1
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Croney K, McCarty J. Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics. J Phys Chem B 2024; 128:3102-3112. [PMID: 38516924 PMCID: PMC11000218 DOI: 10.1021/acs.jpcb.3c07972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
The yeast cytosine deaminase (yCD) enzyme/5-fluorocytosine prodrug system is a promising candidate for targeted chemotherapeutics. After conversion of the prodrug into the toxic chemotherapeutic drug, 5-fluorouracil (5-FU), the slow product release from the enzyme limits the overall catalytic efficiency of the enzyme/prodrug system. Here, we present a computational study of the product release of the anticancer drug, 5-FU, from yCD using metadynamics. We present a comparison of the 5-FU drug to the natural enzyme product, uracil. We use volume-based metadynamics to compute the free energy landscape for product release and show a modest binding affinity for the product to the enzyme, consistent with experiments. Next, we use infrequent metadynamics to estimate the unbiased release rate from Kramers time-dependent rate theory and find a favorable comparison to experiment with a slower rate of product release for the 5-FU system. Our work demonstrates how adaptive sampling methods can be used to study the protein-ligand unbinding process for engineering enzyme/prodrug systems and gives insights into the molecular mechanism of product release for the yCD/5-FU system.
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Affiliation(s)
- Kayla
A. Croney
- Department of Chemistry, Western
Washington University, Bellingham, Washington 98225, United States
| | - James McCarty
- Department of Chemistry, Western
Washington University, Bellingham, Washington 98225, United States
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2
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Mosa FES, AlRawashdeh S, El-Kadi AOS, Barakat K. Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations. J Chem Inf Model 2024; 64:2021-2034. [PMID: 38457778 DOI: 10.1021/acs.jcim.4c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that mediates biological signals to control various complicated cellular functions. It plays a crucial role in environmental sensing and xenobiotic metabolism. Dysregulation of AhR is associated with health concerns, including cancer and immune system disorders. Upon binding to AhR ligands, AhR, along with heat shock protein 90 and other partner proteins undergoes a transformation in the nucleus, heterodimerizes with the aryl hydrocarbon receptor nuclear translocator (ARNT), and mediates numerous biological functions by inducing the transcription of various AhR-responsive genes. In this manuscript, the 3-dimensional structure of the entire human AhR is obtained using an artificial intelligence tool, and molecular dynamics (MD) simulations are performed to study different structural conformations. These conformations provide insights into the protein's function and movement in response to ligand binding. Understanding the dynamic behavior of AhR will contribute to the development of targeted therapies for associated health conditions. Therefore, we employ well-tempered metadynamics (WTE-metaD) simulations to explore the conformational landscape of AhR and obtain a better understanding of its functional behavior. Our computational results are in excellent agreement with previous experimental findings, revealing the closed and open states of helix α1 in the basic helix-loop-helix (bHLH domain) in the cytoplasm at the atomic level. We also predict the inactive form of AhR and identify Arginine 42 as a key residue that regulates switching between closed and open conformations in existing AhR modulators.
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Affiliation(s)
- Farag E S Mosa
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Sara AlRawashdeh
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Ayman O S El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1, Canada
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3
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Saar A, Ghahremanpour MM, Tirado-Rives J, Jorgensen WL. Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors. J Chem Inf Model 2023; 63:7210-7218. [PMID: 37934762 DOI: 10.1021/acs.jcim.3c01453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Absolute binding free energy (ABFE) calculations can be an important part of the drug discovery process by identifying molecules that have the potential to be strong binders for a biomolecular target. Recent work has used free energy perturbation (FEP) theory for these calculations, focusing on a set of 16 inhibitors of the severe acute respiratory syndrome coronavirus 2 main protease (Mpro). Herein, the same data set is evaluated by metadynamics (MetaD), four different docking programs, and molecular mechanics with generalized Born and surface area solvation. MetaD yields a Kendall τ distance of 0.28 and Pearson r2 of 0.49, which reflect somewhat less accuracy than that from the ABFE FEP results. Notably, it is demonstrated that an ensemble docking protocol by which each ligand is docked into the 13 crystal structures in this data set provides improved performance, particularly when docking is carried out with Glide XP (Kendall τ distance = 0.20, Pearson r2 = 0.71), Glide SP (Kendall τ distance = 0.19, Pearson r2 = 0.66), or AutoDock 4 (Kendall τ distance = 0.21, Pearson r2 = 0.55). The best results are obtained with "superconsensus" docking by averaging the 52 results for each compound using the 4 docking protocols and all 13 crystal structures (Kendall τ distance = 0.18, Pearson r2 = 0.73).
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Affiliation(s)
- Anastasia Saar
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | | | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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4
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Bobrovs R, Drunka L, Kanepe I, Jirgensons A, Caflisch A, Salvalaglio M, Jaudzems K. Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. J Chem Inf Model 2023; 63:6890-6899. [PMID: 37801405 DOI: 10.1021/acs.jcim.3c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Predicting the interaction modes and binding affinities of virtual compound libraries is of great interest in drug development. It reduces the cost and time of lead compound identification and selection. Here we apply path-based metadynamics simulations to characterize the binding of potential inhibitors to the Plasmodium falciparum aspartic protease plasmepsin V (plm V), a validated antimalarial drug target that has a highly mobile binding site. The potential plm V binders were identified in a high-throughput virtual screening (HTVS) campaign and were experimentally verified in a fluorescence resonance energy transfer (FRET) assay. Our simulations allowed us to estimate compound binding energies and revealed relevant states along binding/unbinding pathways in atomistic resolution. We believe that the method described allows the prioritization of compounds for synthesis and enables rational structure-based drug design for targets that undergo considerable conformational changes upon inhibitor binding.
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Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Laura Drunka
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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5
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Motta S, Siani P, Donadoni E, Frigerio G, Bonati L, Di Valentin C. Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles. NANOSCALE 2023; 15:7909-7919. [PMID: 37066796 DOI: 10.1039/d3nr00397c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Inorganic nanoparticles show promising properties that allow them to be efficiently used as drug carriers. The main limitation in this type of application is currently the drug loading capacity, which can be overcome with a proper functionalization of the nanoparticle surface. In this study, we present, for the first time, a computational approach based on metadynamics to estimate the binding free energy of the doxorubicin drug (DOX) to a functionalized TiO2 nanoparticle under different pH conditions. On a thermodynamic basis, we demonstrate the robustness of our approach to capture the overall mechanism behind the pH-triggered release of DOX due to environmental pH changes. Notably, binding free energy estimations align well with what is expected for a pH-sensitive drug delivery system. Based on our results, we envision the use of metadynamics as a promising computational tool for the rational design and in silico optimization of organic ligands with improved drug carrier properties.
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Affiliation(s)
- Stefano Motta
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Edoardo Donadoni
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Giulia Frigerio
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Laura Bonati
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
- BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, Italy
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6
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Afshinpour M, Mahdiuni H. Arginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies. J Biomol Struct Dyn 2023; 41:13580-13594. [PMID: 36762692 DOI: 10.1080/07391102.2023.2175374] [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: 07/21/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023]
Abstract
Metabolic and signaling mechanisms in mammalian cells are facilitated by the transportation of L-arginine (Arg) across the plasma membrane through cationic amino acid transporter (CAT) proteins. Due to a lack of argininosuccinate synthase (ASS) activity in various tumor cells such as acute myeloid leukemia, acute lymphocytic leukemia, and chronic lymphocytic leukemia, these tumor entities are arginine-auxotrophic and therefore depend on the uptake of the amino acid arginine. Cationic amino acid transporter-1 (CAT-1) is the leading arginine importer expressed in the aforementioned tumor entities. Hence, in the present study, to investigate the transportation mechanism of arginine in CAT-1, we performed molecular dynamics (MD) simulation methods on the modeled human CAT-1. The MM-PBSA approach was conducted to determine the critical residues interacting with arginine within the corresponding binding site of CAT-1. In addition, we found out that the water molecules have the leading role in forming the transportation channel within CAT-1. The conductive structure of CAT-1 was formed only when the water molecules were continuously distributed across the channel. Steered molecular dynamics (SMD) simulation approach showed various energy barriers against arginine transportation through CAT-1, especially while crossing the bottlenecks of the related channel. These findings at the molecular level might shed light on identifying the crucial amino acids in the binding of arginine to eukaryotic CATs and also provide fundamental insights into the arginine transportation mechanisms through CAT-1. Understanding the transportation mechanism of arginine is essential to developing CAT-1 blockers, which can be potential medications for some types of cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maral Afshinpour
- Bioinformatics Lab., Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Hamid Mahdiuni
- Bioinformatics Lab., Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
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7
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Salyha N, Oliynyk I. Hypoxia modeling techniques: A review. Heliyon 2023; 9:e13238. [PMID: 36718422 PMCID: PMC9877323 DOI: 10.1016/j.heliyon.2023.e13238] [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: 08/19/2022] [Revised: 01/08/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Hypoxia is the main cause and effect of a large number of diseases, including the most recent one facing the world, the coronavirus disease (COVID-19). Hypoxia is divided into short-term, long-term, and periodic, it can be the result of diseases, climate change, or living and traveling in the high mountain regions of the world. Since each type of hypoxia can be a cause and a consequence of various physiological changes, the methods for modeling these hypoxias are also different. There are many techniques for modeling hypoxia under experimental conditions. The most common animal for modeling hypoxia is a rat. Hypoxia models (hypoxia simulations) in rats are a tool to study the effect of various conditions on the oxygen supply of the body. These models can provide a necessary information to understand hypoxia and also provide effective treatment, highlighting the importance of various reactions of the body to hypoxia. The main parameters when choosing a model should be reproducibility and the goal that the scientist wants to achieve. Hypoxia in rats can be reproduced both ways exogenously and endogenously. The reason for writing this review was the aim to systematize the models of rats available in the literature in order to facilitate their selection by scientists. The relative strengths and limitations of each model need to be identified and understood in order to evaluate the information obtained from these models and extrapolate these results to humans to develop the necessary generalizations. Despite these problems, animal models have been and remain vital to understanding the mechanisms involved in the development and progression of hypoxia. The eligibility criteria for the selected studies was a comprehensive review of the methods and results obtained from the studies. This made it possible to make generalizations and give recommendations on the application of these methods. The review will assist scientists in choosing an appropriate hypoxia simulation method, as well as assist in interpreting the results obtained with these methods.
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Affiliation(s)
- Nataliya Salyha
- Institute of Animal Biology NAAS, Lviv, Ukraine,Corresponding author
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8
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Jiang T, Liu Z, Liu W, Chen J, Zheng Z, Duan M. The Conformational Transition Pathways and Hidden Intermediates in DFG-Flip Process of c-Met Kinase Revealed by Metadynamics Simulations. J Chem Inf Model 2022; 62:3651-3663. [PMID: 35848778 DOI: 10.1021/acs.jcim.2c00770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein kinases intrinsically translate their conformations between active and inactive states, which is key to their enzymatic activities. The conformational flipping of the three-residue conservative motif, Asp-Phe-Gly (DFG), is crucial for many kinases' biological functions. Obtaining a detailed demonstration of the DFG flipping process and its corresponding dynamical and thermodynamical features could broaden our understanding of kinases' conformation-activity relationship. In this study, we employed metadynamics simulation, a widely used enhanced sampling technique, to analyze the conformational transition pathways of the DFG flipping for the c-Met kinase. The corresponding free energy landscape suggested two distinct transition pathways between the "DFG-in" and "DFG-out" states of the DFG-flip from c-Met. On the basis of the orientation direction of the F1223 residue, we correspondingly named the two pathways the "DFG-up" path, featuring forming a commonly discovered "DFG-up" transition state, and the "DFG-down" path, a unique transition pathway with F1223 rotating along the opposite direction away from the hydrophobic cavity. The free energies along the two pathways were then calculated using the Path Collective Variable (PCV) metadynamics simulation. The simulation results showed that, though having similar free energy barriers, the free energy cuve for the DFG-down path suggested a two-step conformational transition mechanism, while that for the DFG-up path showed the one-step transition feature. The c-Met DFG flipping mechanism and the new intermediate state discovered in this work could provide a deeper understanding of the conformation-activity relationship for c-Met and, possibly, reveal a new conformational state as the drug target for c-Met and other similar kinases.
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Affiliation(s)
- Tao Jiang
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Zhenhao Liu
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Wenlang Liu
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Jiawen Chen
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, P. R. China
| | - Zheng Zheng
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, P. R. China
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9
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Bobrovs R, Basens EE, Drunka L, Kanepe I, Matisone S, Velins KK, Andrianov V, Leitis G, Zelencova-Gopejenko D, Rasina D, Jirgensons A, Jaudzems K. Exploring Aspartic Protease Inhibitor Binding to Design-Selective Antimalarials. J Chem Inf Model 2022; 62:3263-3273. [PMID: 35712895 DOI: 10.1021/acs.jcim.2c00422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selectivity is a major issue in the development of drugs targeting pathogen aspartic proteases. Here, we explore the selectivity-determining factors by studying specifically designed malaria aspartic protease (plasmepsin) open-flap inhibitors. Metadynamics simulations are used to uncover the complex binding/unbinding pathways of these inhibitors and describe the critical transition states in atomistic resolution. The simulation results are compared with experimentally determined enzymatic activities. Our findings demonstrate that plasmepsin inhibitor selectivity can be achieved by targeting the flap loop with hydrophobic substituents that enable ligand binding under the flap loop, as such a behavior is not observed for several other aspartic proteases. The ability to estimate the selectivity of compounds before they are synthesized is of considerable importance in drug design; therefore, we expect that our approach will be useful in selective inhibitor designs against not only aspartic proteases but also other enzyme classes.
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Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Laura Drunka
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Sofija Matisone
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Victor Andrianov
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Gundars Leitis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | | | - Dace Rasina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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Motta S, Callea L, Bonati L, Pandini A. PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations. J Chem Theory Comput 2022; 18:1957-1968. [PMID: 35213804 PMCID: PMC8908765 DOI: 10.1021/acs.jctc.1c01163] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Understanding the
process of ligand–protein recognition
is important to unveil biological mechanisms and to guide drug discovery
and design. Enhanced-sampling molecular dynamics is now routinely
used to simulate the ligand binding process, resulting in the need
for suitable tools for the analysis of large data sets of binding
events. Here, we designed, implemented, and tested PathDetect-SOM,
a tool based on self-organizing maps to build concise visual models
of the ligand binding pathways sampled along single simulations or
replicas. The tool performs a geometric clustering of the trajectories
and traces the pathways over an easily interpretable 2D map and, using
an approximate transition matrix, it can build a graph model of concurrent
pathways. The tool was tested on three study cases representing different
types of problems and simulation techniques. A clear reconstruction
of the sampled pathways was derived in all cases, and useful information
on the energetic features of the processes was recovered. The tool
is available at https://github.com/MottaStefano/PathDetect-SOM.
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Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Lara Callea
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Alessandro Pandini
- Department of Computer Science, Brunel University London, Uxbridge UB8 3PH, U.K.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, U.K
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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