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Malani M, Hiremath MS, Sharma S, Jhunjhunwala M, Gayen S, Hota C, Nirmal J. Interaction of systemic drugs causing ocular toxicity with organic cation transporter: an artificial intelligence prediction. J Biomol Struct Dyn 2024; 42:5207-5218. [PMID: 37340665 DOI: 10.1080/07391102.2023.2226717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
Chronic disease patients (cancer, arthritis, cardiovascular diseases) undergo long-term systemic drug treatment. Membrane transporters in ocular barriers could falsely recognize these drugs and allow their trafficking into the eye from systemic circulation. Hence, despite their pharmacological activity, these drugs accumulate and cause toxicity at the non-target site, such as the eye. Since around 40% of clinically used drugs are organic cation in nature, it is essential to understand the role of organic cation transporter (OCT1) in ocular barriers to facilitate the entry of systemic drugs into the eye. We applied machine learning techniques and computer simulation models (molecular dynamics and metadynamics) in the current study to predict the potential OCT1 substrates. Artificial intelligence models were developed using a training dataset of a known substrates and non-substrates of OCT1 and predicted the potential OCT1 substrates from various systemic drugs causing ocular toxicity. Computer simulation studies was performed by developing the OCT1 homology model. Molecular dynamic simulations equilibrated the docked protein-ligand complex. And metadynamics revealed the movement of substrates across the transporter with minimum free energy near the binding pocket. The machine learning model showed an accuracy of about 80% and predicted the potential substrates for OCT1 among systemic drugs causing ocular toxicity - not known earlier, such as cyclophosphamide, bupivacaine, bortezomib, sulphanilamide, tosufloxacin, topiramate, and many more. However, further invitro and invivo studies are required to confirm these predictions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manisha Malani
- Translational Pharmaceutics Research Laboratory, Birla Institute of Technology and Science-Pilani, Hyderabad, Telangana, India
| | - Manthan S Hiremath
- Translational Pharmaceutics Research Laboratory, Birla Institute of Technology and Science-Pilani, Hyderabad, Telangana, India
| | - Surbhi Sharma
- Department of Computer Science and Information Systems (CSIS), Birla Institute of Technology & Science-Pilani, Hyderabad, Telangana, India
| | - Manisha Jhunjhunwala
- Department of Computer Science and Information Systems (CSIS), Birla Institute of Technology & Science-Pilani, Hyderabad, Telangana, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Chittaranjan Hota
- Department of Computer Science and Information Systems (CSIS), Birla Institute of Technology & Science-Pilani, Hyderabad, Telangana, India
| | - Jayabalan Nirmal
- Translational Pharmaceutics Research Laboratory, Birla Institute of Technology and Science-Pilani, Hyderabad, Telangana, India
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Kasten A, Cascorbi I. Understanding the impact of ABCG2 polymorphisms on drug pharmacokinetics: focus on rosuvastatin and allopurinol. Expert Opin Drug Metab Toxicol 2024; 20:519-528. [PMID: 38809523 DOI: 10.1080/17425255.2024.2362184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/28/2024] [Indexed: 05/30/2024]
Abstract
INTRODUCTION In addition to the well-established understanding of the pharmacogenetics of drug-metabolizing enzymes, there is growing data on the effects of genetic variation in drug transporters, particularly ATP-binding cassette (ABC) transporters. However, the evidence that these genetic variants can be used to predict drug effects and to adjust individual dosing to avoid adverse events is still limited. AREAS COVERED This review presents a summary of the current literature from the PubMed database as of February 2024 regarding the impact of genetic variants on ABCG2 function and their relevance to the clinical use of the HMG-CoA reductase inhibitor rosuvastatin and the xanthine oxidase inhibitor allopurinol. EXPERT OPINION Although there are pharmacogenetic guidelines for the ABCG2 missense variant Q141K, there is still some conflicting data regarding the clinical benefits of these recommendations. Some caution appears to be warranted in homozygous ABCG2 Q141K carriers when rosuvastatin is administered at higher doses and such information is already included in the drug label. The benefit of dose adaption to lower possible side effects needs to be evaluated in prospective clinical studies.
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Affiliation(s)
- Anne Kasten
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany
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3
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da Silva Zanzarini I, Henrique Kita D, Scheiffer G, Karoline Dos Santos K, de Paula Dutra J, Augusto Pastore M, Gomes de Moraes Rego F, Picheth G, Ambudkar SV, Pulvirenti L, Cardullo N, Rotuno Moure V, Muccilli V, Tringali C, Valdameri G. Magnolol derivatives as specific and noncytotoxic inhibitors of breast cancer resistance protein (BCRP/ABCG2). Bioorg Chem 2024; 146:107283. [PMID: 38513324 PMCID: PMC11069345 DOI: 10.1016/j.bioorg.2024.107283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/20/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
The breast cancer resistance protein (BCRP/ABCG2) transporter mediates the efflux of numerous antineoplastic drugs, playing a central role in multidrug resistance related to cancer. The absence of successful clinical trials using specific ABCG2 inhibitors reveals the urge to identify new compounds to attend this critical demand. In this work, a series of 13 magnolol derivatives was tested as ABCG2 inhibitors. Only two compounds, derivatives 10 and 11, showed partial and complete ABCG2 inhibitory effect, respectively. This inhibition was selective toward ABCG2, since none of the 13 compounds inhibited neither P-glycoprotein nor MRP1. Both inhibitors (10 and 11) were not transported by ABCG2 and demonstrated a low cytotoxic profile even at high concentrations (up to 100 µM). 11 emerged as the most promising compound of the series, considering the ratio between cytotoxicity (IG50) and ABCG2 inhibition potency (IC50), showing a therapeutic ratio (TR) higher than observed for 10 (10.5 versus 1.6, respectively). This derivative showed a substrate-independent and a mixed type of inhibition. The effect of compound 11 on the ABCG2 ATPase activity and thermostability revealed allosteric protein changes. This compound did not affect the expression levels of ABCG2 and increased the binding of the conformational-sensitive antibody 5D3. A docking study showed that 11 did not share the same binding site with ABCG2 substrate mitoxantrone. Finally, 11 could revert the chemoresistance to SN-38 mediated by ABCG2.
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Affiliation(s)
- Isadora da Silva Zanzarini
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Diogo Henrique Kita
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil; Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gustavo Scheiffer
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Kelly Karoline Dos Santos
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Julia de Paula Dutra
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Matteo Augusto Pastore
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | | | - Geraldo Picheth
- Department of Clinical Analysis, Federal University of Parana, Curitiba, Brazil
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Luana Pulvirenti
- Istituto di Chimica Biomolecolare del Consiglio Nazionale delle Ricerche (ICB-CNR), Catania, Italy
| | - Nunzio Cardullo
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Vivian Rotuno Moure
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Vera Muccilli
- Department of Chemical Sciences, University of Catania, Catania, Italy.
| | - Corrado Tringali
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Glaucio Valdameri
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil.
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Gao Y, Wei C, Luo L, Tang Y, Yu Y, Li Y, Xing J, Pan X. Membrane-assisted tariquidar access and binding mechanisms of human ATP-binding cassette transporter P-glycoprotein. Front Mol Biosci 2024; 11:1364494. [PMID: 38560519 PMCID: PMC10979361 DOI: 10.3389/fmolb.2024.1364494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
The human multidrug transporter P-glycoprotein (P-gp) is physiologically essential and of key relevance to biomedicine. Recent structural studies have shed light on the mode of inhibition of the third-generation inhibitors for human P-gp, but the molecular mechanism by which these inhibitors enter the transmembrane sites remains poorly understood. In this study, we utilized all-atom molecular dynamics (MD) simulations to characterize human P-gp dynamics under a potent inhibitor, tariquidar, bound condition, as well as the atomic-level binding pathways in an explicit membrane/water environment. Extensive unbiased simulations show that human P-gp remains relatively stable in tariquidar-free and bound states, while exhibiting a high dynamic binding mode at either the drug-binding pocket or the regulatory site. Free energy estimations by partial nudged elastic band (PNEB) simulations and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method identify two energetically favorable binding pathways originating from the cytoplasmic gate with an extended tariquidar conformation. Interestingly, free tariquidar in the lipid membrane predominantly adopts extended conformations similar to those observed at the regulatory site. These results suggest that membrane lipids may preconfigure tariquidar into an active ligand conformation for efficient binding to the regulatory site. However, due to its conformational plasticity, tariquidar ultimately moves toward the drug-binding pocket in both pathways, explaining how it acts as a substrate at low concentrations. Our molecular findings propose a membrane-assisted mechanism for the access and binding of the third-generation inhibitors to the binding sites of human P-gp, and offer deeper insights into the molecule design of more potent inhibitors against P-gp-mediated drug resistance.
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Affiliation(s)
- Yingjie Gao
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Caiyan Wei
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Lanxin Luo
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Yang Tang
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yongzhen Yu
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yaling Li
- Department of Pharmacy, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Juan Xing
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Xianchao Pan
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
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Dudas B, Miteva MA. Computational and artificial intelligence-based approaches for drug metabolism and transport prediction. Trends Pharmacol Sci 2024; 45:39-55. [PMID: 38072723 DOI: 10.1016/j.tips.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/07/2024]
Abstract
Drug metabolism and transport, orchestrated by drug-metabolizing enzymes (DMEs) and drug transporters (DTs), are implicated in drug-drug interactions (DDIs) and adverse drug reactions (ADRs). Reliable and precise predictions of DDIs and ADRs are critical in the early stages of drug development to reduce the rate of drug candidate failure. A variety of experimental and computational technologies have been developed to predict DDIs and ADRs. Recent artificial intelligence (AI) approaches offer new opportunities for better predicting and understanding the complex processes related to drug metabolism and transport. We summarize the role of major DMEs and DTs, and provide an overview of current progress in computational approaches for the prediction of drug metabolism, transport, and DDIs, with an emphasis on AI including machine learning (ML) and deep learning (DL) modeling.
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Affiliation(s)
- Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Maria A Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France.
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Dutra JDP, Scheiffer G, Kronenberger T, Gomes LJC, Zanzarini I, dos Santos KK, Tonduru AK, Poso A, Rego FGDM, Picheth G, Valdameri G, Moure VR. Structural and molecular characterization of lopinavir and ivermectin as breast cancer resistance protein (BCRP/ABCG2) inhibitors. EXCLI JOURNAL 2023; 22:1155-1172. [PMID: 38204967 PMCID: PMC10776880 DOI: 10.17179/excli2023-6427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 01/12/2024]
Abstract
A current clinical challenge in cancer is multidrug resistance (MDR) mediated by ABC transporters. Breast cancer resistance protein (BCRP) or ABCG2 transporter is one of the most important ABC transporters implicated in MDR and the use of inhibitors is a promising approach to overcome the resistance in cancer. This study aimed to characterize the molecular mechanism of ABCG2 inhibitors identified by a repurposing drug strategy using antiviral, anti-inflammatory and antiparasitic agents. Lopinavir and ivermectin can be considered as pan-inhibitors of ABC transporters, since both compounds inhibited ABCG2, P-glycoprotein and MRP1. They inhibited ABCG2 activity showing IC50 values of 25.5 and 23.4 µM, respectively. These drugs were highly cytotoxic and not transported by ABCG2. Additionally, these drugs increased the 5D3 antibody binding and did not affect the mRNA and protein expression levels. Cell-based analysis of the type of inhibition suggested a non-competitive inhibition, which was further corroborated by in silico approaches of molecular docking and molecular dynamics simulations. These results showed an overlap of the lopinavir and ivermectin binding sites on ABCG2, mainly interacting with E446 residue. However, the substrate mitoxantrone occupies a different site, binding to the F436 region, closer to the L554/L555 plug. In conclusion, these results revealed the mechanistic basis of lopinavir and ivermectin interaction with ABCG2. See also the Graphical abstract(Fig. 1).
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Affiliation(s)
- Julia de Paula Dutra
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Gustavo Scheiffer
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- (a) Department of Internal Medicine VIII, University Hospital Tuebingen, Otfried-Müller-Strasse 14, Tuebingen DE 72076, Germany, (b) Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany, (c) Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany, (d) Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | - Lucas Julian Cruz Gomes
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Isadora Zanzarini
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Kelly Karoline dos Santos
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Arun K. Tonduru
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- (a) Department of Internal Medicine VIII, University Hospital Tuebingen, Otfried-Müller-Strasse 14, Tuebingen DE 72076, Germany, (b) Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany, (c) Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany, (d) Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | | | - Geraldo Picheth
- Graduate Program in Pharmaceutical Sciences, Federal University of Parana, Curitiba, PR, Brazil
| | - Glaucio Valdameri
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Vivian Rotuno Moure
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
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Pakuła K, Sequeiros-Borja C, Biała-Leonhard W, Pawela A, Banasiak J, Bailly A, Radom M, Geisler M, Brezovsky J, Jasiński M. Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters. Cell Mol Life Sci 2023; 80:105. [PMID: 36952129 PMCID: PMC10036432 DOI: 10.1007/s00018-023-04751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Abstract
ABCG46 of the legume Medicago truncatula is an ABC-type transporter responsible for highly selective translocation of the phenylpropanoids, 4-coumarate, and liquiritigenin, over the plasma membrane. To investigate molecular determinants of the observed substrate selectivity, we applied a combination of phylogenetic and biochemical analyses, AlphaFold2 structure prediction, molecular dynamics simulations, and mutagenesis. We discovered an unusually narrow transient access path to the central cavity of MtABCG46 that constitutes an initial filter responsible for the selective translocation of phenylpropanoids through a lipid bilayer. Furthermore, we identified remote residue F562 as pivotal for maintaining the stability of this filter. The determination of individual amino acids that impact the selective transport of specialized metabolites may provide new opportunities associated with ABCGs being of interest, in many biological scenarios.
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Affiliation(s)
- Konrad Pakuła
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614, Poznan, Poland
| | - Carlos Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Wanda Biała-Leonhard
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aleksandra Pawela
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Joanna Banasiak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aurélien Bailly
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Marcin Radom
- Department of Structural Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z.Noskowskiego12/14, 61-704, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Markus Geisler
- Department of Biology, University of Fribourg, Chem. du Musée 10, 1700, Fribourg, Switzerland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109, Warsaw, Poland.
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznan, Poland.
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632, Poznan, Poland.
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Rasouli A, Yu Q, Dehghani-Ghahnaviyeh S, Wen PC, Kowal J, Locher KP, Tajkhorshid E. Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. Proc Natl Acad Sci U S A 2023; 120:e2213437120. [PMID: 36580587 PMCID: PMC9910490 DOI: 10.1073/pnas.2213437120] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/20/2022] [Indexed: 12/31/2022] Open
Abstract
ABCG2 is an ATP-binding cassette (ABC) transporter that extrudes a wide range of xenobiotics and drugs from the cell and contributes to multidrug resistance in cancer cells. Following our recent structural characterization of topotecan-bound ABCG2, here, we present cryo-EM structures of ABCG2 under turnover conditions in complex with a special modulator and slow substrate, tariquidar, in nanodiscs. The structures reveal that similar to topotecan, tariquidar induces two distinct ABCG2 conformations under turnover conditions (turnover-1 and turnover-2). μs-scale molecular dynamics simulations of drug-bound and apo ABCG2 in native-like lipid bilayers, in both topotecan- and tariquidar-bound states, characterize the ligand size as a major determinant of its binding stability. The simulations highlight direct lipid-drug interactions for the smaller topotecan, which exhibits a highly dynamic binding mode. In contrast, the larger tariquidar occupies most of the available volume in the binding pocket, thus leaving little space for lipids to enter the cavity and interact with it. Similarly, when simulating ABCG2 in the apo inward-open state, we also observe spontaneous penetration of phospholipids into the binding cavity. The captured phospholipid diffusion pathway into ABCG2 offers a putative general path to recruit any hydrophobic/amphiphilic substrates directly from the membrane. Our simulations also reveal that ABCG2 rejects cholesterol as a substrate, which is omnipresent in plasma membranes that contain ABCG2. At the same time, cholesterol is found to prohibit the penetration of phospholipids into ABCG2. These molecular findings have direct functional ramifications on ABCG2's function as a transporter.
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Affiliation(s)
- Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, University of Illinois, Urbana, IL61801
- Center for Biophysics and Quantitative Biology University of Illinois, Urbana, IL61801
| | - Qin Yu
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, University of Illinois, Urbana, IL61801
- Center for Biophysics and Quantitative Biology University of Illinois, Urbana, IL61801
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, University of Illinois, Urbana, IL61801
- Center for Biophysics and Quantitative Biology University of Illinois, Urbana, IL61801
| | - Julia Kowal
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Kaspar P. Locher
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, University of Illinois, Urbana, IL61801
- Center for Biophysics and Quantitative Biology University of Illinois, Urbana, IL61801
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9
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Constantinescu T, Mihis AG. Two Important Anticancer Mechanisms of Natural and Synthetic Chalcones. Int J Mol Sci 2022; 23:11595. [PMID: 36232899 PMCID: PMC9570335 DOI: 10.3390/ijms231911595] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
ATP-binding cassette subfamily G and tubulin pharmacological mechanisms decrease the effectiveness of anticancer drugs by modulating drug absorption and by creating tubulin assembly through polymerization. A series of natural and synthetic chalcones have been reported to have very good anticancer activity, with a half-maximal inhibitory concentration lower than 1 µM. By modulation, it is observed in case of the first mechanism that methoxy substituents on the aromatic cycle of acetophenone residue and substitution of phenyl nucleus by a heterocycle and by methoxy or hydroxyl groups have a positive impact. To inhibit tubulin, compounds bind to colchicine binding site. Presence of methoxy groups, amino groups or heterocyclic substituents increase activity.
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Affiliation(s)
- Teodora Constantinescu
- Department of Chemistry, Faculty of Pharmacy, Iuliu Hatieganu University, 400012 Cluj-Napoca, Romania
| | - Alin Grig Mihis
- Advanced Materials and Applied Technologies Laboratory, Institute of Research-Development-Innovation in Applied Natural Sciences, “Babes-Bolyai” University, Fantanele Str. 30, 400294 Cluj-Napoca, Romania
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10
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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11
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Farhat D, Rezaei F, Ristovski M, Yang Y, Stancescu A, Dzimkova L, Samnani S, Couture JF, Lee JY. Structural analysis of cholesterol binding and sterol selectivity by ABCG5/G8. J Mol Biol 2022; 434:167795. [PMID: 35988751 DOI: 10.1016/j.jmb.2022.167795] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/30/2022] [Accepted: 08/15/2022] [Indexed: 01/08/2023]
Abstract
The ATP-binding cassette (ABC) sterol transporters are responsible for maintaining cholesterol homeostasis in mammals by participating in reverse cholesterol transport (RCT) or transintestinal cholesterol efflux (TICE). The heterodimeric ABCG5/G8 carries out selective sterol excretion, preventing the abnormal accumulation of plant sterols in human bodies, while homodimeric ABCG1 contributes to the biogenesis and metabolism of high-density lipoproteins. A sterol-binding site on ABCG5/G8 was proposed at the interface of the transmembrane domain and the core of lipid bilayers. In this study, we have determined the crystal structure of ABCG5/G8 in a cholesterol-bound state. The structure combined with amino acid sequence analysis shows that in the proximity of the sterol-binding site, a highly conserved phenylalanine array supports functional implications for ABCG cholesterol/sterol transporters. Lastly, in silico docking analysis of cholesterol and stigmasterol (a plant sterol) suggests sterol-binding selectivity on ABCG5/G8, but not ABCG1. Together, our results provide a structural basis for cholesterol binding on ABCG5/G8 and the sterol selectivity by ABCG transporters.
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Affiliation(s)
- Danny Farhat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Fatemeh Rezaei
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Milica Ristovski
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Translational and Molecular Medicine Program, Faculty of Medicine, University of Ottawa, Ontario, Ottawa, Canada
| | - Yidai Yang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Albert Stancescu
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Biochemistry Program, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lucia Dzimkova
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Biochemistry Program, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Sabrina Samnani
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Biochemistry Program, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jyh-Yeuan Lee
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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12
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Tordai H, Suhajda E, Sillitoe I, Nair S, Varadi M, Hegedus T. Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology. Int J Mol Sci 2022; 23:8877. [PMID: 36012140 PMCID: PMC9408558 DOI: 10.3390/ijms23168877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 02/06/2023] Open
Abstract
The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.
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Affiliation(s)
- Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
| | - Erzsebet Suhajda
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, 1111 Budapest, Hungary
- Wigner Research Centre for Physics, 1121 Budapest, Hungary
| | - Ian Sillitoe
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Sreenath Nair
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Mihaly Varadi
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Tamas Hegedus
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, 1052 Budapest, Hungary
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13
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Dudas B, Decleves X, Cisternino S, Perahia D, Miteva M. ABCG2/BCRP transport mechanism revealed through kinetically excited targeted molecular dynamics simulations. Comput Struct Biotechnol J 2022; 20:4195-4205. [PMID: 36016719 PMCID: PMC9389183 DOI: 10.1016/j.csbj.2022.07.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
ABCG2/BCRP is an ABC transporter that plays an important role in tissue protection by exporting endogenous substrates and xenobiotics. ABCG2 is of major interest due to its involvement in multidrug resistance (MDR), and understanding its complex efflux mechanism is essential to preventing MDR and drug-drug interactions (DDI). ABCG2 export is characterized by two major conformational transitions between inward- and outward-facing states, the structures of which have been resolved. Yet, the entire transport cycle has not been characterized to date. Our study bridges the gap between the two extreme conformations by studying connecting pathways. We developed an innovative approach to enhance molecular dynamics simulations, ‘kinetically excited targeted molecular dynamics’, and successfully simulated the transitions between inward- and outward-facing states in both directions and the transport of the endogenous substrate estrone 3-sulfate. We discovered an additional pocket between the two substrate-binding cavities and found that the presence of the substrate in the first cavity is essential to couple the movements between the nucleotide-binding and transmembrane domains. Our study shed new light on the complex efflux mechanism, and we provided transition pathways that can help to identify novel substrates and inhibitors of ABCG2 and probe new drug candidates for MDR and DDI.
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14
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Hegedűs T, Geisler M, Lukács GL, Farkas B. Ins and outs of AlphaFold2 transmembrane protein structure predictions. Cell Mol Life Sci 2022; 79:73. [PMID: 35034173 PMCID: PMC8761152 DOI: 10.1007/s00018-021-04112-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/25/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
Abstract
Transmembrane (TM) proteins are major drug targets, but their structure determination, a prerequisite for rational drug design, remains challenging. Recently, the DeepMind's AlphaFold2 machine learning method greatly expanded the structural coverage of sequences with high accuracy. Since the employed algorithm did not take specific properties of TM proteins into account, the reliability of the generated TM structures should be assessed. Therefore, we quantitatively investigated the quality of structures at genome scales, at the level of ABC protein superfamily folds and for specific membrane proteins (e.g. dimer modeling and stability in molecular dynamics simulations). We tested template-free structure prediction with a challenging TM CASP14 target and several TM protein structures published after AlphaFold2 training. Our results suggest that AlphaFold2 performs well in the case of TM proteins and its neural network is not overfitted. We conclude that cautious applications of AlphaFold2 structural models will advance TM protein-associated studies at an unexpected level.
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Affiliation(s)
- Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
- TKI, Eötvös Loránd Research Network, Budapest, Hungary.
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Bianka Farkas
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
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