51
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Radan M, Djikic T, Obradovic D, Nikolic K. Application of in vitro PAMPA technique and in silico computational methods for blood-brain barrier permeability prediction of novel CNS drug candidates. Eur J Pharm Sci 2021; 168:106056. [PMID: 34740787 DOI: 10.1016/j.ejps.2021.106056] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/09/2021] [Accepted: 10/31/2021] [Indexed: 11/17/2022]
Abstract
Permeability assessment of small molecules through the blood-brain barrier (BBB) plays a significant role in the development of effective central nervous system (CNS) drug candidates. Since in vivo methods for BBB permeability estimation require a lot of time and resources, in silico and in vitro approaches are becoming increasingly popular nowadays for faster and more economical predictions in early phases of drug discovery. In this work, through application of in vitro parallel artificial membrane permeability assay (PAMPA-BBB) and in silico computational methods we aimed to examine the passive permeability of eighteen compounds, which affect serotonin and dopamine levels in the CNS. The data set was consisted of novel six human dopamine transporter (hDAT) substrates that were previously identified as the most promising lead compounds for further optimisation to achieve neuroprotective effect, twelve approved CNS drugs, and their related compounds. Firstly, PAMPA methods was used to experimentally determine effective BBB permeability (Pe) for all studied compounds and obtained results were further submitted for quantitative structure permeability relationship (QSPR) analysis. QSPR models were built by using three different statistical methods: stepwise multiple linear regression (MLR), partial least square (PLS), and support-vector machine (SVM), while their predictive capability was tested through internal and external validation. Obtained statistical parameters (MLR- R2pred=-0.10; PLS- R2pred=0.64, r2m=0.69, r/2m=0.44; SVM- R2pred=0.57, r2m=0.72, r/2m=0.55) indicated that the SVM model is superior over others. The most important molecular descriptors (H0p and SolvEMt_3D) were identified and used to propose structural modifications of the examined compounds in order to improve their BBB permeability. Moreover, steered molecular dynamics (SMD) simulation was employed to comprehensively investigate the permeability pathway of compounds through a lipid bilayer. Taken together, the created QSPR model could be used as a reliable and fast pre-screening tool for BBB permeability prediction of structurally related CNS compounds, while performed MD simulations provide a good foundation for future in silico examination.
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Affiliation(s)
- Milica Radan
- University of Belgrade - Faculty of Pharmacy, Department of Pharmaceutical, Chemistry, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Teodora Djikic
- University of Belgrade - Faculty of Pharmacy, Department of Pharmaceutical, Chemistry, Vojvode Stepe 450, 11000 Belgrade, Serbia.
| | - Darija Obradovic
- University of Belgrade - Faculty of Pharmacy, Department of Pharmaceutical, Chemistry, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Katarina Nikolic
- University of Belgrade - Faculty of Pharmacy, Department of Pharmaceutical, Chemistry, Vojvode Stepe 450, 11000 Belgrade, Serbia.
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52
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Cui D, Kong N, Ding L, Guo Y, Yang W, Yan F. Ultrathin 2D Titanium Carbide MXene (Ti 3 C 2 T x ) Nanoflakes Activate WNT/HIF-1α-Mediated Metabolism Reprogramming for Periodontal Regeneration. Adv Healthc Mater 2021; 10:e2101215. [PMID: 34586717 DOI: 10.1002/adhm.202101215] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/08/2021] [Indexed: 12/17/2022]
Abstract
Periodontal defect regeneration in severe periodontitis relies on the differentiation and proliferation of periodontal ligament cells (PDLCs). Recently, an emerging 2D nanomaterial, MXene (Ti3 C2 Tx ), has gained more and more attention due to the extensive antibacterial and anticancer activity, while its potential biomedical application on tissue regeneration remains unclear. Through a combination of experimental and multiscale simulation schemes, Ti3 C2 Tx has exhibited satisfactory biocompatibility and induced distinguish osteogenic differentiation of human PDLCs (hPDLCs), with upregulated osteogenesis-related genes. Ti3 C2 Tx manages to activate the Wnt/β-catenin signaling pathway by enhancing the Wnt-Frizzled complex binding, thus stabilizing HIF-1α and altering metabolic reprogramming into glycolysis. In vivo, hPDLCs pretreated by Ti3 C2 Tx display excellent performance in new bone formation and osteoclast inhibition with enhanced RUNX2, HIF-1α, and β-catenin in an experimental rat model of periodontal fenestration defects, indicating that this material has high efficiency of periodontal regeneration promotion. It is demonstrated in this work that Ti3 C2 Tx has highly efficient therapeutic effects in osteogenic differentiation and periodontal defect repairment.
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Affiliation(s)
- Di Cui
- Nanjing Stomatological Hospital Medical School of Nanjing University Nanjing Jiangsu 210008 China
| | - Na Kong
- School of Life and Environmental Science Deakin University Waurn Ponds Victoria 3216 Australia
| | - Liang Ding
- Nanjing Stomatological Hospital Medical School of Nanjing University Nanjing Jiangsu 210008 China
| | - Yachong Guo
- Kuang Yaming Honors School Nanjing University Nanjing 210023 China
- Institute Theory of Polymers Leibniz‐Institut für Polymerforschung Dresden Dresden 01069 Germany
| | - Wenrong Yang
- School of Life and Environmental Science Deakin University Waurn Ponds Victoria 3216 Australia
| | - Fuhua Yan
- Nanjing Stomatological Hospital Medical School of Nanjing University Nanjing Jiangsu 210008 China
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53
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Meng F, Xi Y, Huang J, Ayers PW. A curated diverse molecular database of blood-brain barrier permeability with chemical descriptors. Sci Data 2021; 8:289. [PMID: 34716354 PMCID: PMC8556334 DOI: 10.1038/s41597-021-01069-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/22/2021] [Indexed: 01/31/2023] Open
Abstract
The highly-selective blood-brain barrier (BBB) prevents neurotoxic substances in blood from crossing into the extracellular fluid of the central nervous system (CNS). As such, the BBB has a close relationship with CNS disease development and treatment, so predicting whether a substance crosses the BBB is a key task in lead discovery for CNS drugs. Machine learning (ML) is a promising strategy for predicting the BBB permeability, but existing studies have been limited by small datasets with limited chemical diversity. To mitigate this issue, we present a large benchmark dataset, B3DB, complied from 50 published resources and categorized based on experimental uncertainty. A subset of the molecules in B3DB has numerical log BB values (1058 compounds), while the whole dataset has categorical (BBB+ or BBB-) BBB permeability labels (7807). The dataset is freely available at https://github.com/theochem/B3DB and https://doi.org/10.6084/m9.figshare.15634230.v3 (version 3). We also provide some physicochemical properties of the molecules. By analyzing these properties, we can demonstrate some physiochemical similarities and differences between BBB+ and BBB- compounds.
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Affiliation(s)
- Fanwang Meng
- grid.25073.330000 0004 1936 8227Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S 4L8 Canada
| | - Yang Xi
- grid.25073.330000 0004 1936 8227Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S 4L8 Canada
| | - Jinfeng Huang
- grid.25073.330000 0004 1936 8227Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S 4L8 Canada
| | - Paul W. Ayers
- grid.25073.330000 0004 1936 8227Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S 4L8 Canada
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54
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Shityakov S, Skorb EV, Förster CY, Dandekar T. Scaffold Searching of FDA and EMA-Approved Drugs Identifies Lead Candidates for Drug Repurposing in Alzheimer's Disease. Front Chem 2021; 9:736509. [PMID: 34751244 PMCID: PMC8571023 DOI: 10.3389/fchem.2021.736509] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/22/2021] [Indexed: 11/24/2022] Open
Abstract
Clinical trials of novel therapeutics for Alzheimer's Disease (AD) have consumed a significant amount of time and resources with largely negative results. Repurposing drugs already approved by the Food and Drug Administration (FDA), European Medicines Agency (EMA), or Worldwide for another indication is a more rapid and less expensive option. Therefore, we apply the scaffold searching approach based on known amyloid-beta (Aβ) inhibitor tramiprosate to screen the DrugCentral database (n = 4,642) of clinically tested drugs. As a result, menadione bisulfite and camphotamide substances with protrombogenic and neurostimulation/cardioprotection effects were identified as promising Aβ inhibitors with an improved binding affinity (ΔGbind) and blood-brain barrier permeation (logBB). Finally, the data was also confirmed by molecular dynamics simulations using implicit solvation, in particular as Molecular Mechanics Generalized Born Surface Area (MM-GBSA) model. Overall, the proposed in silico pipeline can be implemented through the early stage rational drug design to nominate some lead candidates for AD, which will be further validated in vitro and in vivo, and, finally, in a clinical trial.
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Affiliation(s)
- Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
| | - Ekaterina V. Skorb
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
| | - Carola Y. Förster
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, Würzburg University Hospital, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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55
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Lynch MJ, Gobbo OL. Advances in Non-Animal Testing Approaches towards Accelerated Clinical Translation of Novel Nanotheranostic Therapeutics for Central Nervous System Disorders. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2632. [PMID: 34685073 PMCID: PMC8538557 DOI: 10.3390/nano11102632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/21/2021] [Accepted: 10/01/2021] [Indexed: 12/11/2022]
Abstract
Nanotheranostics constitute a novel drug delivery system approach to improving systemic, brain-targeted delivery of diagnostic imaging agents and pharmacological moieties in one rational carrier platform. While there have been notable successes in this field, currently, the clinical translation of such delivery systems for the treatment of neurological disorders has been limited by the inadequacy of correlating in vitro and in vivo data on blood-brain barrier (BBB) permeation and biocompatibility of nanomaterials. This review aims to identify the most contemporary non-invasive approaches for BBB crossing using nanotheranostics as a novel drug delivery strategy and current non-animal-based models for assessing the safety and efficiency of such formulations. This review will also address current and future directions of select in vitro models for reducing the cumbersome and laborious mandate for testing exclusively in animals. It is hoped these non-animal-based modelling approaches will facilitate researchers in optimising promising multifunctional nanocarriers with a view to accelerating clinical testing and authorisation applications. By rational design and appropriate selection of characterised and validated models, ranging from monolayer cell cultures to organ-on-chip microfluidics, promising nanotheranostic particles with modular and rational design can be screened in high-throughput models with robust predictive power. Thus, this article serves to highlight abbreviated research and development possibilities with clinical translational relevance for developing novel nanomaterial-based neuropharmaceuticals for therapy in CNS disorders. By generating predictive data for prospective nanomedicines using validated in vitro models for supporting clinical applications in lieu of requiring extensive use of in vivo animal models that have notable limitations, it is hoped that there will be a burgeoning in the nanotherapy of CNS disorders by virtue of accelerated lead identification through screening, optimisation through rational design for brain-targeted delivery across the BBB and clinical testing and approval using fewer animals. Additionally, by using models with tissue of human origin, reproducible therapeutically relevant nanomedicine delivery and individualised therapy can be realised.
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Affiliation(s)
- Mark J. Lynch
- School of Pharmacy and Pharmaceutical Sciences, Panoz Building, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Oliviero L. Gobbo
- School of Pharmacy and Pharmaceutical Sciences, Panoz Building, Trinity College Dublin, D02 PN40 Dublin, Ireland
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56
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Kim S, Yang JU, Ahn JH, Ko IO, Kim JY, Lee YJ, Park JA. Porphyrin-Based Tumor-Targeting Theranostic Agent: Gd-TDAP. ACS Med Chem Lett 2021; 12:1459-1463. [PMID: 34531954 PMCID: PMC8436409 DOI: 10.1021/acsmedchemlett.1c00283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/11/2021] [Indexed: 12/11/2022] Open
Abstract
The aim of this work was to evaluate a tumor-targeting porphyrin-based gadolinium complex (Gd-TDAP) for use as an MR/optical imaging agent and potential therapeutic agent. Gd-TDAP had higher longitudinal relaxivity (11.8 mM-1 s-1) than a commercial MRI contrast agent (Omniscan; 3.7 mM-1 s-1) in HSA solution (0.67 mM) at 3 T. The tumor-targeting characteristics were confirmed by T1-weighted MR imaging and optical imaging using an orthotopic brain tumor mouse model, which showed 1.3-fold higher uptake in tumor compared to normal brain tissues. The cell fraction data using U87MG glioblastoma cells indicated the potential for gadolinium neutron capture therapy (Gd-NCT), which requires gadolinium to be inside the cell nucleus. In addition, porphyrin derivatives can be used for photodynamic therapy (PDT), and the results demonstrated that Gd-TDAP has great potential not only as a bimodal imaging agent but also for treatment.
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Affiliation(s)
- Soyeon Kim
- Division
of Applied RI, Korea Institute of Radiological
& Medical Sciences (KIRAMS), Seoul 01812, Korea
- Department
of Medical & Biological Engineering, Kyungpook National University, Daegu 41566, Korea
| | - Ji-ung Yang
- Division
of Applied RI, Korea Institute of Radiological
& Medical Sciences (KIRAMS), Seoul 01812, Korea
- Department
of Medical & Biological Engineering, Kyungpook National University, Daegu 41566, Korea
| | - Jae Hun Ahn
- Division
of Applied RI, Korea Institute of Radiological
& Medical Sciences (KIRAMS), Seoul 01812, Korea
- Graduate
School of Translational Medicine, Seoul
National University College of Medicine, Seoul 03080, Korea
| | - In Ok Ko
- Division
of Applied RI, Korea Institute of Radiological
& Medical Sciences (KIRAMS), Seoul 01812, Korea
| | - Jung Young Kim
- Division
of Applied RI, Korea Institute of Radiological
& Medical Sciences (KIRAMS), Seoul 01812, Korea
| | - Yong Jin Lee
- Division
of Applied RI, Korea Institute of Radiological
& Medical Sciences (KIRAMS), Seoul 01812, Korea
| | - Ji-Ae Park
- Division
of Applied RI, Korea Institute of Radiological
& Medical Sciences (KIRAMS), Seoul 01812, Korea
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57
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Physiologically Based Pharmacokinetic (PBPK) Modeling for Predicting Brain Levels of Drug in Rat. Pharmaceutics 2021; 13:pharmaceutics13091402. [PMID: 34575476 PMCID: PMC8471455 DOI: 10.3390/pharmaceutics13091402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
One of the main obstacles in neurological disease treatment is the presence of the blood-brain barrier. New predictive high-throughput screening tools are essential to avoid costly failures in the advanced phases of development and to contribute to the 3 Rs policy. The objective of this work was to jointly develop a new in vitro system coupled with a physiological-based pharmacokinetic (PBPK) model able to predict brain concentration levels of different drugs in rats. Data from in vitro tests with three different cells lines (MDCK, MDCK-MDR1 and hCMEC/D3) were used together with PK parameters and three scaling factors for adjusting the model predictions to the brain and plasma profiles of six model drugs. Later, preliminary quantitative structure-property relationships (QSPRs) were constructed between the scaling factors and the lipophilicity of drugs. The predictability of the model was evaluated by internal validation. It was concluded that the PBPK model, incorporating the barrier resistance to transport, the disposition within the brain and the drug-brain binding combined with MDCK data, provided the best predictions for passive diffusion and carrier-mediated transported drugs, while in the other cell lines, active transport influence can bias predictions.
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58
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Paul R, Paul S. Translocation of Endo-Functionalized Molecular Tubes across Different Lipid Bilayers: Atomistic Molecular Dynamics Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10376-10387. [PMID: 34415773 DOI: 10.1021/acs.langmuir.1c01594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Various artificial receptors, such as calixarenes, cyclodextrins, cucurbit[n]urils, and their acyclic compounds, pliiar[n]arenes, deep cavitands, and molecular tweezers, can permeate the lipid membranes and they are used as drug carriers to improve the drug solubility, stability, and bioavailability. Inspired by these, we have employed atomistic molecular dynamics simulation to examine the effects of endo-functionalized molecular tubes or naphthotubes (host-1a and host-1b) on seven different types of model lipid bilayers and the permeation properties of these receptors through these model lipid bilayers. Lipid types include six model lipid bilayers (POPC, POPE, DOPC, POPG, DPPE, POPE/POPG) and one realistic membrane (Yeast). We observe that these receptors are spontaneously translocated toward these model lipid bilayer head regions and do not proceed further into these lipid bilayer tail regions (reside at the interface between lipid head and lipid tail region), except for the DPPE-containing systems. In the DPPE model lipid bilayer-containing systems (1a-dppe and 1b-dppe), receptor molecules are only adsorbed on the bilayer surface and reside at the interface between lipid head and water. This finding is also supported by the biased free-energy profiles of these translocation processes. Passive transport of these receptors may be possible through these model lipid bilayers (due to low barrier height), except for DPPE bilayer-containing systems (that have a very high energy barrier at the center). The results from these simulations provide insight into the biocompatibility of host-1a or host-1b in microscopic detail. Based on this work, more research is needed to fully comprehend the role of these synthesized receptors as a prospective drug carrier.
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Affiliation(s)
- Rabindranath Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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59
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Dutta A, Vreeken J, Ghiringhelli LM, Bereau T. Data-driven equation for drug-membrane permeability across drugs and membranes. J Chem Phys 2021; 154:244114. [PMID: 34241352 DOI: 10.1063/5.0053931] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Drug efficacy depends on its capacity to permeate across the cell membrane. We consider the prediction of passive drug-membrane permeability coefficients. Beyond the widely recognized correlation with hydrophobicity, we additionally consider the functional relationship between passive permeation and acidity. To discover easily interpretable equations that explain the data well, we use the recently proposed sure-independence screening and sparsifying operator (SISSO), an artificial-intelligence technique that combines symbolic regression with compressed sensing. Our study is based on a large in silico dataset of 0.4 × 106 small molecules extracted from coarse-grained simulations. We rationalize the equation suggested by SISSO via an analysis of the inhomogeneous solubility-diffusion model in several asymptotic acidity regimes. We further extend our analysis to the dependence on lipid-membrane composition. Lipid-tail unsaturation plays a key role but surprisingly contributes stepwise rather than proportionally. Our results are in line with previously observed changes in permeability, suggesting the distinction between liquid-disordered and liquid-ordered permeation. Together, compressed sensing with analytically derived asymptotes establish and validate an accurate, broadly applicable, and interpretable equation for passive permeability across both drug and lipid-tail chemistry.
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Affiliation(s)
- Arghya Dutta
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jilles Vreeken
- CISPA Helmholtz Center for Information Security, Saarbrücken, Germany
| | - Luca M Ghiringhelli
- The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany
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60
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B3Pred: A Random-Forest-Based Method for Predicting and Designing Blood-Brain Barrier Penetrating Peptides. Pharmaceutics 2021; 13:pharmaceutics13081237. [PMID: 34452198 PMCID: PMC8399279 DOI: 10.3390/pharmaceutics13081237] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 12/14/2022] Open
Abstract
The blood–brain barrier is a major obstacle in treating brain-related disorders, as it does not allow the delivery of drugs into the brain. We developed a method for predicting blood–brain barrier penetrating peptides to facilitate drug delivery into the brain. These blood–brain barrier penetrating peptides (B3PPs) can act as therapeutics, as well as drug delivery agents. We trained, tested, and evaluated our models on blood–brain barrier peptides obtained from the B3Pdb database. First, we computed a wide range of peptide features. Then, we selected relevant peptide features. Finally, we developed numerous machine-learning-based models for predicting blood–brain barrier peptides using the selected features. The random-forest-based model performed the best with respect to the top 80 selected features and achieved a maximal 85.08% accuracy with an AUROC of 0.93. We also developed a webserver, B3pred, that implements our best models. It has three major modules that allow users to predict/design B3PPs and scan B3PPs in a protein sequence.
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61
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Lawson C, Ahmed Alta TB, Moschou G, Skamnaki V, Solovou TGA, Topham C, Hayes J, Snape TJ. Novel diarylamides and diarylureas with N-substitution dependent activity against medulloblastoma. Eur J Med Chem 2021; 225:113751. [PMID: 34391032 DOI: 10.1016/j.ejmech.2021.113751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 01/06/2023]
Abstract
Medulloblastoma - highly aggressive and heterogeneous tumours of the cerebellum - account for 15-20% of all childhood brain tumours, and are the most common high-grade childhood embryonal tumour of the central nervous system. Herein, potent in vitro anticancer activity against two established medulloblastoma cell lines of the sonic hedgehog subgroup, namely DAOY (p53 mutant) and ONS-76 (p53 wild type), has been achieved. A number of first-generation diarylamides and diarylureas were evaluated and activity is likely to be, in-part, conformation-dependent. The most active compound from this first-generation set of compounds, 1-naphthyl derivative 4b, was selected and a second-generation of compounds were optimised and tested for activity against the medulloblastoma cell lines. This process resulted in drug-like compounds with up to sixty times the activity (sub-micromolar) of the first-generation - thus providing potent new leads for further study.
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Affiliation(s)
- Christopher Lawson
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, UK
| | | | - Georgia Moschou
- School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT, UK
| | - Vasiliki Skamnaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larisa, Greece
| | - Theodora G A Solovou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larisa, Greece
| | - Caroline Topham
- School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT, UK
| | - Joseph Hayes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, UK
| | - Timothy J Snape
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, UK; Leicester School of Pharmacy, De Montfort University, Leicester, LE1 9BH, UK.
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62
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Shin HK, Lee S, Oh HN, Yoo D, Park S, Kim WK, Kang MG. Development of blood brain barrier permeation prediction models for organic and inorganic biocidal active substances. CHEMOSPHERE 2021; 277:130330. [PMID: 33780678 DOI: 10.1016/j.chemosphere.2021.130330] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 05/04/2023]
Abstract
Biocidal products are broadly used in homes and industries. However, the safety of biocidal active substances (BASs) is not yet fully understood. In particular, the neurotoxic action of BASs needs to be studied as diverse epidemiological studies have reported associations between exposure to BASs and neural diseases. In this study, we developed in silico models to predict the blood-brain barrier (BBB) permeation of organic and inorganic BASs. Due to a lack of BBB data for BASs, the chemical space of BASs and BBB dataset were compared in order to select BBB data that were structurally similar to BASs. In silico models to predict log-scaled BBB penetration were developed using support vector regression for organic BASs and multiple linear regression for inorganic BASs. The model for organic BASs was developed with 231 compounds (training set: 153 and test set: 78) and achieved good prediction accuracy on an external test set (R2 = 0.64), and the model outperformed the model for pharmaceuticals. The model for inorganic BASs was developed with 11 compounds (R2 = 0.51). Applicability domain (AD) analysis of the models clarified molecular structures reliably predicted by the models. Therefore, the models developed in this study can be used for predicting BBB permeable BASs in human. These models were developed according to the Quantitative Structure-Activity Relationship validation principles proposed by the Organization for Economic Cooperation and Development.
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Affiliation(s)
- Hyun Kil Shin
- Toxicoinformatics group, Department of predictive toxicology, Korea institute of toxicology, Daejeon 34114, Republic of Korea
| | - Sangwoo Lee
- Bio-system Research Group, Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Ha-Na Oh
- Bio-system Research Group, Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Donggon Yoo
- Bio-system Research Group, Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea; Human and Environmental Toxicology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Seungmin Park
- Bio-system Research Group, Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea; Human and Environmental Toxicology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Woo-Keun Kim
- Bio-system Research Group, Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea; Human and Environmental Toxicology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Myung-Gyun Kang
- Toxicoinformatics group, Department of predictive toxicology, Korea institute of toxicology, Daejeon 34114, Republic of Korea.
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63
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Bennion BJ, Malfatti MA, Be NA, Enright HA, Hok S, Cadieux CL, Carpenter TS, Lao V, Kuhn EA, McNerney MW, Lightstone FC, Nguyen TH, Valdez CA. Development of a CNS-permeable reactivator for nerve agent exposure: an iterative, multi-disciplinary approach. Sci Rep 2021; 11:15567. [PMID: 34330964 PMCID: PMC8324913 DOI: 10.1038/s41598-021-94963-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
Nerve agents have experienced a resurgence in recent times with their use against civilian targets during the attacks in Syria (2012), the poisoning of Sergei and Yulia Skripal in the United Kingdom (2018) and Alexei Navalny in Russia (2020), strongly renewing the importance of antidote development against these lethal substances. The current standard treatment against their effects relies on the use of small molecule-based oximes that can efficiently restore acetylcholinesterase (AChE) activity. Despite their efficacy in reactivating AChE, the action of drugs like 2-pralidoxime (2-PAM) is primarily limited to the peripheral nervous system (PNS) and, thus, provides no significant protection to the central nervous system (CNS). This lack of action in the CNS stems from their ionic nature that, on one end makes them very powerful reactivators and on the other renders them ineffective at crossing the Blood Brain Barrier (BBB) to reach the CNS. In this report, we describe the use of an iterative approach composed of parallel chemical and in silico syntheses, computational modeling, and a battery of detailed in vitro and in vivo assays that resulted in the identification of a promising, novel CNS-permeable oxime reactivator. Additional experiments to determine acute and chronic toxicity are ongoing.
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Affiliation(s)
- Brian J Bennion
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Michael A Malfatti
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Nicholas A Be
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Heather A Enright
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Saphon Hok
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - C Linn Cadieux
- United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, 21010, USA
| | - Timothy S Carpenter
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Victoria Lao
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Edward A Kuhn
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - M Windy McNerney
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- Affiliation: Mental Illness Research, Education and Clinical Center, Veterans Affairs, Palo Alto, CA, 94304, USA
- Affiliation: Department of Psychiatry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Felice C Lightstone
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Tuan H Nguyen
- Global Security Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Carlos A Valdez
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
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Faulkner C, de Leeuw NH. Predicting the Membrane Permeability of Fentanyl and Its Analogues by Molecular Dynamics Simulations. J Phys Chem B 2021; 125:8443-8449. [PMID: 34286980 PMCID: PMC8389899 DOI: 10.1021/acs.jpcb.1c05438] [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: 11/30/2022]
Abstract
![]()
The lipid membrane
is considered a crucial component of opioid
general anesthesia. The main drug used for the induction and maintenance
of opioid anesthesia is fentanyl and its various analogues. However,
these drugs have different clinical effects, and detailed atomic-level
insight into the drug–membrane interactions could lead to a
better understanding how these drugs exert their anesthetic properties.
In this study, we have used extensive umbrella sampling molecular
dynamics simulations to study the permeation process of fentanyl and
three of its analogues into a variety of simple phospholipid membrane
models. Our simulations show that we can accurately predict the permeability
coefficients of these drug molecules, which is an important process
in understanding how pharmaceuticals reach their molecular targets.
We were also able to show that one phospholipid provides more accurate
predictions than other lipids commonly used in these types of permeation
studies, which will aid future studies of these types of processes.
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Affiliation(s)
- Christopher Faulkner
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Nora H de Leeuw
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.,School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
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Augustine R, Aqel AH, Kalva SN, Joshy KS, Nayeem A, Hasan A. Bioengineered microfluidic blood-brain barrier models in oncology research. Transl Oncol 2021; 14:101087. [PMID: 33865030 PMCID: PMC8066424 DOI: 10.1016/j.tranon.2021.101087] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/25/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Metastasis is the major reason for most brain tumors with up to a 50% chance of occurrence in patients with other types of malignancies. Brain metastasis occurs if cancer cells succeed to cross the 'blood-brain barrier' (BBB). Moreover, changes in the structure and function of BBB can lead to the onset and progression of diseases including neurological disorders and brain-metastases. Generating BBB models with structural and functional features of intact BBB is highly important to better understand the molecular mechanism of such ailments and finding novel therapeutic agents targeting them. Hence, researchers are developing novel in vitro BBB platforms that can recapitulate the structural and functional characteristics of BBB. Brain endothelial cells-based in vitro BBB models have thus been developed to investigate the mechanism of brain metastasis through BBB and facilitate the testing of brain targeted anticancer drugs. Bioengineered constructs integrated with microfluidic platforms are vital tools for recapitulating the features of BBB in vitro closely as possible. In this review, we outline the fundamentals of BBB biology, recent developments in the microfluidic BBB platforms, and provide a concise discussion of diverse types of bioengineered BBB models with an emphasis on the application of them in brain metastasis and cancer research in general. We also provide insights into the challenges and prospects of the current bioengineered microfluidic platforms in cancer research.
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Affiliation(s)
- Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, 2713 Doha, Qatar; Biomedical Research Center (BRC), Qatar University, PO Box 2713 Doha, Qatar.
| | - Ahmad H Aqel
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, 2713 Doha, Qatar; Biomedical Research Center (BRC), Qatar University, PO Box 2713 Doha, Qatar
| | - Sumama Nuthana Kalva
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, 2713 Doha, Qatar; Biomedical Research Center (BRC), Qatar University, PO Box 2713 Doha, Qatar
| | - K S Joshy
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, 2713 Doha, Qatar; Biomedical Research Center (BRC), Qatar University, PO Box 2713 Doha, Qatar
| | - Ajisha Nayeem
- Department of Biotechnology, St. Mary's College, Thrissur 680020, Kerala, India
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, 2713 Doha, Qatar; Biomedical Research Center (BRC), Qatar University, PO Box 2713 Doha, Qatar.
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66
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Alsenan S, Al-Turaiki I, Hafez A. A deep learning approach to predict blood-brain barrier permeability. PeerJ Comput Sci 2021; 7:e515. [PMID: 34179448 PMCID: PMC8205267 DOI: 10.7717/peerj-cs.515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/08/2021] [Indexed: 06/13/2023]
Abstract
The blood-brain barrier plays a crucial role in regulating the passage of 98% of the compounds that enter the central nervous system (CNS). Compounds with high permeability must be identified to enable the synthesis of brain medications for the treatment of various brain diseases, such as Parkinson's, Alzheimer's, and brain tumors. Throughout the years, several models have been developed to solve this problem and have achieved acceptable accuracy scores in predicting compounds that penetrate the blood-brain barrier. However, predicting compounds with "low" permeability has been a challenging task. In this study, we present a deep learning (DL) classification model to predict blood-brain barrier permeability. The proposed model addresses the fundamental issues presented in former models: high dimensionality, class imbalances, and low specificity scores. We address these issues to enhance the high-dimensional, imbalanced dataset before developing the classification model: the imbalanced dataset is addressed using oversampling techniques and the high dimensionality using a non-linear dimensionality reduction technique known as kernel principal component analysis (KPCA). This technique transforms the high-dimensional dataset into a low-dimensional Euclidean space while retaining invaluable information. For the classification task, we developed an enhanced feed-forward deep learning model and a convolutional neural network model. In terms of specificity scores (i.e., predicting compounds with low permeability), the results obtained by the enhanced feed-forward deep learning model outperformed those obtained by other models in the literature that were developed using the same technique. In addition, the proposed convolutional neural network model surpassed models used in other studies in multiple accuracy measures, including overall accuracy and specificity. The proposed approach solves the problem inevitably faced with obtaining low specificity resulting in high false positive rate.
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Affiliation(s)
- Shrooq Alsenan
- Information Systems Department, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Isra Al-Turaiki
- Information Technology Department, College of Computer and Information Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Alaaeldin Hafez
- Information Systems Department, College of Computer and Information Sciences, King Saud University, Riyadh, Saudi Arabia
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Synthesis and Characterization of Some New Quinoxalin-2( 1H)one and 2-Methyl-3 H-quinazolin-4-one Derivatives Targeting the Onset and Progression of CRC with SRA, Molecular Docking, and ADMET Analyses. Molecules 2021; 26:molecules26113121. [PMID: 34071141 PMCID: PMC8197120 DOI: 10.3390/molecules26113121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 01/09/2023] Open
Abstract
The pathogenesis of colorectal cancer is a multifactorial process. Dysbiosis and the overexpression of COX-2 and LDHA are important effectors in the initiation and development of the disease through chromosomal instability, PGE2 biosynthesis, and induction of the Warburg effect, respectively. Herein, we report the in vitro testing of some new quinoxalinone and quinazolinone Schiff’s bases as: antibacterial, COX-2 and LDHA inhibitors, and anticolorectal agents on HCT-116 and LoVo cells. Moreover, molecular docking and SAR analyses were performed to identify the structural features contributing to the biological activities. Among the synthesized molecules, the most active cytotoxic agent, (6d) was also a COX-2 inhibitor. In silico ADMET studies predicted that (6d) would have high Caco-2 permeability, and %HIA (99.58%), with low BBB permeability, zero hepatotoxicity, and zero risk of sudden cardiac arrest, or mutagenicity. Further, (6d) is not a potential P-gp substrate, instead, it is a possible P-gpI and II inhibitor, therefore, it can prevent or reverse the multidrug resistance of the anticancer drugs. Collectively, (6d) can be considered as a promising lead suitable for further optimization to develop anti-CRC agents or glycoproteins inhibitors.
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68
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Lind C, Pandey P, Pastor RW, MacKerell AD. Functional Group Distributions, Partition Coefficients, and Resistance Factors in Lipid Bilayers Using Site Identification by Ligand Competitive Saturation. J Chem Theory Comput 2021; 17:3188-3202. [PMID: 33929848 DOI: 10.1021/acs.jctc.1c00089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules such as metabolites and drugs must pass through the membrane of the cell, a barrier primarily comprising phospholipid bilayers and embedded proteins. To better understand the process of passive diffusion, knowledge of the ability of various functional groups to partition across bilayers and the associated energetics would be of utility. In the present study, the site identification by ligand competitive saturation (SILCS) methodology has been applied to sample the distributions of a diverse set of chemical solutes representing the functional groups of small molecules across phospholipid bilayers composed of 0.9:0.1 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/cholesterol and a mixture of 0.52:0.18:0.3 1,2-dioleoyl-sn-glycero-3-phospho-l-serine/1,2-dioleoyl-sn-glycero-3-phosphocholine/cholesterol used in parallel artificial membrane permeability assay experiments. A combination of oscillating chemical potential grand canonical Monte Carlo and molecular dynamics in the SILCS simulations was applied to achieve solute sampling through the bilayers and surrounding aqueous environment from which the distribution of solutes and the functional groups they represent were obtained. Results show differential distribution of aliphatic versus aromatic groups with the former having increased sampling in the center of the bilayers versus in the region of the glycerol linker for the latter. Variations in the distribution of different polar groups are evident, with large differences between negative acetate and positive methylammonium with accumulation of the polar-neutral and acetate solutes above the bilayer head groups. Conversion of the distributions to absolute free energies allows for a detailed understanding of energetics of functional groups in different regions of the bilayers and for calculation of absolute free-energy profiles of multifunctional drug-like molecules across the bilayers from which partition coefficients and resistance factors suitable for insertion into the homogenous solubility-diffusion equation for calculation of permeability were obtained. Comparisons of the calculated bilayer/solution partition coefficients with 1-octanol/water experimental data for both drug-like molecules and the solutes show overall good agreement, validating the calculated distributions and associated absolute free-energy profiles.
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Affiliation(s)
- Christoffer Lind
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Poonam Pandey
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
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69
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Design and synthesis of novel tacrine-indole hybrids as potential multitarget-directed ligands for the treatment of Alzheimer's disease. Future Med Chem 2021; 13:785-804. [PMID: 33829876 DOI: 10.4155/fmc-2020-0184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The authors report on the synthesis and biological evaluation of new compounds whose structure combines tacrine and indole moieties. Tacrine-indole heterodimers were designed to inhibit cholinesterases and β-amyloid formation, and to cross the blood-brain barrier. The most potent new acetylcholinesterase inhibitors were compounds 3c and 4d (IC50 = 25 and 39 nM, respectively). Compound 3c displayed considerably higher selectivity for acetylcholinesterase relative to human plasma butyrylcholinesterase in comparison to compound 4d (selectivity index: IC50 [butyrylcholinesterase]/IC50 [acetylcholinesterase] = 3 and 0.6, respectively). Furthermore, compound 3c inhibited β-amyloid-dependent amyloid nucleation in the yeast-based prion nucleation assay and displayed no dsDNA destabilizing interactions with DNA. Compounds 3c and 4d displayed a high probability of crossing the blood-brain barrier. The results support the potential of 3c for future development as a dual-acting therapeutic agent in the prevention and/or treatment of Alzheimer's disease.
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70
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Hudáčová M, Hamuľaková S, Konkoľová E, Jendželovský R, Vargová J, Ševc J, Fedoročko P, Soukup O, Janočková J, Ihnatova V, Kučera T, Bzonek P, Novakova N, Jun D, Junova L, Korábečný J, Kuča K, Kožurková M. Synthesis of New Biscoumarin Derivatives, In Vitro Cholinesterase Inhibition, Molecular Modelling and Antiproliferative Effect in A549 Human Lung Carcinoma Cells. Int J Mol Sci 2021; 22:ijms22083830. [PMID: 33917200 PMCID: PMC8068036 DOI: 10.3390/ijms22083830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/29/2022] Open
Abstract
A series of novel C4-C7-tethered biscoumarin derivatives (12a–e) linked through piperazine moiety was designed, synthesized, and evaluated biological/therapeutic potential. Biscoumarin 12d was found to be the most effective inhibitor of both acetylcholinesterase (AChE, IC50 = 6.30 µM) and butyrylcholinesterase (BChE, IC50 = 49 µM). Detailed molecular modelling studies compared the accommodation of ensaculin (well-established coumarin derivative tested in phase I of clinical trials) and 12d in the human recombinant AChE (hAChE) active site. The ability of novel compounds to cross the blood–brain barrier (BBB) was predicted with a positive outcome for compound 12e. The antiproliferative effects of newly synthesized biscoumarin derivatives were tested in vitro on human lung carcinoma cell line (A549) and normal colon fibroblast cell line (CCD-18Co). The effect of derivatives on cell proliferation was evaluated by MTT assay, quantification of cell numbers and viability, colony-forming assay, analysis of cell cycle distribution and mitotic activity. Intracellular localization of used derivatives in A549 cells was confirmed by confocal microscopy. Derivatives 12d and 12e showed significant antiproliferative activity in A549 cancer cells without a significant effect on normal CCD-18Co cells. The inhibition of hAChE/human recombinant BChE (hBChE), the antiproliferative activity on cancer cells, and the ability to cross the BBB suggest the high potential of biscoumarin derivatives. Beside the treatment of cancer, 12e might be applicable against disorders such as schizophrenia, and 12d could serve future development as therapeutic agents in the prevention and/or treatment of Alzheimer’s disease.
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Affiliation(s)
- Monika Hudáčová
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia; (M.H.); (E.K.); (M.K.)
| | - Slávka Hamuľaková
- Department of Organic Chemistry, Institute of Chemical Sciences, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Kosice, Slovakia
- Correspondence:
| | - Eva Konkoľová
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia; (M.H.); (E.K.); (M.K.)
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Rastislav Jendželovský
- Department of Cellular Biology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia; (R.J.); (J.V.); (J.Š.); (P.F.)
| | - Jana Vargová
- Department of Cellular Biology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia; (R.J.); (J.V.); (J.Š.); (P.F.)
| | - Juraj Ševc
- Department of Cellular Biology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia; (R.J.); (J.V.); (J.Š.); (P.F.)
| | - Peter Fedoročko
- Department of Cellular Biology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia; (R.J.); (J.V.); (J.Š.); (P.F.)
| | - Ondrej Soukup
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic; (O.S.); (V.I.); (T.K.); (P.B.); (D.J.); (L.J.); (J.K.)
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; (J.J.); (N.N.); (K.K.)
| | - Jana Janočková
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; (J.J.); (N.N.); (K.K.)
| | - Veronika Ihnatova
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic; (O.S.); (V.I.); (T.K.); (P.B.); (D.J.); (L.J.); (J.K.)
| | - Tomáš Kučera
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic; (O.S.); (V.I.); (T.K.); (P.B.); (D.J.); (L.J.); (J.K.)
| | - Petr Bzonek
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic; (O.S.); (V.I.); (T.K.); (P.B.); (D.J.); (L.J.); (J.K.)
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; (J.J.); (N.N.); (K.K.)
| | - Nikola Novakova
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; (J.J.); (N.N.); (K.K.)
| | - Daniel Jun
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic; (O.S.); (V.I.); (T.K.); (P.B.); (D.J.); (L.J.); (J.K.)
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; (J.J.); (N.N.); (K.K.)
| | - Lucie Junova
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic; (O.S.); (V.I.); (T.K.); (P.B.); (D.J.); (L.J.); (J.K.)
| | - Jan Korábečný
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defense, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic; (O.S.); (V.I.); (T.K.); (P.B.); (D.J.); (L.J.); (J.K.)
- National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
| | - Kamil Kuča
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; (J.J.); (N.N.); (K.K.)
| | - Mária Kožurková
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia; (M.H.); (E.K.); (M.K.)
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; (J.J.); (N.N.); (K.K.)
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Polymerizable Matrix Metalloproteinases' Inhibitors with Potential Application for Dental Restorations. Biomedicines 2021; 9:biomedicines9040366. [PMID: 33807479 PMCID: PMC8065691 DOI: 10.3390/biomedicines9040366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/26/2021] [Indexed: 12/21/2022] Open
Abstract
Collagen cleavage by matrix metalloproteinase (MMP) is considered a major cause of dental resins long term failure. Most MMP inhibitors display significant toxicity and are unsuitable for dental resins’ applications. Here we report a study of a new class of inhibitors that display the unique property of being co-polymerizable with other vinyl compounds present in commercial dental resins, limiting their release and potential toxicity. Computational affinity towards the active site of different MMP-1; -2; -8; -9 and -13 of several compounds showed interesting properties and were synthesized. These free compounds were tested concerning their toxicity upon contact with two different cell types, with no substantial decrease in cell viability at high concentrations. Even so, compound’s safety can be further improved upon copolymerization with commercial dental resins, limiting their release.
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72
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Siwy CM, Delfing BM, Lockhart C, Smith AK, Klimov DK. Partitioning of Aβ Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer. J Phys Chem B 2021; 125:2658-2676. [PMID: 33656350 DOI: 10.1021/acs.jpcb.0c11253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used all-atom replica-exchange umbrella sampling molecular dynamics simulations to investigate the partitioning of the charged tetrapeptide KLVF and its neutral apolar counterpart VVIA into the blood-brain barrier (BBB)-mimetic bilayer. Our findings allowed us to reconstruct the partitioning mechanism for these two Aβ peptide fragments. Despite dissimilar sequences, their permeation shares significant common features. Computations of free energies and permeabilities show that partitioning of both peptides is highly unfavorable, ruling out passive transport. The peptides experience multiple rotational transitions within the bilayer and typically cause considerable lipid disorder and bilayer thinning. Near the bilayer midplane, they lose almost entirely their solvation shell and the interactions with the lipid headgroups. The peptides cause complex reorganization within the proximal bilayer region. Upon insertion, they induce striking cholesterol influx reversed by its depletion and the influx of DMPC when the peptides reach the midplane. The differences in partitioning mechanisms are due to the much higher polarity of KLVF peptide, the permeation of which is more unfavorable and which exclusively assumes vertical orientations within the bilayer. In contrast, VVIA positions itself flat between the leaflets, causing minor disorder and even thickening of the BBB-mimetic bilayer. Due to the high density of the cholesterol-rich BBB bilayer, the unfavorable work associated with the peptide insertion provides a significant, but not dominant, contribution to the partition free energy, which is still governed by dehydration and loss of peptide-headgroup interactions. Comparison with experiments indicates that KLVF and VVIA permeation is similar to that of proline tetrapeptide, mannitol, or cimetidine, all of which exhibit no passive transport.
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Affiliation(s)
- Christopher M Siwy
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Bryan M Delfing
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Christopher Lockhart
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Amy K Smith
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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73
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Fernandes E, Benfeito S, Cagide F, Gonçalves H, Bernstorff S, Nieder JB, Cd Real Oliveira ME, Borges F, Lúcio M. Lipid Nanosystems and Serum Protein as Biomimetic Interfaces: Predicting the Biodistribution of a Caffeic Acid-Based Antioxidant. Nanotechnol Sci Appl 2021; 14:7-27. [PMID: 33603350 PMCID: PMC7882595 DOI: 10.2147/nsa.s289355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/16/2021] [Indexed: 11/30/2022] Open
Abstract
Purpose AntiOxCIN3 is a novel mitochondriotropic antioxidant developed to minimize the effects of oxidative stress on neurodegenerative diseases. Prior to an investment in pre-clinical in vivo studies, it is important to apply in silico and biophysical cell-free in vitro studies to predict AntiOxCIN3 biodistribution profile, respecting the need to preserve animal health in accordance with the EU principles (Directive 2010/63/EU). Accordingly, we propose an innovative toolbox of biophysical studies and mimetic models of biological interfaces, such as nanosystems with different compositions mimicking distinct membrane barriers and human serum albumin (HSA). Methods Intestinal and cell membrane permeation of AntiOxCIN3 was predicted using derivative spectrophotometry. AntiOxCIN3 –HSA binding was evaluated by intrinsic fluorescence quenching, synchronous fluorescence, and dynamic/electrophoretic light scattering. Steady-state and time-resolved fluorescence quenching was used to predict AntiOxCIN3-membrane orientation. Fluorescence anisotropy, synchrotron small- and wide-angle X-ray scattering were used to predict lipid membrane biophysical impairment caused by AntiOxCIN3 distribution. Results and Discussion We found that AntiOxCIN3 has the potential to permeate the gastrointestinal tract. However, its biodistribution and elimination from the body might be affected by its affinity to HSA (>90%) and by its steady-state volume of distribution (VDSS=1.89± 0.48 L∙Kg−1). AntiOxCIN3 is expected to locate parallel to the membrane phospholipids, causing a bilayer stiffness effect. AntiOxCIN3 is also predicted to permeate through blood-brain barrier and reach its therapeutic target – the brain. Conclusion Drug interactions with biological interfaces may be evaluated using membrane model systems and serum proteins. This knowledge is important for the characterization of drug partitioning, positioning and orientation of drugs in membranes, their effect on membrane biophysical properties and the study of serum protein binding. The analysis of these interactions makes it possible to collect valuable knowledge on the transport, distribution, accumulation and, eventually, therapeutic impact of drugs which may aid the drug development process.
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Affiliation(s)
- Eduarda Fernandes
- Departamento de Física da Universidade do Minho, CF-UM-UP, Centro de Física das Universidades do Minho e Porto, Campus de Gualtar, Braga, 4710-057, Portugal.,Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Sofia Benfeito
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Fernando Cagide
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Sigrid Bernstorff
- Elettra-Sincrotrone Trieste S. C.p.A.,, Basovizza, Trieste, I-34149, Italy
| | - Jana B Nieder
- Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - M Elisabete Cd Real Oliveira
- Departamento de Física da Universidade do Minho, CF-UM-UP, Centro de Física das Universidades do Minho e Porto, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Fernanda Borges
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Marlene Lúcio
- Departamento de Física da Universidade do Minho, CF-UM-UP, Centro de Física das Universidades do Minho e Porto, Campus de Gualtar, Braga, 4710-057, Portugal.,CBMA, Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Campus de Gualtar, Braga 4710-057, Portugal
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74
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Carecho R, Carregosa D, Dos Santos CN. Low Molecular Weight (poly)Phenol Metabolites Across the Blood-Brain Barrier: The Underexplored Journey. Brain Plast 2021; 6:193-214. [PMID: 33782650 PMCID: PMC7990460 DOI: 10.3233/bpl-200099] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The world of (poly)phenols arising from dietary sources has been significantly amplified with the discovery of low molecular weight (LMW) (poly)phenol metabolites resulting from phase I and phase II metabolism and microbiota transformations. These metabolites, which are known to reach human circulation have been studied to further explore their interesting properties, especially regarding neuroprotection. Nevertheless, once in circulation, their distribution to target tissues, such as the brain, relies on their ability to cross the blood-brain barrier (BBB), one of the most controlled barriers present in humans. This represents a key step of an underexplored journey towards the brain. Present review highlights the main findings related to the ability of LMW (poly)phenol metabolites to reach the brain, considering different studies: in silico, in vitro, and in vivo. The mechanisms associated with the transport of these LMW (poly)phenol metabolites across the BBB and possible transporters will be discussed. Overall, the transport of these LMW (poly)phenol metabolites is crucial to elucidate which compounds may exert direct neuroprotective effects, so it is imperative to continue dissecting their potential to cross the BBB and the mechanisms behind their permeation.
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Affiliation(s)
- Rafael Carecho
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, Lisboa, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, Oeiras, Portugal
| | - Diogo Carregosa
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, Lisboa, Portugal.,iBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, Apartado 12, Oeiras, Portugal
| | - Cláudia Nunes Dos Santos
- CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, Lisboa, Portugal.,iBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, Apartado 12, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, Oeiras, Portugal
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75
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Chen G, Shen Z, Li Y. A machine-learning-assisted study of the permeability of small drug-like molecules across lipid membranes. Phys Chem Chem Phys 2021; 22:19687-19696. [PMID: 32830206 DOI: 10.1039/d0cp03243c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Study of the permeability of small organic molecules across lipid membranes plays a significant role in designing potential drugs in the field of drug discovery. Approaches to design promising drug molecules have gone through many stages, from experiment-based trail-and-error approaches, to the well-established avenue of the quantitative structure-activity relationship, and currently to the stage guided by machine learning (ML) and artificial intelligence techniques. In this work, we present a study of the permeability of small drug-like molecules across lipid membranes by two types of ML models, namely the least absolute shrinkage and selection operator (LASSO) and deep neural network (DNN) models. Molecular descriptors and fingerprints are used for featurization of organic molecules. Using molecular descriptors, the LASSO model uncovers that the electro-topological, electrostatic, polarizability, and hydrophobicity/hydrophilicity properties are the most important physical properties to determine the membrane permeability of small drug-like molecules. Additionally, with molecular fingerprints, the LASSO model suggests that certain chemical substructures can significantly affect the permeability of organic molecules, which closely connects to the identified main physical properties. Moreover, the DNN model using molecular fingerprints can help develop a more accurate mapping between molecular structures and their membrane permeability than LASSO models. Our results provide deep understanding of drug-membrane interactions and useful guidance for the inverse molecular design of drug-like molecules. Last but not least, while the current focus is on the permeability of drug-like molecules, the methodology of this work is general and can be applied for other complex physical chemistry problems to gain molecular insights.
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Affiliation(s)
- Guang Chen
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
| | - Zhiqiang Shen
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
| | - Ying Li
- Department of Mechanical Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
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76
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Salgin-Goksen U, Telli G, Erikci A, Dedecengiz E, Tel BC, Kaynak FB, Yelekci K, Ucar G, Gokhan-Kelekci N. New 2-Pyrazoline and Hydrazone Derivatives as Potent and Selective Monoamine Oxidase A Inhibitors. J Med Chem 2021; 64:1989-2009. [PMID: 33533632 DOI: 10.1021/acs.jmedchem.0c01504] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Thirty compounds having 1-[2-(5-substituted-2-benzoxazolinone-3-yl) acetyl]-3,5-disubstitutedphenyl-2-pyrazoline structure and nine compounds having N'-(1,3-disubstitutedphenylallylidene)-2-(5-substituted-2-benzoxazolinone-3-yl)acetohydrazide skeleton were synthesized and evaluated as monoamine oxidase (MAO) inhibitors. All of the compounds exhibited selective MAO-A inhibitor activity in the nanomolar or low micromolar range. The results of the molecular docking for hydrazone derivatives supported the in vitro results. Five compounds, 6 (0.008 μM, Selectivity Index (SI): 9.70 × 10-4), 7 (0.009 μM, SI: 4.55 × 10-5), 14 (0.001 μM, SI: 8.00 × 10-4), 21 (0.009 μM, SI: 1.37 × 10-5), and 42 (0.010 μM, SI: 5.40 × 10-6), exhibiting the highest inhibition and selectivity toward hMAO-A and nontoxic to hepatocytes were assessed for antidepressant activity as acute and subchronic in mice. All of these five compounds showed significant antidepressant activity with subchronic administration consistent with the increase in the brain serotonin levels and the compounds crossed the blood-brain barrier according to parallel artificial membrane permeation assay. Compounds 14, 21, and 42 exhibited an ex vivo MAO-A profile, which is highly consistent with the in vitro data.
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Affiliation(s)
- Umut Salgin-Goksen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey.,Turkish Medicines and Medical Devices Agency, Analyses and Control Laboratories, 06100 Ankara, Turkey
| | - Gokcen Telli
- Department of Pharmacology, Faculty of Pharmacy, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey
| | - Acelya Erikci
- Department of Biochemistry, Faculty of Pharmacy, Lokman Hekim University, 06510 Söğütözü, Ankara, Turkey
| | - Ezgi Dedecengiz
- Department of Physics Engineering, Faculty of Engineering, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Banu Cahide Tel
- Department of Pharmacology, Faculty of Pharmacy, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey
| | - F Betul Kaynak
- Department of Physics Engineering, Faculty of Engineering, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Kemal Yelekci
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083 Fatih, Istanbul, Turkey
| | - Gulberk Ucar
- Department of Biochemistry, Faculty of Pharmacy, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey
| | - Nesrin Gokhan-Kelekci
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey
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77
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Campora M, Canale C, Gatta E, Tasso B, Laurini E, Relini A, Pricl S, Catto M, Tonelli M. Multitarget Biological Profiling of New Naphthoquinone and Anthraquinone-Based Derivatives for the Treatment of Alzheimer's Disease. ACS Chem Neurosci 2021; 12:447-461. [PMID: 33428389 PMCID: PMC7880572 DOI: 10.1021/acschemneuro.0c00624] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
![]()
Two
series of naphthoquinone and anthraquinone derivatives decorated
with an aromatic/heteroaromatic chain have been synthesized and evaluated
as potential promiscuous agents capable of targeting different factors
playing a key role in Alzheimer’s disease (AD) pathogenesis.
On the basis of the in vitro biological profiling,
most of them exhibited a significant ability to inhibit amyloid aggregation,
PHF6 tau sequence aggregation, acetylcholinesterase (AChE), and monoamine
oxidase (MAO) B. In particular, naphthoquinone 2 resulted
as one of the best performing multitarget-directed ligand (MTDL) experiencing
a high potency profile in inhibiting β-amyloid (Aβ40) aggregation (IC50 = 3.2 μM), PHF6 tau
fragment (91% at 10 μM), AChE enzyme (IC50 = 9.2
μM) jointly with a remarkable inhibitory activity against MAO
B (IC50 = 7.7 nM). Molecular modeling studies explained
the structure–activity relationship (SAR) around the binding
modes of representative compound 2 in complex with hMAO
B and hAChE enzymes, revealing inhibitor/protein key contacts and
the likely molecular rationale for enzyme selectivity. Compound 2 was also demonstrated to be a strong inhibitor of Aβ42 aggregation, with potency comparable to quercetin. Accordingly,
atomic force microscopy (AFM) revealed that the most promising naphthoquinones 2 and 5 and anthraquinones 11 and 12 were able to impair Aβ42 fibrillation,
deconstructing the morphologies of its fibrillar aggregates. Moreover,
the same compounds exerted a moderate neuroprotective effect against
Aβ42 toxicity in primary cultures of cerebellar granule
cells. Therefore, our findings demonstrate that these molecules may
represent valuable chemotypes toward the development of promising
candidates for AD therapy.
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Affiliation(s)
- Marta Campora
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Claudio Canale
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Elena Gatta
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Bruno Tasso
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Annalisa Relini
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
| | - Marco Catto
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
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78
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Yee SM, Gillams RJ, McLain SE, Lorenz CD. Effects of lipid heterogeneity on model human brain lipid membranes. SOFT MATTER 2021; 17:126-135. [PMID: 33155582 DOI: 10.1039/d0sm01766c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cell membranes naturally contain a heterogeneous lipid distribution. However, homogeneous bilayers are commonly preferred and utilised in computer simulations due to their relative simplicity, and the availability of lipid force field parameters. Recently, experimental lipidomics data for the human brain cell membranes under healthy and Alzheimer's disease (AD) conditions were investigated, since disruption to the lipid composition has been implicated in neurodegenerative disorders, including AD [R. B. Chan et al., J. Biol. Chem., 2012, 287, 2678-2688]. In order to observe the effects of lipid complexity on the various bilayer properties, molecular dynamics simulations were used to study four membranes with increasing heterogeneity: a pure POPC membrane, a POPC and cholesterol membrane in a 1 : 1 ratio (POPC-CHOL), and to our knowledge, the first realistic models of a healthy brain membrane and an Alzheimer's diseased brain membrane. Numerous structural, interfacial, and dynamical properties, including the area per lipid, interdigitation, dipole potential, and lateral diffusion of the two simple models, POPC and POPC-CHOL, were analysed and compared to those of the complex brain models consisting of 27 lipid components. As the membranes gain heterogeneity, a number of alterations were found in the structural and dynamical properties, and more significant differences were observed in the lateral diffusion. Additionally, we observed snorkeling behaviour of the lipid tails that may play a role in the permeation of small molecules across biological membranes. In this work, atomistic description of realistic brain membrane models is provided, which can add insight towards the permeability and transport pathways of small molecules across these membrane barriers.
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Affiliation(s)
- Sze May Yee
- Department of Physics, King's College London, London WC2R 2LS, UK.
| | - Richard J Gillams
- School of Electronics and Computer Science, and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sylvia E McLain
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
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79
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Coimbra JTS, Feghali R, Ribeiro RP, Ramos MJ, Fernandes PA. The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer. RSC Adv 2020; 11:899-908. [PMID: 35423709 PMCID: PMC8693363 DOI: 10.1039/d0ra09995c] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
The number of hydrogen bond donors and acceptors is a fundamental molecular descriptor to predict the oral bioavailability of small drug candidates. In fact, the most widely used oral bioavailability rules (such as the Lipinsky's rule-of-five and the Veber rules) make use of this molecular descriptor. It is generally assumed that hydrogen bond donors and acceptors impact on passive diffusion across cell membranes, a fundamental event during drug absorption and distribution. Although the relationship between the number of these motifs and the probability of having good oral bioavailability has been studied and described for more than 20 years, little attention has been given to their spatial distribution in the molecule. In this paper, we used molecular dynamics to describe the effect of intramolecular hydrogen bonding on the passive diffusion of a small drug (piracetam) through a lipid membrane. The results indicated that the formation of an intramolecular hydrogen bond decreases the barrier for translocation by ca. 4 kcal mol-1 and increases the permeability of the tested molecule, partially compensating the desolvation penalty arising from the penetration of the drug into the biological membrane core. This effect was apparent in simulations where the formation of this interaction was prevented with the help of modified potentials, and in simulations with a similar compound to piracetam that was not able to form this intramolecular hydrogen bond due to a larger distance between the hydrogen bond donor and acceptor groups. These results were also supported by coarse-grained methods, which are becoming an important resource for sampling a larger chemical space of molecules, with reduced computational effort. Furthermore, entropy and enthalpy derived profiles were also obtained as the compounds translocated across the membrane, suggesting that, even though the process of formation of internal hydrogen bonds is entropically unfavorable, the enthalpic gain is such that the formation of these interactions is beneficial for the passive diffusion across cell membranes.
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Affiliation(s)
- João T S Coimbra
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
| | - Ralph Feghali
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
| | - Rui P Ribeiro
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
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80
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Naresh P, Selvaraj A, Shyam Sundar P, Murugesan S, Sathianarayanan S, Namboori P K K, Jubie S. Targeting a conserved pocket (n-octyl-β-D-glucoside) on the dengue virus envelope protein by small bioactive molecule inhibitors. J Biomol Struct Dyn 2020; 40:4866-4878. [PMID: 33345726 DOI: 10.1080/07391102.2020.1862707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dengue virus enters the cell by receptor-mediated endocytosis followed by a viral envelope (DENVE) protein-mediated membrane fusion. A small detergent molecule n-octyl-β-D-glucoside (βOG) occupies the hydrophobic pocket which is located in the hinge region plays a major role in the rearrangement. It has been reported that mutations occurred in this binding pocket lead to the alterations of pH threshold for fusion. In addition to this event, the protonation of histidine residues present in the hydrophobic pocket would also impart the conformational change of the E protein evidence this pocket as a promising target. The present study identified novel cinnamic acid analogs as significant blockers of the hydrophobic pocket through molecular modeling studies against DENVE. A library of seventy-two analogs of cinnamic acid was undertaken for the discovery process of DENV inhibitors. A Molecular docking study was used to analyze the binding mechanism between these compounds and DENV followed by ADMET prediction. Binding energies were predicted by the MMGBSA study. The Molecular dynamic simulation was utilized to confirm the stability of potential compound binding. The compounds CA and SCA derivatives have been tested against HSV-1 & 2 viruses. From the computational results, the compounds CA1, CA2, SCA 60, SCA 57, SCA 37, SCA 58, and SCA 14 exhibited favorable interaction energy. The compounds have in-vitro antiviral activity; the results clearly indicate that the compounds showed the activity against both the viruses (HSV-1 & HSV-2). Our study provides valuable information on the discovery of small molecules DENVE inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P Naresh
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Tamilnadu, India
| | - A Selvaraj
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Tamilnadu, India
| | - P Shyam Sundar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Tamilnadu, India
| | - S Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, BITS Pilani, Pilani Campus, Vidya Vihar, Pilani, Rajasthan, India
| | - S Sathianarayanan
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Ponekkara, Kochi, Kerala, India
| | - Krishnan Namboori P K
- Amrita Molecular Modeling and Synthesis (AMMAS) Research Lab, Amrita Vishwavidyapeetham, Coimbatore, Tamilnadu, India
| | - S Jubie
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Tamilnadu, India
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81
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Radchenko EV, Dyabina AS, Palyulin VA. Towards Deep Neural Network Models for the Prediction of the Blood-Brain Barrier Permeability for Diverse Organic Compounds. Molecules 2020; 25:molecules25245901. [PMID: 33322142 PMCID: PMC7763607 DOI: 10.3390/molecules25245901] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 11/24/2022] Open
Abstract
Permeation through the blood–brain barrier (BBB) is among the most important processes controlling the pharmacokinetic properties of drugs and other bioactive compounds. Using the fragmental (substructural) descriptors representing the occurrence number of various substructures, as well as the artificial neural network approach and the double cross-validation procedure, we have developed a predictive in silico LogBB model based on an extensive and verified dataset (529 compounds), which is applicable to diverse drugs and drug-like compounds. The model has good predictivity parameters (Q2=0.815, RMSEcv=0.318) that are similar to or better than those of the most reliable models available in the literature. Larger datasets, and perhaps more sophisticated network architectures, are required to realize the full potential of deep neural networks. The analysis of fragment contributions reveals patterns of influence consistent with the known concepts of structural characteristics that affect the BBB permeability of organic compounds. The external validation of the model confirms good agreement between the predicted and experimental LogBB values for most of the compounds. The model enables the evaluation and optimization of the BBB permeability of potential neuroactive agents and other drug compounds.
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82
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Ciura K, Ulenberg S, Kapica H, Kawczak P, Belka M, Bączek T. Assessment of blood–brain barrier permeability using micellar electrokinetic chromatography and P_VSA-like descriptors. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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83
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Lee BL, Kuczera K, Lee KH, Childs EW, Jas GS. Unassisted N-acetyl-phenylalanine-amide transport across membrane with varying lipid size and composition: kinetic measurements and atomistic molecular dynamics simulation. J Biomol Struct Dyn 2020; 40:1445-1460. [PMID: 33034537 DOI: 10.1080/07391102.2020.1827037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Biological membranes are essential to preserve structural integrity and regulate functional properties through the permeability of nutrients, pharmaceutical drugs, and neurotransmitters of a living cell. The movement of acetylated and amidated phenylalanine (NAFA) across 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane bilayers is investigated to probe physical transport. The rate of transport is measured experimentally applying parallel artificial membrane permeation assay (PAMPA). At the physiological temperature, 310 K, the measured time constants in the neutral pH were ∼6 h in DOPC and ∼3 h in POPC, while in a more acidic condition, at a pH 4.8, the time constants were ∼8 h in both lipids. Computationally, we have expanded our transport study of three aromatic dipeptides across a bilayer composed of DOPC18. In this study, we have examined the effects of lipid composition and bilayer size on the passive transport of NAFA by simulating the dipeptide in three different bilayers, with 50 DOPC lipids, 50 POPC lipids, and 40 POPC molecules. Specifically, atomistic molecular dynamics simulations with umbrella sampling were used to calculate the potential of mean force for the passive permeation of NAFA across the bilayers. Diffusion constants were then calculated by numerically solving the Smoluchowski equation. Permeability coefficients and mean first passage times were then calculated. Structural properties - Ramachandran plots, sidechain torsions, peptide insertion angles, radial distribution functions, and proximal peptide water molecules - were also examined to determine the effect of system size and lipid type. In terms of systems size, we observed a small decrease in the highest barrier of the potential of mean force and fewer sampled sidechain dihedral angle conformations with 40 versus 50 POPC lipids due to weaker membrane deformations within a smaller lipid bilayer. In terms of lipid type, DOPC contains two monounsaturated acyl chains compared to only one such acyl chain in POPC; therefore, DOPC bilayers are less ordered and more easily deformed, as seen by a much broader potential of mean force profile. The NAFA in DOPC lipid also transitioned to an internally hydrogen-bonded backbone conformation at lower membrane depths than in POPC. Similarly, as for other aromatic dipeptides, NAFA tends to insert into the membrane sidechain-first, remains mostly desolvated in the membrane center, and exhibits slow reorientations within the bilayer in both DOPC and POPC. With a joint experimental and computational study we have gained a new insight into the rate of transport and the underlying microscopic mechanism in different lipid bilayer conditions of the simplest hydrophobic aromatic dipeptide.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Brent L Lee
- Department of Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas, Lawrence, KS, USA.,Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Kyung-Hoon Lee
- Department of Biology, Chowan University, Murfreesboro, NC, USA
| | - Ed W Childs
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA, USA
| | - Gouri S Jas
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
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84
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Krämer A, Ghysels A, Wang E, Venable RM, Klauda JB, Brooks BR, Pastor RW. Membrane permeability of small molecules from unbiased molecular dynamics simulations. J Chem Phys 2020; 153:124107. [PMID: 33003739 PMCID: PMC7519415 DOI: 10.1063/5.0013429] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
Permeation of many small molecules through lipid bilayers can be directly observed in molecular dynamics simulations on the nano- and microsecond timescale. While unbiased simulations provide an unobstructed view of the permeation process, their feasibility for computing permeability coefficients depends on various factors that differ for each permeant. The present work studies three small molecules for which unbiased simulations of permeation are feasible within less than a microsecond, one hydrophobic (oxygen), one hydrophilic (water), and one amphiphilic (ethanol). Permeabilities are computed using two approaches: counting methods and a maximum-likelihood estimation for the inhomogeneous solubility diffusion (ISD) model. Counting methods yield nearly model-free estimates of the permeability for all three permeants. While the ISD-based approach is reasonable for oxygen, it lacks precision for water due to insufficient sampling and results in misleading estimates for ethanol due to invalid model assumptions. It is also demonstrated that simulations using a Langevin thermostat with collision frequencies of 1/ps and 5/ps yield oxygen permeabilities and diffusion constants that are lower than those using Nosé-Hoover by statistically significant margins. In contrast, permeabilities from trajectories generated with Nosé-Hoover and the microcanonical ensemble do not show statistically significant differences. As molecular simulations become more affordable and accurate, calculation of permeability for an expanding range of molecules will be feasible using unbiased simulations. The present work summarizes theoretical underpinnings, identifies pitfalls, and develops best practices for such simulations.
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Affiliation(s)
- Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - An Ghysels
- IBiTech - BioMMeda, Ghent University, Corneel Heymanslaan 10, Block B - Entrance 36, 9000 Gent, Belgium
| | - Eric Wang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, USA
| | - Richard M. Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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85
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Siwy CM, Delfing BM, Smith AK, Klimov DK. Partitioning of Benzoic Acid into 1,2-Dimyristoyl- sn-glycero-3-phosphocholine and Blood-Brain Barrier Mimetic Bilayers. J Chem Inf Model 2020; 60:4030-4046. [PMID: 32672960 DOI: 10.1021/acs.jcim.0c00590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using an all-atom explicit water model and replica exchange umbrella sampling simulations, we investigated the molecular mechanisms of benzoic acid partitioning into two model lipid bilayers. The first was formed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids, whereas the second was composed of an equimolar mixture of DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine, palmitoylsphingomyelin, and cholesterol to constitute a blood-brain barrier (BBB) mimetic bilayer. Comparative analysis of benzoic acid partitioning into the two bilayers has revealed qualitative similarities. Partitioning into the DMPC and BBB bilayers is thermodynamically favorable although insertion into the former lowers the free energy of benzoic acid by approximately an additional 1 kcal mol-1. The partitioning energetics for the two bilayers is also largely similar based on the balance of benzoic acid interactions with apolar fatty acid tails, polar lipid headgroups, and water. In both bilayers, benzoic acid retains a considerable number of residual water molecules until reaching the bilayer midplane where it experiences nearly complete dehydration. Upon insertion into the bilayers, benzoic acid undergoes several rotations primarily determined by the interactions with the lipid headgroups. Nonetheless, in addition to the depth of the free energy minimum, the BBB bilayer differs from the DMPC counterpart by a much deeper location of the free energy minimum and the appearance of a high free energy barrier and positioning of benzoic acid near the midplane. Furthermore, DMPC and BBB bilayers exhibit different structural responses to benzoic acid insertion. Taken together, the BBB mimetic bilayer is preferable for an accurate description of benzoic acid partitioning.
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Affiliation(s)
- Christopher M Siwy
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Bryan M Delfing
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Amy K Smith
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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86
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Bennett WFD, He S, Bilodeau CL, Jones D, Sun D, Kim H, Allen JE, Lightstone FC, Ingólfsson HI. Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning. J Chem Inf Model 2020; 60:5375-5381. [DOI: 10.1021/acs.jcim.0c00318] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- W. F. Drew Bennett
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
| | - Stewart He
- Global Security Computing Applications, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
| | - Camille L. Bilodeau
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
| | - Derek Jones
- Global Security Computing Applications, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
| | - Delin Sun
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
| | - Hyojin Kim
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
| | - Jonathan E. Allen
- Global Security Computing Applications, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
| | - Felice C. Lightstone
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
| | - Helgi I. Ingólfsson
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California, United States
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87
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Radaic A, Martins-de-Souza D. The state of the art of nanopsychiatry for schizophrenia diagnostics and treatment. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2020; 28:102222. [DOI: 10.1016/j.nano.2020.102222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/18/2020] [Accepted: 05/02/2020] [Indexed: 02/07/2023]
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88
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Martinotti C, Ruiz-Perez L, Deplazes E, Mancera RL. Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes. Chemphyschem 2020; 21:1486-1514. [PMID: 32452115 DOI: 10.1002/cphc.202000219] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
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Affiliation(s)
- Carlo Martinotti
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
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89
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Flieger J, Orzeł A, Kowalska-Kępczyńska A, Pizoń M, Trębacz H, Majerek D, Plech T, Płaziński W. Teicoplanin-Modified HPLC Column as a Source of Experimental Parameters for Prediction of the Anticonvulsant Activity of 1,2,4-Triazole-3-Thiones by the Regression Models. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E2650. [PMID: 32532041 PMCID: PMC7321613 DOI: 10.3390/ma13112650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 11/16/2022]
Abstract
The cell membrane is a complex system that consists of lipids, proteins, polysaccharides, and amphiphilic phospholipids. It plays an important role in ADME processes that are responsible for the final pharmaceutical effects of xenobiotics (bioavailability, activity). To study drug-membrane interaction at the molecular level, several high-performance liquid chromatography (HPLC) membrane model systems have been proposed which are mimicking mainly its lipid character. The aim of this work was to study interactions of new synthesized antiepileptic compounds of 4-alkyl-5-(3-chlorophenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione derivatives with Chirobiotic column containing glycoprotein ligand attached to the silica matrix. The affinity of the analytes to immobilized glycoprotein ligand was examined chromatographically in reversed-phase mode. The thermodynamics of interactions between bioactive compounds and teicoplanin was studied in terms of the van't Hoff linear relationship ln k vs. 1/T in the range of 5-45 °C. Change in enthalpy (ΔH°), change in entropy (ΔS°) and change in Gibbs free energy (ΔG°) were estimated utilizing graphical extrapolation and interpolation methods. The density functional theory (DFT) approach and docking simulations were used to get the molecular interpretation and prove the obtained experimental results. Cross-correlations of chromatographic and thermodynamic parameters with non-empirical topological and quantum chemical indices suggest that the polarizability of analytes appears to be responsible for the interactions of the tested molecules with teicoplanin and, ultimately, their retention on the column. Experimental and theoretical parameters were subjected to statistical analysis using regression models. Partial least squares (PLS) regression model showed the usefulness of the experimentally measured parameter φ0 (MeOH) to discriminate between anticonvulsant active and inactive 1,2,4-triazole-3-thione derivatives. Obtained results point out the usefulness of interaction of potential anticonvulsants with glycoprotein class of compounds to anticipate their activity.
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Affiliation(s)
- Jolanta Flieger
- Department of Analytical Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland;
| | - Anna Orzeł
- Faculty of Medicine, Medical University of Lublin, Aleje Racławickie 1, 20-059 Lublin, Poland;
| | - Anna Kowalska-Kępczyńska
- Department of Biochemical Diagnostics, Medical University of Lublin, Staszica 16, 20-081 Lublin, Poland;
| | - Magdalena Pizoń
- Department of Analytical Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland;
| | - Hanna Trębacz
- Chair and Department of Biophysics, Medical University of Lublin, Jaczewskiego 4, 20-090 Lublin, Poland;
| | - Dariusz Majerek
- Department of Applied Mathematics, University of Technology, Nadbystrzycka 38D, 20-618 Lublin, Poland;
| | - Tomasz Plech
- Department of Pharmacology, Faculty of Nursing and Health Sciences, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland;
| | - Wojciech Płaziński
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland;
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90
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Thai NQ, Theodorakis PE, Li MS. Fast Estimation of the Blood-Brain Barrier Permeability by Pulling a Ligand through a Lipid Membrane. J Chem Inf Model 2020; 60:3057-3067. [PMID: 32469527 PMCID: PMC7588033 DOI: 10.1021/acs.jcim.9b00834] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The blood–brain barrier (BBB)
is a physical barrier that
regulates the homeostasis of the neural microenvironment. A relative
estimate of the BBB permeability, which is important for drug design,
may be experimentally provided by the logBB (the blood–brain
concentration ratio) and the logPS (permeability–surface-area
product), while many computational methods aim to identify key properties
that correlate well with these quantities. Although currently existing
computational methods (e.g., quantitative structure activity relation)
have made a significant contribution in screening various compounds
that could potentially translocate through the BBB, they are unable
to provide a physical explanation of the underlying processes and
they can often be computationally demanding. Here, we use steered
molecular dynamics simulation to estimate the BBB permeability of
various compounds on the basis of simple lipid–membrane models
by computing the nonequilibrium work, Wneq, produced by pulling the compounds through the membrane. We found
that the values of Wneq correlate remarkably
well with logBB and logPS for a range of compounds and different membrane
types and pulling speeds, independently of the choice of force field.
Moreover, our results provide insight into the role of hydrogen bonds,
the energetic barriers, and the forces exerted on the ligands during
their pulling. Our method is computationally easy to implement and
fast. Therefore, we anticipate that it could provide a reliable prescreening
tool for estimating the relative permeability of the BBB to various
substances.
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Affiliation(s)
- Nguyen Quoc Thai
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam.,Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City 870000, Dong Thap, Vietnam
| | | | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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91
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Çevik UA, Osmaniye D, Levent S, Sağlik BN, Çavuşoğlu BK, Özkay Y, Kaplancikl ZA. Synthesis and characterization of a new series of thiadiazole derivatives as potential anticancer agents. HETEROCYCL COMMUN 2020. [DOI: 10.1515/hc-2020-0002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
AbstractCancer is one of the most common causes of death in the world. Despite the importance of combating cancer in healthcare systems and research centers, toxicity in normal tissues and the low efficiency of anticancer drugs are major problems in chemotherapy. Nowadays the aim of many medical research projects is to discover new safer and more effective anticancer agents. 1,3,4-Thiadiazole compounds are important fragments in medicinal chemistry because of their wide range of biological activities, including anticancer activities. The aim of this study was to determine the capacity of newly synthesized 1,3,4-thiadiazole compounds as chemotherapeutic agents. The structures of the obtained compounds were elucidated using 1H-NMR, 13C-NMR and mass spectrometry. Although the thiadiazole derivatives did not prove to be significantly cytotoxic to the tumour tissue cultures, compound 4i showed activity against the C6 rat brain cancer cell line (IC50 0.097 mM) at the tested concentrations.
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Affiliation(s)
- Ulviye Acar Çevik
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
- Anadolu University, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, 26470, Eskişehir, Turkey
| | - Derya Osmaniye
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
- Anadolu University, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, 26470, Eskişehir, Turkey
| | - Serkan Levent
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
- Anadolu University, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, 26470, Eskişehir, Turkey
| | - Begüm Nurpelin Sağlik
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
- Anadolu University, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, 26470, Eskişehir, Turkey
| | - Betül Kaya Çavuşoğlu
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
- Anadolu University, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, 26470, Eskişehir, Turkey
| | - Yusuf Özkay
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
- Anadolu University, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, 26470, Eskişehir, Turkey
| | - Zafer Asım Kaplancikl
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
- Anadolu University, Faculty of Pharmacy, Doping and Narcotic Compounds Analysis Laboratory, 26470, Eskişehir, Turkey
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92
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Hoffmann C, Centi A, Menichetti R, Bereau T. Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations. Sci Data 2020; 7:51. [PMID: 32054852 PMCID: PMC7018832 DOI: 10.1038/s41597-020-0391-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/22/2020] [Indexed: 02/07/2023] Open
Abstract
The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes-exhaustively enumerating all 105 CG dimers-and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability.
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Affiliation(s)
| | - Alessia Centi
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Roberto Menichetti
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- Physics Department, University of Trento, 38123, Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, 38123, Trento, Italy
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany.
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93
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Janicka M, Sztanke M, Sztanke K. Predicting the Blood-Brain Barrier Permeability of New Drug-Like Compounds via HPLC with Various Stationary Phases. Molecules 2020; 25:molecules25030487. [PMID: 31979316 PMCID: PMC7037052 DOI: 10.3390/molecules25030487] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 11/30/2022] Open
Abstract
The permeation of the blood-brain barrier is a very important consideration for new drug candidate molecules. In this research, the reversed-phase liquid chromatography with different columns (Purosphere RP-18e, IAM.PC.DD2 and Cosmosil Cholester) was used to predict the penetration of the blood-brain barrier by 65 newly-synthesized drug-like compounds. The linear free energy relationships (LFERs) model (log BB = c + eE + sS + aA + bB + vV) was established for a training set of 23 congeneric biologically active azole compounds with known experimental log BB (BB = Cblood/Cbrain) values (R2 = 0.9039). The reliability and predictive potency of the model were confirmed by leave-one-out cross validation as well as leave-50%-out cross validation. Multiple linear regression (MLR) was used to develop the quantitative structure-activity relationships (QSARs) to predict the log BB values of compounds that were tested, taking into account the chromatographic lipophilicity (log kw), polarizability and topological polar surface area. The excellent statistics of the developed MLR equations (R2 > 0.8 for all columns) showed that it is possible to use the HPLC technique and retention data to produce reliable blood-brain barrier permeability models and to predict the log BB values of our pharmaceutically important molecules.
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Affiliation(s)
- Małgorzata Janicka
- Department of Physical Chemistry, Faculty of Chemistry, Institute of Chemical Science, Maria Curie-Skłodowska University, Maria Curie-Skłodowska Sq. 3, 20-031 Lublin, Poland;
| | - Małgorzata Sztanke
- Chair and Department of Medical Chemistry, Medical University, 4A Chodźki Street, 20-093 Lublin, Poland
- Correspondence: (M.S.); (K.S.); Tel.: +48-814486195 (M.S. & K.S.)
| | - Krzysztof Sztanke
- Laboratory of Bioorganic Synthesis and Analysis, Chair and Department of Medical Chemistry, Medical University, 4A Chodźki Street, 20-093 Lublin, Poland
- Correspondence: (M.S.); (K.S.); Tel.: +48-814486195 (M.S. & K.S.)
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94
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Kecel-Gunduz S, Budama-Kilinc Y, Cakir-Koc R, Zorlu T, Bicak B, Kokcu Y, E Ozel A, Akyuz S. In Silico design of AVP (4-5) peptide and synthesis, characterization and in vitro activity of chitosan nanoparticles. ACTA ACUST UNITED AC 2020; 28:139-157. [PMID: 31942695 DOI: 10.1007/s40199-019-00325-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 12/23/2019] [Indexed: 02/03/2023]
Abstract
BACKGROUND Arginine-vasopressin (AVP) is a neuropeptide and provides learning and memory modulation. The AVP (4-5) dipeptide corresponds to the N-terminal fragment of the major vasopressin metabolite AVP (4-9), has a neuroprotective effect and used in the treatment of Alzheimer's and Parkinson's disease. METHODS The main objective of the present study is to evaluate the molecular mechanism of AVP (4-5) dipeptide and to develop and synthesize chitosan nanoparticle formulation using modified version of ionic gelation method, to increase drug effectiveness. For peptide loaded chitosan nanoparticles, the synthesized experiment medium was simulated for the first time by molecular dynamics method and used to determine the stability of the peptide, and the binding mechanism to protein (HSP70) was also investigated by molecular docking calculations. A potential pharmacologically features of the peptide was also characterized by ADME (Absorption, Distribution, Metabolism and Excretion) analysis. The characterization, in vitro release study, encapsulation efficiency and loading capacity of the peptide loaded chitosan nanoparticles (CS NPs) were performed by Dynamic Light Scattering (DLS), UV-vis absorption (UV), Scanning Electron Microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy techniques. Additionally, in vitro cytotoxicity of the peptide on human neuroblastoma cells (SH-SY5Y) was examined with XTT assay and the statistical analysis was evaluated. RESULTS The results showed that; hydrodynamic size, zeta potential and polydispersity index (PdI) of the peptide-loaded CS NPs were 167.6 nm, +13.2 mV, and 0.211, respectively. In vitro release study of the peptide-loaded CS NPs showed that 17.23% of the AVP (4-5)-NH2 peptide was released in the first day, while 61.13% of AVP (4-5)-NH2 peptide was released in the end of the 10th day. The encapsulation efficiency and loading capacity were 99% and 10%, respectively. According to the obtained results from XTT assay, toxicity on SHSY-5Y cells in the concentration from 0.01 μg/μL to 30 μg/μL were evaluated and no toxicity was observed. Also, neuroprotective effect was showed against H2O2 treatment. CONCLUSION The experimental medium of peptide-loaded chitosan nanoparticles was created for the first time with in silico system and the stability of the peptide in this medium was carried out by molecular dynamics studies. The binding sites of the peptide with the HSP70 protein were determined by molecular docking analysis. The size and morphology of the prepared NPs capable of crossing the blood-brain barrier (BBB) were monitored using DLS and SEM analyses, and the encapsulation efficiency and loading capacity were successfully performed with UV Analysis. In vitro release studies and in vitro cytotoxicity analysis on SHSY-5Y cell lines of the peptide were conducted for the first time. Grapical abstract.
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Affiliation(s)
- Serda Kecel-Gunduz
- Physics Department, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.
| | - Yasemin Budama-Kilinc
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, 34220, Istanbul, Turkey
| | - Rabia Cakir-Koc
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, 34220, Istanbul, Turkey
| | - Tolga Zorlu
- Graduate School of Natural and Applied Science, Yildiz Technical University, 34220, Istanbul, Turkey.,Department of Physical Chemistry and EMaS, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Bilge Bicak
- Physics Department, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.,Institute of Graduate Studies in Sciences, Istanbul University, 34452, Istanbul, Turkey
| | - Yagmur Kokcu
- Institute of Graduate Studies in Sciences, Istanbul University, 34452, Istanbul, Turkey
| | - Aysen E Ozel
- Physics Department, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey
| | - Sevim Akyuz
- Physics Department, Science and Letters Faculty, Istanbul Kultur University, Atakoy Campus, Bakirkoy, 34156, Istanbul, Turkey
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95
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Pre-Treatment with Laminarin Protects Hippocampal CA1 Pyramidal Neurons and Attenuates Reactive Gliosis Following Transient Forebrain Ischemia in Gerbils. Mar Drugs 2020; 18:md18010052. [PMID: 31940961 PMCID: PMC7024340 DOI: 10.3390/md18010052] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/19/2022] Open
Abstract
Transient brain ischemia triggers selective neuronal death/loss, especially in vulnerable regions of the brain including the hippocampus. Laminarin, a polysaccharide originating from brown seaweed, has various pharmaceutical properties including an antioxidant function. To the best of our knowledge, few studies have been conducted on the protective effects of laminarin against ischemic injury induced by ischemic insults. In this study, we histopathologically investigated the neuroprotective effects of laminarin in the Cornu Ammonis 1 (CA1) field of the hippocampus, which is very vulnerable to ischemia-reperfusion injury, following transient forebrain ischemia (TFI) for five minutes in gerbils. The neuroprotective effect was examined by cresyl violet staining, Fluoro-Jade B histofluorescence staining and immunohistochemistry for neuronal-specific nuclear protein. Additionally, to study gliosis (glial changes), we performed immunohistochemistry for glial fibrillary acidic protein to examine astrocytes, and ionized calcium-binding adaptor molecule 1 to examine microglia. Furthermore, we examined alterations in pro-inflammatory M1 microglia by using double immunofluorescence. Pretreatment with 10 mg/kg laminarin failed to protect neurons in the hippocampal CA1 field and did not attenuate reactive gliosis in the field following TFI. In contrast, pretreatment with 50 or 100 mg/kg laminarin protected neurons, attenuated reactive gliosis and reduced pro-inflammatory M1 microglia in the CA1 field following TFI. Based on these results, we firmly propose that 50 mg/kg laminarin can be strategically applied to develop a preventative against injuries following cerebral ischemic insults.
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96
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Juračka J, Šrejber M, Melíková M, Bazgier V, Berka K. MolMeDB: Molecules on Membranes Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5523873. [PMID: 31250015 PMCID: PMC6597476 DOI: 10.1093/database/baz078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/16/2022]
Abstract
Biological membranes act as barriers or reservoirs for many compounds within the human body. As such, they play an important role in pharmacokinetics and pharmacodynamics of drugs and other molecular species. Until now, most membrane/drug interactions have been inferred from simple partitioning between octanol and water phases. However, the observed variability in membrane composition and among compounds themselves stretches beyond such simplification as there are multiple drug–membrane interactions. Numerous experimental and theoretical approaches are used to determine the molecule–membrane interactions with variable accuracy, but there is no open resource for their critical comparison. For this reason, we have built Molecules on Membranes Database (MolMeDB), which gathers data about over 3600 compound–membrane interactions including partitioning, penetration and positioning. The data have been collected from scientific articles published in peer-reviewed journals and complemented by in-house calculations from high-throughput COSMOmic approach to set up a baseline for further comparison. The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method or dataset and we offer the collected data openly for further reuse and we are open to further additions. MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions.
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Affiliation(s)
- Jakub Juračka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Martin Šrejber
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michaela Melíková
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Václav Bazgier
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
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97
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El-Sayed NF, El-Hussieny M, Ewies EF, Fouad MA, Boulos LS. New phosphazine and phosphazide derivatives as multifunctional ligands targeting acetylcholinesterase and β-Amyloid aggregation for treatment of Alzheimer's disease. Bioorg Chem 2019; 95:103499. [PMID: 31838287 DOI: 10.1016/j.bioorg.2019.103499] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022]
Abstract
Phosphazine and phosphazide derivatives are described herein as a new class of selective and potent acetylcholinesterase (AChE) inhibitors and β-amyloid aggregation inhibitors. Phosphazines (5-7) were synthesized smoothly via a redox-condensation reaction of 1,2-bis(diphenylphosphino)ethane with different amines derivatives in the presence of dialkyl azodicarboxylate (Staudinger reaction) while phosphazides (8) via electrophilic attack of azido derivatives. Structures of the synthesized compounds were justified on the basis of compatible elementary and spectroscopic analyses. All the compounds were evaluated for their acetylcholinesterase inhibitory activity. The most three potent compounds (5b-c and 8b) showing AChE IC50 values (29.85-34.96 nM) comparable to that of donepezil (34.42 nM) were subjected to further investigation by testing their butyrylcholinesterase, MMP-2 and self-induced Aβ aggregation inhibition activity. Especially, the coumarin phosphazide derivative (8b) presented the best AChE inhibition selectivity index (IC50 = 34.96 nM, AChE/BuChE; 3.81) together with good inhibition ability against MMP-2 (IC50 = 441.33 nM) and self-induced Aβ1-42 aggregation (IC50 = 337.77 nM). In addition, the inhibition of metal-induced Aβ aggregation by 8b was confirmed by thioflavine T fluorescence. The most potent effect of 8b was observed on the Zn2+-induced Aβ42 aggregation. Kinetic study of compound 8b suggested it to be a competitive AChE inhibitor. Also, it specifically chelates metal and is predicted to be permeable to BBB. It also possesses low toxicity on SH-SY5Y neuroblastoma cells with a safety index of 15.37. In addition, it was demonstrated that compound 8b can improve the cognitive impairment of scopolamine-induced model in mice with % alternations and transfer latency time comparable to that of donepezil. Also, a docking study was carried out and it was in accordance with the in vitro results. These promising in vitro and in vivo findings highlight compound 8b as a possible drug candidate in searching for new multifunctional AD drugs.
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Affiliation(s)
- Naglaa F El-Sayed
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 ElBohouth St., (Former El Tahrir) Dokki, P.O. 12622, Giza, Egypt
| | - Marwa El-Hussieny
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 ElBohouth St., (Former El Tahrir) Dokki, P.O. 12622, Giza, Egypt
| | - Ewies F Ewies
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 ElBohouth St., (Former El Tahrir) Dokki, P.O. 12622, Giza, Egypt.
| | - Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt.
| | - Leila S Boulos
- Organometallic and Organometalloid Chemistry Department, National Research Centre, 33 ElBohouth St., (Former El Tahrir) Dokki, P.O. 12622, Giza, Egypt
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98
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Wood I, Fabian L, Moglioni A, Cabeça LF, de Paula E, Pickholz M. Combining nuclear magnetic resonance with molecular dynamics simulations to address sumatriptan interaction with model membranes. Chem Phys Lipids 2019; 225:104792. [DOI: 10.1016/j.chemphyslip.2019.104792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/21/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
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99
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Rajagopal N, Irudayanathan FJ, Nangia S. Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface. Int J Mol Sci 2019; 20:E5583. [PMID: 31717316 PMCID: PMC6888702 DOI: 10.3390/ijms20225583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
The selectivity of the blood-brain barrier (BBB) is primarily maintained by tight junctions (TJs), which act as gatekeepers of the paracellular space by blocking blood-borne toxins, drugs, and pathogens from entering the brain. The BBB presents a significant challenge in designing neurotherapeutics, so a comprehensive understanding of the TJ architecture can aid in the design of novel therapeutics. Unraveling the intricacies of TJs with conventional experimental techniques alone is challenging, but recently developed computational tools can provide a valuable molecular-level understanding of TJ architecture. We employed the computational methods toolkit to investigate claudin-5, a highly expressed TJ protein at the BBB interface. Our approach started with the prediction of claudin-5 structure, evaluation of stable dimer conformations and nanoscale assemblies, followed by the impact of lipid environments, and posttranslational modifications on these claudin-5 assemblies. These led to the study of TJ pores and barriers and finally understanding of ion and small molecule transport through the TJs. Some of these in silico, molecular-level findings, will need to be corroborated by future experiments. The resulting understanding can be advantageous towards the eventual goal of drug delivery across the BBB. This review provides key insights gleaned from a series of state-of-the-art nanoscale simulations (or computational nanoscopy studies) performed on the TJ architecture.
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Affiliation(s)
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
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100
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Design of novel monoamine oxidase-B inhibitors based on piperine scaffold: Structure-activity-toxicity, drug-likeness and efflux transport studies. Eur J Med Chem 2019; 185:111770. [PMID: 31711793 DOI: 10.1016/j.ejmech.2019.111770] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/06/2019] [Accepted: 10/06/2019] [Indexed: 02/02/2023]
Abstract
Piperine has been associated with neuroprotective effects and monoamine oxidase (MAO) inhibition, thus being an attractive scaffold to develop new antiparkinsonian agents. Accordingly, we prepared a small library of piperine derivatives and screened the inhibitory activities towards human MAO isoforms (hMAO-A and hMAO-B). Structure-activity relationship (SAR) studies pointed out that the combination of α-cyano and benzyl ester groups increased both potency and selectivity towards hMAO-B. Kinetic experiments with compounds 7, 10 and 15 indicated a competitive hMAO-B inhibition mechanism. Compounds 15 and 16, at 10 μM, caused a small but significant decrease in P-gp efflux activity in Caco-2 cells. Compound 15 stands out as the most potent piperine-based hMAO-B inhibitor (IC50 = 47.4 nM), displaying favourable drug-like properties and a broad safety window. Compound 15 is thus a suitable candidate for lead optimization and the development of multitarget-directed ligands.
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