1
|
Gaur V, Kumar N, Vyas A, Chowdhury D, Singh J, Bera S. Identification of potential inhibitors against Escherichia coli Mur D enzyme to combat rising drug resistance: an in-silico approach. J Biomol Struct Dyn 2023:1-11. [PMID: 38149858 DOI: 10.1080/07391102.2023.2297007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Indiscriminate use of anti-microbial agents has resulted in the inception, frequency, and spread of antibiotic resistance among targeted bacterial pathogens and the commensal flora. Mur enzymes, playing a crucial role in cell-wall synthesis, are one of the most appropriate targets for developing novel inhibitors against antibiotic-resistant bacterial pathogens. In the present study, in-silico high-throughput virtual (HTVS) and Standard-Precision (SP) screening was carried out with 0.3 million compounds from several small-molecule libraries against the E. coli Mur D enzyme (PDB ID 2UUP). The docked complexes were further subjected to extra-precision (XP) docking calculations, and highest Glide-score compound was further subjected to molecular simulation studies. The top six virtual hits (S1-S6) displayed a glide score (G-score) within the range of -9.013 to -7.126 kcal/mol and compound S1 was found to have the highest stable interactions with the Mur D enzyme (2UUP) of E. coli. The stability of compound S1 with the Mur D (2UUP) complex was validated by a 100-ns molecular dynamics simulation. Binding free energy calculation by the MM-GBSA strategy of the S1-2UUP (Mur D) complex established van der Waals, hydrogen bonding, lipophilic, and Coulomb energy terms as significant favorable contributors for ligand binding. The final lead molecules were subjected to ADMET predictions to study their pharmacokinetic properties and displayed promising results, except for certain modifications required to improve QPlogHERG values. So, the compounds screened against the Mur D enzyme can be further studied as preparatory points for in-vivo studies to develop potential drugs. HIGHLIGHTSE.coli is a common cause of urinary tract infections.E.coli MurD enzyme is a suitable target for drug development.Novel inhibitors against E.coli MurD enzyme were identified.Molecular dynamics studies identified in-silico potential of identified compound.ADMET predictions and Lipinski's rule of five studies showed promising results.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Vinita Gaur
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles' University, Udaipur, Rajasthan, India
| | - Ashish Vyas
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Debabrata Chowdhury
- School of Medicine - Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Joginder Singh
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Surojit Bera
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| |
Collapse
|
2
|
Wanat K, Brzezińska E. Chromatographic Data in Statistical Analysis of BBB Permeability Indices. MEMBRANES 2023; 13:623. [PMID: 37504989 PMCID: PMC10384010 DOI: 10.3390/membranes13070623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 07/29/2023]
Abstract
Blood-brain barrier (BBB) permeability is an essential phenomena when considering the treatment of neurological disorders as well as in the case of central nervous system (CNS) adverse effects caused by peripherally acting drugs. The presented work contains statistical analyses and the correlation assessment of the analyzed group of active pharmaceutical ingredients (APIs) with their BBB-permeability data collected from the literature (such as computational log BB; Kp,uu,brain, and CNS+/- groups). A number of regression models were constructed in order to observe the connections between the APIs' physicochemical properties in combination with their retention data from the chromatographic experiments (TLC and HPLC) and the indices of bioavailability in the CNS. Conducted analyses confirm that descriptors significant in BBB permeability modeling are hydrogen bond acceptors and donors, physiological charge, or energy of the lowest unoccupied molecular orbital. These molecular descriptors were the basis, along with the chromatographic data from the TLC in log BB regression analyses. Normal-phase TLC data showed a significant contribution to the creation of the log BB regression model using the multiple linear regression method. The model using them showed a good predictive value at the level of R2 = 0.87. Models for Kp,uu,brain resulted in lower statistics: R2 = 0.56 for the group of 23 APIs with the participation of k IAM.
Collapse
Affiliation(s)
- Karolina Wanat
- Department of Analytical Chemistry, Faculty of Pharmacy, Medical University of Lodz, 90-419 Lodz, Poland
| | - Elżbieta Brzezińska
- Department of Analytical Chemistry, Faculty of Pharmacy, Medical University of Lodz, 90-419 Lodz, Poland
| |
Collapse
|
3
|
Karolina W, Agata R, Elżbieta B. Computational Approach to Drug Penetration across the Blood-Brain and Blood-Milk Barrier Using Chromatographic Descriptors. Cells 2023; 12:cells12030421. [PMID: 36766764 PMCID: PMC9913351 DOI: 10.3390/cells12030421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Drug penetration through biological barriers is an important aspect of pharmacokinetics. Although the structure of the blood-brain and blood-milk barriers is different, a connection can be found in the literature between drugs entering the central nervous system (CNS) and breast milk. This study was created to reveal such a relationship with the use of statistical modelling. The basic physicochemical properties of 37 active pharmaceutical compounds (APIs) and their chromatographic retention data (TLC and HPLC) were incorporated into calculations as molecular descriptors (MDs). Chromatography was performed in a thin layer format (TLC), where the plates were impregnated with bovine serum albumin to mimic plasma protein binding. Two columns were used in high performance liquid chromatography (HPLC): one with immobilized human serum albumin (HSA), and the other containing an immobilized artificial membrane (IAM). Statistical methods including multiple linear regression (MLR), cluster analysis (CA) and random forest regression (RF) were performed with satisfactory results: the MLR model explains 83% of the independent variable variability related to CNS bioavailability; while the RF model explains up to 87%. In both cases, the parameter related to breast milk penetration was included in the created models. A significant share of reversed-phase TLC retention values was also noticed in the RF model.
Collapse
|
4
|
Faramarzi S, Kim MT, Volpe DA, Cross KP, Chakravarti S, Stavitskaya L. Development of QSAR models to predict blood-brain barrier permeability. Front Pharmacol 2022; 13:1040838. [PMID: 36339562 PMCID: PMC9633177 DOI: 10.3389/fphar.2022.1040838] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/10/2022] [Indexed: 07/29/2023] Open
Abstract
Assessing drug permeability across the blood-brain barrier (BBB) is important when evaluating the abuse potential of new pharmaceuticals as well as developing novel therapeutics that target central nervous system disorders. One of the gold-standard in vivo methods for determining BBB permeability is rodent log BB; however, like most in vivo methods, it is time-consuming and expensive. In the present study, two statistical-based quantitative structure-activity relationship (QSAR) models were developed to predict BBB permeability of drugs based on their chemical structure. The in vivo BBB permeability data were harvested for 921 compounds from publicly available literature, non-proprietary drug approval packages, and University of Washington's Drug Interaction Database. The cross-validation performance statistics for the BBB models ranged from 82 to 85% in sensitivity and 80-83% in negative predictivity. Additionally, the performance of newly developed models was assessed using an external validation set comprised of 83 chemicals. Overall, performance of individual models ranged from 70 to 75% in sensitivity, 70-72% in negative predictivity, and 78-86% in coverage. The predictive performance was further improved to 93% in coverage by combining predictions across the two software programs. These new models can be rapidly deployed to predict blood brain barrier permeability of pharmaceutical candidates and reduce the use of experimental animals.
Collapse
Affiliation(s)
- Sadegh Faramarzi
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, United States
| | - Marlene T. Kim
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, United States
| | - Donna A. Volpe
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, United States
| | | | | | - Lidiya Stavitskaya
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, United States
| |
Collapse
|
5
|
de Oliveira ECL, da Costa KS, Taube PS, Lima AH, Junior CDSDS. Biological Membrane-Penetrating Peptides: Computational Prediction and Applications. Front Cell Infect Microbiol 2022; 12:838259. [PMID: 35402305 PMCID: PMC8992797 DOI: 10.3389/fcimb.2022.838259] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/21/2022] [Indexed: 12/14/2022] Open
Abstract
Peptides comprise a versatile class of biomolecules that present a unique chemical space with diverse physicochemical and structural properties. Some classes of peptides are able to naturally cross the biological membranes, such as cell membrane and blood-brain barrier (BBB). Cell-penetrating peptides (CPPs) and blood-brain barrier-penetrating peptides (B3PPs) have been explored by the biotechnological and pharmaceutical industries to develop new therapeutic molecules and carrier systems. The computational prediction of peptides’ penetration into biological membranes has been emerged as an interesting strategy due to their high throughput and low-cost screening of large chemical libraries. Structure- and sequence-based information of peptides, as well as atomistic biophysical models, have been explored in computer-assisted discovery strategies to classify and identify new structures with pharmacokinetic properties related to the translocation through biomembranes. Computational strategies to predict the permeability into biomembranes include cheminformatic filters, molecular dynamics simulations, artificial intelligence algorithms, and statistical models, and the choice of the most adequate method depends on the purposes of the computational investigation. Here, we exhibit and discuss some principles and applications of these computational methods widely used to predict the permeability of peptides into biomembranes, exhibiting some of their pharmaceutical and biotechnological applications.
Collapse
Affiliation(s)
- Ewerton Cristhian Lima de Oliveira
- Institute of Technology, Federal University of Pará, Belém, Brazil
- *Correspondence: Kauê Santana da Costa, ; Ewerton Cristhian Lima de Oliveira,
| | - Kauê Santana da Costa
- Laboratory of Computational Simulation, Institute of Biodiversity, Federal University of Western Pará, Santarém, Brazil
- *Correspondence: Kauê Santana da Costa, ; Ewerton Cristhian Lima de Oliveira,
| | - Paulo Sérgio Taube
- Laboratory of Computational Simulation, Institute of Biodiversity, Federal University of Western Pará, Santarém, Brazil
| | - Anderson H. Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | | |
Collapse
|
6
|
Liu L, Zhang L, Feng H, Li S, Liu M, Zhao J, Liu H. Prediction of the Blood-Brain Barrier (BBB) Permeability of Chemicals Based on Machine-Learning and Ensemble Methods. Chem Res Toxicol 2021; 34:1456-1467. [PMID: 34047182 DOI: 10.1021/acs.chemrestox.0c00343] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ability of chemicals to enter the blood-brain barrier (BBB) is a key factor for central nervous system (CNS) drug development. Although many models for BBB permeability prediction have been developed, they have insufficient accuracy (ACC) and sensitivity (SEN). To improve performance, ensemble models were built to predict the BBB permeability of compounds. In this study, in silico ensemble-learning models were developed using 3 machine-learning algorithms and 9 molecular fingerprints from 1757 chemicals (integrated from 2 published data sets) to predict BBB permeability. The best prediction performance of the base classifier models was achieved by a prediction model based on an random forest (RF) and a MACCS molecular fingerprint with an ACC of 0.910, an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.957, a SEN of 0.927, and a specificity of 0.867 in 5-fold cross-validation. The prediction performance of the ensemble models is better than that of most of the base classifiers. The final ensemble model has also demonstrated good accuracy for an external validation and can be used for the early screening of CNS drugs.
Collapse
Affiliation(s)
- Lili Liu
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Li Zhang
- School of Life Science, Liaoning University, Shenyang 110036, China.,Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Shenyang, Liaoning University, Shenyang 110036, China.,Technology Innovation Center for Computer Simulating and Information Processing of Bio-macromolecules of Shenyang, Shenyang 110036, China
| | - Huawei Feng
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Shimeng Li
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Miao Liu
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Jian Zhao
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Hongsheng Liu
- Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Shenyang, Liaoning University, Shenyang 110036, China.,Technology Innovation Center for Computer Simulating and Information Processing of Bio-macromolecules of Shenyang, Shenyang 110036, China.,School of Pharmacy, Liaoning University, Shenyang 110036, China
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Pamies D, Zurich MG, Hartung T. Organotypic Models to Study Human Glioblastoma: Studying the Beast in Its Ecosystem. iScience 2020; 23:101633. [PMID: 33103073 PMCID: PMC7569333 DOI: 10.1016/j.isci.2020.101633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma is a very aggressive primary brain tumor in adults, with very low survival rates and no curative treatments. The high failure rate of drug development for this cancer is linked to the high-cost, time-consuming, and inefficient models used to study the disease. Advances in stem cell and in vitro cultures technologies are promising, however, and here we present the advantages and limitations of available organotypic culture models and discuss their possible applications for studying glioblastoma.
Collapse
Affiliation(s)
- David Pamies
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
- Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Marie-Gabrielle Zurich
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
- Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT) Europe, University of Konstanz, Konstanz, Germany
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| |
Collapse
|
9
|
Gupta M, Bogdanowicz T, Reed MA, Barden CJ, Weaver DF. The Brain Exposure Efficiency (BEE) Score. ACS Chem Neurosci 2020; 11:205-224. [PMID: 31815431 DOI: 10.1021/acschemneuro.9b00650] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The blood-brain barrier (BBB), composed of microvascular tight junctions and glial cell sheathing, selectively controls drug permeation into the central nervous system (CNS) by either passive diffusion or active transport. Computational techniques capable of predicting molecular brain penetration are important to neurological drug design. A novel prediction algorithm, termed the Brain Exposure Efficiency Score (BEE), is presented. BEE addresses the need to incorporate the role of trans-BBB influx and efflux active transporters by considering key brain penetrance parameters, namely, steady state unbound brain to plasma ratio of drug (Kp,uu) and dose normalized unbound concentration of drug in brain (Cu,b). BEE was devised using quantitative structure-activity relationships (QSARs) and molecular modeling studies on known transporter proteins and their ligands. The developed algorithms are provided as a user-friendly open source calculator to assist in optimizing a brain penetrance strategy during the early phases of small molecule molecular therapeutic design.
Collapse
Affiliation(s)
- Mayuri Gupta
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Thomas Bogdanowicz
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Mark A. Reed
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Christopher J. Barden
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Donald F. Weaver
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5G 2C4, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2 Canada
| |
Collapse
|
10
|
Dichiara M, Amata B, Turnaturi R, Marrazzo A, Amata E. Tuning Properties for Blood-Brain Barrier Permeation: A Statistics-Based Analysis. ACS Chem Neurosci 2020; 11:34-44. [PMID: 31793759 DOI: 10.1021/acschemneuro.9b00541] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the effort to define a set of rules useful in tuning the properties for a successful blood-brain barrier (BBB) permeation, we statistically analyzed a set of 328 compounds and correlated their experimental in vivo logBB with a series of computed descriptors. Contingency tables were constructed, observed and expected distributions were calculated, and chi-square (χ2) distributions were evaluated. This allowed to point out a significant dependence of certain physicochemical properties in influencing the BBB permeation. Of over 15 computed descriptors, 9 resulted to be particularly important showing highly significant χ2 distribution: polar surface area (χ2 = 66.79; p = 1.08 × 10-13), nitrogen and oxygen count (χ2 = 51.17; p = 2.06 × 10-10), logP (χ2 = 47.38; p = 1.27 × 10-9), nitrogen count (χ2 = 38.29; p = 9.77 × 10-8), logD (χ2 = 36.80; p = 36.80), oxygen count (χ2 = 35.83; p = 3.13 × 10-7), ionization state (χ2 = 33.02, p = 3.19 × 10-7), hydrogen bond acceptors (χ2 = 30.80; p = 3.36 × 10-6), and hydrogen bond donors (χ2 = 29.29; p = 6.81 × 10-6). Other parameters describing the mass and size of the molecules (molecular weight: 11.18; p = 2.46 × 10-2) resulted in being not significant since the population within the observed and expected distribution was similar. Depending on the combination of the significant descriptors, we set a three cases probabilistic scenario (BBB+, BBB-, BBB+/BBB-) that would prospectively be used to tune properties for BBB permeation.
Collapse
Affiliation(s)
- Maria Dichiara
- Department of Drug Sciences, Medicinal Chemistry Section, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Benedetto Amata
- Department of Drug Sciences, Medicinal Chemistry Section, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Rita Turnaturi
- Department of Drug Sciences, Medicinal Chemistry Section, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Agostino Marrazzo
- Department of Drug Sciences, Medicinal Chemistry Section, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Emanuele Amata
- Department of Drug Sciences, Medicinal Chemistry Section, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| |
Collapse
|
11
|
Ghosh S, Lalani R, Patel V, Bhowmick S, Misra A. Surface engineered liposomal delivery of therapeutics across the blood brain barrier: recent advances, challenges and opportunities. Expert Opin Drug Deliv 2019; 16:1287-1311. [DOI: 10.1080/17425247.2019.1676721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Saikat Ghosh
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, India
- Formulation Development Department-Novel Drug Delivery Systems, Sun Pharmaceutical Industries Ltd, Vadodara, India
| | - Rohan Lalani
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, India
- Formulation Development Department-Novel Drug Delivery Systems, Sun Pharmaceutical Industries Ltd, Vadodara, India
| | - Vivek Patel
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Subhas Bhowmick
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, India
- Formulation Development Department-Novel Drug Delivery Systems, Sun Pharmaceutical Industries Ltd, Vadodara, India
| | - Ambikanandan Misra
- Department of Pharmaceutics, Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, India
| |
Collapse
|
12
|
Saxena D, Sharma A, Siddiqui MH, Kumar R. Blood Brain Barrier Permeability Prediction Using Machine Learning Techniques: An Update. Curr Pharm Biotechnol 2019; 20:1163-1171. [DOI: 10.2174/1389201020666190821145346] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/01/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022]
Abstract
Blood Brain Barrier (BBB) is the collection of vessels of blood with special properties of
permeability that allow a limited range of drug and compounds to pass through it. The BBB plays a vital
role in maintaining balance between intracellular and extracellular environment for brain. Brain Capillary
Endothelial Cells (BECs) act as vehicle for transport and the transport mechanisms across BBB
involve active and passive diffusion of compounds. Efficient prediction models of BBB permeability
can be vital at the preliminary stages of drug development. There have been persistent efforts in identifying
the prediction of BBB permeability of compounds employing multiple machine learning methods
in an attempt to minimize the attrition rate of drug candidates taking up preclinical and clinical trials.
However, there is an urgent need to review the progress of such machine learning derived prediction
models in the prediction of BBB permeability. In the current article, we have analyzed the recently developed
prediction model for BBB permeability using machine learning.
Collapse
Affiliation(s)
- Deeksha Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow-226028, Uttar Pradesh, India
| | - Anju Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow-226028, Uttar Pradesh, India
| | - Mohammed H. Siddiqui
- Department of Bioengineering, Integral University, Dasauli, P.O. Basha, Kursi Road, Lucknow, Uttar Pradesh, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow-226028, Uttar Pradesh, India
| |
Collapse
|
13
|
Panduwawala TD, Iqbal S, Thompson AL, Genov M, Pretsch A, Pretsch D, Liu S, Ebright RH, Howells A, Maxwell A, Moloney MG. Functionalised bicyclic tetramates derived from cysteine as antibacterial agents. Org Biomol Chem 2019; 17:5615-5632. [PMID: 31120090 PMCID: PMC6686852 DOI: 10.1039/c9ob01076a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Routes to bicyclic tetramates derived from cysteine permitting ready incorporation of functionality at two different points around the periphery of a heterocyclic skeleton are reported. This has enabled the identification of systems active against Gram-positive bacteria, some of which show gyrase and RNA polymerase inhibitory activity. In particular, tetramates substituted with glycosyl side chains, chosen to impart polarity and aqueous solubility, show high antibacterial activity coupled with modest gyrase/polymerase activity in two cases. An analysis of physicochemical properties indicates that the antibacterially active tetramates generally occupy physicochemical space with MW of 300-600, clog D7.4 of -2.5 to 4 and rel. PSA of 11-22%. This work demonstrates that biologically active 3D libraries are readily available by manipulation of a tetramate skeleton.
Collapse
Affiliation(s)
- Tharindi D Panduwawala
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, UK.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Abstract
One hundred ten compounds of diverse structures (actives and excipients used in pharmaceutical preparations) were studied by RP-18 HPLC with acetonitrile-pH 7.4 phosphate buffer 1 : 1 (v/v) as the mobile phase. The relationships between the BBB permeation coefficients and the chromatographic parameters log k and (log k)/PSA were compared to those between the blood-brain barrier (BBB) permeation parameters and the RP-18 TLC descriptors Rf and Rf/PSA known from our earlier studies. It was found that the correlations between the BBB permeability and the HPLC data are slightly worse than those achieved for the thin-layer chromatographic data. MLR analysis based upon the physicochemical data confirmed the value of the molecular descriptors, related to the CNS bioavailability. These variables, combined with the HPLC data, made it possible to generate computational models, explaining 70–96% of the total variance of the CNS bioavailability. Contrary to TLC Rf, the advantage of the modification of HPLC log k with PSA (polar surface area) has not been confirmed and the results obtained with log k are superior to those obtained after a novel (log k)/PSA parameter has been introduced. Establishing a firm threshold limit of (log k)/PSA, log k, or even k and k/PSA to distinguish between the CNS+ and CNS− compounds was impossible. On the other hand, discriminant function analyses involving log k and (log k)/PSA as discriminating variables separated the CNS+ and CNS− compounds with the success rate ca. 90%. On the basis of these results, it was concluded that the RP-18 HPLC analytical models are entirely successful in studies and predictions of the BBB permeability.
Collapse
|
15
|
Haj E, Losev Y, Guru KrishnaKumar V, Pichinuk E, Engel H, Raveh A, Gazit E, Segal D. Integrating in vitro and in silico approaches to evaluate the "dual functionality" of palmatine chloride in inhibiting and disassembling Tau-derived VQIVYK peptide fibrils. Biochim Biophys Acta Gen Subj 2018; 1862:1565-1575. [PMID: 29634991 DOI: 10.1016/j.bbagen.2018.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common neurodegenerative disorder which is characterized by the deposits of intra-cellular tau protein and extra-cellular amyloid-β (Aβ) peptides in the human brain. Understanding the mechanism of protein aggregation and finding compounds that are capable of inhibiting its aggregation is considered to be highly important for disease therapy. METHODS We used an in vitro High-Throughput Screening for the identification of potent inhibitors of tau aggregation using a proxy model; a highly aggregation-prone hexapeptide fragment 306VQIVYK311 derived from tau. Using ThS fluorescence assay we screened a library of 2401 FDA approved, bio-active and natural compounds in attempt to find molecules which can efficiently modulate tau aggregation. RESULTS Among the screened compounds, palmatine chloride (PC) alkaloid was able to dramatically reduce the aggregation propensity of PHF6 at sub-molar concentrations. PC was also able to disassemble preformed aggregates of PHF6 and reduce the amyloid content in a dose-dependent manner. Insights obtained from MD simulation showed that PC interacted with the key residues of PHF6 responsible for β-sheet formation, which could likely be the mechanism of inhibition and disassembly. Furthermore, PC could effectively inhibit the aggregation of full-length tau and disassemble preformed aggregates. CONCLUSIONS We found that PC possesses "dual functionality" towards PHF6 and full-length tau, i.e. inhibit their aggregation and disassemble pre-formed fibrils. GENERAL SIGNIFICANCE The "dual functionality" of PC is valuable as a disease modifying strategy for AD, and other tauopathies, by inhibiting their progress and reducing the effect of fibrils already present in the brain.
Collapse
Affiliation(s)
- Esraa Haj
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Yelena Losev
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - V Guru KrishnaKumar
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel; Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Edward Pichinuk
- BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Hamutal Engel
- BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Avi Raveh
- BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel; BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 69978, Israel; The Interdisciplinary Sagol School of Neurosciences, Tel-Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|
16
|
Liu H, Dong K, Zhang W, Summerfield SG, Terstappen GC. Prediction of brain:blood unbound concentration ratios in CNS drug discovery employing in silico and in vitro model systems. Drug Discov Today 2018; 23:1357-1372. [PMID: 29548981 DOI: 10.1016/j.drudis.2018.03.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/03/2018] [Accepted: 03/08/2018] [Indexed: 12/15/2022]
Abstract
Recent years have seen a paradigm shift away from optimizing the brain:blood concentration ratio toward the more relevant brain:blood unbound concentration ratio (Kp,uu,br) in CNS drug discovery. Here, we review the recent developments in the in silico and in vitro model systems to predict the Kp,uu,br of discovery compounds with special emphasis on the in-vitro-in-vivo correlation. We also discuss clinical 'translation' of rodent Kp,uu,br and highlight the future directions for improvement in brain penetration prediction. Important in this regard are in silico Kp,uu,br models built on larger datasets of high quality, calibration and deeper understanding of experimental in vitro transporter systems, and better understanding of blood-brain barrier transporters and their in vivo relevance aside from P-gp and BCRP.
Collapse
Affiliation(s)
- Houfu Liu
- Platform Technology and Science, GlaxoSmithKline R&D Center, Shanghai, China.
| | - Kelly Dong
- Platform Technology and Science, GlaxoSmithKline R&D Center, Shanghai, China
| | - Wandong Zhang
- Platform Technology and Science, GlaxoSmithKline R&D Center, Shanghai, China
| | - Scott G Summerfield
- Bioanalysis, Immunogenicity and Biomarker, Platform Technology and Science, GlaxoSmithKline, Ware, UK
| | - Georg C Terstappen
- Platform Technology and Science, GlaxoSmithKline R&D Center, Shanghai, China
| |
Collapse
|
17
|
Modarres HP, Janmaleki M, Novin M, Saliba J, El-Hajj F, RezayatiCharan M, Seyfoori A, Sadabadi H, Vandal M, Nguyen MD, Hasan A, Sanati-Nezhad A. In vitro models and systems for evaluating the dynamics of drug delivery to the healthy and diseased brain. J Control Release 2018; 273:108-130. [PMID: 29378233 DOI: 10.1016/j.jconrel.2018.01.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/12/2022]
Abstract
The blood-brain barrier (BBB) plays a crucial role in maintaining brain homeostasis and transport of drugs to the brain. The conventional animal and Transwell BBB models along with emerging microfluidic-based BBB-on-chip systems have provided fundamental functionalities of the BBB and facilitated the testing of drug delivery to the brain tissue. However, developing biomimetic and predictive BBB models capable of reasonably mimicking essential characteristics of the BBB functions is still a challenge. In addition, detailed analysis of the dynamics of drug delivery to the healthy or diseased brain requires not only biomimetic BBB tissue models but also new systems capable of monitoring the BBB microenvironment and dynamics of barrier function and delivery mechanisms. This review provides a comprehensive overview of recent advances in microengineering of BBB models with different functional complexity and mimicking capability of healthy and diseased states. It also discusses new technologies that can make the next generation of biomimetic human BBBs containing integrated biosensors for real-time monitoring the tissue microenvironment and barrier function and correlating it with the dynamics of drug delivery. Such integrated system addresses important brain drug delivery questions related to the treatment of brain diseases. We further discuss how the combination of in vitro BBB systems, computational models and nanotechnology supports for characterization of the dynamics of drug delivery to the brain.
Collapse
Affiliation(s)
- Hassan Pezeshgi Modarres
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada
| | - Mohsen Janmaleki
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada
| | - Mana Novin
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada
| | - John Saliba
- Biomedical Engineering, Department of Mechanical Engineering, Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Fatima El-Hajj
- Biomedical Engineering, Department of Mechanical Engineering, Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Mahdi RezayatiCharan
- Breast Cancer Research Center (BCRC), ACECR, Tehran, Iran; School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Amir Seyfoori
- Breast Cancer Research Center (BCRC), ACECR, Tehran, Iran; School of Metallurgy and Materials Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Hamid Sadabadi
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada
| | - Milène Vandal
- Departments of Clinical Neurosciences, Cell Biology and Anatomy, Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Minh Dang Nguyen
- Departments of Clinical Neurosciences, Cell Biology and Anatomy, Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Anwarul Hasan
- Biomedical Engineering, Department of Mechanical Engineering, Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon; Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha, 2713, Qatar
| | - Amir Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada.
| |
Collapse
|
18
|
In vitro prediction of gastrointestinal absorption of novel β-hydroxy-β-arylalkanoic acids using PAMPA technique. Eur J Pharm Sci 2017; 100:36-41. [DOI: 10.1016/j.ejps.2017.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/19/2016] [Accepted: 01/06/2017] [Indexed: 11/22/2022]
|
19
|
Approaches for the discovery of novel positron emission tomography radiotracers for brain imaging. Clin Transl Imaging 2017. [DOI: 10.1007/s40336-017-0221-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
20
|
The role of multidrug resistance protein (MRP-1) as an active efflux transporter on blood-brain barrier (BBB) permeability. Mol Divers 2017; 21:355-365. [PMID: 28050687 DOI: 10.1007/s11030-016-9715-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/16/2016] [Indexed: 01/30/2023]
Abstract
Drugs acting on central nervous system (CNS) may take longer duration to reach the market as these compounds have a higher attrition rate in clinical trials due to the complexity of the brain, side effects, and poor blood-brain barrier (BBB) permeability compared to non-CNS-acting compounds. The roles of active efflux transporters with BBB are still unclear. The aim of the present work was to develop a predictive model for BBB permeability that includes the MRP-1 transporter, which is considered as an active efflux transporter. A support vector machine model was developed for the classification of MRP-1 substrates and non-substrates, which was validated with an external data set and Y-randomization method. An artificial neural network model has been developed to evaluate the role of MRP-1 on BBB permeation. A total of nine descriptors were selected, which included molecular weight, topological polar surface area, ClogP, number of hydrogen bond donors, number of hydrogen bond acceptors, number of rotatable bonds, P-gp, BCRP, and MRP-1 substrate probabilities for model development. We identified 5 molecules that fulfilled all criteria required for passive permeation of BBB, but they all have a low logBB value, which suggested that the molecules were effluxed by the MRP-1 transporter.
Collapse
|
21
|
Enciso M, Meftahi N, Walker ML, Smith BJ. BioPPSy: An Open-Source Platform for QSAR/QSPR Analysis. PLoS One 2016; 11:e0166298. [PMID: 27832156 PMCID: PMC5104412 DOI: 10.1371/journal.pone.0166298] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022] Open
Abstract
The reliability of quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR) models is often difficult to assess due to the problems of accessing the tools and data used to build the models. We present here BioPPSy, which aims to fill this gap by providing an easy-to-use open-source software platform. We demonstrate the program capabilities by calculating three key properties used in drug discovery, aqueous solubility, Caco-2 cell permeability and blood-brain barrier permeability. A comparison is made with a number of previously reported methods, taken from the literature, for each property. The software, including source code, current models and databases, is available from https://sourceforge.net/projects/bioppsy/.
Collapse
Affiliation(s)
- Marta Enciso
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Nastaran Meftahi
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Michael L. Walker
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Brian J. Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
- * E-mail:
| |
Collapse
|
22
|
Dolgikh E, Watson IA, Desai PV, Sawada GA, Morton S, Jones TM, Raub TJ. QSAR Model of Unbound Brain-to-Plasma Partition Coefficient, K p,uu,brain: Incorporating P-glycoprotein Efflux as a Variable. J Chem Inf Model 2016; 56:2225-2233. [PMID: 27684523 DOI: 10.1021/acs.jcim.6b00229] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report development and prospective validation of a QSAR model of the unbound brain-to-plasma partition coefficient, Kp,uu,brain, based on the in-house data set of ∼1000 compounds. We discuss effects of experimental variability, explore the applicability of both regression and classification approaches, and evaluate a novel, model-within-a-model approach of including P-glycoprotein efflux prediction as an additional variable. When tested on an independent test set of 91 internal compounds, incorporation of P-glycoprotein efflux information significantly improves the model performance resulting in an R2 of 0.53, RMSE of 0.57, Spearman's Rho correlation coefficient of 0.73, and qualitative prediction accuracy of 0.8 (kappa = 0.6). In addition to improving the performance, one of the key advantages of this approach is the larger chemical space coverage provided indirectly through incorporation of the in vitro, higher throughput data set that is 4 times larger than the in vivo data set.
Collapse
Affiliation(s)
- Elena Dolgikh
- Global Scientific Informatics, ‡Advanced Analytics, §Computational ADME, ∥IT Informatics and ⊥Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana 46285, United States
| | - Ian A Watson
- Global Scientific Informatics, ‡Advanced Analytics, §Computational ADME, ∥IT Informatics and ⊥Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana 46285, United States
| | - Prashant V Desai
- Global Scientific Informatics, ‡Advanced Analytics, §Computational ADME, ∥IT Informatics and ⊥Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana 46285, United States
| | - Geri A Sawada
- Global Scientific Informatics, ‡Advanced Analytics, §Computational ADME, ∥IT Informatics and ⊥Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana 46285, United States
| | - Stuart Morton
- Global Scientific Informatics, ‡Advanced Analytics, §Computational ADME, ∥IT Informatics and ⊥Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana 46285, United States
| | - Timothy M Jones
- Global Scientific Informatics, ‡Advanced Analytics, §Computational ADME, ∥IT Informatics and ⊥Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana 46285, United States
| | - Thomas J Raub
- Global Scientific Informatics, ‡Advanced Analytics, §Computational ADME, ∥IT Informatics and ⊥Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana 46285, United States
| |
Collapse
|
23
|
A Genetic Algorithm Based Support Vector Machine Model for Blood-Brain Barrier Penetration Prediction. BIOMED RESEARCH INTERNATIONAL 2015; 2015:292683. [PMID: 26504797 PMCID: PMC4609370 DOI: 10.1155/2015/292683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/07/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023]
Abstract
Blood-brain barrier (BBB) is a highly complex physical barrier determining what substances are allowed to enter the brain. Support vector machine (SVM) is a kernel-based machine learning method that is widely used in QSAR study. For a successful SVM model, the kernel parameters for SVM and feature subset selection are the most important factors affecting prediction accuracy. In most studies, they are treated as two independent problems, but it has been proven that they could affect each other. We designed and implemented genetic algorithm (GA) to optimize kernel parameters and feature subset selection for SVM regression and applied it to the BBB penetration prediction. The results show that our GA/SVM model is more accurate than other currently available log BB models. Therefore, to optimize both SVM parameters and feature subset simultaneously with genetic algorithm is a better approach than other methods that treat the two problems separately. Analysis of our log BB model suggests that carboxylic acid group, polar surface area (PSA)/hydrogen-bonding ability, lipophilicity, and molecular charge play important role in BBB penetration. Among those properties relevant to BBB penetration, lipophilicity could enhance the BBB penetration while all the others are negatively correlated with BBB penetration.
Collapse
|
24
|
Zeng H, Wu X. Alzheimer's disease drug development based on Computer-Aided Drug Design. Eur J Med Chem 2015; 121:851-863. [PMID: 26415837 DOI: 10.1016/j.ejmech.2015.08.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/01/2015] [Accepted: 08/21/2015] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder characterized by the excessive deposition of amyloids in the brain. The pathological features mainly include the extracellular amyloid plaques and intracellular neurofibrillary tangles, which are the production of amyloid precursor protein (APP) processed by the α-, β- and γ-secretases. Based on the amyloid cascade hypotheses of AD, a large number of amyloid-β agents and secretase inhibitors against AD have been recently developed by using computational methods. This review article describes pathophysiology of AD and the structure of the Aβ plaques, β- and γ-secretases, and discusses the recent advances in the development of the amyloid agents for AD therapy and diagnosis by using Computer-Aided Drug Design approach.
Collapse
Affiliation(s)
- Huahui Zeng
- Science & Technology Department, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China; Department of Nuclear Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China.
| | - Xiangxiang Wu
- Science & Technology Department, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China.
| |
Collapse
|
25
|
Abstract
The blood-brain barrier (BBB) is a microvascular unit which selectively regulates the permeability of drugs to the brain. With the rise in CNS drug targets and diseases, there is a need to be able to accurately predict a priori which compounds in a company database should be pursued for favorable properties. In this review, we will explore the different computational tools available today, as well as underpin these to the experimental methods used to determine BBB permeability. These include in vitro models and the in vivo models that yield the dataset we use to generate predictive models. Understanding of how these models were experimentally derived determines our accurate and predicted use for determining a balance between activity and BBB distribution.
Collapse
|
26
|
Brito-Sánchez Y, Marrero-Ponce Y, Barigye SJ, Yaber-Goenaga I, Morell Pérez C, Le-Thi-Thu H, Cherkasov A. Towards Better BBB Passage Prediction Using an Extensive and Curated Data Set. Mol Inform 2015; 34:308-30. [PMID: 27490276 DOI: 10.1002/minf.201400118] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/20/2015] [Indexed: 12/25/2022]
Abstract
In the present report, the challenging task of drug delivery across the blood-brain barrier (BBB) is addressed via a computational approach. The BBB passage was modeled using classification and regression schemes on a novel extensive and curated data set (the largest to the best of our knowledge) in terms of log BB. Prior to the model development, steps of data analysis that comprise chemical data curation, structural, cutoff and cluster analysis (CA) were conducted. Linear Discriminant Analysis (LDA) and Multiple Linear Regression (MLR) were used to fit classification and correlation functions. The best LDA-based model showed overall accuracies over 85 % and 83 % for the training and test sets, respectively. Also a MLR-based model with acceptable explanation of more than 69 % of the variance in the experimental log BB was developed. A brief and general interpretation of proposed models allowed the estimation on how 'near' our computational approach is to the factors that determine the passage of molecules through the BBB. In a final effort some popular and powerful Machine Learning methods were considered. Comparable or similar performance was observed respect to the simpler linear techniques. Most of the compounds with anomalous behavior were put aside into a set denoted as controversial set and discussion regarding to these compounds is provided. Finally, our results were compared with methodologies previously reported in the literature showing comparable to better results. The results could represent useful tools available and reproducible by all scientific community in the early stages of neuropharmaceutical drug discovery/development projects.
Collapse
Affiliation(s)
- Yoan Brito-Sánchez
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6, Canada.,Unit of Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research, International Network (CAMD-BIR International Network), Los Laureles L76MD, Nuevo Bosque, 130015, Cartagena de Indias, Bolivar, Colombia. Homepage: http://www.uv.es/yoma/ Homepage: http://sites.google.com/site/ymponce/home
| | - Yovani Marrero-Ponce
- Unit of Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research, International Network (CAMD-BIR International Network), Los Laureles L76MD, Nuevo Bosque, 130015, Cartagena de Indias, Bolivar, Colombia. Homepage: http://www.uv.es/yoma/ Homepage: http://sites.google.com/site/ymponce/home. .,Grupo de Investigación en Estudios Químicos y Biológicos, Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, Parque Industrial y Tecnológico Carlos Vélez Pombo Km 1 vía Turbaco, 130010, Cartagena de Indias, Bolívar, Colombia. .,Facultad de Química Farmacéutica, Universidad de Cartagena, Cartagena de Indias, Bolívar, Colombia.
| | - Stephen J Barigye
- Unit of Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research, International Network (CAMD-BIR International Network), Los Laureles L76MD, Nuevo Bosque, 130015, Cartagena de Indias, Bolivar, Colombia. Homepage: http://www.uv.es/yoma/ Homepage: http://sites.google.com/site/ymponce/home.,Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000, Lavras, MG, Brazil
| | - Iván Yaber-Goenaga
- Grupo de Investigación en Estudios Químicos y Biológicos, Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, Parque Industrial y Tecnológico Carlos Vélez Pombo Km 1 vía Turbaco, 130010, Cartagena de Indias, Bolívar, Colombia
| | - Carlos Morell Pérez
- Center of Studies on Informatics, Universidad "Marta Abreu" de Las Villas, Santa Clara, 54830, Villa Clara, Cuba
| | - Huong Le-Thi-Thu
- School of Medicine and Pharmacy, Vietnam National University, Hanoi (VNU) 144 Xuan Thuy, CauGiay, Hanoi, Vietnam
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6, Canada
| |
Collapse
|
27
|
Varadharajan S, Winiwarter S, Carlsson L, Engkvist O, Anantha A, Kogej T, Fridén M, Stålring J, Chen H. Exploring In Silico Prediction of the Unbound Brain-to-Plasma Drug Concentration Ratio: Model Validation, Renewal, and Interpretation. J Pharm Sci 2015; 104:1197-206. [DOI: 10.1002/jps.24301] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/14/2014] [Accepted: 11/18/2014] [Indexed: 01/13/2023]
|
28
|
Garg P, Dhakne R, Belekar V. Role of breast cancer resistance protein (BCRP) as active efflux transporter on blood-brain barrier (BBB) permeability. Mol Divers 2014; 19:163-72. [PMID: 25502234 DOI: 10.1007/s11030-014-9562-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 11/26/2014] [Indexed: 11/26/2022]
Abstract
Nowadays most of the CNS acting therapeutic molecules are failing in clinical trials due to efflux transporters at the blood brain barrier (BBB) which imparts resistance and poor ADMET properties of these molecules. CNS acting drug molecules interact with the BBB prior to their target site, so there is a need to develop predictive models for BBB permeability which can be used in the initial phases of drug discovery process. Most of the drug molecules are transported to the brain via passive diffusion which is explored extensively; on the other hand, the role of active efflux transporters in BBB permeability is unclear. Our aim is to develop predictive models for BBB permeability that include active efflux transporters. An in silico model has been developed to assess the role of BCRP on BBB permeation. Eight descriptors were selected, which also include BCRP substrate probabilities used for model development and show a relationship between BCRP and logBB. From our analysis, it was found that 11 molecules satisfied all criteria required for BBB permeation but have low logBB values. These 11 molecules are predicted as BCRP substrates from the model developed, suggesting that the molecules are effluxed by the BCRP transporter. This predictive ability was further validated by docking of these 11 molecules into BCRP protein. This study provides a new mechanistic insight into correlation of low logBB values and efflux mechanism of BCRP in BBB.
Collapse
Affiliation(s)
- Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Punjab, 160062, India,
| | | | | |
Collapse
|
29
|
Carpenter TS, Kirshner DA, Lau EY, Wong SE, Nilmeier JP, Lightstone FC. A method to predict blood-brain barrier permeability of drug-like compounds using molecular dynamics simulations. Biophys J 2014; 107:630-641. [PMID: 25099802 PMCID: PMC4129472 DOI: 10.1016/j.bpj.2014.06.024] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 06/10/2014] [Accepted: 06/16/2014] [Indexed: 02/06/2023] Open
Abstract
The blood-brain barrier (BBB) is formed by specialized tight junctions between endothelial cells that line brain capillaries to create a highly selective barrier between the brain and the rest of the body. A major problem to overcome in drug design is the ability of the compound in question to cross the BBB. Neuroactive drugs are required to cross the BBB to function. Conversely, drugs that target other parts of the body ideally should not cross the BBB to avoid possible psychotropic side effects. Thus, the task of predicting the BBB permeability of new compounds is of great importance. Two gold-standard experimental measures of BBB permeability are logBB (the concentration of drug in the brain divided by concentration in the blood) and logPS (permeability surface-area product). Both methods are time-consuming and expensive, and although logPS is considered the more informative measure, it is lower throughput and more resource intensive. With continual increases in computer power and improvements in molecular simulations, in silico methods may provide viable alternatives. Computational predictions of these two parameters for a sample of 12 small molecule compounds were performed. The potential of mean force for each compound through a 1,2-dioleoyl-sn-glycero-3-phosphocholine bilayer is determined by molecular dynamics simulations. This system setup is often used as a simple BBB mimetic. Additionally, one-dimensional position-dependent diffusion coefficients are calculated from the molecular dynamics trajectories. The diffusion coefficient is combined with the free energy landscape to calculate the effective permeability (Peff) for each sample compound. The relative values of these permeabilities are compared to experimentally determined logBB and logPS values. Our computational predictions correlate remarkably well with both logBB (R(2) = 0.94) and logPS (R(2) = 0.90). Thus, we have demonstrated that this approach may have the potential to provide reliable, quantitatively predictive BBB permeability, using a relatively quick, inexpensive method.
Collapse
Affiliation(s)
- Timothy S Carpenter
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Daniel A Kirshner
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Edmond Y Lau
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Sergio E Wong
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Jerome P Nilmeier
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Felice C Lightstone
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California.
| |
Collapse
|
30
|
Seo YJ, Kang Y, Muench L, Reid A, Caesar S, Jean L, Wagner F, Holson E, Haggarty SJ, Weiss P, King P, Carter P, Volkow ND, Fowler JS, Hooker JM, Kim SW. Image-guided synthesis reveals potent blood-brain barrier permeable histone deacetylase inhibitors. ACS Chem Neurosci 2014; 5:588-96. [PMID: 24780082 DOI: 10.1021/cn500021p] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Recent studies have revealed that several histone deacetylase (HDAC) inhibitors, which are used to study/treat brain diseases, show low blood-brain barrier (BBB) penetration. In addition to low HDAC potency and selectivity observed, poor brain penetrance may account for the high doses needed to achieve therapeutic efficacy. Here we report the development and evaluation of highly potent and blood-brain barrier permeable HDAC inhibitors for CNS applications based on an image-guided approach involving the parallel synthesis and radiolabeling of a series of compounds based on the benzamide HDAC inhibitor, MS-275 as a template. BBB penetration was optimized by rapid carbon-11 labeling and PET imaging in the baboon model and using the imaging derived data on BBB penetration from each compound to feed back into the design process. A total of 17 compounds were evaluated, revealing molecules with both high binding affinity and BBB permeability. A key element conferring BBB penetration in this benzamide series was a basic benzylic amine. These derivatives exhibited 1-100 nM inhibitory activity against recombinant human HDAC1 and HDAC2. Three of the carbon-11 labeled aminomethyl benzamide derivatives showed high BBB penetration (∼0.015%ID/cc) and regional binding heterogeneity in the brain (high in thalamus and cerebellum). Taken together this approach has afforded a strategy and a predictive model for developing highly potent and BBB permeable HDAC inhibitors for CNS applications and for the discovery of novel candidate molecules for small molecule probes and drugs.
Collapse
Affiliation(s)
- Young Jun Seo
- Biosciences
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
- Department
of Chemistry, Chonbuk National University, Jeonju, 561-756, South Korea
| | - Yeona Kang
- Biosciences
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Lisa Muench
- Laboratory
of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, Upton, New York 11973, United States
| | - Alicia Reid
- Physical,
Environmental and Computer Sciences, Medgar Evers College, Brooklyn, New York 11225, United States
| | - Shannon Caesar
- Biosciences
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Logan Jean
- Biosciences
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Florence Wagner
- Stanley Center
for Psychiatric Research, Broad Institute of Massachusetts Institute
of Technology and Harvard University, Cambridge, Massachusetts 02142, United States
| | - Edward Holson
- Stanley Center
for Psychiatric Research, Broad Institute of Massachusetts Institute
of Technology and Harvard University, Cambridge, Massachusetts 02142, United States
| | - Stephen J. Haggarty
- Center for
Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02142, United States
| | - Philipp Weiss
- Institut
für Organische Chemie, Johannes-Gutenberg Universität Mainz, Duesbergweg 10-14, Mainz 55122, Germany
| | - Payton King
- Biosciences
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Pauline Carter
- Biosciences
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Nora D. Volkow
- Laboratory
of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, Upton, New York 11973, United States
- National Institute
on Drug Abuse, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Joanna S. Fowler
- Biosciences
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jacob M. Hooker
- Biosciences
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
- Athinoula
A. Martinos Center for Biomedical Imaging, Department of Radiology,
Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Sung Won Kim
- Laboratory
of Neuroimaging, National Institute on Alcohol Abuse and Alcoholism, Upton, New York 11973, United States
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| |
Collapse
|
31
|
Jiang P, Mukthavaram R, Mukthavavam R, Chao Y, Bharati IS, Fogal V, Pastorino S, Cong X, Nomura N, Gallagher M, Abbasi T, Vali S, Pingle SC, Makale M, Kesari S. Novel anti-glioblastoma agents and therapeutic combinations identified from a collection of FDA approved drugs. J Transl Med 2014; 12:13. [PMID: 24433351 PMCID: PMC3898565 DOI: 10.1186/1479-5876-12-13] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 01/10/2014] [Indexed: 01/23/2023] Open
Abstract
Background Glioblastoma (GBM) is a therapeutic challenge, associated with high mortality. More effective GBM therapeutic options are urgently needed. Hence, we screened a large multi-class drug panel comprising the NIH clinical collection (NCC) that includes 446 FDA-approved drugs, with the goal of identifying new GBM therapeutics for rapid entry into clinical trials for GBM. Methods Screens using human GBM cell lines revealed 22 drugs with potent anti-GBM activity, including serotonergic blockers, cholesterol-lowering agents (statins), antineoplastics, anti-infective, anti-inflammatories, and hormonal modulators. We tested the 8 most potent drugs using patient-derived GBM cancer stem cell-like lines. Notably, the statins were active in vitro; they inhibited GBM cell proliferation and induced cellular autophagy. Moreover, the statins enhanced, by 40-70 fold, the pro-apoptotic activity of irinotecan, a topoisomerase 1 inhibitor currently used to treat a variety of cancers including GBM. Our data suggest that the mechanism of action of statins was prevention of multi-drug resistance protein MDR-1 glycosylation. This drug combination was synergistic in inhibiting tumor growth in vivo. Compared to animals treated with high dose irinotecan, the drug combination showed significantly less toxicity. Results Our data identifies a novel combination from among FDA-approved drugs. In addition, this combination is safer and well tolerated compared to single agent irinotecan. Conclusions Our study newly identifies several FDA-approved compounds that may potentially be useful in GBM treatment. Our findings provide the basis for the rational combination of statins and topoisomerase inhibitors in GBM.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Santosh Kesari
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, UC San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
32
|
|
33
|
Raevsky O, Solodova S, Lagunin A, Poroikov V. Computer modeling of blood brain barrier permeability of physiologically active compounds. ACTA ACUST UNITED AC 2014; 60:161-81. [DOI: 10.18097/pbmc20146002161] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
At present work discusses the current level of computer modeling the relationship structure of organic compounds and drugs and their ability to penetrate the BBB. All descriptors that influence to this permeability within classification and regression QSAR models are generalized and analyzed. The crucial role of H-bond in processes both passive, and active transport across BBB is observed. It is concluded that further research should be focused on interpretation the spatial structure of a full-size P-glycoprotein molecule with high resolution and the creation of QSAR models describing the quantitative relationship between structure and active transport of substances across BBB.
Collapse
Affiliation(s)
- O.A. Raevsky
- Institute of Physiologically Active Compounds, Russian Academy of Science
| | - S.L. Solodova
- Institute of Physiologically Active Compounds, Russian Academy of Science
| | - A.A. Lagunin
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences
| | - V.V. Poroikov
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences
| |
Collapse
|
34
|
Dander A, Mueller LA, Gallasch R, Pabinger S, Emmert-Streib F, Graber A, Dehmer M. [COMMODE] a large-scale database of molecular descriptors using compounds from PubChem. SOURCE CODE FOR BIOLOGY AND MEDICINE 2013; 8:22. [PMID: 24225386 PMCID: PMC3831596 DOI: 10.1186/1751-0473-8-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/29/2013] [Indexed: 11/11/2022]
Abstract
Background Molecular descriptors have been extensively used in the field of structure-oriented drug design and structural chemistry. They have been applied in QSPR and QSAR models to predict ADME-Tox properties, which specify essential features for drugs. Molecular descriptors capture chemical and structural information, but investigating their interpretation and meaning remains very challenging. Results This paper introduces a large-scale database of molecular descriptors called COMMODE containing more than 25 million compounds originated from PubChem. About 2500 DRAGON-descriptors have been calculated for all compounds and integrated into this database, which is accessible through a web interface at http://commode.i-med.ac.at.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Matthias Dehmer
- UMIT, Division for Bioinformatics and Translational Research, Eduard Wallnoefer Zentrum 1, A-6060 Hall in Tyrol, Austria.
| |
Collapse
|
35
|
Can we predict blood brain barrier permeability of ligands using computational approaches? Interdiscip Sci 2013; 5:95-101. [DOI: 10.1007/s12539-013-0158-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 08/21/2012] [Accepted: 12/01/2012] [Indexed: 12/14/2022]
|
36
|
Raevsky OA, Solodova SL, Lagunin AA, Poroikov VV. Computer modeling of blood brain barrier permeability for physiologically active compounds. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2013. [DOI: 10.1134/s199075081302008x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
37
|
He Y, Chong FHT, Lim J, Lee RJT, Yap CW. Determination of the Potential of Drug Candidates to Cause Severe Skin Disorders Using Computational Modeling. Mol Inform 2013; 32:303-12. [PMID: 27481525 DOI: 10.1002/minf.201200086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 02/20/2013] [Indexed: 11/11/2022]
Abstract
Efficient and accurate prediction for drugs' potential to cause rare and severe adverse drug reactions (ADRs) is needed to facilitate the evaluation of risk-benefit ratio of drug candidates during drug development. Severe skin disorders like the Stevens Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN), which are life-threatening dermatological conditions, are such ADRs that have not received sufficient attention so far. In this study, a total of 1127 marketed drugs were screened for their potential to cause SJS/TEN, of which 255 were found to cause SJS/TEN and 239 were unlikely to cause SJS/TEN. One-class classification method was used to develop multiple prediction models. An applicability domain was determined to define the applicability of the model. Ensemble method was used to develop ensemble models to improve prediction ability. The final ensemble model achieved a sensitivity and specificity of 81 % and 67.4 %, respectively, when estimated using the external 5-fold cross validation method, and a sensitivity of 66.7 % when assessed using an external positive set. The results suggest the methods used in this study are potentially useful for facilitating the prediction of rare and severe ADRs.
Collapse
Affiliation(s)
- Yuye He
- Pharmaceutical Data Exploration Laboratory, Department of Pharmacy, National University of Singapore, Singapore tel: 065-65165971, fax: 065-67791554
| | | | | | | | - Chun Wei Yap
- Pharmaceutical Data Exploration Laboratory, Department of Pharmacy, National University of Singapore, Singapore tel: 065-65165971, fax: 065-67791554.
| |
Collapse
|
38
|
Dolghih E, Jacobson MP. Predicting efflux ratios and blood-brain barrier penetration from chemical structure: combining passive permeability with active efflux by P-glycoprotein. ACS Chem Neurosci 2013; 4:361-7. [PMID: 23421687 DOI: 10.1021/cn3001922] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In order to reach their pharmacologic targets, successful central nervous system (CNS) drug candidates have to cross a complex protective barrier separating brain from the blood. Being able to predict a priori which molecules can successfully penetrate this barrier could be of significant value in CNS drug discovery. Herein we report a new computational approach that combines two mechanism-based models, for passive permeation and for active efflux by P-glycoprotein, to provide insight into the multiparameter optimization problem of designing small molecules able to access the CNS. Our results indicate that this approach is capable of distinguishing compounds with high/low efflux ratios as well as CNS+/CNS- compounds and provides advantage over estimating P-glycoprotein efflux or passive permeability alone when trying to predict these emergent properties. We also demonstrate that this method could be useful for rank-ordering chemically similar compounds and that it can provide detailed mechanistic insight into the relationship between chemical structure and efflux ratios and/or CNS penetration, offering guidance as to how compounds could be modified to improve their access into the brain.
Collapse
Affiliation(s)
- Elena Dolghih
- Department of Pharmaceutical
Chemistry, University of California, San
Francisco, San Francisco, California 94158, United States
| | - Matthew P. Jacobson
- Department of Pharmaceutical
Chemistry, University of California, San
Francisco, San Francisco, California 94158, United States
| |
Collapse
|
39
|
In vitro, in vivo and in silico models of drug distribution into the brain. J Pharmacokinet Pharmacodyn 2013; 40:301-14. [DOI: 10.1007/s10928-013-9303-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 01/31/2013] [Indexed: 10/27/2022]
|
40
|
Manallack DT, Prankerd RJ, Yuriev E, Oprea TI, Chalmers DK. The significance of acid/base properties in drug discovery. Chem Soc Rev 2013; 42:485-96. [PMID: 23099561 PMCID: PMC3641858 DOI: 10.1039/c2cs35348b] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
While drug discovery scientists take heed of various guidelines concerning drug-like character, the influence of acid/base properties often remains under-scrutinised. Ionisation constants (pK(a) values) are fundamental to the variability of the biopharmaceutical characteristics of drugs and to underlying parameters such as logD and solubility. pK(a) values affect physicochemical properties such as aqueous solubility, which in turn influences drug formulation approaches. More importantly, absorption, distribution, metabolism, excretion and toxicity (ADMET) are profoundly affected by the charge state of compounds under varying pH conditions. Consideration of pK(a) values in conjunction with other molecular properties is of great significance and has the potential to be used to further improve the efficiency of drug discovery. Given the recent low annual output of new drugs from pharmaceutical companies, this review will provide a timely reminder of an important molecular property that influences clinical success.
Collapse
Affiliation(s)
- David T Manallack
- Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052, Australia.
| | | | | | | | | |
Collapse
|
41
|
Lanevskij K, Japertas P, Didziapetris R. Improving the prediction of drug disposition in the brain. Expert Opin Drug Metab Toxicol 2013; 9:473-86. [PMID: 23294027 DOI: 10.1517/17425255.2013.754423] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Ability to cross the blood-brain barrier is one of the key ADME characteristics of all drug candidates regardless of their target location in the body. While good brain penetration is essential for CNS drugs, it may lead to serious side effects in case of peripherally-targeted molecules. Despite a high demand of computational methods for estimating brain transport early in drug discovery, achieving good prediction accuracy still remains a challenging task. AREAS COVERED This article reviews various measures employed to quantify brain delivery and recent advances in QSAR approaches for predicting these properties from the compound's structure. Additionally, the authors discuss the classification models attempting to distinguish between permeable and impermeable chemicals. EXPERT OPINION Recent research in the field of brain penetration modeling showed an increasing understanding of the processes involved in drug disposition, although most models of brain/plasma partitioning still rely on purely statistical considerations. Preferably, new models should incorporate mechanistic knowledge since it is the prerequisite for guiding drug design efforts in the desired direction. To increase the efficiency of computational tools, a broader view is necessary, involving rate and extent of brain penetration, as well as plasma and brain tissue binding strength, instead of relying on any single property.
Collapse
Affiliation(s)
- Kiril Lanevskij
- VšĮ Aukštieji algoritmai, A. Mickeviciaus 29, LT-08117 Vilnius, Lithuania.
| | | | | |
Collapse
|
42
|
Martins IF, Teixeira AL, Pinheiro L, Falcao AO. A Bayesian Approach to in Silico Blood-Brain Barrier Penetration Modeling. J Chem Inf Model 2012; 52:1686-97. [DOI: 10.1021/ci300124c] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
| | - Ana L. Teixeira
- CQB - Centro de Quimica e Bioquimica,
Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | | |
Collapse
|
43
|
Translational CNS medicines research. Drug Discov Today 2012; 17:1068-78. [PMID: 22580061 DOI: 10.1016/j.drudis.2012.05.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 03/22/2012] [Accepted: 05/02/2012] [Indexed: 12/31/2022]
Abstract
The major imperative of the pharmaceutical industry is to effectively translate insights gained from basic research into new medicines. This task is toughest for CNS disorders. Compared with non-CNS drugs, CNS drugs take longer to get to market and their attrition rate is greater. This is principally because of the complexity of the human brain (the cause of many brain disorders remains unknown), the liability of CNS drugs to cause CNS side effects (which limits their use) and the requirement of CNS medicines to cross the blood-CNS barrier (BCNSB) (which restricts their ability to interact with their CNS target). In this review we consider the factors that are important in translating neuroscience research into CNS medicines.
Collapse
|
44
|
Duffy BC, Zhu L, Decornez H, Kitchen DB. Early phase drug discovery: cheminformatics and computational techniques in identifying lead series. Bioorg Med Chem 2012; 20:5324-42. [PMID: 22938785 DOI: 10.1016/j.bmc.2012.04.062] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/24/2012] [Accepted: 04/27/2012] [Indexed: 01/31/2023]
Abstract
Early drug discovery processes rely on hit finding procedures followed by extensive experimental confirmation in order to select high priority hit series which then undergo further scrutiny in hit-to-lead studies. The experimental cost and the risk associated with poor selection of lead series can be greatly reduced by the use of many different computational and cheminformatic techniques to sort and prioritize compounds. We describe the steps in typical hit identification and hit-to-lead programs and then describe how cheminformatic analysis assists this process. In particular, scaffold analysis, clustering and property calculations assist in the design of high-throughput screening libraries, the early analysis of hits and then organizing compounds into series for their progression from hits to leads. Additionally, these computational tools can be used in virtual screening to design hit-finding libraries and as procedures to help with early SAR exploration.
Collapse
Affiliation(s)
- Bryan C Duffy
- AMRI, 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | | | | | | |
Collapse
|
45
|
Kühne S, Untucht C, Steinert M, Wätzig H. Fast investigations from biological matrices using CE – Test of a blood–brain barrier model. Electrophoresis 2012; 33:395-401. [DOI: 10.1002/elps.201100282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sascha Kühne
- Technische Universität Braunschweig, Institut für Pharmazeutische Chemie, Braunschweig, Germany
| | - Christopher Untucht
- Technische Universität Braunschweig, Institut für Mikrobiologie, Braunschweig, Germany
| | - Michael Steinert
- Technische Universität Braunschweig, Institut für Mikrobiologie, Braunschweig, Germany
| | - Hermann Wätzig
- Technische Universität Braunschweig, Institut für Pharmazeutische Chemie, Braunschweig, Germany
| |
Collapse
|
46
|
Abstract
In silico tools specifically developed for prediction of pharmacokinetic parameters are of particular interest to pharmaceutical industry because of the high potential of discarding inappropriate molecules during an early stage of drug development itself with consequent saving of vital resources and valuable time. The ultimate goal of the in silico models of absorption, distribution, metabolism, and excretion (ADME) properties is the accurate prediction of the in vivo pharmacokinetics of a potential drug molecule in man, whilst it exists only as a virtual structure. Various types of in silico models developed for successful prediction of the ADME parameters like oral absorption, bioavailability, plasma protein binding, tissue distribution, clearance, half-life, etc. have been briefly described in this chapter.
Collapse
Affiliation(s)
- A K Madan
- Pt. BD Sharma University of Health Sciences, Rohtak, India.
| | | |
Collapse
|
47
|
Liu J, Yu LF, Eaton JB, Caldarone B, Cavino K, Ruiz C, Terry M, Fedolak A, Wang D, Ghavami A, Lowe DA, Brunner D, Lukas RJ, Kozikowski AP. Discovery of isoxazole analogues of sazetidine-A as selective α4β2-nicotinic acetylcholine receptor partial agonists for the treatment of depression. J Med Chem 2011; 54:7280-8. [PMID: 21905669 DOI: 10.1021/jm200855b] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Depression, a common neurological condition, is one of the leading causes of disability and suicide worldwide. Standard treatment, targeting monoamine transporters selective for the neurotransmitters serotonin and noradrenaline, is not able to help many patients that are poor responders. This study advances the development of sazetidine-A analogues that interact with α4β2 nicotinic acetylcholine receptors (nAChRs) as partial agonists and that possess favorable antidepressant profiles. The resulting compounds that are highly selective for the α4β2 subtype of nAChR over α3β4-nAChRs are partial agonists at the α4β2 subtype and have excellent antidepressant behavioral profiles as measured by the mouse forced swim test. Preliminary absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies for one promising ligand revealed an excellent plasma protein binding (PPB) profile, low CYP450-related metabolism, and low cardiovascular toxicity, suggesting it is a promising lead as well as a drug candidate to be advanced through the drug discovery pipeline.
Collapse
Affiliation(s)
- Jianhua Liu
- Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
In silico prediction of unbound brain-to-plasma concentration ratio using machine learning algorithms. J Mol Graph Model 2011; 29:985-95. [DOI: 10.1016/j.jmgm.2011.04.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/08/2011] [Accepted: 04/12/2011] [Indexed: 11/22/2022]
|
49
|
Bolboacă SD, Jäntschi L. Predictivity approach for quantitative structure-property models. Application for blood-brain barrier permeation of diverse drug-like compounds. Int J Mol Sci 2011; 12:4348-64. [PMID: 21845082 PMCID: PMC3155355 DOI: 10.3390/ijms12074348] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/09/2011] [Accepted: 06/24/2011] [Indexed: 01/13/2023] Open
Abstract
The goal of the present research was to present a predictivity statistical approach applied on structure-based prediction models. The approach was applied to the domain of blood-brain barrier (BBB) permeation of diverse drug-like compounds. For this purpose, 15 statistical parameters and associated 95% confidence intervals computed on a 2 × 2 contingency table were defined as measures of predictivity for binary quantitative structure-property models. The predictivity approach was applied on a set of compounds comprised of 437 diverse molecules, 122 with measured BBB permeability and 315 classified as active or inactive. A training set of 81 compounds (~2/3 of 122 compounds assigned randomly) was used to identify the model and a test set of 41 compounds was used as the internal validation set. The molecular descriptor family on vertices cutting was the computation tool used to generate and calculate structural descriptors for all compounds. The identified model was assessed using the predictivity approach and compared to one model previously reported. The best-identified classification model proved to have an accuracy of 69% in the training set (95%CI [58.53–78.37]) and of 73% in the test set (95%CI [58.32–84.77]). The predictive accuracy obtained on the external set proved to be of 73% (95%CI [67.58–77.39]). The classification model proved to have better abilities in the classification of inactive compounds (specificity of ~74% [59.20–85.15]) compared to abilities in the classification of active compounds (sensitivity of ~64% [48.47–77.70]) in the training and external sets. The overall accuracy of the previously reported model seems not to be statistically significantly better compared to the identified model (~81% [71.45–87.80] in the training set, ~93% [78.12–98.17] in the test set and ~79% [70.19–86.58] in the external set). In conclusion, our predictivity approach allowed us to characterize the model obtained on the investigated set of compounds as well as compare it with a previously reported model. According to the obtained results, the reported model should be chosen if a correct classification of inactive compounds is desired and the previously reported model should be chosen if a correct classification of active compounds is most wanted.
Collapse
Affiliation(s)
- Sorana D. Bolboacă
- “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 13 Emil Isac, 400023 Cluj, Romania; E-Mail:
| | - Lorentz Jäntschi
- University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 3-5 Calea Mănăştur, 400372 Cluj, Romania
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +4-0264-401-775; Fax: +4-0264-401-768
| |
Collapse
|
50
|
Lanevskij K, Dapkunas J, Juska L, Japertas P, Didziapetris R. QSAR Analysis of Blood–Brain Distribution: The Influence of Plasma and Brain Tissue Binding. J Pharm Sci 2011; 100:2147-60. [DOI: 10.1002/jps.22442] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/11/2010] [Accepted: 11/16/2010] [Indexed: 11/07/2022]
|