1
|
Williams J, Siramshetty V, Nguyễn ÐT, Padilha EC, Kabir M, Yu KR, Wang AQ, Zhao T, Itkin M, Shinn P, Mathé EA, Xu X, Shah P. Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability. Bioorg Med Chem 2022; 56:116588. [PMID: 35030421 PMCID: PMC9843724 DOI: 10.1016/j.bmc.2021.116588] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 01/19/2023]
Abstract
Membrane permeability plays an important role in oral drug absorption. Caco-2 and Madin-Darby Canine Kidney (MDCK) cell culture systems have been widely used for assessing intestinal permeability. Since most drugs are absorbed passively, Parallel Artificial Membrane Permeability Assay (PAMPA) has gained popularity as a low-cost and high-throughput method in early drug discovery when compared to high-cost, labor intensive cell-based assays. At the National Center for Advancing Translational Sciences (NCATS), PAMPA pH 5 is employed as one of the Tier I absorption, distribution, metabolism, and elimination (ADME) assays. In this study, we have developed a quantitative structure activity relationship (QSAR) model using our ∼6500 compound PAMPA pH 5 permeability dataset. Along with ensemble decision tree-based methods such as Random Forest and eXtreme Gradient Boosting, we employed deep neural network and a graph convolutional neural network to model PAMPA pH 5 permeability. The classification models trained on a balanced training set provided accuracies ranging from 71% to 78% on the external set. Of the four classifiers, the graph convolutional neural network that directly operates on molecular graphs offered the best classification performance. Additionally, an ∼85% correlation was obtained between PAMPA pH 5 permeability and in vivo oral bioavailability in mice and rats. These results suggest that data from this assay (experimental or predicted) can be used to rank-order compounds for preclinical in vivo testing with a high degree of confidence, reducing cost and attrition as well as accelerating the drug discovery process. Additionally, experimental data for 486 compounds (PubChem AID: 1645871) and the best models have been made publicly available (https://opendata.ncats.nih.gov/adme/).
Collapse
Affiliation(s)
- Jordan Williams
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Vishal Siramshetty
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ðắc-Trung Nguyễn
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Elias Carvalho Padilha
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Md Kabir
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Kyeong-Ri Yu
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States,Department of Surgery, Virginia Commonwealth University Health Systems, 1200 E Broad St, Richmond, Virginia 23298, United States
| | - Amy Q. Wang
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Tongan Zhao
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Misha Itkin
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ewy A. Mathé
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Xu
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States,Corresponding Author: Pranav Shah,
| |
Collapse
|
2
|
Faulkner C, de Leeuw NH. Predicting the Membrane Permeability of Fentanyl and Its Analogues by Molecular Dynamics Simulations. J Phys Chem B 2021; 125:8443-8449. [PMID: 34286980 PMCID: PMC8389899 DOI: 10.1021/acs.jpcb.1c05438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The lipid membrane
is considered a crucial component of opioid
general anesthesia. The main drug used for the induction and maintenance
of opioid anesthesia is fentanyl and its various analogues. However,
these drugs have different clinical effects, and detailed atomic-level
insight into the drug–membrane interactions could lead to a
better understanding how these drugs exert their anesthetic properties.
In this study, we have used extensive umbrella sampling molecular
dynamics simulations to study the permeation process of fentanyl and
three of its analogues into a variety of simple phospholipid membrane
models. Our simulations show that we can accurately predict the permeability
coefficients of these drug molecules, which is an important process
in understanding how pharmaceuticals reach their molecular targets.
We were also able to show that one phospholipid provides more accurate
predictions than other lipids commonly used in these types of permeation
studies, which will aid future studies of these types of processes.
Collapse
Affiliation(s)
- Christopher Faulkner
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Nora H de Leeuw
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.,School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| |
Collapse
|
3
|
Sharifian Gh M. Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules. Mol Pharm 2021; 18:2122-2141. [PMID: 33914545 DOI: 10.1021/acs.molpharmaceut.1c00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to measure the passive membrane permeation of drug-like molecules is of fundamental biological and pharmaceutical importance. Of significance, passive diffusion across the cellular membranes plays an effective role in the delivery of many pharmaceutical agents to intracellular targets. Hence, approaches for quantitative measurement of membrane permeability have been the topics of research for decades, resulting in sophisticated biomimetic systems coupled with advanced techniques. In this review, recent developments in experimental approaches along with theoretical models for quantitative and real-time analysis of membrane transport of drug-like molecules through mimetic and living cell membranes are discussed. The focus is on time-resolved fluorescence-based, surface plasmon resonance, and second-harmonic light scattering approaches. The current understanding of how properties of the membrane and permeant affect the permeation process is discussed.
Collapse
Affiliation(s)
- Mohammad Sharifian Gh
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States
| |
Collapse
|
4
|
Lomize AL, Pogozheva ID. Physics-Based Method for Modeling Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. J Chem Inf Model 2019; 59:3198-3213. [PMID: 31259555 DOI: 10.1021/acs.jcim.9b00224] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assessment of permeability is a critical step in the drug development process for selection of drug candidates with favorable ADME properties. We have developed a novel physics-based method for fast computational modeling of passive permeation of diverse classes of molecules across lipid membranes. The method is based on heterogeneous solubility-diffusion theory and operates with all-atom 3D structures of solutes and the anisotropic solvent model of the lipid bilayer characterized by transbilayer profiles of dielectric and hydrogen bonding capacity parameters. The optimal translocation pathway of a solute is determined by moving an ensemble of representative conformations of the molecule through the dioleoyl-phosphatidylcholine (DOPC) bilayer and optimizing their rotational orientations in every point of the transmembrane trajectory. The method calculates (1) the membrane-bound state of the solute molecule; (2) free energy profile of the solute along the permeation pathway; and (3) the permeability coefficient obtained by integration over the transbilayer energy profile and assuming a constant size-dependent diffusivity along the membrane normal. The accuracy of the predictions was evaluated against experimental permeability coefficients measured in pure lipid membranes (for 78 compounds, R2 was 0.88 and rmse was 1.15 log units), PAMPA-DS (for 280 compounds, R2 was 0.75 and rmse was 1.59 log units), BBB (for 182 compounds, R2 was 0.69 and rmse was 0.87 log units), and Caco-2/MDCK assays (for 165 compounds, R2 was 0.52 and rmse was 0.89 log units).
Collapse
Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| |
Collapse
|
5
|
In Silico Prediction of PAMPA Effective Permeability Using a Two-QSAR Approach. Int J Mol Sci 2019; 20:ijms20133170. [PMID: 31261723 PMCID: PMC6651837 DOI: 10.3390/ijms20133170] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/12/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Oral administration is the preferred and predominant route of choice for medication. As such, drug absorption is one of critical drug metabolism and pharmacokinetics (DM/PK) parameters that should be taken into consideration in the process of drug discovery and development. The cell-free in vitro parallel artificial membrane permeability assay (PAMPA) has been adopted as the primary screening to assess the passive diffusion of compounds in the practical applications. A classical quantitative structure–activity relationship (QSAR) model and a machine learning (ML)-based QSAR model were derived using the partial least square (PLS) scheme and hierarchical support vector regression (HSVR) scheme to elucidate the underlying passive diffusion mechanism and to predict the PAMPA effective permeability, respectively, in this study. It was observed that HSVR executed better than PLS as manifested by the predictions of the samples in the training set, test set, and outlier set as well as various statistical assessments. When applied to the mock test, which was designated to mimic real challenges, HSVR also showed better predictive performance. PLS, conversely, cannot cover some mechanistically interpretable relationships between descriptors and permeability. Accordingly, the synergy of predictive HSVR and interpretable PLS models can be greatly useful in facilitating drug discovery and development by predicting passive diffusion.
Collapse
|
6
|
Diukendjieva A, Tsakovska I, Alov P, Pencheva T, Pajeva I, Worth AP, Madden JC, Cronin MT. Advances in the prediction of gastrointestinal absorption: Quantitative Structure-Activity Relationship (QSAR) modelling of PAMPA permeability. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.comtox.2018.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
7
|
Khan MSS, Majid AMSA, Iqbal MA, Majid ASA, Al-Mansoub M, Haque RSMA. Designing the angiogenic inhibitor for brain tumor via disruption of VEGF and IL17A expression. Eur J Pharm Sci 2016; 93:304-18. [PMID: 27552907 DOI: 10.1016/j.ejps.2016.08.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/30/2016] [Accepted: 08/18/2016] [Indexed: 02/08/2023]
Abstract
Glioblastoma multiforme is a highly malignant, heterogenic, and drug resistant tumor. The blood-brain barrier (BBB), systemic cytotoxicity, and limited specificity are the main obstacles in designing brain tumor drugs. In this study a computational approach was used to design brain tumor drugs that could downregulate VEGF and IL17A in glioblastoma multiforme type four. Computational screening tools were used to evaluate potential candidates for antiangiogenic activity, target binding, BBB permeability, and ADME physicochemical properties. Additionally, in vitro cytotoxicity, migration, invasion, tube formation, apoptosis, ROS and ELISA assays were conducted for molecule 6 that was deemed most likely to succeed. The efflux ratio of membrane permeability and calculated docking scores of permeability to glycoproteins (P-gps) were used to determine the BBB permeability of the molecules. The results showed BBB permeation for molecule 6, with the predicted efficiency of 0.55kcal/mol and binding affinity of -37kj/mol corresponding to an experimental efflux ratio of 0.625 and predicted -15kj/mol of binding affinity for P-gps. Molecule 6 significantly affected the angiogenesis pathways by 2-fold downregulation of IL17A and VEGF through inactivation of active sites of HSP90 (predicted binding: -37kj/mol, predicted efficiency: 0.55kcal/mol) and p23 (predicted binding: 12kj/mol, predicted efficiency: 0.17kcal/mol) chaperon proteins. Additionally, molecule 6 activated the 17.38% relative fold of ROS level at 18.3μg/mL and upregulated the caspase which lead the potential synergistic apoptosis through the antiangiogenic activity of molecule 6 and thereby the highly efficacious anticancer upshot. The results indicate that the binding of the molecules to the therapeutic target is not essential to produce a lethal effect on cancer cells of the brain and that antiangiogenic efficiency is much more important.
Collapse
Affiliation(s)
- Md Shamsuddin Sultan Khan
- EMAN Cancer Research Laboratory, Department of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia.
| | - Amin Malik Shah Abdul Majid
- EMAN Cancer Research Laboratory, Department of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia.
| | - Muhammad Adnan Iqbal
- The School of Chemical Sciences, Universiti Sains Malaysia (USM), 11800 Penang, Malaysia
| | - Aman Shah Abdul Majid
- EMAN Cancer Research Laboratory, Department of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia; QUEST International University, Ipoh, Perak, Malaysia
| | - Majed Al-Mansoub
- EMAN Cancer Research Laboratory, Department of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
| | | |
Collapse
|
8
|
Leung SSF, Sindhikara D, Jacobson MP. Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. J Chem Inf Model 2016; 56:924-9. [PMID: 27135806 DOI: 10.1021/acs.jcim.6b00005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We investigate the relationship between passive permeability and molecular size, in the context of solubility-diffusion theory, using a diverse compound set with molecular weights ranging from 151 to 828, which have all been characterized in a consistent manner using the RRCK cell monolayer assay. Computationally, each compound was subjected to extensive conformational search and physics-based permeability prediction, and multiple linear regression analyses were subsequently performed to determine, empirically, the relative contributions of hydrophobicity and molecular size to passive permeation in the RRCK assay. Additional analyses of Log D and PAMPA data suggest that these measurements are not size selective, a possible reason for their sometimes weak correlation with cell-based permeability.
Collapse
Affiliation(s)
- Siegfried S F Leung
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Daniel Sindhikara
- Schrödinger, Inc., 120 West 45th Street, 17th Floor, New York, New York 10036, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| |
Collapse
|
9
|
Cardenas AE, Elber R. Computational study of peptide permeation through membrane: Searching for hidden slow variables. Mol Phys 2013; 111:3565-3578. [PMID: 26203198 PMCID: PMC4507298 DOI: 10.1080/00268976.2013.842010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Atomically detailed molecular dynamics trajectories in conjunction with Milestoning are used to analyze the different contributions of coarse variables to the permeation process of a small peptide (N-acetyl-L-tryptophanamide, NATA) through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane. The peptide reverses its overall orientation as it permeates through the biological bilayer. The large change in orientation is investigated explicitly but is shown to impact the free energy landscape and permeation time only moderately. Nevertheless, a significant difference in permeation properties of the two halves of the membrane suggests the presence of other hidden slow variables. We speculate, based on calculation of the potential of mean force, that a conformational transition of NATA makes significant contribution to these differences. Other candidates for hidden slow variables may include water permeation and collective motions of phospholipids.
Collapse
Affiliation(s)
- Alfredo E. Cardenas
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin TX 78712, USA
| | - Ron Elber
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin TX 78712, USA
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin TX 78712, USA
| |
Collapse
|
10
|
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
|
11
|
Swift RV, Amaro RE. Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR? Chem Biol Drug Des 2013; 81:61-71. [PMID: 23066853 PMCID: PMC3527668 DOI: 10.1111/cbdd.12074] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
It is widely recognized that adsorption, distribution, metabolism, excretion, and toxicology liabilities kill the majority of drug candidates that progress to clinical trials. The development of computational models to predict small molecule membrane permeability is therefore of considerable scientific and public health interest. Empirical qualitative structure permeability relationship models of permeability have been a mainstay in industrial applications, but lack a deep understanding of the underlying biologic physics. Others and we have shown that implicit solvent models to predict passive permeability for small molecules exhibit mediocre predictive performance when validated across experimental test sets. Given the vast increase in computer power, more efficient parallelization schemes, and extension of current atomistic simulation codes to general use graphical processing units, the development and application of physical models based on all-atom simulations may now be feasible. Preliminary results from rigorous free energy calculations using all-atom simulations indicate that performance relative to implicit solvent models may be improved, but many outstanding questions remain. Here, we review the current state-of-the-art physical models for passive membrane permeability prediction and present a prospective look at promising new directions for all-atom approaches.
Collapse
|
12
|
Leung SSF, Mijalkovic J, Borrelli K, Jacobson MP. Testing physical models of passive membrane permeation. J Chem Inf Model 2012; 52:1621-36. [PMID: 22621168 PMCID: PMC3383340 DOI: 10.1021/ci200583t] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The biophysical basis of passive membrane permeability is well-understood, but most methods for predicting membrane permeability in the context of drug design are based on statistical relationships that indirectly capture the key physical aspects. Here, we investigate molecular mechanics-based models of passive membrane permeability and evaluate their performance against different types of experimental data, including parallel artificial membrane permeability assays (PAMPA), cell-based assays, in vivo measurements, and other in silico predictions. The experimental data sets we use in these tests are diverse, including peptidomimetics, congeneric series, and diverse FDA approved drugs. The physical models are not specifically trained for any of these data sets; rather, input parameters are based on standard molecular mechanics force fields, such as partial charges, and an implicit solvent model. A systematic approach is taken to analyze the contribution from each component in the physics-based permeability model. A primary factor in determining rates of passive membrane permeation is the conformation-dependent free energy of desolvating the molecule, and this measure alone provides good agreement with experimental permeability measurements in many cases. Other factors that improve agreement with experimental data include deionization and estimates of entropy losses of the ligand and the membrane, which lead to size-dependence of the permeation rate.
Collapse
Affiliation(s)
- Siegfried S. F. Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94158
| | - Jona Mijalkovic
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94158
| | - Kenneth Borrelli
- Schrödinger, Inc. 120 West 4 Street, 32 Floor, New York, New York, 10036
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94158
| |
Collapse
|
13
|
Rafi SB, Hearn BR, Vedantham P, Jacobson MP, Renslo AR. Predicting and improving the membrane permeability of peptidic small molecules. J Med Chem 2012; 55:3163-9. [PMID: 22394492 DOI: 10.1021/jm201634q] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We evaluate experimentally and computationally the membrane permeability of matched sets of peptidic small molecules bearing natural or bioisosteric unnatural amino acids. We find that the intentional introduction of hydrogen bond acceptor-donor pairs in such molecules can improve membrane permeability while retaining or improving other favorable drug-like properties. We employ an all-atom force field based method to calculate changes in free energy associated with the transfer of the peptidic molecules from water to membrane. This computational method correctly predicts rank order experimental permeability trends within congeneric series and is much more predictive than calculations (e.g., clogP) that do not consider three-dimensional conformation.
Collapse
Affiliation(s)
- Salma B Rafi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
| | | | | | | | | |
Collapse
|
14
|
Rand AC, Leung SSF, Eng H, Rotter CJ, Sharma R, Kalgutkar AS, Zhang Y, Varma MV, Farley KA, Khunte B, Limberakis C, Price DA, Liras S, Mathiowetz AM, Jacobson MP, Lokey RS. Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance(). MEDCHEMCOMM 2012; 3:1282-1289. [PMID: 23133740 DOI: 10.1039/c2md20203d] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A series of cyclic peptides were designed and prepared to investigate the physicochemical properties that affect oral bioavailabilty of this chemotype in rats. In particular, the ionization state of the peptide was examined by the incorporation of naturally occurring amino acid residues that are charged in differing regions of the gut. In addition, data was generated in a variety of in vitro assays and the usefulness of this data in predicting the subsequent oral bioavailability observed in the rat is discussed.
Collapse
Affiliation(s)
- Arthur C Rand
- Department of Chemistry, University of California Santa Cruz, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Swift RV, Amaro RE. Modeling the pharmacodynamics of passive membrane permeability. J Comput Aided Mol Des 2011; 25:1007-17. [PMID: 22042376 PMCID: PMC3223344 DOI: 10.1007/s10822-011-9480-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 10/17/2011] [Indexed: 11/17/2022]
Abstract
Small molecule permeability through cellular membranes is critical to a better understanding of pharmacodynamics and the drug discovery endeavor. Such permeability may be estimated as a function of the free energy change of barrier crossing by invoking the barrier domain model, which posits that permeation is limited by passage through a single “barrier domain” and assumes diffusivity differences among compounds of similar structure are negligible. Inspired by the work of Rezai and co-workers (JACS 128:14073–14080, 2006), we estimate this free energy change as the difference in implicit solvation free energies in chloroform and water, but extend their model to include solute conformational affects. Using a set of eleven structurally diverse FDA approved compounds and a set of thirteen congeneric molecules, we show that the solvation free energies are dominated by the global minima, which allows solute conformational distributions to be effectively neglected. For the set of tested compounds, the best correlation with experiment is obtained when the implicit chloroform global minimum is used to evaluate the solvation free energy difference.
Collapse
Affiliation(s)
- Robert V Swift
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697-3958, USA
| | | |
Collapse
|
16
|
Dolghih E, Bryant C, Renslo AR, Jacobson MP. Predicting binding to p-glycoprotein by flexible receptor docking. PLoS Comput Biol 2011; 7:e1002083. [PMID: 21731480 PMCID: PMC3121697 DOI: 10.1371/journal.pcbi.1002083] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 04/22/2011] [Indexed: 01/07/2023] Open
Abstract
P-glycoprotein (P-gp) is an ATP-dependent transport protein that is selectively expressed at entry points of xenobiotics where, acting as an efflux pump, it prevents their entering sensitive organs. The protein also plays a key role in the absorption and blood-brain barrier penetration of many drugs, while its overexpression in cancer cells has been linked to multidrug resistance in tumors. The recent publication of the mouse P-gp crystal structure revealed a large and hydrophobic binding cavity with no clearly defined sub-sites that supports an “induced-fit” ligand binding model. We employed flexible receptor docking to develop a new prediction algorithm for P-gp binding specificity. We tested the ability of this method to differentiate between binders and nonbinders of P-gp using consistently measured experimental data from P-gp efflux and calcein-inhibition assays. We also subjected the model to a blind test on a series of peptidic cysteine protease inhibitors, confirming the ability to predict compounds more likely to be P-gp substrates. Finally, we used the method to predict cellular metabolites that may be P-gp substrates. Overall, our results suggest that many P-gp substrates bind deeper in the cavity than the cyclic peptide in the crystal structure and that specificity in P-gp is better understood in terms of physicochemical properties of the ligands (and the binding site), rather than being defined by specific sub-sites. With many drugs failing in the preclinical stages of drug discovery due to undesirable ADMETox (absorption, distribution, metabolism, excretion and toxicity) properties, improvement of these properties early on in the process, alongside the optimization of the compound activity, is emerging as a new focus in the pharmaceutical field. One of the key players affecting pharmacokinetic profiles of many clinically relevant compounds is an active efflux transporter, P-glycoprotein. Expressed predominantly at various physiological barriers, it can influence drug absorption (intestinal epithelium, colon), drug elimination (kidney proximal tubules) and drug penetration of the blood-brain barrier (endothelial brain cells). Moreover, its increased expression in cancer cells has been linked to resistance to multiple drugs in tumors. In this study we describe a computational approach that allows prediction of which compounds are more likely to interact with P-gp. We have tested the ability of this method to differentiate between binders and nonbinders of P-gp by using consistently measured in vitro experimental data. We also implemented a blind test on a series of peptidic cysteine protease inhibitors with encouraging outcome. Overall, our results suggest that this method provides a qualitative, quick, and inexpensive way of evaluating potential drug efflux problem at the early stages of drug development.
Collapse
Affiliation(s)
- Elena Dolghih
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.
| | | | | | | |
Collapse
|
17
|
Sugano K, Cucurull‐Sanchez L, Bennett J. Membrane Permeability – Measurement and Prediction in Drug Discovery. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/9783527627448.ch6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|