1
|
Kaste JAM, Walker BJ, Shachar-Hill Y. Reaction-diffusion modeling provides insights into biophysical carbon-concentrating mechanisms in land plants. PLANT PHYSIOLOGY 2024; 196:1374-1390. [PMID: 38857179 PMCID: PMC11444298 DOI: 10.1093/plphys/kiae324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 06/12/2024]
Abstract
Carbon-concentrating mechanisms (CCMs) have evolved numerous times in photosynthetic organisms. They elevate the concentration of CO2 around the carbon-fixing enzyme rubisco, thereby increasing CO2 assimilatory flux and reducing photorespiration. Biophysical CCMs, like the pyrenoid-based CCM (PCCM) of Chlamydomonas reinhardtii or carboxysome systems of cyanobacteria, are common in aquatic photosynthetic microbes, but in land plants appear only among the hornworts. To predict the likely efficiency of biophysical CCMs in C3 plants, we used spatially resolved reaction-diffusion models to predict rubisco saturation and light use efficiency. We found that the energy efficiency of adding individual CCM components to a C3 land plant is highly dependent on the permeability of lipid membranes to CO2, with values in the range reported in the literature that are higher than those used in previous modeling studies resulting in low light use efficiency. Adding a complete PCCM into the leaf cells of a C3 land plant was predicted to boost net CO2 fixation, but at higher energetic costs than those incurred by photorespiratory losses without a CCM. Two notable exceptions were when substomatal CO2 levels are as low as those found in land plants that already use biochemical CCMs and when gas exchange is limited, such as with hornworts, making the use of a biophysical CCM necessary to achieve net positive CO2 fixation under atmospheric CO2 levels. This provides an explanation for the uniqueness of hornworts' CCM among land plants and the evolution of pyrenoids multiple times.
Collapse
Affiliation(s)
- Joshua A M Kaste
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI 48823, USA
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI 48824, USA
| | - Berkley J Walker
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State University, 612 Wilson Rd, East Lansing, MI 48824, USA
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI 48824, USA
| |
Collapse
|
2
|
Jalali P, Nowroozi A, Moradi S, Shahlaei M. Exploration of lipid bilayer mechanical properties using molecular dynamics simulation. Arch Biochem Biophys 2024; 761:110151. [PMID: 39265694 DOI: 10.1016/j.abb.2024.110151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 08/22/2024] [Accepted: 09/09/2024] [Indexed: 09/14/2024]
Abstract
Important biological structures known for their exceptional mechanical qualities, lipid bilayers are essential to many cellular functions. Fluidity, elasticity, permeability, stiffness, tensile strength, compressibility, shear viscosity, line tension, and curvature elasticity are some of the fundamental characteristics affecting their behavior. The purpose of this review is to examine these characteristics in more detail by molecular dynamics simulation, elucidating their importance and the elements that lead to their appearance in lipid bilayers. Comprehending the mechanical characteristics of lipid bilayers is critical for creating medications, drug delivery systems, and biomaterials that interact with biological membranes because it allows one to understand how these materials respond to different stresses and deformations. The influence of mechanical characteristics on important lipid bilayer properties is examined in this review. The mechanical properties of lipid bilayers were clarified through the use of molecular dynamics simulation analysis techniques, including bilayer thickness, stress-strain analysis, lipid bilayer area compressibility, membrane bending rigidity, and time- or ensemble-averaged the area per lipid evaluation. We explain the significance of molecular dynamics simulation analysis methods, providing important new information about the stability and dynamic behavior of the bilayer. In the end, we hope to use molecular dynamics simulation to provide a comprehensive understanding of the mechanical properties and behavior of lipid bilayers, laying the groundwork for further studies and applications. Taken together, careful investigation of these mechanical aspects deepens our understanding of the adaptive capacities and functional roles of lipid bilayers in biological environments.
Collapse
Affiliation(s)
- Parvin Jalali
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| |
Collapse
|
3
|
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
|
4
|
Chuang YC, Haas NW, Pepin R, Behringer MG, Oda Y, LaSarre B, Harwood CS, McKinlay JB. Bacterial adenine cross-feeding stems from a purine salvage bottleneck. THE ISME JOURNAL 2024; 18:wrae034. [PMID: 38452196 PMCID: PMC10976475 DOI: 10.1093/ismejo/wrae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/19/2023] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
Diverse ecosystems host microbial relationships that are stabilized by nutrient cross-feeding. Cross-feeding can involve metabolites that should hold value for the producer. Externalization of such communally valuable metabolites is often unexpected and difficult to predict. Previously, we discovered purine externalization by Rhodopseudomonas palustris by its ability to rescue an Escherichia coli purine auxotroph. Here we found that an E. coli purine auxotroph can stably coexist with R. palustris due to purine cross-feeding. We identified the cross-fed purine as adenine. Adenine was externalized by R. palustris under diverse growth conditions. Computational modeling suggested that adenine externalization occurs via diffusion across the cytoplasmic membrane. RNAseq analysis led us to hypothesize that adenine accumulation and externalization stem from a salvage pathway bottleneck at the enzyme encoded by apt. Ectopic expression of apt eliminated adenine externalization, supporting our hypothesis. A comparison of 49 R. palustris strains suggested that purine externalization is relatively common, with 16 strains exhibiting the trait. Purine externalization was correlated with the genomic orientation of apt, but apt orientation alone could not always explain purine externalization. Our results provide a mechanistic understanding of how a communally valuable metabolite can participate in cross-feeding. Our findings also highlight the challenge in identifying genetic signatures for metabolite externalization.
Collapse
Affiliation(s)
- Ying-Chih Chuang
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
- Biochemistry Program, Indiana University, Bloomington, IN 47405, United States
| | - Nicholas W Haas
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Robert Pepin
- Department of Chemistry, Indiana University, Bloomington, IN 47405, United States
| | - Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, United States
| | - Yasuhiro Oda
- Department of Microbiology, University of Washington, Seattle, WA 98195, United States
| | - Breah LaSarre
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, United States
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, WA 98195, United States
| | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| |
Collapse
|
5
|
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
|
6
|
Stergiopoulos C, Tsakanika LA, Ochsenkühn-Petropoulou M, Kakoulidou AT, Tsopelas F. APPLICATION OF MICELLAR LIQUID CHROMATOGRAPHY TO MODEL ECOTOXICITY OF PESTICIDES. COMPARISON WITH IMMOBILIZED ARTIFICIAL MEMBRANE CHROMATOGRAPHY AND N-OCTANOL-WATER PARTITIONING. J Chromatogr A 2023; 1696:463951. [PMID: 37054635 DOI: 10.1016/j.chroma.2023.463951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
The potential of Micellar Liquid Chromatography (MLC) to model ecotoxicological endpoints for a series of pesticides was investigated. To exploit the flexibility in MLC conditions, different surfactants were employed and retention mechanism was tracked and compared to Immobilized Artificial Membrane (IAM) chromatographic retention and n-octanol- water partitioning, logP. Neutral polyoxyethylene (23) lauryl ether (Brij-35), anionic sodium dodecyl sulfate (SDS) and cationic cetyltrimethylammonium bromide (CTAB) were used in presence of PBS at pH=7.40 and acetonitrile as organic modifier when necessary. Similarities/ dissimilarities between MLC retention and IAM or logP were investigated by Principal Component Analysis (PCA) and Liner Solvation Energy Relationships (LSER). LSER revealed that hydrogen bonding acidity is the most important factor for differentiation between MLC and IAM or logP. The impact of hydrogen bonding is exemplified in the relationships of MLC retention factors with IAM or logP, which necessitate the inclusion of a relevant descriptor. PCA further revealed that MLC retention factors are clustered together with IAM indices and logP within a broader ellipse formed by ecotoxicological endpoints, involving LC50/ EC50 values of six aquatic organisms namely Rainbow Trout, Fathead Minnow, Bluegill Sunfish, Sheepshead Minnow, Eastern Oyster and Water Flea as well as LD50 values of Honey Bee, thus justifying their use to construct relevant models. Satisfactory specific models for individual organisms, as well as general fish models, were obtained, in most cases, upon combination of MLC retention factors with Molecular Weight (MW) or/ and hydrogen bond parameters. All models were evaluated and compared to previously reported IAM and logP based models using an external validation data set. Predictions with Brij-35 and SDS based models were comparable, although slightly inferior than those obtained with IAM, while they were in all cases better than those obtained with logP. CTAB led to a satisfactory prediction model for Honey Bee, but it was found less suitable for aquatic organisms.
Collapse
Affiliation(s)
- Chrysanthos Stergiopoulos
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, Athens 157 80, Greece
| | - Lamprini-Areti Tsakanika
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, Athens 157 80, Greece
| | - Maria Ochsenkühn-Petropoulou
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, Athens 157 80, Greece
| | - Anna Tsantili- Kakoulidou
- Department of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 157 71, Greece
| | - Fotios Tsopelas
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, Athens 157 80, Greece.
| |
Collapse
|
7
|
Linker S, Schellhaas C, Kamenik AS, Veldhuizen MM, Waibl F, Roth HJ, Fouché M, Rodde S, Riniker S. Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes. J Med Chem 2023; 66:2773-2788. [PMID: 36762908 PMCID: PMC9969412 DOI: 10.1021/acs.jmedchem.2c01837] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Indexed: 02/11/2023]
Abstract
Cyclic peptides extend the druggable target space due to their size, flexibility, and hydrogen-bonding capacity. However, these properties impact also their passive membrane permeability. As the "journey" through membranes cannot be monitored experimentally, little is known about the underlying process, which hinders rational design. Here, we use molecular simulations to uncover how cyclic peptides permeate a membrane. We show that side chains can act as "molecular anchors", establishing the first contact with the membrane and enabling insertion. Once inside, the peptides are positioned between headgroups and lipid tails─a unique polar/apolar interface. Only one of two distinct orientations at this interface allows for the formation of the permeable "closed" conformation. In the closed conformation, the peptide crosses to the lower leaflet via another "anchoring" and flipping mechanism. Our findings provide atomistic insights into the permeation process of flexible cyclic peptides and reveal design considerations for each step of the process.
Collapse
Affiliation(s)
- Stephanie
M. Linker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Christian Schellhaas
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Anna S. Kamenik
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Mac M. Veldhuizen
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Hans-Jörg Roth
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Marianne Fouché
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
8
|
Physicochemical and biopharmaceutical aspects influencing skin permeation and role of SLN and NLC for skin drug delivery. Heliyon 2022; 8:e08938. [PMID: 35198788 PMCID: PMC8851252 DOI: 10.1016/j.heliyon.2022.e08938] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 01/30/2022] [Accepted: 02/08/2022] [Indexed: 12/28/2022] Open
Abstract
The skin is a complex and multifunctional organ, in which the static versus dynamic balance is responsible for its constant adaptation to variations in the external environment that is continuously exposed. One of the most important functions of the skin is its ability to act as a protective barrier, against the entry of foreign substances and against the excessive loss of endogenous material. Human skin imposes physical, chemical and biological limitations on all types of permeating agents that can cross the epithelial barrier. For a molecule to be passively permeated through the skin, it must have properties, such as dimensions, molecular weight, pKa and hydrophilic-lipophilic gradient, appropriate to the anatomy and physiology of the skin. These requirements have limited the number of commercially available products for dermal and transdermal administration of drugs. To understand the mechanisms involved in the drug permeation process through the skin, the approach should be multidisciplinary in order to overcome biological and pharmacotechnical barriers. The study of the mechanisms involved in the permeation process, and the ways to control it, can make this route of drug administration cease to be a constant promise and become a reality. In this work, we address the physicochemical and biopharmaceutical aspects encountered in the pathway of drugs through the skin, and the potential added value of using solid lipid nanoparticles (SLN) and nanostructured lipid vectors (NLC) to drug permeation/penetration through this route. The technology and architecture for obtaining lipid nanoparticles are described in detail, namely the composition, production methods and the ability to release pharmacologically active substances, as well as the application of these systems in the vectorization of various pharmacologically active substances for dermal and transdermal applications. The characteristics of these systems in terms of dermal application are addressed, such as biocompatibility, occlusion, hydration, emollience and the penetration of pharmacologically active substances. The advantages of using these systems over conventional formulations are described and explored from a pharmaceutical point of view.
Collapse
|
9
|
Petris PC, Becherer P, Fraaije JGEM. Alkane/Water Partition Coefficient Calculation Based on the Modified AM1 Method and Internal Hydrogen Bonding Sampling Using COSMO-RS. J Chem Inf Model 2021; 61:3453-3462. [PMID: 34165298 PMCID: PMC8317156 DOI: 10.1021/acs.jcim.0c01478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
We introduce a physics-based
model for calculating partition coefficients
of solutes between water and alkanes, using a combination of a semi-empirical
method for COSMO charge density calculation and statistical sampling
of internal hydrogen bonds (IHBs). We validate the model on the experimental
partition data (∼3500 molecules) of small organics, drug-like
molecules, and statistical assessment of modeling of proteins and
ligand drugs. The model combines two novel algorithms: a bond-correction
method for improving the calculation of COSMO charge density from
AM1 calculations and a sampling method to deal with IHBs. From a comparison
of simulated and experimental partition coefficients, we find a root-mean-square
deviation of roughly one log 10 unit. From IHB analysis, we know that
IHBs can be present in two states: open (in water) and closed (in
apolar solvent). The difference can lead to a shift of as much as
two log 10 units per IHB; not taking this effect into account can
lead to substantial errors. The method takes a few minutes of calculation
time on a single core, per molecule. Although this is still much slower
than quantitative structure–activity relationship, it is much
faster than molecular simulations and can be readily incorporated
into any screening method.
Collapse
Affiliation(s)
- Panagiotis C Petris
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.,Siemens Industry Software Netherlands B.V., Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Paul Becherer
- Siemens Industry Software Netherlands B.V., Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Johannes G E M Fraaije
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.,Siemens Industry Software Netherlands B.V., Galileiweg 8, 2333 BD Leiden, The Netherlands
| |
Collapse
|
10
|
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
|
11
|
Fu BM, Zhao Z, Zhu D. Blood-Brain Barrier (BBB) Permeability and Transport Measurement In Vitro and In Vivo. Methods Mol Biol 2021; 2367:105-122. [PMID: 32803538 PMCID: PMC7889748 DOI: 10.1007/7651_2020_308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Quantification of the blood-brain barrier (BBB) permeability and transport in brain tissue is crucial in understanding brain disorders and developing systemic and non-systemic drug delivery strategies to the brain. This chapter summarizes BBB permeability measurement in vitro (Part I) and the in vivo non-invasive methods for quantifying the BBB permeability to solutes and brain tissue transport in rat brain by employing intravital multiphoton microscopy and a curving fitting method by using an unsteady mass transfer mathematical model (Part II).
Collapse
Affiliation(s)
- Bingmei M Fu
- Department of Biomedical Engineering, The City College of the City University of New York, New York, NY, USA.
| | - Zhen Zhao
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Donghui Zhu
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.
| |
Collapse
|
12
|
Hammouda AN, Elmagbari FM, Jackson GE, Vicatos GM, Bonomo RP, Valora G. Stability, Structure, and Permeability Studies of Copper Tripeptide Species in Aqueous Solution. Aust J Chem 2021. [DOI: 10.1071/ch21040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The use of copper complexes to alleviate inflammation associated with rheumatoid arthritis (RA) is well known. This study focuses on designing a new drug that could be used to increase the bioavailability of copper and hence be more effective. The ligand chosen was sarcosyl-l-lysyl-l-lysine (Sar-Lys-Lys). The thermodynamic stability of H+, CuII, NiII, and ZnII complexes of Sar-Lys-Lys was measured in an aqueous solution at 298±0.01°C and an ionic strength of 0.15M (NaCl) using glass electrode potentiometry. UV-Vis, ESR, and 1H NMR spectroscopy was used to investigate the solution structures of the different species. At physiological pH, the ligand was found to coordinate via two amide nitrogens, the terminal amine, and the terminal carboxy group. The ε-amino group of lysine did not coordinate with the metal ion. Dermal absorption is the preferred method of administration and so this study used partition coefficients and tissue permeability studies to assess the bioavailability of the different complexes. Sar-Lys-Lys was found to increase the copper lipophilicity by a factor of 10 and increased tissue permeability by 30%.
Collapse
|
13
|
Rotem R, Micale A, Rizzuto MA, Migliavacca M, Giustra M, Salvioni L, Tasin F, Prosperi D, Colombo M. Modeling the interaction of amphiphilic polymer nanoparticles with biomembranes to Guide rational design of drug delivery systems. Colloids Surf B Biointerfaces 2020; 196:111366. [PMID: 32992287 DOI: 10.1016/j.colsurfb.2020.111366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/05/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022]
Abstract
Nanoparticle assisted drug delivery to the cytoplasm is limited by sequestration of nanoparticles in endosomes. Endosomal escape through polymer-induced membrane destabilization is one of a few well characterized mechanisms to overcome it. Aiming to utilize this method in vivo, it is necessary to understand how modulating the structural and chemical features of the polymer and the presence of proteins in biological fluids can affect this activity. Here, as a model for the endosomal membrane, we use the membrane of red blood cells to evaluate the membrane destabilization ability of a model amphiphilic polymer in the presence of blood plasma using a hemolysis assay. This allows determination of red blood cells membrane permeabilization through the quantification of hemoglobin leakage. Our results showed a strong inhibitory effect of plasma, and that hemolytic activity can be improved by chemical modification of the polymeric micelle, reducing its interaction with plasma proteins. Finally, a second mechanism of pH-induced direct diffusion is proposed and tested using an oil/water partitioning model. These results offer a body of knowledge to improve delivery of drugs across biological membranes using carefully designed polymeric nanocarriers.
Collapse
Affiliation(s)
- Rany Rotem
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Angelo Micale
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Maria Antonietta Rizzuto
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Martina Migliavacca
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Marco Giustra
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Lucia Salvioni
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Federico Tasin
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Davide Prosperi
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy; Nanomedicine Laboratory, ICS Maugeri S.p.A. SB, via S. Maugeri 10, 27100, Pavia, Italy.
| | - Miriam Colombo
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy.
| |
Collapse
|
14
|
Klein VG, Townsend CE, Testa A, Zengerle M, Maniaci C, Hughes SJ, Chan KH, Ciulli A, Lokey RS. Understanding and Improving the Membrane Permeability of VH032-Based PROTACs. ACS Med Chem Lett 2020; 11:1732-1738. [PMID: 32939229 PMCID: PMC7488288 DOI: 10.1021/acsmedchemlett.0c00265] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/30/2020] [Indexed: 01/03/2023] Open
Abstract
![]()
Proteolysis targeting
chimeras (PROTACs) are catalytic heterobifunctional
molecules that can selectively degrade a protein of interest by recruiting
a ubiquitin E3 ligase to the target, leading to its ubiquitylation
and degradation by the proteasome. Most degraders lie outside the
chemical space associated with most membrane-permeable drugs. Although
many PROTACs have been described with potent activity in cells, our
understanding of the relationship between structure and permeability
in these compounds remains limited. Here, we describe a label-free
method for assessing the permeability of several VH032-based PROTACs
and their components by combining a parallel artificial membrane permeability
assay (PAMPA) and a lipophilic permeability efficiency (LPE) metric.
Our results show that the combination of these two cell-free membrane
permeability assays provides new insight into PROTAC structure–permeability
relationships and offers a conceptual framework for predicting the
physicochemical properties of PROTACs in order to better inform the
design of more permeable and more effective degraders.
Collapse
Affiliation(s)
- Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Michael Zengerle
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Chiara Maniaci
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Scott J. Hughes
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Kwok-Ho Chan
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| |
Collapse
|
15
|
Erimban S, Daschakraborty S. Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study. Phys Chem Chem Phys 2020; 22:6335-6350. [DOI: 10.1039/c9cp05999g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Passive permeation of CD across lipid bilayer is almost impossible. Forced permeation results membrane rupture.
Collapse
Affiliation(s)
- Shakkira Erimban
- Department of Chemistry
- Indian Institute of Technology Patna
- Bihar 801106
- India
| | | |
Collapse
|
16
|
Abstract
Approximately 75% of all disease-relevant human proteins, including those involved in intracellular protein-protein interactions (PPIs), are undruggable with the current drug modalities (i.e., small molecules and biologics). Macrocyclic peptides provide a potential solution to these undruggable targets because their larger sizes (relative to conventional small molecules) endow them the capability of binding to flat PPI interfaces with antibody-like affinity and specificity. Powerful combinatorial library technologies have been developed to routinely identify cyclic peptides as potent, specific inhibitors against proteins including PPI targets. However, with the exception of a very small set of sequences, the vast majority of cyclic peptides are impermeable to the cell membrane, preventing their application against intracellular targets. This Review examines common structural features that render most cyclic peptides membrane impermeable, as well as the unique features that allow the minority of sequences to enter the cell interior by passive diffusion, endocytosis/endosomal escape, or other mechanisms. We also present the current state of knowledge about the molecular mechanisms of cell penetration, the various strategies for designing cell-permeable, biologically active cyclic peptides against intracellular targets, and the assay methods available to quantify their cell-permeability.
Collapse
Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| |
Collapse
|
17
|
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
|
18
|
Lomize AL, Hage JM, Schnitzer K, Golobokov K, LaFaive MB, Forsyth AC, Pogozheva ID. PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. J Chem Inf Model 2019; 59:3094-3099. [PMID: 31259547 DOI: 10.1021/acs.jcim.9b00225] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The PerMM web server and database were developed for quantitative analysis and visualization of passive translocation of bioactive molecules across lipid membranes. The server is the first physics-based web tool that calculates membrane binding energies and permeability coefficients of diverse molecules through artificial and natural membranes (phospholipid bilayers, PAMPA-DS, blood-brain barrier, and Caco-2/MDCK cell membranes). It also visualizes the transmembrane translocation pathway as a sequence of translational and rotational positions of a permeant as it moves across the lipid bilayer, along with the corresponding changes in solvation energy. The server can be applied for prediction of permeability coefficients of compounds with diverse chemical scaffolds to facilitate selection and optimization of potential drug leads. The complementary PerMM database allows comparison of computationally and experimentally determined permeability coefficients for more than 500 compounds in different membrane systems. The website and database are freely accessible at https://permm.phar.umich.edu/ .
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
| | - Jacob M Hage
- Department of Electrical Engineering and Computer Science, College of Engineering , University of Michigan , 1221 Beal Ave , Ann Arbor , Michigan 48109-2102 , United States
| | - Kevin Schnitzer
- Department of Electrical Engineering and Computer Science, College of Engineering , University of Michigan , 1221 Beal Ave , Ann Arbor , Michigan 48109-2102 , United States
| | - Konstantin Golobokov
- Department of Electrical Engineering and Computer Science, College of Engineering , University of Michigan , 1221 Beal Ave , Ann Arbor , Michigan 48109-2102 , United States
| | - Mitchell B LaFaive
- Department of Electrical Engineering and Computer Science, College of Engineering , University of Michigan , 1221 Beal Ave , Ann Arbor , Michigan 48109-2102 , United States
| | - Alexander C Forsyth
- Department of Computer Science, College of Literature, Science, and the Arts , University of Michigan , 2260 Hayward Street , Ann Arbor , Michigan 48109-2121 , 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
|
19
|
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
|
20
|
Stergiopoulos C, Makarouni D, Tsantili-Kakoulidou A, Ochsenkühn-Petropoulou M, Tsopelas F. Immobilized artificial membrane chromatography as a tool for the prediction of ecotoxicity of pesticides. CHEMOSPHERE 2019; 224:128-139. [PMID: 30818191 DOI: 10.1016/j.chemosphere.2019.02.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 05/27/2023]
Abstract
The potential of Immobilized Artificial Membrane (IAM) chromatography to predict ecotoxicological endpoints of pesticides was investigated. For this purpose, retention factors of 39 structurally-diverse pesticides were measured on an IAM stationary phase. A representative test set of 6 pesticides was carefully selected. The training set, involving the remaining pesticides for which experimental data were available, served to establish linear IAM models with LC50/EC50 values in a series of aquatic organisms involving Rainbow Trout, Fathead Minnow, Bluegill Sunfish, Sheepshead Minnow, Eastern Oyster and Water Flea as well as LD50 values in honey bee, compiled from literature sources. For reasons of comparison, corresponding models were derived by replacing IAM retention factors with octanol-water partition coefficients (logP). Considering the similar regression equations obtained for the 4 fish species, general models to predict toxicity in fish were established. Most models were improved upon inclusion of additional physicochemical parameters. The positive contribution of Molecular Weight to ecotoxicity along with the positive sign of hydrogen bond indices in most cases implies that toxic action is manifested mainly by accumulation on the membrane rather than through diffusion across them. IAM models are generally followed by better statistics and superior predictive performance than those based on experimental or computed logP. Predictions based on IAM chromatography were comparable or even superior with those performed by EPI Suite Software. Hence, IAM retention factors are suggested as promising indices in order to screen or rank chemicals with respect to their ecotoxicological risk, especially in the case of new entities.
Collapse
Affiliation(s)
- Chrysanthos Stergiopoulos
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, 157 80 Athens, Greece
| | - Dimitra Makarouni
- Vioryl, Chemical and Agricultural Industry, Research S.A., 28th klm Athens- Lamia national road, 19014, Afidnes, Greece
| | - Anna Tsantili-Kakoulidou
- Department of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 157 71 Athens, Greece
| | - Maria Ochsenkühn-Petropoulou
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, 157 80 Athens, Greece
| | - Fotios Tsopelas
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, 157 80 Athens, Greece.
| |
Collapse
|
21
|
Brocke SA, Degen A, MacKerell AD, Dutagaci B, Feig M. Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. J Chem Inf Model 2019; 59:1147-1162. [PMID: 30540459 PMCID: PMC6433486 DOI: 10.1021/acs.jcim.8b00648] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipid membrane permeation of drug molecules was investigated with Heterogeneous Dielectric Generalized Born (HDGB)-based models using solubility-diffusion theory and machine learning. Free energy profiles were obtained for neutral molecules by the standard HDGB and Dynamic HDGB (DHDGB) to account for the membrane deformation upon insertion of drugs. We also obtained hybrid free energy profiles where the neutralization of charged molecules was taken into account upon membrane insertion. The evaluation of the predictions was done against experimental permeability coefficients from Parallel Artificial Membrane Permeability Assays (PAMPA), and effects of partial charge sets, CGenFF, AM1-BCC, and OPLS, on the performance of the predictions were discussed. (D)HDGB-based models improved the predictions over the two-state implicit membrane models, and partial charge sets seemed to have a strong impact on the predictions. Machine learning increased the accuracy of the predictions, although it could not outperform the physics-based approach in terms of correlations.
Collapse
Affiliation(s)
- Stephanie A. Brocke
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Alexandra Degen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, USA
- University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland 21201, USA
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| |
Collapse
|
22
|
Mircioiu C, Voicu V, Anuta V, Tudose A, Celia C, Paolino D, Fresta M, Sandulovici R, Mircioiu I. Mathematical Modeling of Release Kinetics from Supramolecular Drug Delivery Systems. Pharmaceutics 2019; 11:E140. [PMID: 30901930 PMCID: PMC6471682 DOI: 10.3390/pharmaceutics11030140] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/07/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022] Open
Abstract
Embedding of active substances in supramolecular systems has as the main goal to ensure the controlled release of the active ingredients. Whatever the final architecture or entrapment mechanism, modeling of release is challenging due to the moving boundary conditions and complex initial conditions. Despite huge diversity of formulations, diffusion phenomena are involved in practically all release processes. The approach in this paper starts, therefore, from mathematical methods for solving the diffusion equation in initial and boundary conditions, which are further connected with phenomenological conditions, simplified and idealized in order to lead to problems which can be analytically solved. Consequently, the release models are classified starting from the geometry of diffusion domain, initial conditions, and conditions on frontiers. Taking into account that practically all solutions of the models use the separation of variables method and integral transformation method, two specific applications of these methods are included. This paper suggests that "good modeling practice" of release kinetics consists essentially of identifying the most appropriate mathematical conditions corresponding to implied physicochemical phenomena. However, in most of the cases, models can be written but analytical solutions for these models cannot be obtained. Consequently, empiric models remain the first choice, and they receive an important place in the review.
Collapse
Affiliation(s)
- Constantin Mircioiu
- Department of Applied Mathematics and Biostatistics, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania.
| | - Victor Voicu
- Department of Clinical Pharmacology, Toxicology and Psychopharmacology, Faculty of Medicine, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania.
| | - Valentina Anuta
- Department of Physical and Colloidal Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania.
| | - Andra Tudose
- Department of Applied Mathematics and Biostatistics, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania.
| | - Christian Celia
- Department of Pharmacy, G. D'Annunzio University of Chieti⁻Pescara, 66100 Chieti, Italy.
| | - Donatella Paolino
- Department of Clinical and Experimental Medicine, "Magna Græcia" University of Catanzaro, Germaneto - Catanzaro (CZ) 88100, Italy.
| | - Massimo Fresta
- Department of Health Sciences, School of Pharmacy, "Magna Græcia" University of Catanzaro, Germaneto - Catanzaro (CZ) 88100, Italy.
| | - Roxana Sandulovici
- Department of Applied Mathematics and Biostatistics, Titu Maiorescu University, 004051 Bucharest, Romania.
| | - Ion Mircioiu
- Department of Biopharmacy and Pharmacokinetics, Titu Maiorescu University, 004051 Bucharest, Romania.
| |
Collapse
|
23
|
Naylor MR, Ly AM, Handford MJ, Ramos DP, Pye CR, Furukawa A, Klein VG, Noland RP, Edmondson Q, Turmon AC, Hewitt WM, Schwochert J, Townsend CE, Kelly CN, Blanco MJ, Lokey RS. Lipophilic Permeability Efficiency Reconciles the Opposing Roles of Lipophilicity in Membrane Permeability and Aqueous Solubility. J Med Chem 2018; 61:11169-11182. [DOI: 10.1021/acs.jmedchem.8b01259] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Andrew M. Ly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Mason J. Handford
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Daniel P. Ramos
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R. Pye
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Akihiro Furukawa
- Modality Research Laboratories, Daiichi Sankyo Company, Ltd., 1-2-58 Hiromachi, Shingawa-ku, Tokyo 140-8710, Japan
| | - Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Ryan P. Noland
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Quinn Edmondson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Alexandra C. Turmon
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - William M. Hewitt
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Colin N. Kelly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria-Jesus Blanco
- Sage Therapeutics, 215 First Street, Suite 220, Cambridge, Massachusetts 02142, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| |
Collapse
|
24
|
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
|
25
|
Raevsky OA, Grigorev VY, Polianczyk DE, Raevskaja OE, Dearden JC. Contribution assessment of multiparameter optimization descriptors in CNS penetration. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:785-800. [PMID: 30274532 DOI: 10.1080/1062936x.2018.1514652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 06/08/2023]
Abstract
Assessment of the influence of six physicochemical properties used in the multiparameter optimization (MPO) approach for chemical penetration of the blood-brain barrier was carried out by means of application of logistic regression and multiple linear regression, using a data set of 578 diverse chemicals. It was found that use of an aggregation MPO-score descriptor did not give satisfactory results with central nervous system (CNS)/non-CNS classification. Thus an application of the MPO approach for CNS penetration is ambiguous. An alternative to the MPO approach in this work contains detailed (quantitative) structure-activity relationship analysis using a number of methods (linear discriminant analysis, random forest, support vector machine, Gaussian process). Three properties (molecular weight, number of H-bond donors and octanol-water partition coefficient) yielded optimal categorical models with modest statistical parameters (accuracy 0.730-0.765 for CNS/non-CNS classification). The poor statistics of regression models for the common data set suggested the presence of subsets with different mechanisms of penetrations. Based on graphic comparison of experimental and calculated Cu,b values, subset clusters have satisfactory statistics. The regression models obtained allowed the estimation of descriptor contributions in log Cu,b. This means that medicinal chemists now have a simple additive scheme for at least preliminary quantitative assessment of this important pharmacokinetic parameter.
Collapse
Affiliation(s)
- O A Raevsky
- a Department of Computer-Aided Molecular Design , Institute of Physiologically Active Compounds, Russian Academy of Science , Russia
| | - V Yu Grigorev
- a Department of Computer-Aided Molecular Design , Institute of Physiologically Active Compounds, Russian Academy of Science , Russia
| | - D E Polianczyk
- a Department of Computer-Aided Molecular Design , Institute of Physiologically Active Compounds, Russian Academy of Science , Russia
| | - O E Raevskaja
- a Department of Computer-Aided Molecular Design , Institute of Physiologically Active Compounds, Russian Academy of Science , Russia
| | - J C Dearden
- b School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , UK
| |
Collapse
|
26
|
Li SK, Chantasart D. Skin Permeation Enhancement in Aqueous Solution: Correlation With Equilibrium Enhancer Concentration and Octanol/Water Partition Coefficient. J Pharm Sci 2018; 108:350-357. [PMID: 30165068 DOI: 10.1016/j.xphs.2018.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/06/2018] [Accepted: 08/16/2018] [Indexed: 11/28/2022]
Abstract
The effectiveness of skin penetration enhancers and the enhancer concentration required for effective skin permeation enhancement are difficult to predict. A comprehensive quantitative structure-enhancement relationship of chemical penetration enhancers for skin permeation is not currently available. The present study (a) investigated the relationship between skin permeation enhancement and chemical enhancer concentration and (b) examined a simple quantitative structure-enhancement relationship for predicting skin permeation enhancement to guide enhancer formulation development. In the present analysis, data from previous skin permeation studies that used the symmetric/equilibrium configuration and skin parallel pathway model were summarized to determine the relationship between enhancement factor and enhancer concentration. Under the equilibrium conditions, semilogarithmic linear relationships between enhancement factor (E) and enhancer aqueous concentration (C) were observed and an enhancer potency parameter (α) was defined. A correlation between the potency parameter α and enhancer octanol/water partition coefficient (Koct) was obtained. The enhancement factor relationship was derived: Log E = 0.32 ∙ C ∙ Koct. The results suggest that a "threshold" of (C ∙ Koct) > 0.5 M is required to induce effective skin permeation enhancement under these conditions. Consistent with the analyses in previous studies, the data suggest that octanol represents the skin barrier microenvironment for the penetration enhancers.
Collapse
Affiliation(s)
- S Kevin Li
- Division of Pharmaceutical Sciences, College of Pharmacy, University of Cincinnati, Cincinnati, Ohio 45267.
| | - Doungdaw Chantasart
- Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| |
Collapse
|
27
|
Lavoie M, Duval JFL, Raven JA, Maps F, Béjaoui B, Kieber DJ, Vincent WF. Carbonate Disequilibrium in the External Boundary Layer of Freshwater Chrysophytes: Implications for Contaminant Uptake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:9403-9411. [PMID: 30016087 DOI: 10.1021/acs.est.8b00843] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The interplay between biological and chemical reactions in the freshwater phytoplankton phycosphere and the resulting modulations of contaminant speciation and uptake is poorly characterized. Here we modeled the effect of algal C and N uptake on carbonate cycling and speciation of selected contaminants in the phycosphere (external boundary layer) of chrysophytes, a key phytoplankton group in oligotrophic systems. We calculated an enrichment in H+ concentration relative to that in the bulk solution (pH 7.0) of approximately 40% or a depletion of approximately 30% for NH4+ or NO3--grown cells, respectively, at the algal membrane surface of a 5-μm radius cell. Such changes are mainly due to direct H+ uptake or release at the plasmalemma if NO3- or NH4+ is the N source, respectively. Due to these pH changes in the external boundary layer, competition between H+ and metals for uptake is enhanced, for NH4+-grown cells which contributes to a decrease in potential metal uptake. Our model suggests that the uptake of protonated weakly acidic organic acids (HA) is greater in NH4+-grown cells compared to that in NO3--grown cells. The account of chemical reactions in the algal external boundary layer could improve ecological risk assessments for a wide range of contaminants.
Collapse
Affiliation(s)
- Michel Lavoie
- Québec-Océan, Takuvik Unité Mixte Internationale (Université Laval-CNRS) and Département de Biologie , Université Laval , Québec , Québec G1V 0A6 , Canada
| | - Jérôme F L Duval
- CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360 , Vandoeuvre-lès-Nancy F-54501 , France
- Université de Lorraine, LIEC, UMR7360 , Vandoeuvre-lès-Nancy F-54501 , France
| | - John A Raven
- Division of Plant Science , University of Dundee at the James Hutton Institute , Invergowrie, Dundee DD2 5DA , United Kingdom
- Functional Plant Biology and Climate Change Cluster (C3) , University of Technology Sydney , Ultimo , New South Wales 2007 , Australia
| | - Frédéric Maps
- Québec-Océan, Takuvik Unité Mixte Internationale (Université Laval-CNRS) and Département de Biologie , Université Laval , Québec , Québec G1V 0A6 , Canada
| | - Béchir Béjaoui
- Laboratoire Milieu Marin (LMM) , Institut National des Sciences et Technologies de la Mer , 28, rue du 2 mars 1934 , 2025 , Salammbô , Tunisie
| | - David J Kieber
- Department of Chemistry , State University of New York, College of Environmental Science and Forestry , Syracuse , New York 13210 , United States
| | - Warwick F Vincent
- Québec-Océan, Takuvik Unité Mixte Internationale (Université Laval-CNRS) and Département de Biologie , Université Laval , Québec , Québec G1V 0A6 , Canada
| |
Collapse
|
28
|
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
|
29
|
Rossi Sebastiano M, Doak BC, Backlund M, Poongavanam V, Over B, Ermondi G, Caron G, Matsson P, Kihlberg J. Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5. J Med Chem 2018; 61:4189-4202. [PMID: 29608068 DOI: 10.1021/acs.jmedchem.8b00347] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conformational flexibility has been proposed to significantly affect drug properties outside rule-of-5 (Ro5) chemical space. Here, we investigated the influence of dynamically exposed polarity on cell permeability and aqueous solubility for a structurally diverse set of drugs and clinical candidates far beyond the Ro5, all of which populated multiple distinct conformations as revealed by X-ray crystallography. Efflux-inhibited (passive) Caco-2 cell permeability correlated strongly with the compounds' minimum solvent-accessible 3D polar surface areas (PSA), whereas aqueous solubility depended less on the specific 3D conformation. Inspection of the crystal structures highlighted flexibly linked aromatic side chains and dynamically forming intramolecular hydrogen bonds as particularly effective in providing "chameleonic" properties that allow compounds to display both high cell permeability and aqueous solubility. These structural features, in combination with permeability predictions based on the correlation to solvent-accessible 3D PSA, should inspire drug design in the challenging chemical space far beyond the Ro5.
Collapse
Affiliation(s)
| | - Bradley C Doak
- Department of Medicinal Chemistry, MIPS , Monash University , 381 Royal Parade , Parkville , Victoria 3052 , Australia
| | - Maria Backlund
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), a Node at the Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Pharmacy, BMC , Uppsala University , Box 580, SE-751 23 Uppsala , Sweden
| | | | - Björn Over
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit , AstraZeneca R&D Gothenburg , SE-431 83 Mölndal , Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences , University of Torino , Quarello 15 , 10135 Torino , Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences , University of Torino , Quarello 15 , 10135 Torino , Italy
| | - Pär Matsson
- Department of Pharmacy, BMC , Uppsala University , Box 580, SE-751 23 Uppsala , Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC , Uppsala University , Box 576, SE-751 23 Uppsala , Sweden
| |
Collapse
|
30
|
Bittermann K, Goss KU. Predicting apparent passive permeability of Caco-2 and MDCK cell-monolayers: A mechanistic model. PLoS One 2017; 12:e0190319. [PMID: 29281711 PMCID: PMC5744993 DOI: 10.1371/journal.pone.0190319] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/12/2017] [Indexed: 01/16/2023] Open
Abstract
Experimentally derived apparent permeabilities, Papp, through cell monolayers such as Caco-2 and MDCK are considered to be an in-vitro gold standard for assessing the uptake efficiency of drugs. Here, we present a mechanistic model that describes 'passive' Papp values (i.e., neglecting active transport) by accounting for the different resistances solutes encounter when permeating a cell monolayer. We described three parallel permeation pathways, namely a cytosolic-, paracellular-, and lateral route, each of which consists of a number of serial resistances. These resistances were accounted for via a mechanistic depiction of the underlying processes that are largely based on literature work. For the present Papp dataset, about as much chemicals are dominated by the cytosolic route as were dominated by the paracellular route, while the lateral route was negligible. For the cytosolic route by far the most chemicals found their main resistance in the various water layers and not in the membrane. Although correlations within the subclasses of chemicals dominated by a specific permeation route were rather poor, we could overall satisfyingly predict Papp for 151 chemicals at a pH of 7.4 (R2 = 0.77, RMSE = 0.48). For a specific evaluation of the intrinsic membrane permeability, Pm, a second experimental dataset based on experiments with black lipid membranes, BLM, was evaluated. Pm could be predicted for 37 chemicals with R2 = 0.91 and RMSE = 0.64 log units.
Collapse
Affiliation(s)
- Kai Bittermann
- Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Kai-Uwe Goss
- Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Department of Chemistry, University of Halle-Wittenberg, Halle, Germany
- * E-mail:
| |
Collapse
|
31
|
Nitsche JM, Kasting GB. A Universal Correlation Predicts Permeability Coefficients of Fluid- and Gel-Phase Phospholipid and Phospholipid-Cholesterol Bilayers for Arbitrary Solutes. J Pharm Sci 2017; 105:1762-1771. [PMID: 27112406 DOI: 10.1016/j.xphs.2016.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 11/24/2022]
Abstract
The permeability of gel-phase phospholipids is typically about an order of magnitude lower than that of the same compositions in the fluid phase, yet a quantitative description of the ordering factors leading to this difference has been elusive. The present analysis examines these factors with particular focus on the area per phospholipid chain, Ac, and its relationship to the minimum area per molecule in the crystalline state, A0. It is shown that fluid- and gel-phase phospholipid permeabilities can be reconciled by postulating a minimum area per chain Ac,0 = 17.1 Å(2), substantially less than one would estimate by dividing the accepted value A0 = 40.8 Å(2) by 2. An extended data set of phospholipid and phospholipid-cholesterol bilayer permeability data extending over 9 orders of magnitude is analyzed and correlated according to the developed relationship (N = 85, s = 0.3024, r(2) = 0.9332). Individual permeability values are consequently predicted to within an average deviation of 10(0.3024) or about a factor of 2. The analysis is broadly applicable in the fluid phase but is restricted to gel-phase phospholipid compositions that do not contain cholesterol. Guidance for the latter scenario is provided.
Collapse
Affiliation(s)
- Johannes M Nitsche
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200.
| | - Gerald B Kasting
- James L. Winkle College of Pharmacy, University of Cincinnati Academic Health Center, Cincinnati, Ohio 45267-0004
| |
Collapse
|
32
|
Modeling the Kinetics of the Permeation of Antibacterial Agents into Growing Bacteria and Its Interplay with Efflux. Antimicrob Agents Chemother 2017; 61:AAC.02576-16. [PMID: 28717042 DOI: 10.1128/aac.02576-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/30/2017] [Indexed: 01/05/2023] Open
Abstract
A mathematical model of the passive permeation of a novel solute into bacteria that explicitly accounts for intracellular dilution through growth was developed. A bacterial cell envelope permeability coefficient of approximately >10-8 cm2 · s-1 is predicted to ensure passive permeation into rapidly replicating bacterial cells. The relative importance of the permeability coefficients of the cytoplasmic and outer membranes of Gram-negative bacteria in determining the overall envelope permeability coefficient was analyzed quantitatively. A mathematical description of the balance between passive influx and active efflux was also developed and shows that bacterial expansion through growth can usually be neglected for compounds likely to be prepared in antibacterial drug discovery programs and the balance between passive inward permeation and active outwardly directed efflux predominates. A new parameter, efflux efficiency (η, where η is equal to k/P, in which k is the rate coefficient for the efflux pump and P is the permeability coefficient for the membrane across which the pump acts), is introduced, and the consequences for the efficiency of efflux pumping by a single pump, two pumps in parallel across either the cytoplasmic or the outer membrane, and two pumps in series, one across the cytoplasmic membrane and one across the outer membrane of Gram-negative bacteria, are explored. The results, showing additive efficiency for two pumps acting across a single membrane and multiplicative efficiency for two pumps acting in series across the cytoplasmic and outer membranes, can be quantitatively related to the ratios between MICs measured against pump-sufficient and pump deletion strains and agree with those of previous experimental and theoretical studies.
Collapse
|
33
|
Langton MJ, Scriven LM, Williams NH, Hunter CA. Triggered Release from Lipid Bilayer Vesicles by an Artificial Transmembrane Signal Transduction System. J Am Chem Soc 2017; 139:15768-15773. [PMID: 28876061 DOI: 10.1021/jacs.7b07747] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The on-demand delivery of drug molecules from nanoscale carriers with spatiotemporal control is a key challenge in modern medicine. Here we show that lipid bilayer vesicles (liposomes) can be triggered to release an encapsulated molecular cargo in response to an external control signal by employing an artificial transmembrane signal transduction mechanism. A synthetic signal transducer embedded in the lipid bilayer membrane acts as a switchable catalyst, catalyzing the formation of surfactant molecules inside the vesicle in response to a change in external pH. The surfactant permeabilizes the lipid bilayer membrane to facilitate release of an encapsulated hydrophilic cargo. In the absence of the pH control signal, the catalyst is inactive, and the cargo remains encapsulated within the vesicle.
Collapse
Affiliation(s)
- Matthew J Langton
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Lorel M Scriven
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Nicholas H Williams
- Department of Chemistry, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Christopher A Hunter
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
34
|
Theodorakis PE, Müller EA, Craster RV, Matar OK. Physical insights into the blood-brain barrier translocation mechanisms. Phys Biol 2017; 14:041001. [PMID: 28586313 DOI: 10.1088/1478-3975/aa708a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The number of individuals suffering from diseases of the central nervous system (CNS) is growing with an aging population. While candidate drugs for many of these diseases are available, most of these pharmaceutical agents cannot reach the brain rendering most of the drug therapies that target the CNS inefficient. The reason is the blood-brain barrier (BBB), a complex and dynamic interface that controls the influx and efflux of substances through a number of different translocation mechanisms. Here, we present these mechanisms providing, also, the necessary background related to the morphology and various characteristics of the BBB. Moreover, we discuss various numerical and simulation approaches used to study the BBB, and possible future directions based on multi-scale methods. We anticipate that this review will motivate multi-disciplinary research on the BBB aiming at the design of effective drug therapies.
Collapse
|
35
|
Subramaniam R, Jagadeesan R, Mathew I, Cen Y, Balaz S. Scalable Synthesis and Purification of Acetylated Phosphatidyl Choline Headgroup. Org Process Res Dev 2017; 21:177-181. [PMID: 30792570 DOI: 10.1021/acs.oprd.6b00261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The acetylated headgroup of the most abundant mammalian phospholipid, 1,2-diacetyl-3-sn-phosphatidyl choline (DAcPC), has several important applications in research. For instance, it can be dissolved in the same amount of water as in the fluid PC bilayer, to create a surrogate of a PC headgroup stratum, for studying solvation of small molecules and the influence of their structure on the process. In contrast to PC derivatives with longer acyl chains, DAcPC does not self-aggregate, rendering the aqueous solution homogeneous and suitable for simplified analyses of interactions of molecules with the headgroups. Several studies have been published where DAcPC was used in a crudely purified form. Here we describe a one-step preparation of DAcPC from commercially available bulk chemicals and purification of the product by crystallization and washing. The process gives a good yield and is easily scalable. The availability of enantiopure, crystalline DAcPC could open the door to more extensive biochemical, pharmacological, and nutritional studies of this interesting chemical.
Collapse
Affiliation(s)
- Rajesh Subramaniam
- Department of Pharmaceutical Sciences, Vermont Campus, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, Unites States
| | - Ramesh Jagadeesan
- Pharmaceutical Development Unit, Kemwell Biopharma Pvt Ltd, 34 Tumkur Road, T-Begur, Nelamangala, Bangalore Rural-562123, India
| | - Iswarya Mathew
- Department of Pharmaceutical Sciences, Vermont Campus, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, Unites States
| | - Yana Cen
- Department of Pharmaceutical Sciences, Vermont Campus, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, Unites States
| | - Stefan Balaz
- Department of Pharmaceutical Sciences, Vermont Campus, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, Unites States
| |
Collapse
|
36
|
Pye CR, Hewitt WM, Schwochert J, Haddad TD, Townsend CE, Etienne L, Lao Y, Limberakis C, Furukawa A, Mathiowetz AM, Price DA, Liras S, Lokey RS. Nonclassical Size Dependence of Permeation Defines Bounds for Passive Adsorption of Large Drug Molecules. J Med Chem 2017; 60:1665-1672. [PMID: 28059508 DOI: 10.1021/acs.jmedchem.6b01483] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Macrocyclic peptides are considered large enough to inhibit "undruggable" targets, but the design of passively cell-permeable molecules in this space remains a challenge due to the poorly understood role of molecular size on passive membrane permeability. Using split-pool combinatorial synthesis, we constructed a library of cyclic, per-N-methlyated peptides spanning a wide range of calculated lipohilicities (0 < AlogP < 8) and molecular weights (∼800 Da < MW < ∼1200 Da). Analysis by the parallel artificial membrane permeability assay revealed a steep drop-off in apparent passive permeability with increasing size in stark disagreement with current permeation models. This observation, corroborated by a set of natural products, helps define criteria for achieving permeability in larger molecular size regimes and suggests an operational cutoff, beyond which passive permeability is constrained by a sharply increasing penalty on membrane permeation.
Collapse
Affiliation(s)
- Cameron R Pye
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - William M Hewitt
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Terra D Haddad
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Lyns Etienne
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Yongtong Lao
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Chris Limberakis
- World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. , Groton, Connecticut 06340, United States
| | - Akihiro Furukawa
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd. , 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Alan M Mathiowetz
- World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. , Cambridge, Massachusetts 02139, United States
| | - David A Price
- World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. , Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. , Cambridge, Massachusetts 02139, United States
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| |
Collapse
|
37
|
Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
|
38
|
Furukawa A, Townsend CE, Schwochert J, Pye CR, Bednarek MA, Lokey RS. Passive Membrane Permeability in Cyclic Peptomer Scaffolds Is Robust to Extensive Variation in Side Chain Functionality and Backbone Geometry. J Med Chem 2016; 59:9503-9512. [PMID: 27690434 DOI: 10.1021/acs.jmedchem.6b01246] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Synthetic and natural cyclic peptides provide a testing ground for studying membrane permeability in nontraditional drug scaffolds. Cyclic peptomers, which incorporate peptide and N-alkylglycine (peptoid) residues, combine the stereochemical and geometric complexity of peptides with the functional group diversity accessible to peptoids. We synthesized cyclic peptomer libraries by split-pool techniques, separately permuting side chain and backbone geometry, and analyzed their membrane permeabilities using the parallel artificial membrane permeability assay. Nearly half of the side chain permutations had permeability coefficients (Papp) > 1 × 10-6 cm/s. Some backbone geometries enhanced permeability due to their ability to form more stable intramolecular hydrogen bond networks compared with other scaffolds. These observations suggest that hexameric cyclic peptomers can have good passive permeability even in the context of extensive side chain and backbone variation, and that high permeability can generally be achieved within a relatively wide lipophilicity range.
Collapse
Affiliation(s)
- Akihiro Furukawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States.,Modality Research Laboratories, Daiichi Sankyo Co., Ltd. , 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R Pye
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria A Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd. , Cambridge CB21 6GH, United Kingdom
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| |
Collapse
|
39
|
pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. Proc Natl Acad Sci U S A 2016; 113:E5354-62. [PMID: 27551079 DOI: 10.1073/pnas.1525145113] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Many carbon-fixing bacteria rely on a CO2 concentrating mechanism (CCM) to elevate the CO2 concentration around the carboxylating enzyme ribulose bisphosphate carboxylase/oxygenase (RuBisCO). The CCM is postulated to simultaneously enhance the rate of carboxylation and minimize oxygenation, a competitive reaction with O2 also catalyzed by RuBisCO. To achieve this effect, the CCM combines two features: active transport of inorganic carbon into the cell and colocalization of carbonic anhydrase and RuBisCO inside proteinaceous microcompartments called carboxysomes. Understanding the significance of the various CCM components requires reconciling biochemical intuition with a quantitative description of the system. To this end, we have developed a mathematical model of the CCM to analyze its energetic costs and the inherent intertwining of physiology and pH. We find that intracellular pH greatly affects the cost of inorganic carbon accumulation. At low pH the inorganic carbon pool contains more of the highly cell-permeable H2CO3, necessitating a substantial expenditure of energy on transport to maintain internal inorganic carbon levels. An intracellular pH ≈8 reduces leakage, making the CCM significantly more energetically efficient. This pH prediction coincides well with our measurement of intracellular pH in a model cyanobacterium. We also demonstrate that CO2 retention in the carboxysome is necessary, whereas selective uptake of HCO3 (-) into the carboxysome would not appreciably enhance energetic efficiency. Altogether, integration of pH produces a model that is quantitatively consistent with cyanobacterial physiology, emphasizing that pH cannot be neglected when describing biological systems interacting with inorganic carbon pools.
Collapse
|
40
|
Korshunov S, Imlay KRC, Imlay JA. The cytochrome bd oxidase of Escherichia coli prevents respiratory inhibition by endogenous and exogenous hydrogen sulfide. Mol Microbiol 2016; 101:62-77. [PMID: 26991114 DOI: 10.1111/mmi.13372] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2016] [Indexed: 12/31/2022]
Abstract
When sulfur compounds are scarce or difficult to process, Escherichia coli adapts by inducing the high-level expression of sulfur-compound importers. If cystine then becomes available, the cystine is rapidly overimported and reduced, leading to a burgeoning pool of intracellular cysteine. Most of the excess cysteine is exported, but some is adventitiously degraded, with the consequent release of sulfide. Sulfide is a potent ligand of copper and heme moieties, raising the prospect that it interferes with enzymes. We observed that when cystine was provided and sulfide levels rose, E. coli became strictly dependent upon cytochrome bd oxidase for continued respiration. Inspection revealed that low-micromolar levels of sulfide inhibited the proton-pumping cytochrome bo oxidase that is regarded as the primary respiratory oxidase. In the absence of the back-up cytochrome bd oxidase, growth failed. Exogenous sulfide elicited the same effect. The potency of sulfide was enhanced when oxygen concentrations were low. Natural oxic-anoxic interfaces are often sulfidic, including the intestinal environment where E. coli dwells. We propose that the sulfide resistance of the cytochrome bd oxidase is a key trait that permits respiration in such habitats.
Collapse
Affiliation(s)
- Sergey Korshunov
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA
| | - Karin R C Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA
| |
Collapse
|
41
|
Leung SSF, Sindhikara D, Jacobson MP. Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. J Chem Inf Model 2016; 56:924-9. [PMID: 27135806 DOI: 10.1021/acs.jcim.6b00005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We investigate the relationship between passive permeability and molecular size, in the context of solubility-diffusion theory, using a diverse compound set with molecular weights ranging from 151 to 828, which have all been characterized in a consistent manner using the RRCK cell monolayer assay. Computationally, each compound was subjected to extensive conformational search and physics-based permeability prediction, and multiple linear regression analyses were subsequently performed to determine, empirically, the relative contributions of hydrophobicity and molecular size to passive permeation in the RRCK assay. Additional analyses of Log D and PAMPA data suggest that these measurements are not size selective, a possible reason for their sometimes weak correlation with cell-based permeability.
Collapse
Affiliation(s)
- Siegfried S F Leung
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Daniel Sindhikara
- Schrödinger, Inc., 120 West 45th Street, 17th Floor, New York, New York 10036, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| |
Collapse
|
42
|
Raevsky OA. CNS Multiparameter Optimization Approach: Is it in Accordance with Occam’s Razor Principle? Mol Inform 2016; 35:94-8. [DOI: 10.1002/minf.201500109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 12/11/2015] [Indexed: 01/30/2023]
|
43
|
Jackson GE, Elmagbari FM, Hammouda AN, Bonomo RP. Solution equilibria and the X-ray structure of Cu(ii) complexation with 3-amino-N-(pyridin-2-ylmethyl)propanamide, a pseudo-mimic of human serum albumin. Dalton Trans 2016; 45:17010-17019. [DOI: 10.1039/c6dt02974d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Copper complexes have anti-inflammatory activity in the treatment of inflammation associated with rheumatoid arthritis (RA).
Collapse
|
44
|
Casalegno M, Raos G, Sello G. From dioxin to dioxin congeners: understanding the differences in hydrophobic aggregation in water and absorption into lipid membranes by means of atomistic simulations. Phys Chem Chem Phys 2016; 18:17731-9. [DOI: 10.1039/c6cp01728b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular dynamics simulations indicate that dioxin likely accumulates in cell membranes more than its congeners (anthracene, tetrahydrodioxin, 3,3′,5,5′-tetrachlorobiphenyl, and 1,2-dihydroxytetrahydrodibenzo-p-dioxin).
Collapse
Affiliation(s)
- Mosé Casalegno
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “G. Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Guido Raos
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “G. Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Guido Sello
- Dipartimento di Chimica
- Università degli Studi di Milano
- I-20133 Milano
- Italy
| |
Collapse
|
45
|
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
|
46
|
Nolte TM, Kettler K, Meesters JAJ, Hendriks AJ, van de Meent D. A semi-empirical model for transport of inorganic nanoparticles across a lipid bilayer: implications for uptake by living cells. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:488-496. [PMID: 25470256 DOI: 10.1002/etc.2812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/17/2014] [Accepted: 11/16/2014] [Indexed: 06/04/2023]
Abstract
Due to increasing application, release of nanoparticles (NPs) and nanomaterials into the environment becomes likely. Knowledge about NP uptake in organisms is crucial for risk assessment including estimations on the behavior of NPs based on their physicochemical properties. In the present study, the authors have applied current scientific knowledge to construct a mathematical model, which estimates the transport of NPs through a model biological membrane. The semi-empirical model developed showed all parameters studied to substantially affect the agglomeration of the NPs in suspension, thereby also affecting passive transport. The authors quantified the effects of pH, ionic strength, organic matter concentration of medium, and NP size of several inorganic NPs on the permeation through the lipid membrane. Model outcomes and experimental results described in literature were strongly correlated for several metal oxide NPs. With caution, the model may be used to explain some of the existing variance in nano-uptake and toxicity experiments.
Collapse
Affiliation(s)
- Tom M Nolte
- Radboud University Nijmegen, Institute for Water and Wetland Research, Department of Environmental Science, Nijmegen, The Netherlands
| | | | | | | | | |
Collapse
|
47
|
Natesan S, Lukacova V, Peng M, Subramaniam R, Lynch S, Wang Z, Tandlich R, Balaz S. Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases. Mol Pharm 2014; 11:3577-95. [PMID: 25179490 PMCID: PMC4186683 DOI: 10.1021/mp5003366] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Solvation of drugs in the core (C)
and headgroup (H) strata of
phospholipid bilayers affects their physiological transport rates
and accumulation. These characteristics, especially a complete drug
distribution profile across the bilayer strata, are tedious to obtain
experimentally, to the point that even simplified preferred locations
are only available for a few dozen compounds. Recently, we showed
that the partition coefficient (P) values in the
system of hydrated diacetyl phosphatidylcholine (DAcPC) and n-hexadecane (C16), as surrogates of the H- and C-strata
of the bilayer composed of the most abundant mammalian phospholipid,
PC, agree well with the preferred bilayer location of compounds. High P values are typical for lipophiles accumulating in the
core, and low P values are characteristic of cephalophiles
preferring the headgroups. This simple pattern does not hold for most
compounds, which usually have more even distribution and may also
accumulate at the H/C interface. To model complete distribution, the
correlates of solvation energies are needed for each drug state in
the bilayer: (1) for the H-stratum it is the DAcPC/W P value, calculated as the ratio of the C16/W and C16/DAcPC (W for
water) P values; (2) for the C-stratum, the C16/W P value; (3) for the H/C interface, the P values for all plausible molecular poses are characterized using
the fragment DAcPC/W and C16/W solvation parameters for the parts
of the molecule embedded in the H- and C-strata, respectively. The
correlates, each scaled by two Collander coefficients, were used in
a nonlinear, mass-balance based model of intrabilayer distribution,
which was applied to the easily measurable overall P values of compounds in the DMPC (M = myristoyl) bilayers and monolayers
as the dependent variables. The calibrated model for 107 neutral compounds
explains 94% of experimental variance, achieves similar cross-validation
levels, and agrees well with the nontrivial, experimentally determined
bilayer locations for 27 compounds. The resulting structure-based
prediction system for intrabilayer distribution will facilitate more
realistic modeling of passive transport and drug interactions with
those integral membrane proteins, which have the binding sites located
in the bilayer, such as some enzymes, influx and efflux transporters,
and receptors. If only overall bilayer accumulation is of interest,
the 1-octanol/W P values suffice to model the studied
set.
Collapse
Affiliation(s)
- Senthil Natesan
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences , Vermont Campus, Colchester, Vermont 05446, United States
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Zocher F, van der Spoel D, Pohl P, Hub JS. Local partition coefficients govern solute permeability of cholesterol-containing membranes. Biophys J 2014; 105:2760-70. [PMID: 24359748 DOI: 10.1016/j.bpj.2013.11.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/31/2013] [Accepted: 11/04/2013] [Indexed: 11/25/2022] Open
Abstract
The permeability of lipid membranes for metabolic molecules or drugs is routinely estimated from the solute's oil/water partition coefficient. However, the molecular determinants that modulate the permeability in different lipid compositions have remained unclear. Here, we combine scanning electrochemical microscopy and molecular-dynamics simulations to study the effect of cholesterol on membrane permeability, because cholesterol is abundant in all animal membranes. The permeability of membranes from natural lipid mixtures to both hydrophilic and hydrophobic solutes monotonously decreases with cholesterol concentration [Chol]. The same is true for hydrophilic solutes and planar bilayers composed of dioleoyl-phosphatidylcholine or dioleoyl-phosphatidyl-ethanolamine. However, these synthetic lipids give rise to a bell-shaped dependence of membrane permeability on [Chol] for very hydrophobic solutes. The simulations indicate that cholesterol does not affect the diffusion constant inside the membrane. Instead, local partition coefficients at the lipid headgroups and at the lipid tails are modulated oppositely by cholesterol, explaining the experimental findings. Structurally, these modulations are induced by looser packing at the lipid headgroups and tighter packing at the tails upon the addition of cholesterol.
Collapse
Affiliation(s)
- Florian Zocher
- Institut für Biophysik, Johannes Kepler Universität, Linz, Austria
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala, Sweden
| | - Peter Pohl
- Institut für Biophysik, Johannes Kepler Universität, Linz, Austria.
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| |
Collapse
|
49
|
Abraham MH. Human Intestinal Absorption—Neutral Molecules and Ionic Species. J Pharm Sci 2014; 103:1956-1966. [DOI: 10.1002/jps.24024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 11/11/2022]
|
50
|
Abstract
Pathogenic spirochetes cause clinically relevant diseases in humans and animals, such as Lyme disease and leptospirosis. The causative agent of Lyme disease, Borrelia burgdorferi, and the causative agent of leptospirosis, Leptospria interrogans, encounter reactive oxygen species (ROS) during their enzootic cycles. This report demonstrated that physiologically relevant concentrations of pyruvate, a potent H2O2 scavenger, and provided passive protection to B. burgdorferi and L. interrogans against H2O2. When extracellular pyruvate was absent, both spirochetes were sensitive to a low dose of H2O2 (≈0.6 µM per h) generated by glucose oxidase (GOX). Despite encoding a functional catalase, L. interrogans was more sensitive than B. burgdorferi to H2O2 generated by GOX, which may be due to the inherent resistance of B. burgdorferi because of the virtual absence of intracellular iron. In B. burgdorferi, the nucleotide excision repair (NER) and the DNA mismatch repair (MMR) pathways were important for survival during H2O2 challenge since deletion of the uvrB or the mutS genes enhanced its sensitivity to H2O2 killing; however, the presence of pyruvate fully protected ΔuvrB and ΔmutS from H2O2 killing further demonstrating the importance of pyruvate in protection. These findings demonstrated that pyruvate, in addition to its classical role in central carbon metabolism, serves as an important H2O2 scavenger for pathogenic spirochetes. Furthermore, pyruvate reduced ROS generated by human neutrophils in response to the Toll-like receptor 2 (TLR2) agonist zymosan. In addition, pyruvate reduced neutrophil-derived ROS in response to B. burgdorferi, which also activates host expression through TLR2 signaling. Thus, pathogenic spirochetes may exploit the metabolite pyruvate, present in blood and tissues, to survive H2O2 generated by the host antibacterial response generated during infection.
Collapse
|