Accurate and efficient prediction of drug partitioning in model membranes is of significant interest to the pharmaceutical industry. Herein, we utilize advanced sampling methods, specifically, the adaptive biasing force methodology to calculate the potential of mean force for a model hydrophobic anticancer drug, camptothecin (CPT), across three model interfaces. We consider an octanol bilayer, a thick octanol/water interface, and a model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/water interface. We characterize the enthalpic and entropic contributions of the drug to the potential of mean force. We show that the rotational entropy of the drug is inversely related to the probability of hydrogen bond formation of the drug with the POPC membrane. In addition, in long-time microsecond simulations of a high concentration of CPT above the POPC membrane, we show that strong drug-drug aromatic interactions shift the spatial orientation of the drug with the membrane. Stacks of hydrophobic drugs form, allowing penetration of the drug just under the POPC head groups. These results imply that inhomogeneous membrane models need to take into account the effect of drug aggregation on the membrane environment.
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Affiliation(s)
- Phu K Tang
- Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, 6S-238, Staten Island, New York 10314, United States.,Ph.D. Program in Chemistry, Biochemistry, and Physics, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Kaushik Chakraborty
- Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, 6S-238, Staten Island, New York 10314, United States
| | - William Hu
- Hunter College High School, New York, New York, 10128, United States
| | - Myungshim Kang
- Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, 6S-238, Staten Island, New York 10314, United States
| | - Sharon M Loverde
- Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, 6S-238, Staten Island, New York 10314, United States.,Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Chemistry, Biochemistry, and Physics, The Graduate Center of the City University of New York, New York, New York 10016, United States
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23
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Zhang H, Shao X, Dehez F, Cai W, Chipot C. Modulation of membrane permeability by carbon dioxide. J Comput Chem 2019; 41:421-426. [PMID: 31479166 DOI: 10.1002/jcc.26063] [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: 05/28/2019] [Revised: 08/02/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
Abstract
Promoting drug delivery across the biological membrane is a common strategy to improve bioavailability. Inspired by the observation that carbonated alcoholic beverages can increase the absorption rate of ethanol, we speculate that carbon dioxide (CO2 ) molecules could also enhance membrane permeability to drugs. In the present work, we have investigated the effect of CO2 on the permeability of a model membrane formed by 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine lipids to three drug-like molecules, namely, ethanol, 2',3'-dideoxyadenosine, and trimethoprim. The free-energy and fractional-diffusivity profiles underlying membrane translocation were obtained from μs-timescale simulations and combined in the framework of the fractional solubility-diffusion model. We find that addition of CO2 in the lipid environment results in an increase of the membrane permeability to the three substrates. Further analysis of the permeation events reveals that CO2 expands and loosens the membrane, which, in turn, facilitates permeation of the drug-like molecules. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Hong Zhang
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, 300071, People's Republic of China
| | - Xueguang Shao
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, 300071, People's Republic of China
| | - François Dehez
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandœuvre-lès-Nancy, F-54506, France.,LPCT, UMR 7019 Université de Lorraine CNRS, Vandœuvre-lès-Nancy, F-54500, France
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, 300071, People's Republic of China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandœuvre-lès-Nancy, F-54506, France.,LPCT, UMR 7019 Université de Lorraine CNRS, Vandœuvre-lès-Nancy, F-54500, France.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
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