1
|
Zhang J, Li R, Yu Y, Sun W, Zhang C, Wang H. Network pharmacology-and molecular docking-based investigation of Danggui blood-supplementing decoction in ischaemic stroke. Growth Factors 2024; 42:13-23. [PMID: 37932893 DOI: 10.1080/08977194.2023.2277755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/27/2023] [Indexed: 11/08/2023]
Abstract
Danggui blood-supplementing decoction (DBsD) is an herbal preparation treating several diseases including stroke. The present study sought to investigate the potential mechanism of DBsD in ischaemic stroke (IS) using network pharmacology, molecular docking, and cell experiment. Based on the protein-protein (PPI) network analysis, MAPK1 (0.51, 12), KNG1 (0.57, 28), and TNF (0.64, 39) were found with relatively good performance in degree and closeness centrality. The functional enrichment analysis revealed that DBsD contributed to IS-related biological processes, molecule function, and presynaptic/postsynaptic cellular components. Pathway enrichment indicated that DBsD might protect IS by modulating multi-signalling pathways including the sphingolipid signalling pathway. Molecular docking verified the stigmasterol-KNG1, bifendate-TNF, and formononetin-MAPK1 pairs. Cell experiments confirmed the involvement of KNG1 and sphingolipid signalling pathway in hippocampal neuronal cell apoptosis. This study showed that DBsD can protect neuronal cell injury after IS through multiple components, multiple targets, and multiple pathways.
Collapse
Affiliation(s)
- Jinling Zhang
- Department of Neurology, The First Affiliated Hospital of Qiqihar Medical College, Qiqihar, Heilongjiang, China
| | - Ruiqing Li
- Department of Neurology, The First Affiliated Hospital of Qiqihar Medical College, Qiqihar, Heilongjiang, China
| | - Yang Yu
- Department of Neurology, The First Affiliated Hospital of Qiqihar Medical College, Qiqihar, Heilongjiang, China
| | - Weijia Sun
- Department of Neurology, The First Affiliated Hospital of Qiqihar Medical College, Qiqihar, Heilongjiang, China
| | - Chengshi Zhang
- Department of Neurology, The First Affiliated Hospital of Qiqihar Medical College, Qiqihar, Heilongjiang, China
| | - Haijun Wang
- Department of Neurology, The First Affiliated Hospital of Qiqihar Medical College, Qiqihar, Heilongjiang, China
| |
Collapse
|
2
|
Fancher AT, Hua Y, Close DA, Xu W, McDermott LA, Strock CJ, Santiago U, Camacho CJ, Johnston PA. Characterization of allosteric modulators that disrupt androgen receptor co-activator protein-protein interactions to alter transactivation-Drug leads for metastatic castration resistant prostate cancer. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:325-343. [PMID: 37549772 DOI: 10.1016/j.slasd.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/06/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Three series of compounds were prioritized from a high content screening campaign that identified molecules that blocked dihydrotestosterone (DHT) induced formation of Androgen Receptor (AR) protein-protein interactions (PPIs) with the Transcriptional Intermediary Factor 2 (TIF2) coactivator and also disrupted preformed AR-TIF2 PPI complexes; the hydrobenzo-oxazepins (S1), thiadiazol-5-piperidine-carboxamides (S2), and phenyl-methyl-indoles (S3). Compounds from these series inhibited AR PPIs with TIF2 and SRC-1, another p160 coactivator, in mammalian 2-hybrid assays and blocked transcriptional activation in reporter assays driven by full length AR or AR-V7 splice variants. Compounds inhibited the growth of five prostate cancer cell lines, with many exhibiting differential cytotoxicity towards AR positive cell lines. Representative compounds from the 3 series substantially reduced both endogenous and DHT-enhanced expression and secretion of the prostate specific antigen (PSA) cancer biomarker in the C4-2 castration resistant prostate cancer (CRPC) cell line. The comparatively weak activities of series compounds in the H3-DHT and/or TIF2 box 3 LXXLL-peptide binding assays to the recombinant ligand binding domain of AR suggest that direct antagonism at the orthosteric ligand binding site or AF-2 surface respectively are unlikely mechanisms of action. Cellular enhanced thermal stability assays (CETSA) indicated that compounds engaged AR and reduced the maximum efficacy and right shifted the EC50 of DHT-enhanced AR thermal stabilization consistent with the effects of negative allosteric modulators. Molecular docking of potent representative hits from each series to AR structures suggest that S1-1 and S2-6 engage a novel binding pocket (BP-1) adjacent to the orthosteric ligand binding site, while S3-11 occupies the AR binding function 3 (BF-3) allosteric pocket. Hit binding poses indicate spaces and residues adjacent to the BP-1 and BF-3 pockets that will be exploited in future medicinal chemistry optimization studies. Small molecule allosteric modulators that prevent/disrupt AR PPIs with coactivators like TIF2 to alter transcriptional activation in the presence of orthosteric agonists might evade the resistance mechanisms to existing prostate cancer drugs and provide novel starting points for medicinal chemistry lead optimization and future development into therapies for metastatic CRPC.
Collapse
Affiliation(s)
- Ashley T Fancher
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; Nucleus Global, 2 Ravinia Drive, Suite 605, Atlanta, GA 30346, USA
| | - Yun Hua
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David A Close
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wei Xu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lee A McDermott
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; PsychoGenics Inc, 215 College Road, Paramus, NJ 07652, USA
| | | | - Ulises Santiago
- Department of Computational and Systems Biology, School of Medicine, at the University of Pittsburgh, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, School of Medicine, at the University of Pittsburgh, USA
| | - Paul A Johnston
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA 15232, USA.
| |
Collapse
|
3
|
Ha EJ, Lwin CT, Durrant JD. LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates. J Cheminform 2020; 12:69. [PMID: 33292486 PMCID: PMC7656723 DOI: 10.1186/s13321-020-00471-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/19/2020] [Indexed: 01/21/2023] Open
Abstract
Structure-based virtual screening (VS) uses computer docking to prioritize candidate small-molecule ligands for subsequent experimental testing. Docking programs evaluate molecular binding in part by predicting the geometry with which a given compound might bind a target receptor (e.g., the docked "pose" relative to a protein target). Candidate ligands predicted to participate in the same intermolecular interactions typical of known ligands (or ligands that bind related proteins) are arguably more likely to be true binders. Some docking programs allow users to apply constraints during the docking process with the goal of prioritizing these critical interactions. But these programs often have restrictive and/or expensive licenses, and many popular open-source docking programs (e.g., AutoDock Vina) lack this important functionality. We present LigGrep, a free, open-source program that addresses this limitation. As input, LigGrep accepts a protein receptor file, a directory containing many docked-compound files, and a list of user-specified filters describing critical receptor/ligand interactions. LigGrep evaluates each docked pose and outputs the names of the compounds with poses that pass all filters. To demonstrate utility, we show that LigGrep can improve the hit rates of test VS targeting H. sapiens poly(ADPribose) polymerase 1 (HsPARP1), H. sapiens peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (HsPin1p), and S. cerevisiae hexokinase-2 (ScHxk2p). We hope that LigGrep will be a useful tool for the computational biology community. A copy is available free of charge at http://durrantlab.com/liggrep/ .
Collapse
Affiliation(s)
- Emily J Ha
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, United States
| | - Cara T Lwin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States.
| |
Collapse
|
4
|
Wierbowski SD, Wingert BM, Zheng J, Camacho CJ. Cross-docking benchmark for automated pose and ranking prediction of ligand binding. Protein Sci 2019; 29:298-305. [PMID: 31721338 DOI: 10.1002/pro.3784] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 11/11/2022]
Abstract
Significant efforts have been devoted in the last decade to improving molecular docking techniques to predict both accurate binding poses and ranking affinities. Some shortcomings in the field are the limited number of standard methods for measuring docking success and the availability of widely accepted standard data sets for use as benchmarks in comparing different docking algorithms throughout the field. In order to address these issues, we have created a Cross-Docking Benchmark server. The server is a versatile cross-docking data set containing 4,399 protein-ligand complexes across 95 protein targets intended to serve as benchmark set and gold standard for state-of-the-art pose and ranking prediction in easy, medium, hard, or very hard docking targets. The benchmark along with a customizable cross-docking data set generation tool is available at http://disco.csb.pitt.edu. We further demonstrate the potential uses of the server in questions outside of basic benchmarking such as the selection of the ideal docking reference structure.
Collapse
Affiliation(s)
| | - Bentley M Wingert
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jim Zheng
- Department of Computer Science, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
5
|
Chen X, Liu H, Xie W, Yang Y, Wang Y, Fan Y, Hua Y, Zhu L, Zhao J, Lu T, Chen Y, Zhang Y. Investigation of Crystal Structures in Structure-Based Virtual Screening for Protein Kinase Inhibitors. J Chem Inf Model 2019; 59:5244-5262. [PMID: 31689093 DOI: 10.1021/acs.jcim.9b00684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein kinases are important drug targets in several therapeutic areas ,and structure-based virtual screening (SBVS) is an important strategy in discovering lead compounds for kinase targets. However, there are multiple crystal structures available for each target, and determining which one is the most favorable is a key step in molecular docking for SBVS due to the ligand induce-fit effect. This work aimed to find the most desirable crystal structures for molecular docking by a comprehensive analysis of the protein kinase database which covers 190 different kinases from all eight main kinase families. Through an integrated self-docking and cross-docking evaluation, 86 targets were eventually evaluated on a total of 2608 crystal structures. Results showed that molecular docking has great capability in reproducing conformation of crystallized ligands and for each target, the most favorable crystal structure was selected, and the AGC family outperformed the other family targets based on RMSD comparison. In addition, RMSD values, GlideScore, and corresponding bioactivity data were compared and demonstrated certain relationships. This work provides great convenience for researchers to directly select the optimal crystal structure in SBVS-based kinase drug design and further validates the effectiveness of molecular docking in drug discovery.
Collapse
Affiliation(s)
- Xingye Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Wuchen Xie
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yan Yang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuchen Wang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuanrong Fan
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Lu Zhu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Junnan Zhao
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China.,State Key Laboratory of Natural Medicines , China Pharmaceutical University , 24 Tongjiaxiang , Nanjing 210009 , China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| |
Collapse
|
6
|
Jaroensuk J, Wong YH, Zhong W, Liew CW, Maenpuen S, Sahili AE, Atichartpongkul S, Chionh YH, Nah Q, Thongdee N, McBee ME, Prestwich EG, DeMott MS, Chaiyen P, Mongkolsuk S, Dedon PC, Lescar J, Fuangthong M. Crystal structure and catalytic mechanism of the essential m 1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa. RNA (NEW YORK, N.Y.) 2019; 25:1481-1496. [PMID: 31399541 PMCID: PMC6795141 DOI: 10.1261/rna.066746.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 07/28/2019] [Indexed: 06/10/2023]
Abstract
The tRNA (m1G37) methyltransferase TrmD catalyzes m1G formation at position 37 in many tRNA isoacceptors and is essential in most bacteria, which positions it as a target for antibiotic development. In spite of its crucial role, little is known about TrmD in Pseudomonas aeruginosa (PaTrmD), an important human pathogen. Here we present detailed structural, substrate, and kinetic properties of PaTrmD. The mass spectrometric analysis confirmed the G36G37-containing tRNAs Leu(GAG), Leu(CAG), Leu(UAG), Pro(GGG), Pro(UGG), Pro(CGG), and His(GUG) as PaTrmD substrates. Analysis of steady-state kinetics with S-adenosyl-l-methionine (SAM) and tRNALeu(GAG) showed that PaTrmD catalyzes the two-substrate reaction by way of a ternary complex, while isothermal titration calorimetry revealed that SAM and tRNALeu(GAG) bind to PaTrmD independently, each with a dissociation constant of 14 ± 3 µM. Inhibition by the SAM analog sinefungin was competitive with respect to SAM (Ki = 0.41 ± 0.07 µM) and uncompetitive for tRNA (Ki = 6.4 ± 0.8 µM). A set of crystal structures of the homodimeric PaTrmD protein bound to SAM and sinefungin provide the molecular basis for enzyme competitive inhibition and identify the location of the bound divalent ion. These results provide insights into PaTrmD as a potential target for the development of antibiotics.
Collapse
Affiliation(s)
- Juthamas Jaroensuk
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Wenhe Zhong
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Abbas E Sahili
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | | | - Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Qianhui Nah
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Narumon Thongdee
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Department of Biotechnology, Faculty of Sciences, Mahidol University, Bangkok 10400, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Mayuree Fuangthong
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand
| |
Collapse
|
7
|
Türková A, Zdrazil B. Current Advances in Studying Clinically Relevant Transporters of the Solute Carrier (SLC) Family by Connecting Computational Modeling and Data Science. Comput Struct Biotechnol J 2019; 17:390-405. [PMID: 30976382 PMCID: PMC6438991 DOI: 10.1016/j.csbj.2019.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/18/2023] Open
Abstract
Organic anion and cation transporting proteins (OATs, OATPs, and OCTs), as well as the Multidrug and Toxin Extrusion (MATE) transporters of the Solute Carrier (SLC) family are playing a pivotal role in the discovery and development of new drugs due to their involvement in drug disposition, drug-drug interactions, adverse drug effects and related toxicity. Computational methods to understand and predict clinically relevant transporter interactions can provide useful guidance at early stages in drug discovery and design, especially if they include contemporary data science approaches. In this review, we summarize the current state-of-the-art of computational approaches for exploring ligand interactions and selectivity for these drug (uptake) transporters. The computational methods discussed here by highlighting interesting examples from the current literature are ranging from semiautomatic data mining and integration, to ligand-based methods (such as quantitative structure-activity relationships, and combinatorial pharmacophore modeling), and finally structure-based methods (such as comparative modeling, molecular docking, and molecular dynamics simulations). We are focusing on promising computational techniques such as fold-recognition methods, proteochemometric modeling or techniques for enhanced sampling of protein conformations used in the context of these ADMET-relevant SLC transporters with a special focus on methods useful for studying ligand selectivity.
Collapse
Affiliation(s)
- Alžběta Türková
- Department of Pharmaceutical Chemistry, Divison of Drug Design and Medicinal Chemistry, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Barbara Zdrazil
- Department of Pharmaceutical Chemistry, Divison of Drug Design and Medicinal Chemistry, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| |
Collapse
|
8
|
A network-centric approach to drugging TNF-induced NF-κB signaling. Nat Commun 2019; 10:860. [PMID: 30808860 PMCID: PMC6391473 DOI: 10.1038/s41467-019-08802-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/30/2019] [Indexed: 01/01/2023] Open
Abstract
Target-centric drug development strategies prioritize single-target potency in vitro and do not account for connectivity and multi-target effects within a signal transduction network. Here, we present a systems biology approach that combines transcriptomic and structural analyses with live-cell imaging to predict small molecule inhibitors of TNF-induced NF-κB signaling and elucidate the network response. We identify two first-in-class small molecules that inhibit the NF-κB signaling pathway by preventing the maturation of a rate-limiting multiprotein complex necessary for IKK activation. Our findings suggest that a network-centric drug discovery approach is a promising strategy to evaluate the impact of pharmacologic intervention in signaling. Chemical perturbation of specific protein–protein interactions is notoriously difficult, yet necessary when complete inhibition of a signalling pathway is detrimental to the cell. Here, the authors use a systems approach and identify two first-in-class small molecules that specifically inhibit TNF-induced NF-κB activation.
Collapse
|
9
|
Pabon NA, Xia Y, Estabrooks SK, Ye Z, Herbrand AK, Süß E, Biondi RM, Assimon VA, Gestwicki JE, Brodsky JL, Camacho CJ, Bar-Joseph Z. Predicting protein targets for drug-like compounds using transcriptomics. PLoS Comput Biol 2018; 14:e1006651. [PMID: 30532261 PMCID: PMC6300300 DOI: 10.1371/journal.pcbi.1006651] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/19/2018] [Accepted: 11/13/2018] [Indexed: 01/07/2023] Open
Abstract
An expanded chemical space is essential for improved identification of small molecules for emerging therapeutic targets. However, the identification of targets for novel compounds is biased towards the synthesis of known scaffolds that bind familiar protein families, limiting the exploration of chemical space. To change this paradigm, we validated a new pipeline that identifies small molecule-protein interactions and works even for compounds lacking similarity to known drugs. Based on differential mRNA profiles in multiple cell types exposed to drugs and in which gene knockdowns (KD) were conducted, we showed that drugs induce gene regulatory networks that correlate with those produced after silencing protein-coding genes. Next, we applied supervised machine learning to exploit drug-KD signature correlations and enriched our predictions using an orthogonal structure-based screen. As a proof-of-principle for this regimen, top-10/top-100 target prediction accuracies of 26% and 41%, respectively, were achieved on a validation of set 152 FDA-approved drugs and 3104 potential targets. We then predicted targets for 1680 compounds and validated chemical interactors with four targets that have proven difficult to chemically modulate, including non-covalent inhibitors of HRAS and KRAS. Importantly, drug-target interactions manifest as gene expression correlations between drug treatment and both target gene KD and KD of genes that act up- or down-stream of the target, even for relatively weak binders. These correlations provide new insights on the cellular response of disrupting protein interactions and highlight the complex genetic phenotypes of drug treatment. With further refinement, our pipeline may accelerate the identification and development of novel chemical classes by screening compound-target interactions. Bioactive compounds often disrupt cellular gene expression in ways that are difficult to predict. While the correlation between a cellular response after treatment with a small molecule and the knockdown of its target protein should be simple to establish, in practice this goal has been difficult to achieve. The main challenges are that data are noisy, drugs are not intended to be active in all cell types, and signals from a bona fide target(s) may be obscured by correlations with knockdowns of other proteins in the same pathway(s). Here, we find that a random forest classification model can detect meaningful correlational patterns when gene expression profiles after compound treatment and gene knockdowns in four or more cell lines are compared. When this approach is enriched by a structure-based screen, novel drug-target interactions can be predicted. We then validated new ligand-protein interactions for four difficult targets. Although the initial compounds are not especially potent in vitro, they are capable of disrupting their target pathway in the cell to an extent that generates a significant and characteristic gene expression profile. Collectively, our studies provide insight on cell-level transcriptomic responses to pharmaceutical intervention and the use of these patterns for target identification. In addition, the method provides a novel drug discovery pipeline to test chemistries without a priori knowledge of their target(s).
Collapse
Affiliation(s)
- Nicolas A. Pabon
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Yan Xia
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Samuel K. Estabrooks
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Zhaofeng Ye
- School of Medicine, Tsinghua University, Beijing, China
| | - Amanda K. Herbrand
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - Evelyn Süß
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - Ricardo M. Biondi
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - Victoria A. Assimon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Jeffrey L. Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Carlos J. Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (CJC); (ZBJ)
| | - Ziv Bar-Joseph
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (CJC); (ZBJ)
| |
Collapse
|
10
|
Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
Collapse
Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
| |
Collapse
|
11
|
Wingert BM, Camacho CJ. Improving small molecule virtual screening strategies for the next generation of therapeutics. Curr Opin Chem Biol 2018; 44:87-92. [PMID: 29920436 DOI: 10.1016/j.cbpa.2018.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/27/2018] [Accepted: 06/04/2018] [Indexed: 01/05/2023]
Abstract
The new generation of post-genomic targets, such as protein-protein interactions (PPIs), often require new chemotypes not well represented in current compound libraries. This is one reason for why traditional high throughput screening (HTS) approaches are not more successful in delivering medicinal chemistry starting points for PPIs. In silico screening methods of an expanded chemical space are then potential alternatives for developing novel chemical probes to modulate PPIs. In this review, we report on the state-of-the-art pipelines for virtual screening, emphasizing prospectively validated methods capable of addressing the challenge of drugging difficult targets in the human interactome. Collectively, we show that optimal strategies for structure based virtual screening vary depending on receptor structure and degree of flexibility.
Collapse
Affiliation(s)
- Bentley M Wingert
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| |
Collapse
|
12
|
Abid H, Harigua-Souiai E, Mejri T, Barhoumi M, Guizani I. Leishmania infantum 5'-Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target. BMC STRUCTURAL BIOLOGY 2017; 17:9. [PMID: 29258562 PMCID: PMC5738077 DOI: 10.1186/s12900-017-0079-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND The 5'-methylthioadenosine phosphorylase (MTAP), an enzyme involved in purine and polyamine metabolism and in the methionine salvage pathway, is considered as a potential drug target against cancer and trypanosomiasis. In fact, Trypanosoma and Leishmania parasites lack de novo purine pathways and rely on purine salvage pathways to meet their requirements. Herein, we propose the first comprehensive bioinformatic and structural characterization of the putative Leishmania infantum MTAP (LiMTAP), using a comparative computational approach. RESULTS Sequence analysis showed that LiMTAP shared higher identity rates with the Trypanosoma brucei (TbMTAP) and the human (huMTAP) homologs as compared to the human purine nucleoside phosphorylase (huPNP). Motifs search using MEME identified more common patterns and higher relatedness of the parasite proteins to the huMTAP than to the huPNP. The 3D structures of LiMTAP and TbMTAP were predicted by homology modeling and compared to the crystal structure of the huMTAP. These models presented conserved secondary structures compared to the huMTAP, with a similar topology corresponding to the Rossmann fold. This confirmed that both LiMTAP and TbMTAP are members of the NP-I family. In comparison to the huMTAP, the 3D model of LiMTAP showed an additional α-helix, at the C terminal extremity. One peptide located in this specific region was used to generate a specific antibody to LiMTAP. In comparison with the active site (AS) of huMTAP, the parasite ASs presented significant differences in the shape and the electrostatic potentials (EPs). Molecular docking of 5'-methylthioadenosine (MTA) and 5'-hydroxyethylthio-adenosine (HETA) on the ASs on the three proteins predicted differential binding modes and interactions when comparing the parasite proteins to the human orthologue. CONCLUSIONS This study highlighted significant structural peculiarities, corresponding to functionally relevant sequence divergence in LiMTAP, making of it a potential drug target against Leishmania.
Collapse
Affiliation(s)
- Hela Abid
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR11IPT04/ LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.,Faculté des Sciences de Bizerte, Université de Carthage, Tunis, Tunisie
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR11IPT04/ LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Thouraya Mejri
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR11IPT04/ LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mourad Barhoumi
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR11IPT04/ LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR11IPT04/ LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.
| |
Collapse
|
13
|
Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2. J Comput Aided Mol Des 2017; 32:45-58. [PMID: 29127581 DOI: 10.1007/s10822-017-0081-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/01/2017] [Indexed: 10/18/2022]
Abstract
Two of the major ongoing challenges in computational drug discovery are predicting the binding pose and affinity of a compound to a protein. The Drug Design Data Resource Grand Challenge 2 was developed to address these problems and to drive development of new methods. The challenge provided the 2D structures of compounds for which the organizers help blinded data in the form of 35 X-ray crystal structures and 102 binding affinity measurements and challenged participants to predict the binding pose and affinity of the compounds. We tested a number of pose prediction methods as part of the challenge; we found that docking methods that incorporate protein flexibility (Induced Fit Docking) outperformed methods that treated the protein as rigid. We also found that using binding pose metadynamics, a molecular dynamics based method, to score docked poses provided the best predictions of our methods with an average RMSD of 2.01 Å. We tested both structure-based (e.g. docking) and ligand-based methods (e.g. QSAR) in the affinity prediction portion of the competition. We found that our structure-based methods based on docking with Smina (Spearman ρ = 0.614), performed slightly better than our ligand-based methods (ρ = 0.543), and had equivalent performance with the other top methods in the competition. Despite the overall good performance of our methods in comparison to other participants in the challenge, there exists significant room for improvement especially in cases such as these where protein flexibility plays such a large role.
Collapse
|
14
|
Kadukova M, Grudinin S. Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2. J Comput Aided Mol Des 2017; 32:151-162. [DOI: 10.1007/s10822-017-0062-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/08/2017] [Indexed: 10/18/2022]
|
15
|
Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge. J Comput Aided Mol Des 2016; 30:695-706. [PMID: 27573981 DOI: 10.1007/s10822-016-9941-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/17/2016] [Indexed: 01/31/2023]
Abstract
Induced fit or protein flexibility can make a given structure less useful for docking and/or scoring. The 2015 Drug Design Data Resource (D3R) Grand Challenge provided a unique opportunity to prospectively test optimal strategies for virtual screening in these type of targets: heat shock protein 90 (HSP90), a protein with multiple ligand-induced binding modes; and mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), a kinase with a large flexible pocket. Using previously known co-crystal structures, we tested predictions from methods that keep the receptor structure fixed and used (a) multiple receptor/ligand co-crystals as binding templates for minimization or docking ("close"), (b) methods that align or dock to a single receptor ("cross"), and (c) a hybrid approach that chose from multiple bound ligands as initial templates for minimization to a single receptor ("min-cross"). Pose prediction using our "close" models resulted in average ligand RMSDs of 0.32 and 1.6 Å for HSP90 and MAP4K4, respectively, the most accurate models of the community-wide challenge. On the other hand, affinity ranking using our "cross" methods performed well overall despite the fact that a fixed receptor cannot model ligand-induced structural changes,. In addition, "close" methods that leverage the co-crystals of the different binding modes of HSP90 also predicted the best affinity ranking. Our studies suggest that analysis of changes on the receptor structure upon ligand binding can help select an optimal virtual screening strategy.
Collapse
|
16
|
Carlson HA, Smith RD, Damm-Ganamet KL, Stuckey JA, Ahmed A, Convery MA, Somers DO, Kranz M, Elkins PA, Cui G, Peishoff CE, Lambert MH, Dunbar JB. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. J Chem Inf Model 2016; 56:1063-77. [PMID: 27149958 DOI: 10.1021/acs.jcim.5b00523] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 2014 CSAR Benchmark Exercise was the last community-wide exercise that was conducted by the group at the University of Michigan, Ann Arbor. For this event, GlaxoSmithKline (GSK) donated unpublished crystal structures and affinity data from in-house projects. Three targets were used: tRNA (m1G37) methyltransferase (TrmD), Spleen Tyrosine Kinase (SYK), and Factor Xa (FXa). A particularly strong feature of the GSK data is its large size, which lends greater statistical significance to comparisons between different methods. In Phase 1 of the CSAR 2014 Exercise, participants were given several protein-ligand complexes and asked to identify the one near-native pose from among 200 decoys provided by CSAR. Though decoys were requested by the community, we found that they complicated our analysis. We could not discern whether poor predictions were failures of the chosen method or an incompatibility between the participant's method and the setup protocol we used. This problem is inherent to decoys, and we strongly advise against their use. In Phase 2, participants had to dock and rank/score a set of small molecules given only the SMILES strings of the ligands and a protein structure with a different ligand bound. Overall, docking was a success for most participants, much better in Phase 2 than in Phase 1. However, scoring was a greater challenge. No particular approach to docking and scoring had an edge, and successful methods included empirical, knowledge-based, machine-learning, shape-fitting, and even those with solvation and entropy terms. Several groups were successful in ranking TrmD and/or SYK, but ranking FXa ligands was intractable for all participants. Methods that were able to dock well across all submitted systems include MDock,1 Glide-XP,2 PLANTS,3 Wilma,4 Gold,5 SMINA,6 Glide-XP2/PELE,7 FlexX,8 and MedusaDock.9 In fact, the submission based on Glide-XP2/PELE7 cross-docked all ligands to many crystal structures, and it was particularly impressive to see success across an ensemble of protein structures for multiple targets. For scoring/ranking, submissions that showed statistically significant achievement include MDock1 using ITScore1,10 with a flexible-ligand term,11 SMINA6 using Autodock-Vina,12,13 FlexX8 using HYDE,14 and Glide-XP2 using XP DockScore2 with and without ROCS15 shape similarity.16 Of course, these results are for only three protein targets, and many more systems need to be investigated to truly identify which approaches are more successful than others. Furthermore, our exercise is not a competition.
Collapse
Affiliation(s)
- Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Richard D Smith
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Kelly L Damm-Ganamet
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Jeanne A Stuckey
- Center for Structural Biology, University of Michigan , 3358E Life Sciences Institute, 210 Washtenaw Ave., Ann Arbor, Michigan 48109-2216, United States
| | - Aqeel Ahmed
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Maire A Convery
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Donald O Somers
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Michael Kranz
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Patricia A Elkins
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Guanglei Cui
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Catherine E Peishoff
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Millard H Lambert
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - James B Dunbar
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| |
Collapse
|
17
|
Zhu X, Shin WH, Kim H, Kihara D. Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014. J Chem Inf Model 2015; 56:1088-99. [PMID: 26691286 DOI: 10.1021/acs.jcim.5b00625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Community Structure-Activity Resource (CSAR) benchmark exercise provides a unique opportunity for researchers to objectively evaluate the performance of protein-ligand docking methods. Patch-Surfer and PL-PatchSurfer, molecular surface-based methods for predicting binding ligands of proteins developed in our group, were tested on both CSAR 2013 and 2014 benchmark exercises in combination with an empirical scoring function-based method, AutoDock, while we only participated in CSAR 2013 using Patch-Surfer. The prediction results for Phase 1 task in CSAR 2013 showed that Patch-Surfer was able to rank all the four designed binding proteins within top ranks, outperforming AutoDock Vina. In Phase 2 of 2013, PL-PatchSurfer correctly selected the correct ligand pose for two target proteins. PL-PatchSurfer performed reasonably well in ranking ligands according to their binding affinity and in selecting near-native ligand poses in 2013 Phase 3 and 2014 Phase 1, respectively, although AutoDock Vina showed better performance. Lastly, in the 2014 Phase 2 exercise, the PL-PatchSurfer scores computed for ligands to target protein pairs correlated well with their pIC50 values, which was better or comparable to results by other participants. Overall, our methods showed fairly good performance in CSAR 2013 and 2014. Unique characteristics of the methods are discussed in comparison with AutoDock.
Collapse
Affiliation(s)
- Xiaolei Zhu
- School of Life Science, Anhui University , Hefei, Anhui 230601, China.,Department of Biology Science, Purdue University , West Lafayette, Indiana 47907, United States
| | - Woong-Hee Shin
- Department of Biology Science, Purdue University , West Lafayette, Indiana 47907, United States
| | - Hyungrae Kim
- Department of Biology Science, Purdue University , West Lafayette, Indiana 47907, United States
| | - Daisuke Kihara
- Department of Biology Science, Purdue University , West Lafayette, Indiana 47907, United States.,Department of Computer Science, Purdue University , West Lafayette, Indiana 47907, United States
| |
Collapse
|