1
|
Obi P, Gc JB, Mariasoosai C, Diyaolu A, Natesan S. Application of Generative Artificial Intelligence in Predicting Membrane Partitioning of Drugs: Combining Denoising Diffusion Probabilistic Models and MD Simulations Reduces the Computational Cost to One-Third. J Chem Theory Comput 2024; 20:5866-5881. [PMID: 38942732 DOI: 10.1021/acs.jctc.4c00315] [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: 06/30/2024]
Abstract
The optimal interaction of drugs with plasma membranes and membranes of subcellular organelles is a prerequisite for desirable pharmacology. Importantly, for drugs targeting the transmembrane lipid-facing sites of integral membrane proteins, the relative affinity of a drug to the bilayer lipids compared to the surrounding aqueous phase affects the partitioning, access, and binding of the drug to the target site. Molecular dynamics (MD) simulations, including enhanced sampling techniques such as steered MD, umbrella sampling (US), and metadynamics, offer valuable insights into the interactions of drugs with the membrane lipids and water in atomistic detail. However, these methods are computationally prohibitive for the high-throughput screening of drug candidates. This study shows that applying denoising diffusion probabilistic models (DDPMs), a generative AI method, to US simulation data reduces the computational cost significantly. Specifically, the models used only partial (one-third) data from the US simulations and reproduced the complete potential of mean force (PMF) profiles for three FDA-approved drugs (β2-adrenergic agonists) and ∼20 biologically relevant chemicals with known experimentally characterized bilayer locations. Intriguingly, the model can predict the solvation-free energies for partitioning and crossing the bilayer, preferred bilayer locations (low-energy well), and orientations of the ligands with high accuracy. The results indicate that DDPMs can be used to characterize the complete membrane partitioning profile of drug molecules using fewer umbrella sampling simulations at select positions along the bilayer normal (z-axis), irrespective of their amphiphilic-lipophilic-cephalophilic characteristics.
Collapse
Affiliation(s)
- Peter Obi
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Jeevan B Gc
- The Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Charles Mariasoosai
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Ayobami Diyaolu
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Senthil Natesan
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| |
Collapse
|
2
|
Matsubara Y, Okabe R, Masayama R, Watanabe NM, Umakoshi H, Kasahara K, Matubayasi N. A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation. J Chem Phys 2024; 161:024108. [PMID: 38984955 DOI: 10.1063/5.0214401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024] Open
Abstract
We propose a theoretical approach to estimate the permeability coefficients of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of our approach involves reformulating the returning probability (RP) theory, a rigorous bimolecular reaction theory, to describe permeation phenomena. This reformulation relies on the parallelism between permeation and bimolecular reaction processes. In the present method, the permeability coefficient is represented in terms of the thermodynamic and kinetic quantities for the reactive (R) phase that exists within the inner region of a membrane. One can evaluate these quantities using multiple MD trajectories starting from phase R. We apply the RP theory to the permeation of ethanol and methylamine at different concentrations (infinitely dilute and 1 mol % conditions of permeants). Under the 1 mol% condition, the present method yields a larger permeability coefficient for ethanol (0.12 ± 0.01 cm s-1) than for methylamine (0.069 ± 0.006 cm s-1), while the values of the permeability coefficient are satisfactorily close to those obtained from the brute-force MD simulations (0.18 ± 0.03 and 0.052 ± 0.005 cm s-1 for ethanol and methylamine, respectively). Moreover, upon analyzing the thermodynamic and kinetic contributions to the permeability, we clarify that a higher concentration dependency of permeability for ethanol, as compared to methylamine, arises from the sensitive nature of ethanol's free-energy barrier within the inner region of the membrane against ethanol concentration.
Collapse
Affiliation(s)
- Yuya Matsubara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ryo Okabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ren Masayama
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nozomi Morishita Watanabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
3
|
Oh M, da Hora GCA, Swanson JMJ. tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation. J Chem Theory Comput 2023; 19:8886-8900. [PMID: 37943658 PMCID: PMC11282584 DOI: 10.1021/acs.jctc.3c00526] [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: 11/12/2023]
Abstract
Molecular simulations are commonly used to understand the mechanism of membrane permeation of small molecules, particularly for biomedical and pharmaceutical applications. However, despite significant advances in computing power and algorithms, calculating an accurate permeation free energy profile remains elusive for many drug molecules because it can require identifying the rate-limiting degrees of freedom (i.e., appropriate reaction coordinates). To resolve this issue, researchers have developed machine learning approaches to identify slow system dynamics. In this work, we apply time-lagged independent component analysis (tICA), an unsupervised dimensionality reduction algorithm, to molecular dynamics simulations with well-tempered metadynamics to find the slowest collective degrees of freedom of the permeation process of trimethoprim through a multicomponent membrane. We show that tICA-metadynamics yields translational and orientational collective variables (CVs) that increase convergence efficiency ∼1.5 times. However, crossing the periodic boundary is shown to introduce artifacts in the translational CV that can be corrected by taking absolute values of molecular features. Additionally, we find that the convergence of the tICA CVs is reached with approximately five membrane crossings and that data reweighting is required to avoid deviations in the translational CV.
Collapse
Affiliation(s)
- Myongin Oh
- Department of Chemistry, University of Utah, 315 South 1400 East, Rm 2020, Salt Lake City, Utah 84112, United States
| | - Gabriel C A da Hora
- Department of Chemistry, University of Utah, 315 South 1400 East, Rm 2020, Salt Lake City, Utah 84112, United States
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, 315 South 1400 East, Rm 2020, Salt Lake City, Utah 84112, United States
| |
Collapse
|
4
|
Jorgensen C, Troendle EP, Ulmschneider JP, Searson PC, Ulmschneider MB. A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood-brain barrier endothelium. J Comput Aided Mol Des 2023; 37:537-549. [PMID: 37573260 PMCID: PMC10505096 DOI: 10.1007/s10822-023-00525-1] [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] [Received: 04/07/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
The treatment of various disorders of the central nervous system (CNS) is often impeded by the limited brain exposure of drugs, which is regulated by the human blood-brain barrier (BBB). The screening of lead compounds for CNS penetration is challenging due to the biochemical complexity of the BBB, while experimental determination of permeability is not feasible for all types of compounds. Here we present a novel method for rapid preclinical screening of libraries of compounds by utilizing advancements in computing hardware, with its foundation in transition-based counting of the flux. This method has been experimentally validated for in vitro permeabilities and provides atomic-level insights into transport mechanisms. Our approach only requires a single high-temperature simulation to rank a compound relative to a library, with a typical simulation time converging within 24 to 72 h. The method offers unbiased thermodynamic and kinetic information to interpret the passive transport of small-molecule drugs across the BBB.
Collapse
Affiliation(s)
- Christian Jorgensen
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
| | | | | | - Peter C Searson
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Oh M, da Hora GCA, Swanson JMJ. tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553477. [PMID: 37645884 PMCID: PMC10462029 DOI: 10.1101/2023.08.16.553477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Molecular simulations are commonly used to understand the mechanism of membrane permeation of small molecules, particularly for biomedical and pharmaceutical applications. However, despite significant advances in computing power and algorithms, calculating an accurate permeation free energy profile remains elusive for many drug molecules because it can require identifying the rate-limiting degrees of freedom (i.e., appropriate reaction coordinates). To resolve this issue, researchers have developed machine learning approaches to identify slow system dynamics. In this work, we apply time-lagged independent component analysis (tICA), an unsupervised dimensionality reduction algorithm, to molecular dynamics simulations with well-tempered metadynamics to find the slowest collective degrees of freedom of the permeation process of trimethoprim through a multicomponent membrane. We show that tICA-metadynamics yields translational and orientational collective variables (CVs) that increase convergence efficiency ∼1.5 times. However, crossing the periodic boundary is shown to introduce artefacts in the translational CV that can be corrected by taking absolute values of molecular features. Additionally, we find that the convergence of the tICA CVs is reached with approximately five membrane crossings, and that data reweighting is required to avoid deviations in the translational CV.
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
Affiliation(s)
| | | | | | - Patrick Trouillas
- INSERM, UMR 1248, F-87000 Limoges, France; CATRIN RCPTM, 779 00 Olomouc, Holice, Czech Republic
| | | |
Collapse
|
9
|
Mitsuta Y, Asada T, Shigeta Y. Calculation of the permeability coefficients of small molecules through lipid bilayers by free-energy reaction network analysis following the explicit treatment of the internal conformation of the solute. Phys Chem Chem Phys 2022; 24:26070-26082. [PMID: 36268802 DOI: 10.1039/d2cp03678a] [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: 06/16/2023]
Abstract
Biomembrane permeation represents a major barrier to pharmacokinetics. During preclinical drug discovery, the coefficients of the permeation of molecules through lipid bilayers account for a valuable property of such molecules. Therefore, the control of the permeation of molecules through lipid bilayers is an essential factor in drug design, and the estimation of the permeation phenomena is a crucial study in pharmacy. Thus, there are many published studies on the theoretical estimations of permeation coefficients. Here, we propose a molecular dynamics (MD) simulation method for estimating the permeation of small molecules through lipid bilayers based on the free-energy reaction network (FERN) analysis. In this method, the collective variables (CVs) of the free energy calculations explicitly include the conformational changes in the rotational bonds of the solute molecules. The advantages of the present method over the other method are that it is possible to estimate reaction pathways and their reaction rates, i.e., permeation coefficients or passage times, in multidimensional space spanned by CVs though conventional methods such as the umbrella sampling method and target MDs often dealt with a few degrees of freedom. To demonstrate the efficacy of our method, we calculate the coefficients of the permeation of three small aromatic peptides, namely N-acetylphenylalanineamide (Ac-Phe-NH2 or NAFA), N-acetyltyrosineamide (Ac-Tyr-NH2 or NAYA), and N-acetyltryptophanamide (Ac-Trp-NH2 or NATA), through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer. In these cases we adopted one CV for the permeation direction and four CVs for the internal rotational coordinates. The results reveal that the permeation coefficients of NAFA, NAYA, and NATA are 1.7 × 10-2, 0.51 × 10-4, and 5.7 × 10-4 cm s-1, respectively. Compared with the experimental data, our simulation results followed the same trend, i.e., NAFA > NATA > NAYA. By analyzing the structures of metastable points of the solute molecules, our simulation result reveals that the aforementioned trend is caused by the differences in stability among their rotamers. Furthermore, we evaluate the statistical fluctuation of the rotamers, and the time scale of flipping the side chain reveals that the structures rigidify as the ligand moves deeper into the membrane.
Collapse
Affiliation(s)
- Yuki Mitsuta
- Department of Chemistry, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan.
- RIMED, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan
| | - Toshio Asada
- Department of Chemistry, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan.
- RIMED, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Jourdain B, Lelièvre T, Zitt PA. Convergence of metadynamics: Discussion of the adiabatic hypothesis. ANN APPL PROBAB 2021. [DOI: 10.1214/20-aap1652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Patel SJ, Van Lehn RC. Analysis of Charged Peptide Loop-Flipping across a Lipid Bilayer Using the String Method with Swarms of Trajectories. J Phys Chem B 2021; 125:5862-5873. [PMID: 34033491 DOI: 10.1021/acs.jpcb.1c02810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The hydrophobic core of the lipid bilayer is conventionally considered a barrier to the translocation of charged species such that the translocation of even single ions occurs on long time scales. In contrast, experiments have revealed that some materials, including peptides, proteins, and nanoparticles, can translocate multiple charged moieties across the bilayer on experimentally relevant time scales. Understanding the molecular mechanisms underlying this behavior is challenging because resolving corresponding free-energy landscapes with molecular simulation techniques is computationally expensive. To address this challenge, we use atomistic molecular dynamics simulations with the swarms-of-trajectories (SOT) string method to analyze charge translocation pathways across single-component lipid bilayers as a function of multiple collective variables. We first demonstrate that the SOT string method can reproduce the free-energy barrier for the translocation of a charged lysine amino acid analogue in good agreement with the literature. We then obtain minimum free-energy pathways for the translocation, or flipping, of charged peptide loops across the lipid bilayer by utilizing trajectories from prior temperature-accelerated molecular dynamics (TAMD) simulations as initial configurations. The corresponding potential of mean force calculations reveal that the protonation of a central membrane-exposed aspartate residue substantially reduces the free-energy barrier for flipping charged loops by modulating the water content of the bilayer. These results provide new insight into the thermodynamics underlying loop-flipping processes and highlight how the combination of TAMD and the SOT string method can be used to understand complex charge translocation mechanisms.
Collapse
Affiliation(s)
- Samarthaben J Patel
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
14
|
Ghorbani M, Wang E, Krämer A, Klauda JB. Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers. J Chem Phys 2021; 153:125101. [PMID: 33003717 DOI: 10.1063/5.0013430] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Permeation of small molecules through membranes is a fundamental biological process, and molecular dynamics simulations have proven to be a promising tool for studying the permeability of membranes by providing a precise characterization of the free energy and diffusivity. In this study, permeation of ethanol through three different membranes of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), PO-phosphatidylethanolamine (POPE), and PO-phosphatidylcholine (POPC) is studied. Permeabilities are calculated and compared with two different approaches based on Fick's first law and the inhomogeneous solubility-diffusion model. Microsecond simulation of double bilayers of these membranes provided a direct measurement of permeability by a flux-based counting method. These simulations show that a membrane of POPC has the highest permeability, followed by POPE and POPS. Due to the membrane-modulating properties of ethanol, the permeability increases as functions of concentration and saturation of the inner leaflet in a double bilayer setting, as opposed to the customary definition as a proportionality constant. This concentration dependence is confirmed by single bilayer simulations at different ethanol concentrations ranging from 1% to 18%, where permeability estimates are available from transition-based counting and the inhomogeneous solubility-diffusion model. We show that the free energy and diffusion profiles for ethanol lack accuracy at higher permeant concentrations due to non-Markovian kinetics caused by collective behavior. In contrast, the counting method provides unbiased estimates. Finally, the permeabilities obtained from single bilayer simulations are combined to represent natural gradients felt by a cellular membrane, which accurately models the non-equilibrium effects on ethanol permeability from single bilayer simulations in equilibrium.
Collapse
Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Eric Wang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Andreas Krämer
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| |
Collapse
|
15
|
Sharifian Gh M. Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules. Mol Pharm 2021; 18:2122-2141. [PMID: 33914545 DOI: 10.1021/acs.molpharmaceut.1c00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to measure the passive membrane permeation of drug-like molecules is of fundamental biological and pharmaceutical importance. Of significance, passive diffusion across the cellular membranes plays an effective role in the delivery of many pharmaceutical agents to intracellular targets. Hence, approaches for quantitative measurement of membrane permeability have been the topics of research for decades, resulting in sophisticated biomimetic systems coupled with advanced techniques. In this review, recent developments in experimental approaches along with theoretical models for quantitative and real-time analysis of membrane transport of drug-like molecules through mimetic and living cell membranes are discussed. The focus is on time-resolved fluorescence-based, surface plasmon resonance, and second-harmonic light scattering approaches. The current understanding of how properties of the membrane and permeant affect the permeation process is discussed.
Collapse
Affiliation(s)
- Mohammad Sharifian Gh
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States
| |
Collapse
|
16
|
Li J, Jin X, Zhang L, Yang Y, Liu R, Li Z. Comparison of Different Chitosan Lipid Nanoparticles for Improved Ophthalmic Tetrandrine Delivery: Formulation, Characterization, Pharmacokinetic and Molecular Dynamics Simulation. J Pharm Sci 2020; 109:3625-3635. [PMID: 32946897 DOI: 10.1016/j.xphs.2020.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/25/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
In this study, three different chitosan, namely carboxymethyl chitosan (CMC), hydroxypropyl chitosan (HPC) and trimethyl chitosan (TMC) were used as cationic materials to prepare tetrandrine lipid nanoparticles (TET-LNPs) for the treatment of glaucoma. In vitro drug release and pre-corneal retention were used to select the optimal chitosan. In vitro drug release curves of three kinds of LNPs showed a sustained release and TMC-TET-LNPs were the slowest. Moreover, compared with CMC-TET-LNPs and HPC-TET-LNPs, TMC-TET-LNPs had longer corneal retention time. Afterwards, the characteristics of TMC-TET-LNPs were investigated. The ocular irritation study revealed no sign of irritation in rabbit eyes. The pharmacokinetic studies showed that the area under the curve of TMC-TET-LNPs was increased by 2.03 times than TET solution (p < 0.01). Furthermore, the drug biofilm interactions were evaluated by molecular dynamics (MD) simulation. In MD simulation, the strong hydrophobic group of TET interacted with the tail of POPC, making it hard to enter the hydrophobic region of the membrane, thereby restricting TET ocular bioavailability. The experiments and MD simulation indicated that TMC-TET-LNPs had great potential for ocular administration and MD simulation could predict transmembrane transport of drugs.
Collapse
Affiliation(s)
- Jinjing Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Xin Jin
- Military Medicine Section, Logistics University of Chinese People's Armed Police Force, 1 Huizhihuan Road, Dongli District, Tianjin 300309, China
| | - Lingling Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Yang Yang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Rui Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China.
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| |
Collapse
|
17
|
Martinotti C, Ruiz-Perez L, Deplazes E, Mancera RL. Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes. Chemphyschem 2020; 21:1486-1514. [PMID: 32452115 DOI: 10.1002/cphc.202000219] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
Collapse
Affiliation(s)
- Carlo Martinotti
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| |
Collapse
|
18
|
Cao Z, Liu L, Hu G, Bian Y, Li H, Wang J, Zhou Y. Interplay of hydrophobic and hydrophilic interactions in sequence-dependent cell penetration of spontaneous membrane-translocating peptides revealed by bias-exchange metadynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183402. [PMID: 32569587 DOI: 10.1016/j.bbamem.2020.183402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/29/2022]
Abstract
Spontaneous Membrane Translocating Peptides (SMTPs) can translocate silently across the bilayer and, thus, have the best potential to improve the delivery of therapeutic molecules to cells without toxicity. However, how their translocation mechanisms are affected by a specific peptide sequence remains poorly understood. Here, bias-exchange metadynamics simulations were employed to investigate the translocation mechanisms of five SMTPs with the same composition of amino acids (LLRLR, LRLLR, LLLRR, RLLLR, and LRLRL). Simulation results yield sequence-dependent free energy barrier using the FESs along the z-directional distance. An in-depth analysis of sequence-dependent interactions in different regions of the bilayers indicates that the free-energy barrier height of a specific sequence is resulted from the accessibility balance of isolated or clustered hydrophobic residues (L) and hydrophilic residues (R) that leads to different levels of resistance for moving of a peptide into the hydrophobic center of the membrane. At the maximal of the free-energy barrier, all peptides have a conformation parallel to the membrane surface with the barrier height determined by their affinity to the hydrophobic region. The appropriate bilayer perturbation and GDM+ pairing are beneficial for peptide translocation. These results provide an improved microscopic understanding of how peptide sequence influences the translocation efficiency and mechanism.
Collapse
Affiliation(s)
- Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Lei Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; College of Information Management, Dezhou University, Dezhou 253023, China.
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Haiyan Li
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China; Institute for Glycomics, School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
| |
Collapse
|
19
|
Li J, Jin X, Yang Y, Zhang L, Liu R, Li Z. Trimethyl chitosan nanoparticles for ocular baicalein delivery: Preparation, optimization, in vitro evaluation, in vivo pharmacokinetic study and molecular dynamics simulation. Int J Biol Macromol 2020; 156:749-761. [PMID: 32320806 DOI: 10.1016/j.ijbiomac.2020.04.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/11/2020] [Accepted: 04/16/2020] [Indexed: 12/20/2022]
Abstract
To improve ocular bioavailability of baicalein (BAI), trimethyl chitosan coated lipid nanoparticles of baicalein (TMC-BAI-LNPs) were prepared, optimized and characterized. The properties of TMC-BAI-LNPs such as morphology, particle size, zeta potential and fourier transform infrared spectroscopy were investigated. Additionally, molecular dynamics simulation was applied as a new method to evaluate drug-biological membrane interactions. Transmission electron microscopy showed that the LNPs were approximately spherical in shape with a smooth surface. TMC-BAI-LNPs had a particle size of 162.8 nm, a positive surface charge with a zeta potential of 26.6 mV. The entrapment efficiency and drug loading values of BAI in the formulation were 90.65% and 2.04%, respectively. Moreover, in vitro drug release revealed that TMC-BAI-LNPs had a sustained release effect. In vivo studies indicated TMC-BAI-LNPs had no ocular irritation and the AUC of TMC-BAI-LNPs was 3.17-fold than that of the control (p < 0.01). Molecular dynamics simulation data showed that BAI had a poor membrane permeability, which limited the ocular bioavailability. The results indicated that TMC-BAI-LNPs might open up a new avenue for ocular administration. Furthermore, molecular dynamics simulation could predict permeability of drugs.
Collapse
Affiliation(s)
- Jinjing Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Xin Jin
- Military Medicine Section, Logistics University of Chinese People's Armed Police Force, 1 Huizhihuan Road, Dongli District, Tianjin 300309, China
| | - Yang Yang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Lingling Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Rui Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China.
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China.
| |
Collapse
|
20
|
Garofalo M, Grazioso G, Cavalli A, Sgrignani J. How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs. Molecules 2020; 25:E1756. [PMID: 32290224 PMCID: PMC7180704 DOI: 10.3390/molecules25071756] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/17/2023] Open
Abstract
The early and late development of new anticancer drugs, small molecules or peptides can be slowed down by some issues such as poor selectivity for the target or poor ADME properties. Computer-aided drug design (CADD) and target drug delivery (TDD) techniques, although apparently far from each other, are two research fields that can give a significant contribution to overcome these problems. Their combination may provide mechanistic understanding resulting in a synergy that makes possible the rational design of novel anticancer based therapies. Herein, we aim to discuss selected applications, some also from our research experience, in the fields of anticancer small organic drugs and peptides.
Collapse
Affiliation(s)
- Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milano, 20133 Milan, Italy
| | - Andrea Cavalli
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), 6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), 6500 Bellinzona, Switzerland
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Lomize AL, Pogozheva ID. Physics-Based Method for Modeling Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. J Chem Inf Model 2019; 59:3198-3213. [PMID: 31259555 DOI: 10.1021/acs.jcim.9b00224] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assessment of permeability is a critical step in the drug development process for selection of drug candidates with favorable ADME properties. We have developed a novel physics-based method for fast computational modeling of passive permeation of diverse classes of molecules across lipid membranes. The method is based on heterogeneous solubility-diffusion theory and operates with all-atom 3D structures of solutes and the anisotropic solvent model of the lipid bilayer characterized by transbilayer profiles of dielectric and hydrogen bonding capacity parameters. The optimal translocation pathway of a solute is determined by moving an ensemble of representative conformations of the molecule through the dioleoyl-phosphatidylcholine (DOPC) bilayer and optimizing their rotational orientations in every point of the transmembrane trajectory. The method calculates (1) the membrane-bound state of the solute molecule; (2) free energy profile of the solute along the permeation pathway; and (3) the permeability coefficient obtained by integration over the transbilayer energy profile and assuming a constant size-dependent diffusivity along the membrane normal. The accuracy of the predictions was evaluated against experimental permeability coefficients measured in pure lipid membranes (for 78 compounds, R2 was 0.88 and rmse was 1.15 log units), PAMPA-DS (for 280 compounds, R2 was 0.75 and rmse was 1.59 log units), BBB (for 182 compounds, R2 was 0.69 and rmse was 0.87 log units), and Caco-2/MDCK assays (for 165 compounds, R2 was 0.52 and rmse was 0.89 log units).
Collapse
Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| |
Collapse
|
23
|
Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
Collapse
Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
| |
Collapse
|
24
|
Tse CH, Comer J, Sang Chu SK, Wang Y, Chipot C. Affordable Membrane Permeability Calculations: Permeation of Short-Chain Alcohols through Pure-Lipid Bilayers and a Mammalian Cell Membrane. J Chem Theory Comput 2019; 15:2913-2924. [DOI: 10.1021/acs.jctc.9b00022] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chi Hang Tse
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine and Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506, United States
| | - Simon Kit Sang Chu
- 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
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - 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, 54506 Vandœuvre-lès-Nancy cedex, France
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| |
Collapse
|
25
|
Issack BB, Peslherbe GH. Accuracy and precision of simulated free energies: water permeation of hydrated DPPC bilayers as a paradigm. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1572141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Bilkiss B. Issack
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
- Département des sciences expérimentales, Université de Saint-Boniface, Winnipeg, Canada
| | - Gilles H. Peslherbe
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| |
Collapse
|
26
|
Wood N, Russo J, Turci F, Royall CP. Coupling of sedimentation and liquid structure: Influence on hard sphere nucleation. J Chem Phys 2018; 149:204506. [DOI: 10.1063/1.5050397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nicholas Wood
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
- Centre for Nanoscience and Quantum Information, Tyndall Avenue, Bristol BS8 1FD, United Kingdom
| | - John Russo
- School of Mathematics, University Walk, Bristol BS8 1TW, United Kingdom
| | - Francesco Turci
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
- Centre for Nanoscience and Quantum Information, Tyndall Avenue, Bristol BS8 1FD, United Kingdom
| | - C. Patrick Royall
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
- Centre for Nanoscience and Quantum Information, Tyndall Avenue, Bristol BS8 1FD, United Kingdom
- School of Chemistry, University of Bristol, Cantock Close, Bristol BS8 1TS, United Kingdom
| |
Collapse
|
27
|
Palaiokostas M, Ding W, Shahane G, Orsi M. Effects of lipid composition on membrane permeation. SOFT MATTER 2018; 14:8496-8508. [PMID: 30346462 DOI: 10.1039/c8sm01262h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Passive permeation through lipid membranes is an essential process in biology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterized by their tendency to form lamellar sheet-like structures, which are predominant in nature. Nonlamellar lipids, when isolated, instead form more geometrically complex nonlamellar phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous lamellar bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as internal distributions of stress and elastic properties, which in turn may alter related biological processes. This work focuses on one such process, i.e., permeation, by utilising atomistic molecular dynamics simulations in order to obtain transfer free energy profiles, diffusion profiles and permeation coefficients for a series of thirteen small molecules and drugs. Each permeant is tested on two bilayer membranes of different lipid composition, i.e., purely lamellar and mixed lamellar/nonlamellar. Our results indicate that the presence of nonlamellar lipids reduces permeation for smaller molecules (molecular weight < 100) but facilitates it for the largest ones (molecular weight > 100). This work represents an advancement towards the development of more realistic in silico permeability assays, which may have a substantial future impact in the area of rational drug design.
Collapse
Affiliation(s)
- Michail Palaiokostas
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | | | | | | |
Collapse
|
28
|
Sun R, Han Y, Swanson JMJ, Tan JS, Rose JP, Voth GA. Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants. J Chem Phys 2018; 149:072310. [PMID: 30134730 DOI: 10.1063/1.5027004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Estimating the permeability coefficient of small molecules through lipid bilayer membranes plays an important role in the development of effective drug candidates. In silico simulations can produce acceptable relative permeability coefficients for a series of small molecules; however, the absolute permeability coefficients from simulations are usually off by orders of magnitude. In addition to differences between the lipid bilayers used in vitro and in silico, the poor convergence of permeation free energy profiles and over-simplified diffusion models have contributed to these discrepancies. In this paper, we present a multidimensional inhomogeneous solubility-diffusion model to study the permeability of a small molecule drug (trimethoprim) passing through a POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) lipid bilayer. Our approach improves the permeation model in three ways: First, the free energy profile (potential of mean force, PMF) is two-dimensional in two key coordinates rather than simply one-dimensional along the direction normal to the bilayer. Second, the 2-D PMF calculation has improved convergence due to application of the recently developed transition-tempered metadynamics with randomly initialized replicas, while third, the local diffusivity coefficient was calculated along the direction of the minimum free energy path on the two-dimensional PMF. The permeability is then calculated as a line integral along the minimum free energy path of the PMF. With this approach, we report a considerably more accurate permeability coefficient (only 2-5 times larger than the experimental value). We also compare our approach with the common practice of computing permeability coefficients based only on the translation of the center of mass of the drug molecule. Our paper concludes with a discussion of approaches for minimizing the computational cost for the purpose of more rapidly screening a large number of drug candidate molecules.
Collapse
Affiliation(s)
- Rui Sun
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yining Han
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jessica M J Swanson
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jeffrey S Tan
- Small Molecule Design and Development, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - John P Rose
- Small Molecule Design and Development, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| |
Collapse
|
29
|
Klug J, Triguero C, Del Pópolo MG, Tribello GA. Using Intrinsic Surfaces To Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes. J Phys Chem B 2018; 122:6417-6422. [DOI: 10.1021/acs.jpcb.8b03661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Joaquín Klug
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
- CONICET and Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, CP5500 Mendoza, Argentina
| | - Carles Triguero
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Mario G. Del Pópolo
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
- CONICET and Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, CP5500 Mendoza, Argentina
| | - Gareth A. Tribello
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| |
Collapse
|
30
|
Tse CH, Comer J, Wang Y, Chipot C. Link between Membrane Composition and Permeability to Drugs. J Chem Theory Comput 2018; 14:2895-2909. [PMID: 29771515 DOI: 10.1021/acs.jctc.8b00272] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Prediction of membrane permeability to small molecules represents an important aspect of drug discovery. First-principles calculations of this quantity require an accurate description of both the thermodynamics and kinetics that underlie translocation of the permeant across the lipid bilayer. In this contribution, the membrane permeability to three drugs, or drug-like molecules, namely, 9-anthroic acid (ANA), 2',3'-dideoxyadenosine (DDA), and hydrocortisone (HYL), are estimated in a pure 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and in a POPC:cholesterol (2:1) mixture. On the basis of independent 2-5-μs free-energy calculations combined with a time-fractional Smoluchowski determination of the diffusivity, the estimated membrane permeabilities to these chemically diverse permeants fall within an order of magnitude from the experimental values obtained in egg-lecithin bilayers, with the exception of HYL in pure POPC. This exception is particularly interesting because the calculated permeability of the sterol-rich bilayer to HYL, in close agreement with the experimental value, is about 600 times lower than that of the pure POPC bilayer to HYL. In contrast, the permeabilities to ANA and DDA differ by less than a factor of 10 between the pure POPC and POPC:cholesterol bilayers. The unusual behavior of HYL, a large, amphiphilic compound, may be linked with the longer range perturbation of the lipid bilayer it induces, compared to ANA and DDA, suggestive of a possibly different translocation mechanism. We find that the tendency of lower permeabilities of the POPC:cholesterol bilayer relative to those of the pure POPC one is a consequence of increased free-energy barriers. Beyond reporting accurate estimates of the membrane permeability, the present contribution also demonstrates that rigorous free-energy calculations and a fractional-diffusion model are key in revealing the molecular phenomena linking the composition of a membrane to its permeability to drugs.
Collapse
Affiliation(s)
- Chi Hang Tse
- Shenzhen Research Institute , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China.,Department of Physics , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine and Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Yi Wang
- Shenzhen Research Institute , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China.,Department of Physics , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Christophe Chipot
- Laboratoire International Associé Centre, National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7019 , Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex , France.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , 405 North Mathews Avenue , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
| |
Collapse
|
31
|
Hsiao YW, Hedström M, Losasso V, Metz S, Crain J, Winn M. Cooperative Modes of Action of Antimicrobial Peptides Characterized with Atomistic Simulations: A Study on Cecropin B. J Phys Chem B 2018; 122:5908-5921. [PMID: 29737852 DOI: 10.1021/acs.jpcb.8b01957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Antimicrobial peptides (AMPs) are widely occurring host defense agents of interest as one route for addressing the growing problem of multidrug-resistant pathogens. Understanding the mechanisms behind their antipathogen activity is instrumental in designing new AMPs. Herein, we present an all-atom molecular dynamics and free energy study on cecropin B (CB) and its constituent domains. We find a cooperative mechanism in which CB inserts into an anionic model membrane with its amphipathic N-terminal segment, supported by the hydrophobic C-terminal segment of a second peptide. The two peptides interact via a Glu···Lys salt bridge and together sustain a pore in the membrane. Using a modified membrane composition, we demonstrate that when the lower leaflet is overall neutral, insertion of the cationic segment is retarded and thus this mode of action is membrane specific. The observed mode of action utilizes a flexible hinge, a common structural motif among AMPs, which allows CB to insert into the membrane using either or both termini. Data from both unbiased trajectories and enhanced sampling simulations indicate that a requirement for CB to be an effective AMP is the interaction of its hydrophobic C-terminal segment with the membrane. Simulations of these segments in isolation reveal their aggregation in the membrane and a different mechanism of supporting pore formation. Together, our results show the complex interaction of different structural motifs of AMPs and, in particular, a potential role for electronegative side chains in an overall cationic AMP.
Collapse
Affiliation(s)
- Ya-Wen Hsiao
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , U.K
| | - Magnus Hedström
- Clay Technology AB , Ideon Science Park , SE-223 70 Lund , Sweden
| | - Valeria Losasso
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , U.K
| | - Sebastian Metz
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , U.K
| | - Jason Crain
- IBM Research , Hartree Centre , Daresbury WA4 4AD , U.K
| | - Martyn Winn
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , U.K
| |
Collapse
|
32
|
Cao Z, Bian Y, Hu G, Zhao L, Kong Z, Yang Y, Wang J, Zhou Y. Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids. Int J Mol Sci 2018; 19:E885. [PMID: 29547563 PMCID: PMC5877746 DOI: 10.3390/ijms19030885] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 11/16/2022] Open
Abstract
Thermodynamics of the permeation of amino acids from water to lipid bilayers is an important first step for understanding the mechanism of cell-permeating peptides and the thermodynamics of membrane protein structure and stability. In this work, we employed bias-exchange metadynamics simulations to simulate the membrane permeation of all 20 amino acids from water to the center of a dipalmitoylphosphatidylcholine (DPPC) membrane (consists of 256 lipids) by using both directional and torsion angles for conformational sampling. The overall accuracy for the free energy profiles obtained is supported by significant correlation coefficients (correlation coefficient at 0.5-0.6) between our results and previous experimental or computational studies. The free energy profiles indicated that (1) polar amino acids have larger free energy barriers than nonpolar amino acids; (2) negatively charged amino acids are the most difficult to enter into the membrane; and (3) conformational transitions for many amino acids during membrane crossing is the key for reduced free energy barriers. These results represent the first set of simulated free energy profiles of membrane crossing for all 20 amino acids.
Collapse
Affiliation(s)
- Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Liling Zhao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Zhenzhen Kong
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Life Science, Shandong Normal University, Jinan 250014, China.
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia.
| |
Collapse
|
33
|
Bonhenry D, Dehez F, Tarek M. Effects of hydration on the protonation state of a lysine analog crossing a phospholipid bilayer – insights from molecular dynamics and free-energy calculations. Phys Chem Chem Phys 2018; 20:9101-9107. [DOI: 10.1039/c8cp00312b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protonation states of amino acids crossing lipid bilayers from multidimensional free energy surfaces.
Collapse
Affiliation(s)
| | | | - Mounir Tarek
- Université de Lorraine
- CNRS
- LPCT
- F-54000 Nancy
- France
| |
Collapse
|
34
|
Comer J, Schulten K, Chipot C. Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles. J Chem Theory Comput 2017; 13:2523-2532. [PMID: 28475319 DOI: 10.1021/acs.jctc.7b00264] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational prediction of membrane permeability to small molecules requires accurate description of both the thermodynamics and kinetics underlying translocation across the lipid bilayer. In this contribution, well-converged, microsecond-long free-energy calculations are combined with a recently developed subdiffusive kinetics framework to describe the membrane permeation of a homologous series of short-tail alcohols, from methanol to 1-butanol, with unprecedented fidelity to the underlying molecular models. While the free-energy profiles exhibit barriers for passage through the center of the bilayer in all cases, the height of these barriers decreases with the length of the aliphatic chain of the alcohol, in quantitative agreement with experimentally determined differential solvation free energies in water and oil. A unique aspect of the subdiffusive model employed herein, which was developed in a previous article, is the determination of a position-dependent fractional order which quantifies the degree to which the motion of the alcohol deviates from classical diffusion along the thickness of the membrane. In the aqueous medium far from the bilayer, this quantity approaches 1.0, the asymptotic limit for purely classical diffusion, whereas it dips below 0.75 near the center of the membrane irrespective of the permeant. Remarkably, the fractional diffusivity near the center of membrane, where its influence on the permeability is the greatest, is similar among the four permeants despite the large difference in molecular weight and lipophilicity between methanol and 1-butanol. The relative permeabilities, which are estimated from the free-energy and fractional diffusivity profiles, are therefore determined predominantly by differences in the former rather than the latter. The predicted relative permeabilities are highly correlated with existing experimental results, albeit they do not agree quantitatively with them. On the other hand, quite unexpectedly, the reported experimental values for the short-tail alcohols are nearly three orders of magnitude lower than the available experimental measurement for water. Plausible explanations for this apparent disagreement between theory and experiment are considered in detail.
Collapse
Affiliation(s)
- Jeffrey Comer
- Institute of Computational Comparative Medicine and Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University , Manhattan, Kansas 66506, United States
| | - Klaus Schulten
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Christophe Chipot
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7565, Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex, France
| |
Collapse
|
35
|
Dickson CJ, Hornak V, Pearlstein RA, Duca JS. Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling. J Am Chem Soc 2016; 139:442-452. [DOI: 10.1021/jacs.6b11215] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Callum J. Dickson
- Computer-Aided Drug Discovery,
Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Computer-Aided Drug Discovery,
Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert A. Pearlstein
- Computer-Aided Drug Discovery,
Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jose S. Duca
- Computer-Aided Drug Discovery,
Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
36
|
Chipot C, Comer J. Subdiffusion in Membrane Permeation of Small Molecules. Sci Rep 2016; 6:35913. [PMID: 27805049 PMCID: PMC5090971 DOI: 10.1038/srep35913] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 10/05/2016] [Indexed: 12/22/2022] Open
Abstract
Within the solubility-diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t0.7, in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids.
Collapse
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°7565, Université de Lorraine, B.P. 70239, 54506, Vandœuvre-lès-Nancy cedex, France
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, 1800 Denison Ave, Kansas State University, Manhattan, Kansas 66506, USA
| |
Collapse
|
37
|
Nitschke N, Atkovska K, Hub JS. Accelerating potential of mean force calculations for lipid membrane permeation: System size, reaction coordinate, solute-solute distance, and cutoffs. J Chem Phys 2016; 145:125101. [DOI: 10.1063/1.4963192] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Naomi Nitschke
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Kalina Atkovska
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Jochen S. Hub
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| |
Collapse
|
38
|
Sun R, Dama JF, Tan JS, Rose JP, Voth GA. Transition-Tempered Metadynamics Is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes. J Chem Theory Comput 2016; 12:5157-5169. [PMID: 27598403 DOI: 10.1021/acs.jctc.6b00206] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metadynamics is an important enhanced sampling technique in molecular dynamics simulation to efficiently explore potential energy surfaces. The recently developed transition-tempered metadynamics (TTMetaD) has been proven to converge asymptotically without sacrificing exploration of the collective variable space in the early stages of simulations, unlike other convergent metadynamics (MetaD) methods. We have applied TTMetaD to study the permeation of drug-like molecules through a lipid bilayer to further investigate the usefulness of this method as applied to problems of relevance to medicinal chemistry. First, ethanol permeation through a lipid bilayer was studied to compare TTMetaD with nontempered metadynamics and well-tempered metadynamics. The bias energies computed from various metadynamics simulations were compared to the potential of mean force calculated from umbrella sampling. Though all of the MetaD simulations agree with one another asymptotically, TTMetaD is able to predict the most accurate and reliable estimate of the potential of mean force for permeation in the early stages of the simulations and is robust to the choice of required additional parameters. We also show that using multiple randomly initialized replicas allows convergence analysis and also provides an efficient means to converge the simulations in shorter wall times and, more unexpectedly, in shorter CPU times; splitting the CPU time between multiple replicas appears to lead to less overall error. After validating the method, we studied the permeation of a more complicated drug-like molecule, trimethoprim. Three sets of TTMetaD simulations with different choices of collective variables were carried out, and all converged within feasible simulation time. The minimum free energy paths showed that TTMetaD was able to predict almost identical permeation mechanisms in each case despite significantly different definitions of collective variables.
Collapse
Affiliation(s)
- Rui Sun
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - James F Dama
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Jeffrey S Tan
- Small Molecule Design & Development, Lilly Corporate Center, Eli Lilly & Company, Indianapolis, Indiana 46285, United States
| | - John P Rose
- Small Molecule Design & Development, Lilly Corporate Center, Eli Lilly & Company, Indianapolis, Indiana 46285, United States
| | - Gregory A Voth
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, The University of Chicago , 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| |
Collapse
|
39
|
Ghaemi Z, Alberga D, Carloni P, Laio A, Lattanzi G. Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations. J Chem Theory Comput 2016; 12:4093-9. [DOI: 10.1021/acs.jctc.5b01126] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhaleh Ghaemi
- SISSA, Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | - Domenico Alberga
- Dipartimento Interateneo di Fisica “M. Merlin”, University of Bari “Aldo Moro”, TIRES & INFN, via Orabona 4, 70126 Bari, Italy
| | - Paolo Carloni
- Computational
Biophysics, German Research School for Simulation Sciences, D-52425 Julich, Germany
- Institute for Advanced Simulation, Forschungszentrum
Julich, D-52425 Julich, Germany
| | - Alessandro Laio
- SISSA, Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | - Gianluca Lattanzi
- Dipartimento
di Medicina Clinica e Sperimentale and INFN - Sez. di Bari, Viale
Pinto, 71122 Foggia, Italy
| |
Collapse
|
40
|
Di Meo F, Fabre G, Berka K, Ossman T, Chantemargue B, Paloncýová M, Marquet P, Otyepka M, Trouillas P. In silico pharmacology: Drug membrane partitioning and crossing. Pharmacol Res 2016; 111:471-486. [PMID: 27378566 DOI: 10.1016/j.phrs.2016.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 01/09/2023]
Abstract
Over the past decade, molecular dynamics (MD) simulations have become particularly powerful to rationalize drug insertion and partitioning in lipid bilayers. MD simulations efficiently support experimental evidences, with a comprehensive understanding of molecular interactions driving insertion and crossing. Prediction of drug partitioning is discussed with respect to drug families (anesthetics; β-blockers; non-steroidal anti-inflammatory drugs; antioxidants; antiviral drugs; antimicrobial peptides). To accurately evaluate passive permeation coefficients turned out to be a complex theoretical challenge; however the recent methodological developments based on biased MD simulations are particularly promising. Particular attention is paid to membrane composition (e.g., presence of cholesterol), which influences drug partitioning and permeation. Recent studies concerning in silico models of membrane proteins involved in drug transport (influx and efflux) are also reported here. These studies have allowed gaining insight in drug efflux by, e.g., ABC transporters at an atomic resolution, explicitly accounting for the mandatory forces induced by the surrounded lipid bilayer. Large-scale conformational changes were thoroughly analyzed.
Collapse
Affiliation(s)
- Florent Di Meo
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Gabin Fabre
- LCSN, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Karel Berka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Tahani Ossman
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Benjamin Chantemargue
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Markéta Paloncýová
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Pierre Marquet
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Michal Otyepka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Patrick Trouillas
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic.
| |
Collapse
|
41
|
Lee CT, Comer J, Herndon C, Leung N, Pavlova A, Swift RV, Tung C, Rowley CN, Amaro RE, Chipot C, Wang Y, Gumbart JC. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J Chem Inf Model 2016; 56:721-33. [PMID: 27043429 DOI: 10.1021/acs.jcim.6b00022] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with the inhomogeneous solubility-diffusion model, which requires calculation of the potential of mean force and position-dependent diffusivity of the solute along the transmembrane axis. In this paper, we assess the efficiency and accuracy of several methods for the calculation of the permeability of a model DMPC bilayer to urea, benzoic acid, and codeine. We compare umbrella sampling, replica exchange umbrella sampling, adaptive biasing force, and multiple-walker adaptive biasing force for the calculation of the transmembrane PMF. No definitive advantage for any of these methods in their ability to predict the membrane permeability coefficient Pm was found, provided that a sufficiently long equilibration is performed. For diffusivities, a Bayesian inference method was compared to a generalized Langevin method, both being sensitive to chosen parameters and the slow relaxation of membrane defects. Agreement within 1.5 log units of the computed Pm with experiment is found for all permeants and methods. Remaining discrepancies can likely be attributed to limitations of the force field as well as slowly relaxing collective movements within the lipid environment. Numerical calculations based on model profiles show that Pm can be reliably estimated from only a few data points, leading to recommendations for calculating Pm from simulations.
Collapse
Affiliation(s)
- Christopher T Lee
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Jeffrey Comer
- Nanotechnology Innovation Center of Kansas State, Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University , P-213 Mosier Hall, Manhattan, Kansas 66506, United States
| | - Conner Herndon
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States
| | - Nelson Leung
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States
| | - Robert V Swift
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chris Tung
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland , St. John's, NL A1B 3X7 Canada
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique and University of Illinois at Urbana-Champaign, UMR n° 7565, Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy, France.,Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, United States
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China.,Shenzhen Research Institute, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , 837 State Street, Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology , 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States
| |
Collapse
|
42
|
Permeability across lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2254-2265. [PMID: 27085977 DOI: 10.1016/j.bbamem.2016.03.032] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 11/22/2022]
Abstract
Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Collapse
|
43
|
Neale C, Pomès R. Sampling errors in free energy simulations of small molecules in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2539-2548. [PMID: 26952019 DOI: 10.1016/j.bbamem.2016.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/14/2022]
Abstract
Free energy simulations are a powerful tool for evaluating the interactions of molecular solutes with lipid bilayers as mimetics of cellular membranes. However, these simulations are frequently hindered by systematic sampling errors. This review highlights recent progress in computing free energy profiles for inserting molecular solutes into lipid bilayers. Particular emphasis is placed on a systematic analysis of the free energy profiles, identifying the sources of sampling errors that reduce computational efficiency, and highlighting methodological advances that may alleviate sampling deficiencies. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Collapse
Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180-3590, USA
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
| |
Collapse
|
44
|
Comer J, Schulten K, Chipot C. Calculation of Lipid-Bilayer Permeabilities Using an Average Force. J Chem Theory Comput 2015; 10:554-64. [PMID: 26580032 DOI: 10.1021/ct400925s] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Calculations of lipid bilayer permeabilities from first principles, using molecular simulations, would be valuable to rapidly assess the bioavailability of drug candidates, as well as to decipher, at the atomic level, the mechanisms that underlie the translocation of permeants. The most common theoretical approach, the solubility-diffusion model, requires determination of the free energy and the diffusivity as functions of the position of the permeant. Quantitative predictions of permeability have, however, been stymied by acute difficulties in calculating the diffusivity, inadequate sampling, and, most insidiously, systematic biases due to imperfections in the force field, simulation parameters, and the inherent limitations of the diffusive model. In the present work, we combine importance-sampling simulations employing an adaptive biasing force with a Bayesian-inference algorithm to determine the free energy and diffusivity with noteworthy precision and spatial resolution. In multimicrosecond simulations, we probe the sensitivity of the permeability estimates to different aspects of the methodology, including the truncation of short-range interactions, the thermostat, the force-field parameters of the permeant, the time scale over which the diffusivity is estimated, and the size of the simulated system. The force-field parameters and time scale dependence of the diffusivities impose the greatest uncertainties on the permeability estimates. Our simulations highlight the importance of membrane distortion due to the presence of the permeant, which may be partially suppressed if the bilayer patch is not large enough. We suggest that improvements to force fields and more robust kinetic models may be needed to reduce systematic errors below a factor of two.
Collapse
Affiliation(s)
- Jeffrey Comer
- Laboratoire International Associé, Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign , Unité Mixte de Recherche n°7565, Université de Lorraine , B.P. 70239 54506 Vandœuvre-lès-Nancy cedex, France
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, 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°7565, Université de Lorraine , B.P. 70239 54506 Vandœuvre-lès-Nancy cedex, France.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, United States
| |
Collapse
|
45
|
Comer J, Schulten K, Chipot C. Diffusive Models of Membrane Permeation with Explicit Orientational Freedom. J Chem Theory Comput 2015; 10:2710-8. [PMID: 26586505 DOI: 10.1021/ct500209j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Accurate calculation of permeabilities from first-principles has been a long-standing challenge for computer simulations, notably in the context of drug discovery, as a route to predict the propensity of small, organic molecules to spontaneously translocate biological membranes. Of equal importance is the understanding of the permeation process and the pathway followed by the permeant from the aqueous medium to the interior of the lipid bilayer, and back out again. A convenient framework for the computation of permeabilities is provided by the solubility-diffusion model, which requires knowledge of the underlying free-energy and diffusivity landscapes. Here, we develop a formalism that includes an explicit description of the orientational motion of the solute as it diffuses across the membrane. Toward this end, we have generalized a recently proposed method that reconciles thermodynamics and kinetics in importance-sampling simulations by means of a Bayesian-inference scheme to reverse-solve the underlying Smoluchowski equation. Performance of the proposed formalism is examined in the model cases of a water and an ethanol molecule crossing a fully hydrated lipid bilayer. Our analysis reveals a conspicuous dependence of the free-energy and rotational diffusivity on the orientation of ethanol when it lies within the headgroup region of the bilayer. Specifically, orientations for which the hydroxyl group lies among the polar lipid head groups, while the ethyl group recedes toward the hydrophobic interior are associated with free-energy minima ∼2kBT deep, as well as significantly slower orientational kinetics compared to the bulk solution or the core of the bilayer. The conspicuous orientational anisotropy of ethanol at the aqueous interface is suggestive of a complete rotation of the permeant as it crosses the hydrophobic interior of the membrane.
Collapse
Affiliation(s)
- Jeffrey Comer
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7565, Université de Lorraine , B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7565, Université de Lorraine , B.P. 70239, 54506 Vandoeuvre-lès-Nancy cedex, France.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign , 405 North Mathews, Urbana, Illinois 61801, United States
| |
Collapse
|
46
|
Awoonor-Williams E, Rowley CN. Molecular simulation of nonfacilitated membrane permeation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1672-87. [PMID: 26706099 DOI: 10.1016/j.bbamem.2015.12.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/05/2015] [Accepted: 12/09/2015] [Indexed: 12/29/2022]
Abstract
This is a review. Non-electrolytic compounds typically cross cell membranes by passive diffusion. The rate of permeation is dependent on the chemical properties of the solute and the composition of the lipid bilayer membrane. Predicting the permeability coefficient of a solute is important in pharmaceutical chemistry and toxicology. Molecular simulation has proven to be a valuable tool for modeling permeation of solutes through a lipid bilayer. In particular, the solubility-diffusion model has allowed for the quantitative calculation of permeability coefficients. The underlying theory and computational methods used to calculate membrane permeability are reviewed. We also discuss applications of these methods to examine the permeability of solutes and the effect of membrane composition on permeability. The application of coarse grain and polarizable models is discussed. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Collapse
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7 Canada
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7 Canada.
| |
Collapse
|
47
|
Hu YF, Lv WJ, Zhao S, Shang YZ, Wang HL, Liu HL. Effect of surfactant SDS on DMSO transport across water/hexane interface by molecular dynamics simulation. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.05.068] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
48
|
Partition, orientation and mobility of ubiquinones in a lipid bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1560-73. [PMID: 26255075 DOI: 10.1016/j.bbabio.2015.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/02/2015] [Accepted: 08/04/2015] [Indexed: 01/11/2023]
Abstract
Ubiquinone is the universal mobile charge carrier involved in biological electron transfer processes. Its redox properties and biological function depend on the molecular partition and lateral diffusion over biological membranes. However, ubiquinone localization and dynamics within lipid bilayers are long debated and still uncertain. Here we present molecular dynamics simulations of several ubiquinone homologs with variable isoprenoid tail lengths complexed to phosphatidylcholine bilayers. Initially, a new force-field parametrization for ubiquinone is derived from and compared to high level quantum chemical data. Free energy profiles for ubiquinone insertion in the lipid bilayer are obtained with the new force-field. The profiles allow for the determination of the equilibrium location of ubiquinone in the membrane as well as for the validation of the simulation model by direct comparison with experimental partition coefficients. A detailed analysis of structural properties and interactions shows that the ubiquinone polar head group is localized at the water-bilayer interface at the same depth of the lipid glycerol groups and oriented normal to the membrane plane. Both the localization and orientation of ubiquinone head groups do not change significantly when increasing the number of isoprenoid units. The isoprenoid tail is extended and packed with the lipid acyl chains. For ubiquinones with long tails, the terminal isoprenoid units have high flexibility. Calculated ubiquinone diffusion coefficients are similar to that found for the phosphatidylcholine lipid. These results may have further implications for the mechanisms of ubiquinone transport and binding to respiratory and photosynthetic protein complexes.
Collapse
|
49
|
A Permeability Study of O2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers. PLoS One 2015; 10:e0122468. [PMID: 26086933 PMCID: PMC4472697 DOI: 10.1371/journal.pone.0122468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 02/15/2015] [Indexed: 11/19/2022] Open
Abstract
We study here the permeability of the hydrophobic O2 molecule through a model DPPC bilayer at 323K and 350K, and of the trace amine p-tyramine through PC bilayers at 310K. The tyramine results are compared to previous experimental work at 298K. Nonequilibrium work methods were used in conjunction to simultaneously obtain both the potential of mean force (PMF) and the position dependent transmembrane diffusion coefficient, D(z), from the simulations. These in turn were used to calculate the permeability coefficient, P, through the inhomogeneous solubility-diffusion model. The results for O2 are consistent with previous simulations, and agree with experimentally measured P values for PC bilayers. A temperature dependence in the permeability of O2 through DPPC was obtained, with P decreasing at higher temperatures. Two relevant species of p-tyramine were simulated, from which the PMF and D(z) were calculated. The charged species had a large energetic barrier to crossing the bilayer of ~ 21 kcal/mol, while the uncharged, deprotonated species had a much lower barrier of ~ 7 kcal/mol. The effective in silico permeability for p-tyramine was calculated by applying three approximations, all of which gave nearly identical results (presented here as a function of the pKa). As the permeability value calculated from simulation was highly dependent on the pKa of the amine group, a further pKa study was performed that also varied the fraction of the uncharged and zwitterionic p-tyramine species. Using the experimental P value together with the simulated results, we were able to label the phenolic group as responsible for the pKa1 and the amine for the pKa2, that together represent all of the experimentally measured pKa values for p-tyramine. This agrees with older experimental results, in contrast to more recent work that has suggested there is a strong ambiguity in the pKa values.
Collapse
|
50
|
Cardenas AE, Elber R. Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation. J Chem Phys 2015; 141:054101. [PMID: 25106564 DOI: 10.1063/1.4891305] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Coarse graining of membrane simulations by translating atomistic dynamics to densities and fields with Milestoning is discussed. The space of the membrane system is divided into cells and the different cells are characterized by order parameters presenting the number densities. The dynamics of the order parameters are probed with Milestoning. The methodology is illustrated here for a phospholipid membrane system (a hydrated bilayer of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) lipid molecules). Significant inhomogeneity in membrane internal number density leads to complex free energy landscape and local maps of transition times. Dynamics and distributions of cavities within the membrane assist the permeation of nonpolar solutes such as xenon atoms. It is illustrated that quantitative and detailed dynamics of water transport through DOPC membrane can be analyzed using Milestoning with fields. The reaction space for water transport includes at least two slow variables: the normal to the membrane plane, and the water density.
Collapse
Affiliation(s)
- Alfredo E Cardenas
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ron Elber
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|