1
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Ashraf GM, Rehan M, Alsayed AO, Somvanshi P, Haque S. Drug repurposing against galectin-3 using simulation-based studies. J Biomol Struct Dyn 2022:1-8. [PMID: 36184598 DOI: 10.1080/07391102.2022.2120538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2022]
Abstract
The protein galectin, which binds to carbohydrates and is involved in a number of therapeutic processes including cell proliferation, inflammatory responses, apoptosis, etc., has been discovered as a potential therapeutic target. Galectin-3 is a stable biomarker that exhibits both increased and decreased expression in a variety of illnesses and infections, regardless of sex, age, or body mass index. The goal of the current study is to apply bioinformatics techniques to examine the possibility of cardiovascular medications to inhibit Galectin-3-related biological activities. Unsupervised clustering techniques, molecular docking, and guided molecular dynamics (MD) simulation were used to create a computational pipeline that was used to screen potential chemical compounds from a library of chemical compounds with related molecular fingerprints. Utilizing input factors such as gene expression, mode of action, and chemical descriptors, clustering enables prioritization of medicinal molecules. Twenty-four compounds were screened and repurposed against Galectin-3 utilizing molecular docking as part of the cluster-facilitated virtual screening technique. The polar interactions that Arg144, Glu184, Arg162, His158, and Asn174 have with Bufalin, Cymarin, and Ouabalin have the highest binding affinities, according to docking studies. Studies using MD simulations confirm the tested compounds' ability to inhibit Galectin-3. Galactin-3 targeted experimental and in vivo animal model-based validation studies using Bufalin, Cymarin, and Ouabalin are also necessary.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alhuseen O Alsayed
- Deanship of Scientific Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pallavi Somvanshi
- School of Computational & Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi, India.,Special Centre of Systems Medicine (SCSM), Jawaharlal Nehru University, New Delhi, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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2
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Park S, Seok C. GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network. J Chem Inf Model 2022; 62:3157-3168. [PMID: 35749367 DOI: 10.1021/acs.jcim.2c00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins interact with numerous water molecules to perform their physiological functions in biological organisms. Most water molecules act as solvent media; hence, their roles may be considered implicitly in theoretical treatments of protein structure and function. However, some water molecules interact intimately with proteins and require explicit treatment to understand their effects. Most physics-based computational methods are limited in their ability to accurately locate water molecules on protein surfaces because of inaccurate energy functions. Instead of relying on an energy function, this study attempts to learn the locations of water molecules from structural data. GalaxyWater-convolutional neural network (CNN) predicts water positions on protein chains, protein-protein interfaces, and protein-compound binding sites using a 3D-CNN model that is trained to generate a water score map on a given protein structure. The training data are compiled from high-resolution protein crystal structures resolved together with water molecules. GalaxyWater-CNN shows improved water prediction performance both in the coverage of crystal water molecules and in the accuracy of the predicted water positions when compared with previous energy-based methods. This method shows a superior performance in predicting water molecules that form hydrogen-bond networks precisely. The web service and the source code of this water prediction method are freely available at https://galaxy.seoklab.org/gwcnn and https://github.com/seoklab/GalaxyWater-CNN, respectively.
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Affiliation(s)
- Sangwoo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.,Galux Inc., Gwanak-gu, Seoul 08738, Republic of Korea
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3
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Heo L, Park S, Seok C. GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential. J Chem Inf Model 2021; 61:2283-2293. [PMID: 33938216 DOI: 10.1021/acs.jcim.0c01434] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins fold and function in water, and protein-water interactions play important roles in protein structure and function. In computational studies on protein structure and interaction, the effect of water is considered either implicitly or explicitly. Implicit water models are frequently used in protein structure prediction and docking because they are computationally much more efficient than explicit water models, which are often employed in molecular dynamics (MD) simulations. However, implicit water models that treat water as a continuous solvent medium cannot account for specific atomistic protein-water interactions that are critical for structure formation and interactions with other molecules. Various methods for predicting water molecules that form specific atomistic interactions with proteins have been developed. Methods involving MD simulations or the integral equation theory tend to produce more accurate results at a higher computational cost than simple geometry- or energy-based methods. Here, we present a novel method for predicting water positions on a protein surface called GalaxyWater-wKGB, which is based on a statistical potential, a water knowledge-based potential based on the generalized Born model (wKGB). This method is accurate and rapid because it does not require conformational sampling or iterative computation owing to the effective statistical treatment employed to derive the potential. The statistical potential describes specific protein atom-water interactions more accurately than conventional potentials by considering the dependence on the degree of solvent accessibility of protein atoms as well as on protein atom-water distances and orientations. The introduction of solvent accessibility allows effective consideration of competing nonspecific protein-water and intraprotein interactions. When tested on high-resolution protein crystal structures, this method could recover similar or larger fractions of crystallographic water 180 times faster than the sophisticated integral equation theory, 3D-RISM. A web service of this water prediction method is freely available at http://galaxy.seoklab.org/wkgb.
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Affiliation(s)
- Lim Heo
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sangwoo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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4
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Ren W, Dokainish HM, Shinobu A, Oshima H, Sugita Y. Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations. J Phys Chem B 2021; 125:2898-2909. [PMID: 33728914 PMCID: PMC10954230 DOI: 10.1021/acs.jpcb.0c11600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conformational changes of proteins upon ligand binding are usually explained in terms of several mechanisms including the induced fit, conformational selection, or their mixtures. Due to the slow time scales, conventional molecular dynamics (cMD) simulations based on the atomistic models cannot easily simulate the open-to-closed conformational transition in proteins. In our previous study, we have developed an enhanced sampling scheme (generalized replica exchange with solute tempering selected surface charged residues: gREST_SSCR) for multidomain proteins and applied it to ligand-mediated conformational changes in the G134R mutant of ribose-binding protein (RBPG134R) in solution. The free-energy landscape (FEL) of RBPG134R in the presence of a ribose at the binding site included the open and closed states and two intermediates, open-like and closed-like forms. Only the open and open-like forms existed in the FEL without a ribose. In the current study, the coupling between the conformational changes and ligand binding is further investigated using coarse-grained MD, multiple atomistic cMD, and free-energy calculations. The ribose is easily dissociated from the binding site of wild-type RBP and RBPG134R in the cMD simulations starting from the open and open-like forms. In contrast, it is stable at the binding site in the simulations from the closed and closed-like forms. The free-energy calculations provide the binding affinities of different structures, supporting the results of cMD simulations. Importantly, cMD simulations from the closed-like structures reveal transitions toward the closed one in the presence of a bound ribose. On the basis of the computational results, we propose a molecular mechanism in which conformational selection and induced fit happen in the first and second halves of the open-to-closed transition in RBP, respectively.
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Affiliation(s)
- Weitong Ren
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hisham M. Dokainish
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ai Shinobu
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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5
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Kim KH. Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies. J Comput Aided Mol Des 2021; 35:371-396. [PMID: 33712973 DOI: 10.1007/s10822-021-00377-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 11/30/2022]
Abstract
It is frequently mentioned that QSARs have not generally lived up to expectations, especially in cases where high predictability is expected yet failed to deliver satisfactory results. Even though outliers can provide an increased opportunity in drug discovery research, outliers in SAR and QSAR can contort predictions and affect the accuracy if proper attention is not given. The percentages of outliers in QSARs have not changed appreciably over the last decade. In our previous studies, we suggested two possible sources of outliers in SAR and QSAR. In this paper, we suggest an additional possible source of outliers in QSAR. We presented several literature examples that show one or more water molecules that play a critical role in protein-ligand binding interactions as observed in their crystal structures. These examples illustrate that failing to account for the effects of water molecules in protein-ligand interactions could mislead interpretation and possibly yield outliers in SAR and QSAR. Examples include cases where QSAR, considering the role of water molecules in protein-ligand crystal structures, provided deeper insight into the understanding and interpretation of the developed QSAR.
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6
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Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins. Curr Res Struct Biol 2020; 2:180-190. [PMID: 34235478 PMCID: PMC8244415 DOI: 10.1016/j.crstbi.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
Two mechanisms, induced fit (IF) and conformational selection (CS), have been proposed to explain ligand recognition coupled conformational changes. The histidine binding protein (HisJ) adopts the CS mechanism, in which a pre-equilibrium is established between the open and the closed states with the ligand binding to the closed state. Despite being structurally similar to HisJ, the maltose binding protein (MBP) adopts the IF mechanism, in which the ligand binds the open state and induces a transition to the closed state. To understand the molecular determinants of this difference, we performed molecular dynamics (MD) simulations of coarse-grained dual structure based models. We find that intra-protein contacts unique to the closed state are sufficient to promote the conformational transition in HisJ, indicating a CS-like mechanism. In contrast, additional ligand-mimicking contacts are required to “induce” the conformational transition in MBP suggesting an IF-like mechanism. In agreement with experiments, destabilizing modifications to two structural features, the spine helix (SH) and the balancing interface (BI), present in MBP but absent in HisJ, reduce the need for ligand-mimicking contacts indicating that SH and BI act as structural restraints that keep MBP in the open state. We introduce an SH like element into HisJ and observe that this can impede the conformational transition increasing the importance of ligand-mimicking contacts. Similarly, simultaneous mutations to BI and SH in MBP reduce the barrier to conformational transitions significantly and promote a CS-like mechanism. Together, our results show that structural restraints present in the protein structure can determine the mechanism of conformational transitions and even simple models that correctly capture such structural features can predict their positions. MD simulations of such models can thus be used, in conjunction with mutational experiments, to regulate protein ligand interactions, and modulate ligand binding affinities. MBP operates by induced fit, HisJ by the conformational selection mechanism. Dual structure based models (dSBMs) encode two structures of a protein. MD simulations of dSBMs can identify the mechanism of conformational transitions. Locks, absent in HisJ, hold MBP open with ligand contacts required for closing. Binding mechanisms can be modified by altering such structural locks.
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Key Words
- BI, Balancing interface
- CS, conformational selection
- CTD, C-terminal domain
- Conformational selection
- Dual structure based models
- FEP, free energy profile
- HisJ, histidine binding protein
- IF, induced fit
- Induced fit
- MBP, maltose binding protein
- MD simulations
- MD, molecular dynamics
- NTD, N-terminal domain
- PBP, periplasmic binding protein
- Periplasmic binding proteins
- SH, spine helix
- Structural restraints
- WT, wild-type
- dSBM, dual structure-based model
- sSBM, single structure-based model
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7
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8
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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9
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Bertin-Jung I, Robert A, Ramalanjaona N, Gulberti S, Bui C, Vincourt JB, Ouzzine M, Jacquinet JC, Lopin-Bon C, Fournel-Gigleux S. A versatile strategy to synthesize N-methyl-anthranilic acid-labelled glycoprobes for fluorescence-based screening assays. Chem Commun (Camb) 2020; 56:10746-10749. [DOI: 10.1039/d0cc03882b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we propose a general strategy to label carbohydrates with N-methyl-anthranilic acid to generate glycotools for fluorescence-based screening and carbohydrate–protein interaction studies.
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Affiliation(s)
- Isabelle Bertin-Jung
- Laboratoire IMoPA UMR 7365 CNRS-Université de Lorraine
- Biopôle de la Faculté de Médecine CS 50184
- 54505 Vandœuvre-lès-Nancy Cedex
- France
| | - Anne Robert
- Laboratoire IMoPA UMR 7365 CNRS-Université de Lorraine
- Biopôle de la Faculté de Médecine CS 50184
- 54505 Vandœuvre-lès-Nancy Cedex
- France
| | - Nick Ramalanjaona
- Laboratoire IMoPA UMR 7365 CNRS-Université de Lorraine
- Biopôle de la Faculté de Médecine CS 50184
- 54505 Vandœuvre-lès-Nancy Cedex
- France
| | - Sandrine Gulberti
- Laboratoire IMoPA UMR 7365 CNRS-Université de Lorraine
- Biopôle de la Faculté de Médecine CS 50184
- 54505 Vandœuvre-lès-Nancy Cedex
- France
| | - Catherine Bui
- Laboratoire IMoPA UMR 7365 CNRS-Université de Lorraine
- Biopôle de la Faculté de Médecine CS 50184
- 54505 Vandœuvre-lès-Nancy Cedex
- France
| | - Jean-Baptiste Vincourt
- Laboratoire IMoPA UMR 7365 CNRS-Université de Lorraine
- Biopôle de la Faculté de Médecine CS 50184
- 54505 Vandœuvre-lès-Nancy Cedex
- France
| | - Mohamed Ouzzine
- Laboratoire IMoPA UMR 7365 CNRS-Université de Lorraine
- Biopôle de la Faculté de Médecine CS 50184
- 54505 Vandœuvre-lès-Nancy Cedex
- France
| | | | | | - Sylvie Fournel-Gigleux
- Laboratoire IMoPA UMR 7365 CNRS-Université de Lorraine
- Biopôle de la Faculté de Médecine CS 50184
- 54505 Vandœuvre-lès-Nancy Cedex
- France
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10
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Shadrack DM, Swai HS, Hassanali A. A computational study on the role of water and conformational fluctuations in Hsp90 in response to inhibitors. J Mol Graph Model 2019; 96:107510. [PMID: 31877402 DOI: 10.1016/j.jmgm.2019.107510] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022]
Abstract
Molecular chaperone Heat Shock Protein 90 (Hsp90) represents an interesting chemotherapeutic target for cancer treatments as it plays a role in cancer proliferation. Thus, continued effort to identify novel inhibitors of this target is an important task. Drug design using computational approach has gained significant attention in recent years. This work aims to propose docking protocols to re-purpose FDA-approved drugs targeting Hsp90. Sensitivity of results to different docking protocols such apo, holo and receptor ensembles (relaxed complex) structures, the role of water and conformational changes of Hsp90, are described. We show that the protein conformation and water have effects on drug binding. Holo relaxed complex receptors ensembles improves the binding energy of ligands to the protein. We also compare and contrast structural stability of three drugs namely: ezetimibe, pitavastatin and vilazodon in the Hsp90 protein. The results obtained serves as a possible basis towards developing Hsp90 inhibitors.
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Affiliation(s)
- Daniel M Shadrack
- Department of Health and Biomedical Sciences, School of Life Science and Bioengieering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania; International Centre for Theoretical Physics, Strada Costiera, 11, 34151, Trieste, Italy; Department of Chemistry, FaNAS, St John's University of Tanzania, P.O.Box 47, Dodoma, Tanzania.
| | - Hulda S Swai
- Department of Health and Biomedical Sciences, School of Life Science and Bioengieering, The Nelson Mandela African Institution of Science and Technology, P.O.Box 447, Arusha, Tanzania
| | - Ali Hassanali
- International Centre for Theoretical Physics, Strada Costiera, 11, 34151, Trieste, Italy.
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11
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The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations. J Comput Aided Mol Des 2019; 33:913-926. [PMID: 31686367 DOI: 10.1007/s10822-019-00239-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/17/2019] [Indexed: 12/13/2022]
Abstract
Misfolded Cu/Zn superoxide dismutase enzyme (SOD1) shows prion-like propagation in neuronal cells leading to neurotoxic aggregates that are implicated in amyotrophic lateral sclerosis (ALS). Tryptophan-32 (W32) in SOD1 is part of a potential site for templated conversion of wild type SOD1. This W32 binding site is located on a convex, solvent exposed surface of the SOD1 suggesting that hydration effects can play an important role in ligand recognition and binding. A recent X-ray crystal structure has revealed that 5-Fluorouridine (5-FUrd) binds at the W32 binding site and can act as a pharmacophore scaffold for the development of anti-ALS drugs. In this study, a new protocol is developed to account for structural (non-displaceable) water molecules in docking simulations and successfully applied to predict the correct docked conformation binding modes of 5-FUrd at the W32 binding site. The docked configuration is within 0.58 Å (RMSD) of the observed configuration. The docking protocol involved calculating a hydration structure around SOD1 using molecular theory of solvation (3D-RISM-KH, 3D-Reference Interaction Site Model-Kovalenko-Hirata) whereby, non-displaceable water molecules are identified for docking simulations. This protocol was also used to analyze the hydrated structure of the W32 binding site and to explain the role of solvation in ligand recognition and binding to SOD1. Structural water molecules mediate hydrogen bonds between 5-FUrd and the receptor, and create an environment favoring optimal placement of 5-FUrd in the W32 binding site.
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12
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Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface. Biomolecules 2019; 9:biom9050162. [PMID: 31035615 PMCID: PMC6572318 DOI: 10.3390/biom9050162] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 01/15/2023] Open
Abstract
Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca2+-dependent species of AFP, however, it has not been clarified how 1 mol of Ca2+-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca2+-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca2+-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca2+-binding site. Firstly, the side-chains of four of the five Ca2+-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca2+-bound state. Second, a Ca2+-binding loop consisting of a segment D94–E99 becomes less flexible by the Ca2+-binding. Third, the Ca2+-binding induces a generation of ice-like clathrate waters around the Ca2+-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca2+-binding enables the ice-binding of this protein.
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13
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Matter H, Güssregen S. Characterizing hydration sites in protein-ligand complexes towards the design of novel ligands. Bioorg Med Chem Lett 2018; 28:2343-2352. [PMID: 29880400 DOI: 10.1016/j.bmcl.2018.05.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 11/18/2022]
Abstract
Water is an essential part of protein binding sites and mediates interactions to ligands. Its displacement by ligand parts affects the free binding energy of resulting protein-ligand complexes. Therefore the characterization of solvation properties is important for design. Of particular interest is the propensity of localized water to be favorably displaced by a ligand. This review discusses two popular computational approaches addressing these questions, namely WaterMap based on statistical mechanics analysis of MD simulations and 3D RISM based on integral equation theory of liquids. The theoretical background and recent applications in structure-based design will be presented.
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Affiliation(s)
- Hans Matter
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany.
| | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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14
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Güssregen S, Matter H, Hessler G, Lionta E, Heil J, Kast SM. Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series. J Chem Inf Model 2017; 57:1652-1666. [DOI: 10.1021/acs.jcim.6b00765] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan Güssregen
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Hans Matter
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Evanthia Lionta
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Jochen Heil
- Physikalische
Chemie III, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Stefan M. Kast
- Physikalische
Chemie III, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
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Ariz-Extreme I, Hub JS. Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM. J Phys Chem B 2017; 121:1506-1519. [PMID: 28128570 DOI: 10.1021/acs.jpcb.6b11279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Membrane channels facilitate the efficient and selective flux of various solutes across biological membranes. A common approach to investigate the selectivity of a channel has been the calculation of potentials of mean force (PMFs) for solute permeation across the pore. PMFs have been frequently computed from molecular dynamics (MD) simulations, yet the three-dimensional reference interaction site model (3D-RISM) has been suggested as a computationally efficient alternative to MD. Whether the two methods yield comparable PMFs for solute permeation has remained unclear. In this study, we calculated potentials of mean force for water, ammonia, urea, molecular oxygen, and methanol across the urea transporter B (UT-B) and aquaporin-1 (AQP1), using 3D-RISM, as well as using MD simulations and umbrella sampling. To allow direct comparison between the PMFs from 3D-RISM and MD, we ensure that all PMFs refer to a well-defined reference area in the bulk or, equivalently, to a well-defined density of channels in the membrane. For PMFs of water permeation, we found reasonable agreement between the two methods, with differences of ≲3 kJ mol-1. In contrast, we found stark discrepancies for the PMFs for all other solutes. Additional calculations confirm that discrepancies between MD and 3D-RISM are not explained by the choice for the closure relation, the definition the reaction coordinate (center of mass-based versus atomic site-based), details of the molecule force field, or fluctuations of the protein. Comparison of the PMFs suggests that 3D-RISM may underestimate effects from hydrophobic solute-channel interactions, thereby, for instance, missing the urea binding sites in UT-B. Furthermore, we speculate that the orientational averages inherent to 3D-RISM might lead to discrepancies in the narrow channel lumen. These findings suggest that current 3D-RISM solvers provide reasonable estimates for the PMF for water permeation, but that they are not suitable to study the selectivity of membrane channels with respect to uncharged nonwater solutes.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
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Tanimoto S, Higashi M, Yoshida N, Nakano H. The ion dependence of carbohydrate binding of CBM36: an MD and 3D-RISM study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:344005. [PMID: 27366974 DOI: 10.1088/0953-8984/28/34/344005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The molecular recognition process of the carbohydrate-binding module family 36 (CBM36) was examined theoretically. The mechanism of xylan binding by CBM36 and the role of Ca(2+) were investigated by the combined use of molecular dynamics simulations and the 3D reference interaction site model method. The CBM36 showed affinity for xylan after Ca(2+) binding, but not after Mg(2+) binding. Free-energy component analysis of the xylan-binding process revealed that the major factor for xylan-binding affinity is the electrostatic interaction between the Ca(2+) and the hydroxyl oxygens of xylan. The van der Waals interaction between the hydrophobic side chain of CBM36 and the glucopyranose ring of xylan also contributes to the stabilization of the xylan-binding state. Dehydration on the formation of the complex has the opposite effect on these interactions. The affinity of CBM36 for xylan results from a balance of the interactions between the binding ion and solvents, hydrophilic residues around xylan, and the hydroxyl oxygens of xylan. When CBM binds Ca(2+), these interactions are well balanced; in contrast, when CBM binds Mg(2+), the dehydration penalty is excessively large.
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Affiliation(s)
- Shoichi Tanimoto
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Overcoming ABC transporter-mediated multidrug resistance: Molecular mechanisms and novel therapeutic drug strategies. Drug Resist Updat 2016; 27:14-29. [DOI: 10.1016/j.drup.2016.05.001] [Citation(s) in RCA: 464] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 04/24/2016] [Accepted: 05/06/2016] [Indexed: 12/15/2022]
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Greenidge PA, Lewis RA, Ertl P. Boosting Pose Ranking Performance via Rescoring with MM-GBSA. Chem Biol Drug Des 2016; 88:317-28. [DOI: 10.1111/cbdd.12763] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/07/2016] [Accepted: 03/30/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Paulette A. Greenidge
- Novartis Institutes for Biomedical Research; Novartis Campus; CH-4056 Basel Switzerland
| | - Richard A. Lewis
- Novartis Institutes for Biomedical Research; Novartis Campus; CH-4056 Basel Switzerland
| | - Peter Ertl
- Novartis Institutes for Biomedical Research; Novartis Campus; CH-4056 Basel Switzerland
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Park H, Lee H, Seok C. High-resolution protein-protein docking by global optimization: recent advances and future challenges. Curr Opin Struct Biol 2015; 35:24-31. [PMID: 26295792 DOI: 10.1016/j.sbi.2015.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/13/2015] [Accepted: 08/03/2015] [Indexed: 01/12/2023]
Abstract
A computational protein-protein docking method that predicts atomic details of protein-protein interactions from protein monomer structures is an invaluable tool for understanding the molecular mechanisms of protein interactions and for designing molecules that control such interactions. Compared to low-resolution docking, high-resolution docking explores the conformational space in atomic resolution to provide predictions with atomic details. This allows for applications to more challenging docking problems that involve conformational changes induced by binding. Recently, high-resolution methods have become more promising as additional information such as global shapes or residue contacts are now available from experiments or sequence/structure data. In this review article, we highlight developments in high-resolution docking made during the last decade, specifically regarding global optimization methods employed by the docking methods. We also discuss two major challenges in high-resolution docking: prediction of backbone flexibility and water-mediated interactions.
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Affiliation(s)
- Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Hasup Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
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