1
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Soleymani F, Paquet E, Viktor HL, Michalowski W. Structure-based protein and small molecule generation using EGNN and diffusion models: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2779-2797. [PMID: 39050782 PMCID: PMC11268121 DOI: 10.1016/j.csbj.2024.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Recent breakthroughs in deep learning have revolutionized protein sequence and structure prediction. These advancements are built on decades of protein design efforts, and are overcoming traditional time and cost limitations. Diffusion models, at the forefront of these innovations, significantly enhance design efficiency by automating knowledge acquisition. In the field of de novo protein design, the goal is to create entirely novel proteins with predetermined structures. Given the arbitrary positions of proteins in 3-D space, graph representations and their properties are widely used in protein generation studies. A critical requirement in protein modelling is maintaining spatial relationships under transformations (rotations, translations, and reflections). This property, known as equivariance, ensures that predicted protein characteristics adapt seamlessly to changes in orientation or position. Equivariant graph neural networks offer a solution to this challenge. By incorporating equivariant graph neural networks to learn the score of the probability density function in diffusion models, one can generate proteins with robust 3-D structural representations. This review examines the latest deep learning advancements, specifically focusing on frameworks that combine diffusion models with equivariant graph neural networks for protein generation.
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Affiliation(s)
- Farzan Soleymani
- Telfer School of Management, University of Ottawa, ON, K1N 6N5, Canada
| | - Eric Paquet
- National Research Council, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
- School of Electrical Engineering and Computer Science, University of Ottawa, ON, K1N 6N5, Canada
| | - Herna Lydia Viktor
- School of Electrical Engineering and Computer Science, University of Ottawa, ON, K1N 6N5, Canada
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2
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Martínez-Valencia D, Bañuelos C, García-Rivera G, Talamás-Lara D, Orozco E. The Entamoeba histolytica Vps26 (EhVps26) retromeric protein is involved in phagocytosis: Bioinformatic and experimental approaches. PLoS One 2024; 19:e0304842. [PMID: 39116045 PMCID: PMC11309391 DOI: 10.1371/journal.pone.0304842] [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: 01/29/2024] [Accepted: 05/21/2024] [Indexed: 08/10/2024] Open
Abstract
The retromer is a cellular structure that recruits and recycles proteins inside the cell. In mammalian and yeast, the retromer components have been widely studied, but very little in parasites. In yeast, it is formed by a SNX-BAR membrane remodeling heterodimer and the cargo selecting complex (CSC), composed by three proteins. One of them, the Vps26 protein, possesses a flexible and intrinsically disordered region (IDR), that facilitates interactions with other proteins and contributes to the retromer binding to the endosomal membrane. In Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, the retromer actively participates during the high mobility and phagocytosis of trophozoites, but the molecular details in these events, are almost unknown. Here, we studied the EhVps26 role in phagocytosis. Bioinformatic analyses of EhVps26 revealed a typical arrestin folding structure of the protein, and a long and charged IDR, as described in other systems. EhVps26 molecular dynamics simulations (MDS) allowed us to predict binding pockets for EhVps35, EhSNX3, and a PX domain-containing protein; these pockets were disorganized in a EhVps26 truncated version lacking the IDR. The AlphaFold2 software predicted the interaction of EhVps26 with EhVps35, EhVps29 and EhSNX3, in a model similar to the reported mammalian crystals. By confocal and transmission electron microscopy, EhVps26 was found in the trophozoites plasma membrane, cytosol, endosomes, and Golgi-like apparatus. During phagocytosis, it followed the erythrocytes pathway, probably participating in cargoes selection and recycling. Ehvps26 gene knocking down evidenced that the EhVps26 protein is necessary for efficient phagocytosis.
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Affiliation(s)
- Diana Martínez-Valencia
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Ciudad de México, México
| | - Cecilia Bañuelos
- Doctorado Transdisciplinario en Desarrollo Científico y Tecnológico para la Sociedad, Cinvestav, Ciudad de México, México
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Ciudad de México, México
| | - Daniel Talamás-Lara
- Laboratorios Nacionales de Servicios Experimentales (LaNSE), Cinvestav, Unidad de Microscopía Electrónica, Ciudad de México, México
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Ciudad de México, México
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3
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Ishitani R, Takemoto M, Tomii K. Protein ligand binding site prediction using graph transformer neural network. PLoS One 2024; 19:e0308425. [PMID: 39106255 DOI: 10.1371/journal.pone.0308425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/23/2024] [Indexed: 08/09/2024] Open
Abstract
Ligand binding site prediction is a crucial initial step in structure-based drug discovery. Although several methods have been proposed previously, including those using geometry based and machine learning techniques, their accuracy is considered to be still insufficient. In this study, we introduce an approach that leverages a graph transformer neural network to rank the results of a geometry-based pocket detection method. We also created a larger training dataset compared to the conventionally used sc-PDB and investigated the correlation between the dataset size and prediction performance. Our findings indicate that utilizing a graph transformer-based method alongside a larger training dataset could enhance the performance of ligand binding site prediction.
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Affiliation(s)
- Ryuichiro Ishitani
- Division of Computational Drug Discovery and Design, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Preferred Networks, Inc., Chiyoda-ku, Tokyo, Japan
| | - Mizuki Takemoto
- Division of Computational Drug Discovery and Design, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Kentaro Tomii
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan
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4
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Abbas A, Ye F. Computational methods and key considerations for in silico design of proteolysis targeting chimera (PROTACs). Int J Biol Macromol 2024; 277:134293. [PMID: 39084437 DOI: 10.1016/j.ijbiomac.2024.134293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/19/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs), as heterobifunctional molecules, have garnered significant attention for their ability to target previously undruggable proteins. Due to the challenges in obtaining crystal structures of PROTAC molecules in the ternary complex, a plethora of computational tools have been developed to aid in PROTAC design. These computational tools can be broadly classified into artificial intelligence (AI)-based or non-AI-based methods. This review aims to provide a comprehensive overview of the latest computational methods for the PROTAC design process, covering both AI and non-AI approaches, from protein selection to ternary complex modeling and prediction. Key considerations for in silico PROTAC design are discussed, along with additional considerations for deploying AI-based models. These considerations are intended to guide subsequent model development in the PROTAC design process. Finally, future directions and recommendations are provided.
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Affiliation(s)
- Amr Abbas
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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5
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Ivashchenko SD, Shulga DA, Ivashchenko VD, Zinovev EV, Vlasov AV. In silico studies of the open form of human tissue transglutaminase. Sci Rep 2024; 14:15981. [PMID: 38987418 PMCID: PMC11236986 DOI: 10.1038/s41598-024-66348-8] [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: 02/07/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
Human tissue transglutaminase (tTG) is an intriguing multifunctional enzyme involved in various diseases, including celiac disease and neurological disorders. Although a number of tTG inhibitors have been developed, the molecular determinants governing ligand binding remain incomplete due to the lack of high-resolution structural data in the vicinity of its active site. In this study, we obtained the complete high-resolution model of tTG by in silico methods based on available PDB structures. We discovered significant differences in the active site architecture between our and known tTG models, revealing an additional loop which affects the ligand binding affinity. We assembled a library of new potential tTG inhibitors based on the obtained complete model of the enzyme. Our library substantially expands the spectrum of possible drug candidates targeting tTG and encompasses twelve molecular scaffolds, eleven of which are novel and exhibit higher binding affinity then already known ones, according to our in silico studies. The results of this study open new directions for structure-based drug design of tTG inhibitors, offering the complete protein model and suggesting a wide range of new compounds for further experimental validation.
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Affiliation(s)
- S D Ivashchenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141701
- Laboratory of Microbiology, BIOTECH University, Moscow, Russia, 125080
| | - D A Shulga
- Department of Chemistry, Moscow State University, Moscow, Russia, 119991
| | - V D Ivashchenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141701
| | - E V Zinovev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141701
| | - A V Vlasov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141701.
- Laboratory of Microbiology, BIOTECH University, Moscow, Russia, 125080.
- Joint Institute for Nuclear Research, Dubna, Russia, 141980.
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6
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Reim T, Ehrt C, Graef J, Günther S, Meents A, Rarey M. SiteMine: Large-scale binding site similarity searching in protein structure databases. Arch Pharm (Weinheim) 2024; 357:e2300661. [PMID: 38335311 DOI: 10.1002/ardp.202300661] [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: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024]
Abstract
Drug discovery and design challenges, such as drug repurposing, analyzing protein-ligand and protein-protein complexes, ligand promiscuity studies, or function prediction, can be addressed by protein binding site similarity analysis. Although numerous tools exist, they all have individual strengths and drawbacks with regard to run time, provision of structure superpositions, and applicability to diverse application domains. Here, we introduce SiteMine, an all-in-one database-driven, alignment-providing binding site similarity search tool to tackle the most pressing challenges of binding site comparison. The performance of SiteMine is evaluated on the ProSPECCTs benchmark, showing a promising performance on most of the data sets. The method performs convincingly regarding all quality criteria for reliable binding site comparison, offering a novel state-of-the-art approach for structure-based molecular design based on binding site comparisons. In a SiteMine showcase, we discuss the high structural similarity between cathepsin L and calpain 1 binding sites and give an outlook on the impact of this finding on structure-based drug design. SiteMine is available at https://uhh.de/naomi.
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Affiliation(s)
- Thorben Reim
- ZBH - Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
| | - Christiane Ehrt
- ZBH - Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
| | - Joel Graef
- ZBH - Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
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7
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Xu Y, Hu X, Wang C, Liu Y, Chen Q, Liu H. De novo design of cavity-containing proteins with a backbone-centered neural network energy function. Structure 2024; 32:424-432.e4. [PMID: 38325370 DOI: 10.1016/j.str.2024.01.006] [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: 04/16/2023] [Revised: 10/04/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
The design of small-molecule-binding proteins requires protein backbones that contain cavities. Previous design efforts were based on naturally occurring cavity-containing backbone architectures. Here, we designed diverse cavity-containing backbones without predefined architectures by introducing tailored restraints into the backbone sampling driven by SCUBA (Side Chain-Unknown Backbone Arrangement), a neural network statistical energy function. For 521 out of 5816 designs, the root-mean-square deviations (RMSDs) of the Cα atoms for the AlphaFold2-predicted structures and our designed structures are within 2.0 Å. We experimentally tested 10 designed proteins and determined the crystal structures of two of them. One closely agrees with the designed model, while the other forms a domain-swapped dimer, where the partial structures are in agreement with the designed structures. Our results indicate that data-driven methods such as SCUBA hold great potential for designing de novo proteins with tailored small-molecule-binding function.
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Affiliation(s)
- Yang Xu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiuhong Hu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chenchen Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yongrui Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Quan Chen
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Haiyan Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China; School of Data Science, University of Science and Technology of China, Hefei, Anhui 230027, China.
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8
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Wang N, Zhu S, Lv D, Wang Y, Khawar MB, Sun H. Allosteric modulation of SHP2: Quest from known to unknown. Drug Dev Res 2023; 84:1395-1410. [PMID: 37583266 DOI: 10.1002/ddr.22100] [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: 04/12/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/17/2023]
Abstract
Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) is a key regulatory factor in the cell cycle and its activating mutations play an important role in the development of various cancers, making it an important target for antitumor drugs. Due to the highly conserved amino acid sequence and positively charged nature of the active site of SHP2, it is difficult to discover inhibitors with high affinity for the catalytic site of SHP2 and sufficient cell permeability, making it considered an "undruggable" target. However, the discovery of allosteric regulation mechanisms provides new opportunities for transforming undruggable targets into druggable ones. Given the limitations of orthosteric inhibitors, SHP2 allosteric inhibitors have become a more selective and safer research direction. In this review, we elucidate the oncogenic mechanism of SHP2 and summarize the discovery methods of SHP2 allosteric inhibitors, providing new strategies for the design and improvement of SHP2 allosteric inhibitors.
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Affiliation(s)
- Ning Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
| | - Shilin Zhu
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Dan Lv
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
- School of Life Sciences, Anqing Normal University, Anqing, China
| | - Yajun Wang
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Muhammad B Khawar
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Haibo Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
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Kubra B, Badshah SL, Faisal S, Sharaf M, Emwas AH, Jaremko M, Abdalla M. Inhibition of the predicted allosteric site of the SARS-CoV-2 main protease through flavonoids. J Biomol Struct Dyn 2023; 41:9103-9120. [PMID: 36404610 DOI: 10.1080/07391102.2022.2140201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/19/2022] [Indexed: 11/22/2022]
Abstract
Since its emergence in 2019, coronavirus infection (COVID-19) has become a global pandemic and killed several million people worldwide. Even though several types of vaccines are available against the COVID-19 virus, SARS-CoV-2, new strains are emerging that pose a constant danger to vaccine effectiveness. In this computational study, we identified and predicted potent allosteric inhibitors of the SARS-CoV-2 main protease (Mpro). Via molecular docking and simulations, more than 100 distinct flavonoids were docked with the allosteric site of Mpro. Docking experiments revealed four top hit compounds (Hesperidin, Schaftoside, Brickellin, and Marein) that bound strongly to the Mpro predicted allosteric site. Simulation analyses further revealed that these continually interacted with the enzyme's allosteric region throughout the simulation time. ADMET and Lipinski drug likenesses were calculated to indicate the therapeutic value of the top four hits: They were non-toxic and exhibited high human intestinal absorption concentrations. These novel allosteric site inhibitors provide a higher chance of drugging SARS-CoV2 Mpro due to the rapid mutation rate of the viral enzyme's active sites. Our findings provide a new avenue for developing novel allosteric inhibitors of SARS-CoV-2 Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bibi Kubra
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, Shandong, China
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Zhu KF, Yuan C, Du YM, Sun KL, Zhang XK, Vogel H, Jia XD, Gao YZ, Zhang QF, Wang DP, Zhang HW. Applications and prospects of cryo-EM in drug discovery. Mil Med Res 2023; 10:10. [PMID: 36872349 PMCID: PMC9986049 DOI: 10.1186/s40779-023-00446-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time- and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy (cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence (AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of medium-resolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.
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Affiliation(s)
- Kong-Fu Zhu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Chuang Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
| | - Yong-Ming Du
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Kai-Lei Sun
- Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Hong Kong, 999077 China
| | - Xiao-Kang Zhang
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055 Guangdong China
| | - Horst Vogel
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
| | - Xu-Dong Jia
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Yuan-Zhu Gao
- Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Qin-Fen Zhang
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Da-Ping Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518000 Guangdong China
| | - Hua-Wei Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
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11
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Datta J, Majumder S, Chaudhuri D, Giri K. In silico investigation of binding propensity of hematoxylin derivative and damnacanthal for their potential inhibitory effect on HIV-1 Vpr from different subtypes. J Biomol Struct Dyn 2023; 41:14977-14988. [PMID: 36858595 DOI: 10.1080/07391102.2023.2184634] [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: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
HIV-1, the causative agent of AIDS leads to many deaths worldwide though few options are available as therapeutics. To deal with the continuous mutation in the virus genome, requirement of new drugs is always there. Subtype variation plays a crucial role in case of HIV-1 therapeutics development. In this study, we want to investigate some pre examined molecules that can be effective for HIV-1 VPR. Inhibition of several protein-protein interactions with the small molecules will lead to identify some molecules as therapeutics other than the conventional drugs. We retrieved the sequences of different subtypes from the database and representative sequences were identified. Representative structures were modelled and validated using MD simulations. Forty molecules, showing anti Vpr activity in vitro were identified from literature survey and those were docked with each subtype representative structures. Two molecules a stable Hematoxylin Derivative (SHD) and Damnacanthal (D3), these were shown to be bind more effectively for all the subtypes. The stability of the protein and those two small molecule complexes were identified again with MD simulation followed by the binding energy calculation. Thus, these molecules can be thought as any option other than the conventional drug targeting HIV-1 Vpr.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Joyeeta Datta
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | | | - Kalyan Giri
- Department of Life Sciences, Presidency University, Kolkata, India
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12
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Adeyelu T, Bordin N, Waman VP, Sadlej M, Sillitoe I, Moya-Garcia AA, Orengo CA. KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units. Biomolecules 2023; 13:277. [PMID: 36830646 PMCID: PMC9953599 DOI: 10.3390/biom13020277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Protein kinases are important targets for treating human disorders, and they are the second most targeted families after G-protein coupled receptors. Several resources provide classification of kinases into evolutionary families (based on sequence homology); however, very few systematically classify functional families (FunFams) comprising evolutionary relatives that share similar functional properties. We have developed the FunFam-MARC (Multidomain ARchitecture-based Clustering) protocol, which uses multi-domain architectures of protein kinases and specificity-determining residues for functional family classification. FunFam-MARC predicts 2210 kinase functional families (KinFams), which have increased functional coherence, in terms of EC annotations, compared to the widely used KinBase classification. Our protocol provides a comprehensive classification for kinase sequences from >10,000 organisms. We associate human KinFams with diseases and drugs and identify 28 druggable human KinFams, i.e., enriched in clinically approved drugs. Since relatives in the same druggable KinFam tend to be structurally conserved, including the drug-binding site, these KinFams may be valuable for shortlisting therapeutic targets. Information on the human KinFams and associated 3D structures from AlphaFold2 are provided via our CATH FTP website and Zenodo. This gives the domain structure representative of each KinFam together with information on any drug compounds available. For 32% of the KinFams, we provide information on highly conserved residue sites that may be associated with specificity.
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Affiliation(s)
- Tolulope Adeyelu
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
- Department of Comparative Biomedical Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Vaishali P. Waman
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Marta Sadlej
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Aurelio A. Moya-Garcia
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, 29071 Málaga, Spain
- Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, 29071 Málaga, Spain
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
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13
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Data-driven analysis and druggability assessment methods to accelerate the identification of novel cancer targets. Comput Struct Biotechnol J 2022; 21:46-57. [PMID: 36514341 PMCID: PMC9732000 DOI: 10.1016/j.csbj.2022.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Over the past few decades, drug discovery has greatly improved the outcomes for patients, but several challenges continue to hinder the rapid development of novel drugs. Addressing unmet clinical needs requires the pursuit of drug targets that have a higher likelihood to lead to the development of successful drugs. Here we describe a bioinformatic approach for identifying novel cancer drug targets by performing statistical analysis to ascertain quantitative changes in expression levels between protein-coding genes, as well as co-expression networks to classify these genes into groups. Subsequently, we provide an overview of druggability assessment methodologies to prioritize and select the best targets to pursue.
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14
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Lerma Romero JA, Meyners C, Christmann A, Reinbold LM, Charalampidou A, Hausch F, Kolmar H. Binding pocket stabilization by high-throughput screening of yeast display libraries. Front Mol Biosci 2022; 9:1023131. [DOI: 10.3389/fmolb.2022.1023131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
Protein dynamics have a great influence on the binding pockets of some therapeutic targets. Flexible protein binding sites can result in transient binding pocket formation which might have a negative impact on drug screening efforts. Here, we describe a protein engineering strategy with FK506-binding protein 51 (FKBP51) as a model protein, which is a promising target for stress-related disorders. High-throughput screening of yeast display libraries of FKBP51 resulted in the identification of variants exhibiting higher affinity binding of conformation-specific FKBP51 selective inhibitors. The gene libraries of a random mutagenesis and site saturation mutagenesis of the FK1 domain of FKBP51 encoding sequence were used to create a yeast surface display library. Fluorescence-activated cell sorting for FKBP51 variants that bind conformation-specific fluorescently labeled ligands with high affinity allowed for the identification of 15 different protein variants with improved binding to either, or both FKBP51-specific ligands used in the screening, with improved affinities up to 34-fold compared to the wild type. These variants will pave the way to a better understanding of the conformational flexibility of the FKBP51 binding pocket and may enable the isolation of new selective ligands that preferably and selectively bind the active site of the protein in its open conformation state.
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15
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Parihar A, Ahmed SS, Sharma P, Choudhary NK, Akter F, Ali MA, Sonia ZF, Khan R. Plant-based bioactive molecules for targeting of endoribonuclease using steered molecular dynamic simulation approach: a highly conserved therapeutic target against variants of SARS-CoV-2. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2113811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Arpana Parihar
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India
| | - Sayeda Samina Ahmed
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Palak Sharma
- NIMS Institute of Allied Medical Science and Technology, NIMS University, Jaipur, India
| | | | - Farjana Akter
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Zannatul Ferdous Sonia
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Raju Khan
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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16
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Mitra D, Das Mohapatra PK. In silico comparative structural and compositional analysis of glycoproteins of RSV to study the nature of stability and transmissibility of RSV A. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2022; 3:312-327. [PMID: 38013803 PMCID: PMC9135598 DOI: 10.1007/s43393-022-00110-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/29/2022]
Abstract
The current scenario of COVID-19 makes us to think about the devastating diseases that kill so many people every year. Analysis of viral proteins contributes many things that are utterly useful in the evolution of therapeutic drugs and vaccines. In this study, sequence and structure of fusion glycoproteins and major surface glycoproteins of respiratory syncytial virus (RSV) were analysed to reveal the stability and transmission rate. RSV A has the highest abundance of aromatic residues. The Kyte-Doolittle scale indicates the hydrophilic nature of RSV A protein which leads to the higher transmission rate of this virus. Intra-protein interactions such as carbonyl interactions, cation-pi, and salt bridges were shown to be greater in RSV A compared to RSV B, which might lead to improved stability. This study discovered the presence of a network aromatic-sulphur interaction in viral proteins. Analysis of ligand binding pocket of RSV proteins indicated that drugs are performing better on RSV B than RSV A. It was also shown that increasing the number of tunnels in RSV A proteins boosts catalytic activity. This study will be helpful in drug discovery and vaccine development.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, WB India
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17
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In search of suitable protein targets for anti-malarial and anti-dengue drug discovery. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Valdés-Jiménez A, Jiménez-González D, Kiper AK, Rinné S, Decher N, González W, Reyes-Parada M, Núñez-Vivanco G. A New Strategy for Multitarget Drug Discovery/Repositioning Through the Identification of Similar 3D Amino Acid Patterns Among Proteins Structures: The Case of Tafluprost and its Effects on Cardiac Ion Channels. Front Pharmacol 2022; 13:855792. [PMID: 35370665 PMCID: PMC8971525 DOI: 10.3389/fphar.2022.855792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/21/2022] [Indexed: 01/01/2023] Open
Abstract
The identification of similar three-dimensional (3D) amino acid patterns among different proteins might be helpful to explain the polypharmacological profile of many currently used drugs. Also, it would be a reasonable first step for the design of novel multitarget compounds. Most of the current computational tools employed for this aim are limited to the comparisons among known binding sites, and do not consider several additional important 3D patterns such as allosteric sites or other conserved motifs. In the present work, we introduce Geomfinder2.0, which is a new and improved version of our previously described algorithm for the deep exploration and discovery of similar and druggable 3D patterns. As compared with the original version, substantial improvements that have been incorporated to our software allow: (i) to compare quaternary structures, (ii) to deal with a list of pairs of structures, (iii) to know how druggable is the zone where similar 3D patterns are detected and (iv) to significantly reduce the execution time. Thus, the new algorithm achieves up to 353x speedup as compared to the previous sequential version, allowing the exploration of a significant number of quaternary structures in a reasonable time. In order to illustrate the potential of the updated Geomfinder version, we show a case of use in which similar 3D patterns were detected in the cardiac ions channels NaV1.5 and TASK-1. These channels are quite different in terms of structure, sequence and function and both have been regarded as important targets for drugs aimed at treating atrial fibrillation. Finally, we describe the in vitro effects of tafluprost (a drug currently used to treat glaucoma, which was identified as a novel putative ligand of NaV1.5 and TASK-1) upon both ion channels’ activity and discuss its possible repositioning as a novel antiarrhythmic drug.
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Affiliation(s)
- Alejandro Valdés-Jiménez
- Center for Bioinformatics, Simulations and Modelling, Faculty of Engineering, University of Talca, Talca, Chile
- Computer Architecture Department, Universitat Politécnica de Catalunya, Barcelona, Spain
| | - Daniel Jiménez-González
- Computer Architecture Department, Universitat Politécnica de Catalunya, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Aytug K. Kiper
- Institute for Physiology and Pathophysiology, Philipps-University Marburg, Marburg, Germany
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Philipps-University Marburg, Marburg, Germany
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Philipps-University Marburg, Marburg, Germany
| | - Wendy González
- Center for Bioinformatics, Simulations and Modelling, Faculty of Engineering, University of Talca, Talca, Chile
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca, Chile
- *Correspondence: Wendy González, ; Miguel Reyes-Parada, ; Gabriel Núñez-Vivanco,
| | - Miguel Reyes-Parada
- Centro de Investigación Biomédica y Aplicada (CIBAP), Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
- *Correspondence: Wendy González, ; Miguel Reyes-Parada, ; Gabriel Núñez-Vivanco,
| | - Gabriel Núñez-Vivanco
- Departamento de Ciencias Naturales y Tecnología, Universidad de Aysén, Coyhaique, Chile
- *Correspondence: Wendy González, ; Miguel Reyes-Parada, ; Gabriel Núñez-Vivanco,
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19
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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20
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Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems. J Biol Phys 2022; 48:1-36. [PMID: 34822073 PMCID: PMC8866630 DOI: 10.1007/s10867-021-09586-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/07/2021] [Indexed: 10/19/2022] Open
Abstract
We give a review on the landscape theory of the equilibrium biological systems and landscape-flux theory of the nonequilibrium biological systems as the global driving force. The emergences of the behaviors, the associated thermodynamics in terms of the entropy and free energy and dynamics in terms of the rate and paths have been quantitatively demonstrated. The hierarchical organization structures have been discussed. The biological applications ranging from protein folding, biomolecular recognition, specificity, biomolecular evolution and design for equilibrium systems as well as cell cycle, differentiation and development, cancer, neural networks and brain function, and evolution for nonequilibrium systems, cross-scale studies of genome structural dynamics and experimental quantifications/verifications of the landscape and flux are illustrated. Together, this gives an overall global physical and quantitative picture in terms of the landscape and flux for the behaviors, dynamics and functions of biological systems.
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21
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Zhang J, Liu Z, Zhao W, Yin X, Zheng X, Liu C, Wang J, Wang E. Discovery of Small Molecule NSC290956 as a Therapeutic Agent for KRas Mutant Non-Small-Cell Lung Cancer. Front Pharmacol 2022; 12:797821. [PMID: 35069209 PMCID: PMC8766838 DOI: 10.3389/fphar.2021.797821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
HRas-GTP has a transient intermediate state with a “non-signaling open conformation” in GTP hydrolysis and nucleotide exchange. Due to the same hydrolysis process and the structural homology, it can be speculated that the active KRas adopts the same characteristics with the “open conformation.” This implies that agents locking this “open conformation” may theoretically block KRas-dependent signaling. Applying our specificity-affinity drug screening approach, NSC290956 was chosen by high affinity and specificity interaction with the “open conformation” structure HRasG60A-GppNp. In mutant KRas-driven non-small-cell lung cancer (NSCLC) model system, NSC290956 effectively suppresses the KRas-GTP state and gives pharmacological KRas inhibition with concomitant blockages of both the MAPK-ERK and AKT-mTOR pathways. The dual inhibitory effects lead to the metabolic phenotype switching from glycolysis to mitochondrial metabolism, which promotes the cancer cell death. In the xenograft model, NSC290956 significantly reduces H358 tumor growth in nude mice by mechanisms similar to those observed in the cells. Our work indicates that NSC290956 can be a promising agent for the mutant KRas-driven NSCLC therapy.
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Affiliation(s)
- Jiaxin Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China.,Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Wenjing Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Xunzhe Yin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Chuanbo Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Jin Wang
- Department of Chemistry and Physics, State University of New York, Stony Brook, NY, United States
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China.,Department of Chemistry, University of Science and Technology of China, Hefei, China
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22
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Dhakal A, McKay C, Tanner JJ, Cheng J. Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions. Brief Bioinform 2022; 23:bbab476. [PMID: 34849575 PMCID: PMC8690157 DOI: 10.1093/bib/bbab476] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/28/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
New drug production, from target identification to marketing approval, takes over 12 years and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the urgent need for more powerful computational methods for drug discovery. Here, we review the computational approaches to predicting protein-ligand interactions in the context of drug discovery, focusing on methods using artificial intelligence (AI). We begin with a brief introduction to proteins (targets), ligands (e.g. drugs) and their interactions for nonexperts. Next, we review databases that are commonly used in the domain of protein-ligand interactions. Finally, we survey and analyze the machine learning (ML) approaches implemented to predict protein-ligand binding sites, ligand-binding affinity and binding pose (conformation) including both classical ML algorithms and recent deep learning methods. After exploring the correlation between these three aspects of protein-ligand interaction, it has been proposed that they should be studied in unison. We anticipate that our review will aid exploration and development of more accurate ML-based prediction strategies for studying protein-ligand interactions.
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Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
| | - Cole McKay
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
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23
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Dai M, Radhakrishnan S, Li R, Tan R, Yan K, Fan G, Liu M. Targeted Protein Degradation: An Important Tool for Drug Discovery for "Undruggable" Tumor Transcription Factors. Technol Cancer Res Treat 2022; 21:15330338221095950. [PMID: 35466792 PMCID: PMC9047787 DOI: 10.1177/15330338221095950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Conventional small-molecule drugs (SMDs) are compounds characterized by low
molecular weight, high cell permeability, and high selectivity. In clinical
translation, SMDs are regarded as good candidates for oral drug formulation. SMD
inhibitors play an important role in cancer treatment; however, resistance and
low effectiveness have been major bottlenecks in clinical application.
Generally, only 20% of cell proteins can potentially be targeted and have been
developed as SMDs; thus, some types of tumor targets are considered
“undruggable.” Among these are transcription factors (TFs), an important class
of proteins that regulate the occurrence, formation, and development of tumors.
It is difficult for SMDs and macromolecular drugs to identify bioactive sites in
TFs and hence for use as pharmacological inhibitors in targeting TF proteins.
For this reason, technologies that enable targeted protein degradation, such as
proteolysis-targeting chimera or molecular glues, could serve as a potential
tool to solve these conundrums.
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Affiliation(s)
- Mengyuan Dai
- Department of Gynecological Oncology, 89674Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Sridhar Radhakrishnan
- Cancer Science Institute of Singapore, 37580National University of Singapore, Singapore, Singapore
| | - Rui Li
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruirong Tan
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Institute for Translational Chinese Medicine, 598782Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Kuo Yan
- Institute of Cell and Neurobiology, Charité Medical University, Berlin, Germany
| | - Gang Fan
- Department of Urology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China.,477382The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Miao Liu
- Department of Pathology, 1861Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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24
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Khan MT, Ali A, Wang Q, Irfan M, Khan A, Zeb MT, Zhang YJ, Chinnasamy S, Wei DQ. Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2-a molecular dynamic study. J Biomol Struct Dyn 2021; 39:3627-3637. [PMID: 32410504 PMCID: PMC7284144 DOI: 10.1080/07391102.2020.1769733] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022]
Abstract
Sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA (ssRNA) virus, responsible for severe acute respiratory disease (COVID-19). A large number of natural compounds are under trial for screening compounds, possessing potential inhibitory effect against the viral infection. Keeping in view the importance of marine compounds in antiviral activity, we investigated the potency of some marine natural products to target SARS-CoV-2 main protease (Mpro) (PDB ID 6MO3). The crystallographic structure of Mpro in an apo form was retrieved from Protein Data Bank and marine compounds from PubChem. These structures were prepared for docking and the complex with good docking score was subjected to molecular dynamic (MD) simulations for a period of 100 ns. To measure the stability, flexibility, and average distance between the target and compounds, root mean square deviations (RMSD), root mean square fluctuation (RMSF), and the distance matrix were calculated. Among five marine compounds, C-1 (PubChem CID 11170714) exhibited good activity, interacting with the active site and surrounding residues, forming many hydrogen and hydrophobic interactions. The C-1 also attained a stable dynamic behavior, and the average distance between compound and target remains constant. In conclusion, marine natural compounds may be used as a potential inhibitor against SARS-CoV-2 for better management of COVID-19.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Pakistan
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Qiankun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Muhammad Tariq Zeb
- Senior Research Officer, In-charge Genomic Laboratory, Veterinary Research Institute, Peshawar, Peshawar, Pakistan
| | - Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, China
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
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25
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Khan MT, Ali A, Wang Q, Irfan M, Khan A, Zeb MT, Zhang YJ, Chinnasamy S, Wei DQ. Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2-a molecular dynamic study. J Biomol Struct Dyn 2021. [PMID: 32410504 DOI: 10.1080/0739110220201769733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA (ssRNA) virus, responsible for severe acute respiratory disease (COVID-19). A large number of natural compounds are under trial for screening compounds, possessing potential inhibitory effect against the viral infection. Keeping in view the importance of marine compounds in antiviral activity, we investigated the potency of some marine natural products to target SARS-CoV-2 main protease (Mpro) (PDB ID 6MO3). The crystallographic structure of Mpro in an apo form was retrieved from Protein Data Bank and marine compounds from PubChem. These structures were prepared for docking and the complex with good docking score was subjected to molecular dynamic (MD) simulations for a period of 100 ns. To measure the stability, flexibility, and average distance between the target and compounds, root mean square deviations (RMSD), root mean square fluctuation (RMSF), and the distance matrix were calculated. Among five marine compounds, C-1 (PubChem CID 11170714) exhibited good activity, interacting with the active site and surrounding residues, forming many hydrogen and hydrophobic interactions. The C-1 also attained a stable dynamic behavior, and the average distance between compound and target remains constant. In conclusion, marine natural compounds may be used as a potential inhibitor against SARS-CoV-2 for better management of COVID-19.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Pakistan
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Qiankun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Muhammad Tariq Zeb
- Senior Research Officer, In-charge Genomic Laboratory, Veterinary Research Institute, Peshawar, Peshawar, Pakistan
| | - Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, China
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
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26
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Wang Z, Chen T, Liu H, Zhao XL, Hu WB, Yang H, Liu YA, Wen K. Pillar[5]arene-Derived endo-Functionalized Molecular Tube for Mimicking Protein-Ligand Interactions. J Org Chem 2021; 86:6467-6477. [PMID: 33872006 DOI: 10.1021/acs.joc.1c00314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Artificial tubular molecular pockets bearing polar functionalities on their inner surface are useful model systems for understanding the mechanisms of protein-ligand interactions in living systems. We herein report a pillar[5]arene-derived molecular tube, [P4-(OH)BPO], whose endo conformational isomer endo-[P4-(OH)BPO] possesses an inwardly pointing hydrogen-bond (H-bond) donor (OH) in its deep cavity and a strong H-bond acceptor (C═O) on its predominantly hydrophobic inner surface, rendering it a perfect protein binding pocket mimetic. A fragment-based drug design model was established using endo-[P4-(OH)BPO] and a library of various shape-complementary fragment ligands (1-38). On the basis of the binding affinity data for "fragment-pocket" complexes G⊂endo-[P4-(OH)BPO] (G = 1-38), two rationally designed "lead molecules" (39 and 40) were identified as being able to enhance binding affinity significantly by forming H-bonds with both the donor and acceptor of endo-[P4-(OH)BPO]. The described work opens new avenues for developing pillar[n]arene-derived protein binding pocket-mimetic systems for studies of protein-ligand interactions and mechanisms of enzymatic reactions.
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Affiliation(s)
- Zhuo Wang
- Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China.,School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Chen
- Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiao-Li Zhao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Wei-Bo Hu
- Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Hui Yang
- Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China.,School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yahu A Liu
- Medicinal Chemistry, ChemBridge Research Laboratories, San Diego, California 92127, United States
| | - Ke Wen
- Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China.,School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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27
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Veale CGL. Into the Fray! A Beginner's Guide to Medicinal Chemistry. ChemMedChem 2021; 16:1199-1225. [PMID: 33591595 DOI: 10.1002/cmdc.202000929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/31/2022]
Abstract
Modern medicinal chemistry is a complex, multidimensional discipline that operates at the interface of the chemical and biological sciences. The medicinal chemistry contribution to drug discovery is typically described in the context of the well-recited linear progression of the drug discovery pipeline. However, compound optimization is idiosyncratic to each project, and clear definitions of hit and lead molecules and the subsequent progress along the pipeline becomes easily blurred. In addition, this description lacks insight into the entangled relationship between chemical and pharmacological properties, and thus provides limited guidance on how innovative medicinal chemistry strategies can be applied to solve optimization problems, regardless of the stage in the pipeline. Through discussion and illustrative examples, this article seeks to provide insights into the finesse of medicinal chemistry and the subtlety of balancing chemical properties pharmacology. In so doing, it aims to serve as an accessible and simple-to-digest guide for anyone who wishes to learn about the underlying principles of medicinal chemistry, in a context that has been decoupled from the pipeline description.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, Scottsville, 3209, South Africa
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28
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Xu Y, Wang S, Hu Q, Gao S, Ma X, Zhang W, Shen Y, Chen F, Lai L, Pei J. CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction. Nucleic Acids Res 2019; 46:W374-W379. [PMID: 29750256 PMCID: PMC6031032 DOI: 10.1093/nar/gky380] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/30/2018] [Indexed: 12/02/2022] Open
Abstract
CavityPlus is a web server that offers protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys. CavPharmer uses a receptor-based pharmacophore modelling program, Pocket, to automatically extract pharmacophore features within cavities. CorrSite identifies potential allosteric ligand-binding sites based on motion correlation analyses between cavities. CovCys automatically detects druggable cysteine residues, which is especially useful to identify novel binding sites for designing covalent allosteric ligands. Overall, CavityPlus provides an integrated platform for analysing comprehensive properties of protein binding cavities. Such analyses are useful for many aspects of drug design and discovery, including target selection and identification, virtual screening, de novo drug design, and allosteric and covalent-binding drug design. The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.
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Affiliation(s)
- Youjun Xu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shiwei Wang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Qiwan Hu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shuaishi Gao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaomin Ma
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Weilin Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yihang Shen
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fangjin Chen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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29
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Chen Z, Zhang X, Peng C, Wang J, Xu Z, Chen K, Shi J, Zhu W. D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. J Chem Inf Model 2019; 59:3353-3358. [DOI: 10.1021/acs.jcim.9b00332] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xinben Zhang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Peng
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
| | - Jiye Shi
- UCB Biopharma SPRL, Chemin du Foriest, Braine-l’ Alleud B-1420, Belgium
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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30
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Stank A, Kokh DB, Horn M, Sizikova E, Neil R, Panecka J, Richter S, Wade RC. TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. Nucleic Acids Res 2019; 45:W325-W330. [PMID: 28431137 PMCID: PMC5570179 DOI: 10.1093/nar/gkx277] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/12/2017] [Indexed: 01/07/2023] Open
Abstract
The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure— generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis—superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket—detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues. A standard sequence conservation score per residue or a differential score per residue, for comparing on- and off-targets, can be calculated and displayed on the binding pocket for an uploaded multiple sequence alignment file, and known protein sequence annotations can be displayed simultaneously. The TRAPP webserver is freely available at http://trapp.h-its.org.
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Affiliation(s)
- Antonia Stank
- Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany.,Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany
| | - Daria B Kokh
- Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany
| | - Max Horn
- Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany
| | - Elena Sizikova
- Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany
| | - Rebecca Neil
- Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany
| | - Joanna Panecka
- Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany
| | - Stefan Richter
- Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany.,Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany
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31
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New Binding Sites, New Opportunities for GPCR Drug Discovery. Trends Biochem Sci 2019; 44:312-330. [PMID: 30612897 DOI: 10.1016/j.tibs.2018.11.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/11/2018] [Accepted: 11/27/2018] [Indexed: 12/29/2022]
Abstract
Many central biological events rely on protein-ligand interactions. The identification and characterization of protein-binding sites for ligands are crucial for the understanding of functions of both endogenous ligands and synthetic drug molecules. G protein-coupled receptors (GPCRs) typically detect extracellular signal molecules on the cell surface and transfer these chemical signals across the membrane, inducing downstream cellular responses via G proteins or β-arrestin. GPCRs mediate many central physiological processes, making them important targets for modern drug discovery. Here, we focus on the most recent breakthroughs in finding new binding sites and binding modes of GPCRs and their potentials for the development of new medicines.
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32
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Krivák R, Hoksza D. P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. J Cheminform 2018; 10:39. [PMID: 30109435 PMCID: PMC6091426 DOI: 10.1186/s13321-018-0285-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 06/29/2018] [Indexed: 01/29/2023] Open
Abstract
Background Ligand binding site prediction from protein structure has many applications related to elucidation of protein function and structure based drug discovery. It often represents only one step of many in complex computational drug design efforts. Although many methods have been published to date, only few of them are suitable for use in automated pipelines or for processing large datasets.
These use cases require stability and speed, which disqualifies many of the recently introduced tools that are either template based or available only as web servers. Results We present P2Rank, a stand-alone template-free tool for prediction of ligand binding sites based on machine learning. It is based on prediction of ligandability of local chemical neighbourhoods that are centered on points placed on the solvent accessible surface of a protein.
We show that P2Rank outperforms several existing tools, which include two widely used stand-alone tools (Fpocket, SiteHound), a comprehensive consensus based tool (MetaPocket 2.0), and a recent deep learning based method (DeepSite). P2Rank belongs to the fastest available tools (requires under 1 s for prediction on one protein), with additional advantage of multi-threaded implementation. Conclusions P2Rank is a new open source software package for ligand binding site prediction from protein structure. It is available as a user-friendly stand-alone command line program and a Java library. P2Rank has a lightweight installation and does not depend on other bioinformatics tools or large structural or sequence databases. Thanks to its speed and ability to make fully automated predictions, it is particularly well suited for processing large datasets or as a component of scalable structural bioinformatics pipelines. Electronic supplementary material The online version of this article (10.1186/s13321-018-0285-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Radoslav Krivák
- Department of Software Engineering, Charles University, Prague, Czech Republic.
| | - David Hoksza
- Department of Software Engineering, Charles University, Prague, Czech Republic.
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33
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Preto J, Gentile F, Winter P, Churchill C, Omar SI, Tuszynski JA. Molecular Dynamics and Related Computational Methods with Applications to Drug Discovery. SPRINGER PROCEEDINGS IN MATHEMATICS & STATISTICS 2018. [DOI: 10.1007/978-3-319-76599-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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34
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Simões T, Lopes D, Dias S, Fernandes F, Pereira J, Jorge J, Bajaj C, Gomes A. Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey. COMPUTER GRAPHICS FORUM : JOURNAL OF THE EUROPEAN ASSOCIATION FOR COMPUTER GRAPHICS 2017; 36:643-683. [PMID: 29520122 PMCID: PMC5839519 DOI: 10.1111/cgf.13158] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Detecting and analyzing protein cavities provides significant information about active sites for biological processes (e.g., protein-protein or protein-ligand binding) in molecular graphics and modeling. Using the three-dimensional structure of a given protein (i.e., atom types and their locations in 3D) as retrieved from a PDB (Protein Data Bank) file, it is now computationally viable to determine a description of these cavities. Such cavities correspond to pockets, clefts, invaginations, voids, tunnels, channels, and grooves on the surface of a given protein. In this work, we survey the literature on protein cavity computation and classify algorithmic approaches into three categories: evolution-based, energy-based, and geometry-based. Our survey focuses on geometric algorithms, whose taxonomy is extended to include not only sphere-, grid-, and tessellation-based methods, but also surface-based, hybrid geometric, consensus, and time-varying methods. Finally, we detail those techniques that have been customized for GPU (Graphics Processing Unit) computing.
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Affiliation(s)
- Tiago Simões
- Instituto de Telecomunicações, Portugal
- Universidade da Beira Interior, Portugal
| | | | - Sérgio Dias
- Instituto de Telecomunicações, Portugal
- Universidade da Beira Interior, Portugal
| | | | - João Pereira
- INESC-ID Lisboa, Portugal
- Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joaquim Jorge
- INESC-ID Lisboa, Portugal
- Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | | | - Abel Gomes
- Instituto de Telecomunicações, Portugal
- Universidade da Beira Interior, Portugal
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35
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Culurgioni S, Tang M, Hall DR, Walsh MA. Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092. J Vis Exp 2017. [PMID: 28994793 PMCID: PMC5752355 DOI: 10.3791/56294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Development of new antimicrobials and vaccines for Streptococcus pneumoniae (pneumococcus) are necessary to halt the rapid rise in multiple resistant strains. Carbohydrate substrate binding proteins (SBPs) represent viable targets for the development of protein-based vaccines and new antimicrobials because of their extracellular localization and the centrality of carbohydrate import for pneumococcal metabolism, respectively. Described here is a rationalized integrated protocol to carry out a comprehensive characterization of SP0092, which can be extended to other carbohydrate SBPs from the pneumococcus and other bacteria. This procedure can aid the structure-based design of inhibitors for this class of proteins. Presented in the first part of this manuscript are protocols for biochemical analysis by thermal shift assay, multi angle light scattering (MALS), and size exclusion chromatography (SEC), which optimize the stability and homogeneity of the sample directed to crystallization trials and so enhance the probability of success. The second part of this procedure describes the characterization of the SBP crystals using a tunable wavelength anomalous diffraction synchrotron beamline, and data collection protocols for measuring data that can be used to resolve the crystallized protein structure.
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Affiliation(s)
- Simone Culurgioni
- Diamond Light Source, Harwell Science & Innovation Campus; Research Complex at Harwell, Harwell Science & Innovation Campus;
| | - Minzhe Tang
- Diamond Light Source, Harwell Science & Innovation Campus; Research Complex at Harwell, Harwell Science & Innovation Campus
| | - David R Hall
- Diamond Light Source, Harwell Science & Innovation Campus
| | - Martin A Walsh
- Diamond Light Source, Harwell Science & Innovation Campus; Research Complex at Harwell, Harwell Science & Innovation Campus
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36
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Sarvagalla S, Coumar MS. Protein-Protein Interactions (PPIs) as an Alternative to Targeting the ATP Binding Site of Kinase. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Most of the developed kinase inhibitor drugs are ATP competitive and suffer from drawbacks such as off-target kinase activity, development of resistance due to mutation in the ATP binding pocket and unfavorable intellectual property situations. Besides the ATP binding pocket, protein kinases have binding sites that are involved in Protein-Protein Interactions (PPIs); these PPIs directly or indirectly regulate the protein kinase activity. Of recent, small molecule inhibitors of PPIs are emerging as an alternative to ATP competitive agents. Rational design of inhibitors for kinase PPIs could be carried out using molecular modeling techniques. In silico tools available for the prediction of hot spot residues and cavities at the PPI sites and the means to utilize this information for the identification of inhibitors are discussed. Moreover, in silico studies to target the Aurora B-INCENP PPI sites are discussed in context. Overall, this chapter provides detailed in silico strategies that are available to the researchers for carrying out structure-based drug design of PPI inhibitors.
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37
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Leelananda SP, Lindert S. Computational methods in drug discovery. Beilstein J Org Chem 2016; 12:2694-2718. [PMID: 28144341 PMCID: PMC5238551 DOI: 10.3762/bjoc.12.267] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022] Open
Abstract
The process for drug discovery and development is challenging, time consuming and expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut, assisting in the expedition of this long process and potentially reducing the cost of research and development. Today CADD has become an effective and indispensable tool in therapeutic development. The human genome project has made available a substantial amount of sequence data that can be used in various drug discovery projects. Additionally, increasing knowledge of biological structures, as well as increasing computer power have made it possible to use computational methods effectively in various phases of the drug discovery and development pipeline. The importance of in silico tools is greater than ever before and has advanced pharmaceutical research. Here we present an overview of computational methods used in different facets of drug discovery and highlight some of the recent successes. In this review, both structure-based and ligand-based drug discovery methods are discussed. Advances in virtual high-throughput screening, protein structure prediction methods, protein-ligand docking, pharmacophore modeling and QSAR techniques are reviewed.
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Affiliation(s)
- Sumudu P Leelananda
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
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38
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Broomhead NK, Soliman ME. Can We Rely on Computational Predictions To Correctly Identify Ligand Binding Sites on Novel Protein Drug Targets? Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites. Cell Biochem Biophys 2016; 75:15-23. [PMID: 27796788 DOI: 10.1007/s12013-016-0769-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 10/19/2016] [Indexed: 11/30/2022]
Abstract
In the field of medicinal chemistry there is increasing focus on identifying key proteins whose biochemical functions can firmly be linked to serious diseases. Such proteins become targets for drug or inhibitor molecules that could treat or halt the disease through therapeutic action or by blocking the protein function respectively. The protein must be targeted at the relevant biologically active site for drug or inhibitor binding to be effective. As insufficient experimental data is available to confirm the biologically active binding site for novel protein targets, researchers often rely on computational prediction methods to identify binding sites. Presented herein is a short review on structure-based computational methods that (i) predict putative binding sites and (ii) assess the druggability of predicted binding sites on protein targets. This review briefly covers the principles upon which these methods are based, where they can be accessed and their reliability in identifying the correct binding site on a protein target. Based on this review, we believe that these methods are useful in predicting putative binding sites, but as they do not account for the dynamic nature of protein-ligand binding interactions, they cannot definitively identify the correct site from a ranked list of putative sites. To overcome this shortcoming, we strongly recommend using molecular docking to predict the most likely protein-ligand binding site(s) and mode(s), followed by molecular dynamics simulations and binding thermodynamics calculations to validate the docking results. This protocol provides a valuable platform for experimental and computational efforts to design novel drugs and inhibitors that target disease-related proteins.
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Affiliation(s)
- Neal K Broomhead
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Mahmoud E Soliman
- Molecular Modelling & Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.
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Docking optimization, variance and promiscuity for large-scale drug-like chemical space using high performance computing architectures. Drug Discov Today 2016; 21:1672-1680. [DOI: 10.1016/j.drudis.2016.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/12/2016] [Accepted: 06/21/2016] [Indexed: 12/27/2022]
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Cao C, Xu S. Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area. Sci Rep 2016; 6:33232. [PMID: 27619067 PMCID: PMC5020399 DOI: 10.1038/srep33232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/23/2016] [Indexed: 12/02/2022] Open
Abstract
Protein ligand-binding site prediction is highly important for protein function determination and structure-based drug design. Over the past twenty years, dozens of computational methods have been developed to address this problem. Soga et al. identified ligand cavities based on the preferences of amino acids for the ligand-binding site (RA) and proposed the propensity for ligand binding (PLB) index to rank the cavities on the protein surface. However, we found that residues exhibit different RAs in response to changes in solvent exposure. Furthermore, previous studies have suggested that some dihedral angles of amino acids in specific regions of the Ramachandran plot are preferred at the functional sites of proteins. Based on these discoveries, the amino acid solvent-accessible surface area and dihedral angles were combined with the RA and PLB to obtain two new indexes, multi-factor RA (MF-RA) and multi-factor PLB (MF-PLB). MF-PLB, PLB and other methods were tested using two benchmark databases and two particular ligand-binding sites. The results show that MF-PLB can improve the success rate of PLB for both ligand-bound and ligand-unbound structures, particularly for top choice prediction.
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Affiliation(s)
- Chen Cao
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
- Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, China
| | - Shutan Xu
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
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Ferreira LG, Oliva G, Andricopulo AD. Protein-protein interaction inhibitors: advances in anticancer drug design. Expert Opin Drug Discov 2016; 11:957-68. [DOI: 10.1080/17460441.2016.1223038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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42
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Villoutreix B. Combining bioinformatics, chemoinformatics and experimental approaches to design chemical probes: Applications in the field of blood coagulation. ANNALES PHARMACEUTIQUES FRANÇAISES 2016; 74:253-66. [DOI: 10.1016/j.pharma.2016.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022]
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Guo Z, Li B, Cheng LT, Zhou S, McCammon JA, Che J. Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach. J Chem Theory Comput 2016; 11:753-65. [PMID: 25941465 PMCID: PMC4410907 DOI: 10.1021/ct500867u] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Indexed: 12/25/2022]
Abstract
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Protein–ligand
binding is a key biological process at the
molecular level. The identification and characterization of small-molecule
binding sites on therapeutically relevant proteins have tremendous
implications for target evaluation and rational drug design. In this
work, we used the recently developed level-set variational implicit-solvent
model (VISM) with the Coulomb field approximation (CFA) to locate
and characterize potential protein–small-molecule binding sites.
We applied our method to a data set of 515 protein–ligand complexes
and found that 96.9% of the cocrystallized ligands bind to the VISM-CFA-identified
pockets and that 71.8% of the identified pockets are occupied by cocrystallized
ligands. For 228 tight-binding protein–ligand complexes (i.e,
complexes with experimental pKd values
larger than 6), 99.1% of the cocrystallized ligands are in the VISM-CFA-identified
pockets. In addition, it was found that the ligand binding orientations
are consistent with the hydrophilic and hydrophobic descriptions provided
by VISM. Quantitative characterization of binding pockets with topological
and physicochemical parameters was used to assess the “ligandability”
of the pockets. The results illustrate the key interactions between
ligands and receptors and can be very informative for rational drug
design.
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Affiliation(s)
- Zuojun Guo
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev 2016; 116:6370-90. [PMID: 27074285 PMCID: PMC4901368 DOI: 10.1021/acs.chemrev.5b00631] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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Allosteric drug development holds
promise for delivering medicines
that are more selective and less toxic than those that target orthosteric
sites. To date, the discovery of allosteric binding sites and lead
compounds has been mostly serendipitous, achieved through high-throughput
screening. Over the past decade, structural data has become more readily
available for larger protein systems and more membrane protein classes
(e.g., GPCRs and ion channels), which are common allosteric drug targets.
In parallel, improved simulation methods now provide better atomistic
understanding of the protein dynamics and cooperative motions that
are critical to allosteric mechanisms. As a result of these advances,
the field of predictive allosteric drug development is now on the
cusp of a new era of rational structure-based computational methods.
Here, we review algorithms that predict allosteric sites based on
sequence data and molecular dynamics simulations, describe tools that
assess the druggability of these pockets, and discuss how Markov state
models and topology analyses provide insight into the relationship
between protein dynamics and allosteric drug binding. In each section,
we first provide an overview of the various method classes before
describing relevant algorithms and software packages.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Christopher T Lee
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Jacob D Durrant
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Robert D Malmstrom
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Victoria A Feher
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
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Bartolowits M, Davisson VJ. Considerations of Protein Subpockets in Fragment-Based Drug Design. Chem Biol Drug Des 2015; 87:5-20. [PMID: 26307335 DOI: 10.1111/cbdd.12631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While the fragment-based drug design approach continues to gain importance, gaps in the tools and methods available in the identification and accurate utilization of protein subpockets have limited the scope. The importance of these features of small molecule-protein recognition is highlighted with several examples. A generalized solution for the identification of subpockets and corresponding chemical fragments remains elusive, but there are numerous advancements in methods that can be used in combination to address subpockets. Finally, additional examples of approaches that consider the relative importance of small-molecule co-dependence of protein conformations are highlighted to emphasize an increased significance of subpockets, especially at protein interfaces.
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Affiliation(s)
- Matthew Bartolowits
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - V Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
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Structural basis for Marburg virus neutralization by a cross-reactive human antibody. Cell 2015; 160:904-912. [PMID: 25723165 DOI: 10.1016/j.cell.2015.01.041] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 01/08/2015] [Accepted: 01/27/2015] [Indexed: 12/14/2022]
Abstract
The filoviruses, including Marburg and Ebola, express a single glycoprotein on their surface, termed GP, which is responsible for attachment and entry of target cells. Filovirus GPs differ by up to 70% in protein sequence, and no antibodies are yet described that cross-react among them. Here, we present the 3.6 Å crystal structure of Marburg virus GP in complex with a cross-reactive antibody from a human survivor, and a lower resolution structure of the antibody bound to Ebola virus GP. The antibody, MR78, recognizes a GP1 epitope conserved across the filovirus family, which likely represents the binding site of their NPC1 receptor. Indeed, MR78 blocks binding of the essential NPC1 domain C. These structures and additional small-angle X-ray scattering of mucin-containing MARV and EBOV GPs suggest why such antibodies were not previously elicited in studies of Ebola virus, and provide critical templates for development of immunotherapeutics and inhibitors of entry.
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Krivák R, Hoksza D. Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. J Cheminform 2015; 7:12. [PMID: 25932051 PMCID: PMC4414931 DOI: 10.1186/s13321-015-0059-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein-ligand binding site prediction from a 3D protein structure plays a pivotal role in rational drug design and can be helpful in drug side-effects prediction or elucidation of protein function. Embedded within the binding site detection problem is the problem of pocket ranking - how to score and sort candidate pockets so that the best scored predictions correspond to true ligand binding sites. Although there exist multiple pocket detection algorithms, they mostly employ a fairly simple ranking function leading to sub-optimal prediction results. RESULTS We have developed a new pocket scoring approach (named PRANK) that prioritizes putative pockets according to their probability to bind a ligand. The method first carefully selects pocket points and labels them by physico-chemical characteristics of their local neighborhood. Random Forests classifier is subsequently applied to assign a ligandability score to each of the selected pocket point. The ligandability scores are finally merged into the resulting pocket score to be used for prioritization of the putative pockets. With the used of multiple datasets the experimental results demonstrate that the application of our method as a post-processing step greatly increases the quality of the prediction of Fpocket and ConCavity, two state of the art protein-ligand binding site prediction algorithms. CONCLUSIONS The positive experimental results show that our method can be used to improve the success rate, validity and applicability of existing protein-ligand binding site prediction tools. The method was implemented as a stand-alone program that currently contains support for Fpocket and Concavity out of the box, but is easily extendible to support other tools. PRANK is made freely available at http://siret.ms.mff.cuni.cz/prank.
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Affiliation(s)
- Radoslav Krivák
- Department of Software Engineering, Charles University in Prague, Prague, Czech Republic
| | - David Hoksza
- Department of Software Engineering, Charles University in Prague, Prague, Czech Republic
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Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015; 28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.
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Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, 3084, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia.,School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
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Kuenemann MA, Sperandio O, Labbé CM, Lagorce D, Miteva MA, Villoutreix BO. In silico design of low molecular weight protein-protein interaction inhibitors: Overall concept and recent advances. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:20-32. [PMID: 25748546 DOI: 10.1016/j.pbiomolbio.2015.02.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) are carrying out diverse functions in living systems and are playing a major role in the health and disease states. Low molecular weight (LMW) "drug-like" inhibitors of PPIs would be very valuable not only to enhance our understanding over physiological processes but also for drug discovery endeavors. However, PPIs were deemed intractable by LMW chemicals during many years. But today, with the new experimental and in silico technologies that have been developed, about 50 PPIs have already been inhibited by LMW molecules. Here, we first focus on general concepts about protein-protein interactions, present a consensual view about ligandable pockets at the protein interfaces and the possibilities of using fast and cost effective structure-based virtual screening methods to identify PPI hits. We then discuss the design of compound collections dedicated to PPIs. Recent financial analyses of the field suggest that LMW PPI modulators could be gaining momentum over biologics in the coming years supporting further research in this area.
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Affiliation(s)
- Mélaine A Kuenemann
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Olivier Sperandio
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France
| | - Céline M Labbé
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France
| | - David Lagorce
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Maria A Miteva
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France.
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50
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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