1
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Puls K, Olivé-Marti AL, Hongnak S, Lamp D, Spetea M, Wolber G. Discovery of Novel, Selective, and Nonbasic Agonists for the Kappa-Opioid Receptor Determined by Salvinorin A-Based Virtual Screening. J Med Chem 2024; 67:13788-13801. [PMID: 39088801 PMCID: PMC11345774 DOI: 10.1021/acs.jmedchem.4c00590] [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: 03/11/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/03/2024]
Abstract
Modulating the kappa-opioid receptor (KOR) is a promising strategy for treating various human diseases. KOR agonists show potential for treating pain, pruritus, and epilepsy, while KOR antagonists show potential for treating depression, anxiety, and addiction. The diterpenoid Salvinorin A (SalA), a secondary metabolite of Salvia divinorum, is a potent and selective KOR agonist. Unlike typical opioids, SalA lacks a basic nitrogen, which encouraged us to search for nonbasic KOR ligands. Through structure-based virtual screening using 3D pharmacophore models based on the binding mode of SalA, we identified novel, nonbasic, potent, and selective KOR agonists. In vitro studies confirmed two virtual hits, SalA-VS-07 and SalA-VS-08, as highly selective for the KOR and showing G protein-biased KOR agonist activity. Both KOR ligands share a novel spiro-moiety and a nonbasic scaffold. Our findings provide novel starting points for developing therapeutics aimed at treating pain and other conditions in which KOR is a central player.
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Affiliation(s)
- Kristina Puls
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2-4, 14195 Berlin, Germany
| | - Aina-Leonor Olivé-Marti
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Siriwat Hongnak
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - David Lamp
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Mariana Spetea
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Gerhard Wolber
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2-4, 14195 Berlin, Germany
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2
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Wang Y, Yin Z. Drug-target interaction prediction through fine-grained selection and bidirectional random walk methodology. Sci Rep 2024; 14:18104. [PMID: 39103483 PMCID: PMC11300600 DOI: 10.1038/s41598-024-69186-w] [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: 05/17/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024] Open
Abstract
The study of drug-target interaction plays an important role in the process of drug development. The subject of DTI forecasting has advanced significantly in the last several years, yielding numerous significant research findings and methodologies. Heterogeneous data sources provide richer information and comprehensive perspectives for drug-target interaction prediction, so many existing methods rely on heterogeneous networks, and graph embedding technology becomes an important technology to extract information from heterogeneous networks. These approaches, however, are less concerned with potential noisy information in heterogeneous networks and more focused on the extent of information extraction in those networks. Based on this, a potential DTI predictive network model called FBRWPC is proposed in this paper. It uses a fine-grained similarity selection program to first integrate similarity on similar networks and then a bidirectional random walk graph embedding learning method with restart to obtain an updated drug target interaction matrix. Through the use of similarity selection and fine-grained selection similarity integration, the framework can effectively filter out the noise present in heterogeneous networks and enhance the model's prediction performance. The experimental findings demonstrate that, even after being split up into four distinct types of data sets, FBRWPC can still retain great prediction performance, a sign of the model's resilience and good generalization.
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Affiliation(s)
- YaPing Wang
- School of Mathematics, Physics and Statistics, Institute for Frontier Medical Technology, Center of Intelligent Computing and Applied Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - ZhiXiang Yin
- School of Mathematics, Physics and Statistics, Institute for Frontier Medical Technology, Center of Intelligent Computing and Applied Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China.
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3
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Sahu M, Vashishth S, Kukreti N, Gulia A, Russell A, Ambasta RK, Kumar P. Synergizing drug repurposing and target identification for neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:111-169. [PMID: 38789177 DOI: 10.1016/bs.pmbts.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Despite dedicated research efforts, the absence of disease-curing remedies for neurodegenerative diseases (NDDs) continues to jeopardize human society and stands as a challenge. Drug repurposing is an attempt to find new functionality of existing drugs and take it as an opportunity to discourse the clinically unmet need to treat neurodegeneration. However, despite applying this approach to rediscover a drug, it can also be used to identify the target on which a drug could work. The primary objective of target identification is to unravel all the possibilities of detecting a new drug or repurposing an existing drug. Lately, scientists and researchers have been focusing on specific genes, a particular site in DNA, a protein, or a molecule that might be involved in the pathogenesis of the disease. However, the new era discusses directing the signaling mechanism involved in the disease progression, where receptors, ion channels, enzymes, and other carrier molecules play a huge role. This review aims to highlight how target identification can expedite the whole process of drug repurposing. Here, we first spot various target-identification methods and drug-repositioning studies, including drug-target and structure-based identification studies. Moreover, we emphasize various drug repurposing approaches in NDDs, namely, experimental-based, mechanism-based, and in silico approaches. Later, we draw attention to validation techniques and stress on drugs that are currently undergoing clinical trials in NDDs. Lastly, we underscore the future perspective of synergizing drug repurposing and target identification in NDDs and present an unresolved question to address the issue.
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Affiliation(s)
- Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Shrutikirti Vashishth
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Neha Kukreti
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ashima Gulia
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ashish Russell
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India.
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4
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Puls K, Wolber G. Solving an Old Puzzle: Elucidation and Evaluation of the Binding Mode of Salvinorin A at the Kappa Opioid Receptor. Molecules 2023; 28:718. [PMID: 36677775 PMCID: PMC9861206 DOI: 10.3390/molecules28020718] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 01/13/2023] Open
Abstract
The natural product Salvinorin A (SalA) was the first nitrogen-lacking agonist discovered for the opioid receptors and exhibits high selectivity for the kappa opioid receptor (KOR) turning SalA into a promising analgesic to overcome the current opioid crisis. Since SalA's suffers from poor pharmacokinetic properties, particularly the absence of gastrointestinal bioavailability, fast metabolic inactivation, and subsequent short duration of action, the rational design of new tailored analogs with improved clinical usability is highly desired. Despite being known for decades, the binding mode of SalA within the KOR remains elusive as several conflicting binding modes of SalA were proposed hindering the rational design of new analgesics. In this study, we rationally determined the binding mode of SalA to the active state KOR by in silico experiments (docking, molecular dynamics simulations, dynophores) in the context of all available mutagenesis studies and structure-activity relationship (SAR) data. To the best of our knowledge, this is the first comprehensive evaluation of SalA's binding mode since the determination of the active state KOR crystal structure. SalA binds above the morphinan binding site with its furan pointing toward the intracellular core while the C2-acetoxy group is oriented toward the extracellular loop 2 (ECL2). SalA is solely stabilized within the binding pocket by hydrogen bonds (C210ECL2, Y3127.35, Y3137.36) and hydrophobic contacts (V1182.63, I1393.33, I2946.55, I3167.39). With the disruption of this interaction pattern or the establishment of additional interactions within the binding site, we were able to rationalize the experimental data for selected analogs. We surmise the C2-substituent interactions as important for SalA and its analogs to be experimentally active, albeit with moderate frequency within MD simulations of SalA. We further identified the non-conserved residues 2.63, 7.35, and 7.36 responsible for the KOR subtype selectivity of SalA. We are confident that the elucidation of the SalA binding mode will promote the understanding of KOR activation and facilitate the development of novel analgesics that are urgently needed.
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Affiliation(s)
| | - Gerhard Wolber
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany
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5
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Li Y, Sun C, Wei JM, Liu J. Drug-Protein interaction prediction by correcting the effect of incomplete information in heterogeneous information. Bioinformatics 2022; 38:5073-5080. [PMID: 36111859 DOI: 10.1093/bioinformatics/btac629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/30/2022] [Accepted: 09/15/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Large-scale heterogeneous data provide diverse perspectives for predicting drug-protein interactions (DPIs). However, the available information on molecular interactions and clinical associations related to drugs or proteins is incomplete because there may be unproven interactions and associations. This incomplete information in the available data is presented in the form of non-interaction and non-correlation, which may mislead the prediction model. Existing methods fuse incomplete and complete information without considering their integrity, so the negative effects of incomplete information still exist. RESULTS We develop a network-based DPI prediction method named BRWCP, which uses the complete information network to correct the prediction results acquired by the incomplete information network. By integrating relevant heterogeneous information that may be incomplete, the feature similarities of drugs and proteins are obtained. Combining the feature similarities and known DPIs, an incomplete information-based drug-protein heterogeneous network is constructed. Then, a bidirectional random walk with pruning algorithm is adopted in this heterogeneous network to predict potential DPIs. Next, the predicted DPIs are combined with the chemical fingerprint similarity of drugs and amino acid sequence similarity of proteins to construct the complete information network. The bidirectional random walk with pruning algorithm is applied in the new network to obtain the final prediction results until it converges. Experimental results show that BRWCP is superior to several state-of-the-art DPI prediction methods, and case studies further confirm its ability to tap potential DPIs. AVAILABILITY AND IMPLEMENTATION The code and data used in BRWCP are available at https://github.com/lyfdomain/BRWCP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yanfei Li
- College of Computer Science, Nankai University, Tianjin 300071, China.,Institute of Big Data, Nankai University, Tianjin 300071, China
| | - Chang Sun
- College of Computer Science, Nankai University, Tianjin 300071, China.,Institute of Big Data, Nankai University, Tianjin 300071, China
| | - Jin-Mao Wei
- College of Computer Science, Nankai University, Tianjin 300071, China.,Institute of Big Data, Nankai University, Tianjin 300071, China
| | - Jian Liu
- College of Computer Science, Nankai University, Tianjin 300071, China.,Institute of Big Data, Nankai University, Tianjin 300071, China
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Spiegel J, Senderowitz H. Towards an Enrichment Optimization Algorithm (EOA)-based Target Specific Docking Functions for Virtual Screening. Mol Inform 2022; 41:e2200034. [PMID: 35790469 PMCID: PMC9786651 DOI: 10.1002/minf.202200034] [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: 02/10/2022] [Accepted: 07/05/2022] [Indexed: 12/30/2022]
Abstract
Docking-based virtual screening (VS) is a common starting point in many drug discovery projects. While ligand-based approaches may sometimes provide better results, the advantage of docking lies in its ability to provide reliable ligand binding modes and approximated binding free energies, two factors that are important for hit selection and optimization. Most docking programs were developed to be as general as possible and consequently their performances on specific targets may be sub-optimal. With this in mind, in this work we present a method for the development of target-specific scoring functions using our recently reported Enrichment Optimization Algorithm (EOA). EOA derives QSAR models in the form of multiple linear regression (MLR) equations by optimizing an enrichment-like metric. Since EOA requires target-specific active and inactive (or decoy) compounds, we retrieved such data for six targets from the DUD-E database, and used them to re-derive the weights associated with the components that make up GOLD's ChemPLP scoring function yielding target-specific, modified functions. We then used the original ChemPLP function in small-scale VS experiments on the six targets and subsequently rescored the resulting poses with the modified functions. In addition, we used the modified functions for compounds re-docking. We found that in many although not all cases, either rescoring the original ChemPLP poses or repeating the entire docking process with the modified functions, yielded better results in terms of AUC and EF1% , two metrics, common for the evaluation of VS performances. While work on additional datasets and docking tools is clearly required, we propose that the results obtained thus far hint to the potential benefits in using EOA-based optimization for the derivation of target-specific functions in the context of virtual screening. To this end, we discuss the downsides of the methods and how it could be improved.
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Affiliation(s)
- Jacob Spiegel
- Department of ChemistryBar-Ilan UniversityRamat-Gan5290002Israel
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7
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In Vitro, In Vivo and In Silico Characterization of a Novel Kappa-Opioid Receptor Antagonist. Pharmaceuticals (Basel) 2022; 15:ph15060680. [PMID: 35745598 PMCID: PMC9229160 DOI: 10.3390/ph15060680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/04/2022] Open
Abstract
Kappa-opioid receptor (KOR) antagonists are promising innovative therapeutics for the treatment of the central nervous system (CNS) disorders. The new scaffold opioid ligand, Compound A, was originally found as a mu-opioid receptor (MOR) antagonist but its binding/selectivity and activation profile at the KOR and delta-opioid receptor (DOR) remain elusive. In this study, we present an in vitro, in vivo and in silico characterization of Compound A by revealing this ligand as a KOR antagonist in vitro and in vivo. In the radioligand competitive binding assay, Compound A bound at the human KOR, albeit with moderate affinity, but with increased affinity than to the human MOR and without specific binding at the human DOR, thus displaying a preferential KOR selectivity profile. Following subcutaneous administration in mice, Compound A effectively reverse the antinociceptive effects of the prototypical KOR agonist, U50,488. In silico investigations were carried out to assess the structural determinants responsible for opioid receptor subtype selectivity of Compound A. Molecular docking, molecular dynamics simulations and dynamic pharmacophore (dynophore) generation revealed differences in the stabilization of the chlorophenyl moiety of Compound A within the opioid receptor binding pockets, rationalizing the experimentally determined binding affinity values. This new chemotype bears the potential for favorable ADMET properties and holds promise for chemical optimization toward the development of potential therapeutics.
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8
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Puls K, Schmidhammer H, Wolber G, Spetea M. Mechanistic Characterization of the Pharmacological Profile of HS-731, a Peripherally Acting Opioid Analgesic, at the µ-, δ-, κ-Opioid and Nociceptin Receptors. Molecules 2022; 27:919. [PMID: 35164182 PMCID: PMC8840597 DOI: 10.3390/molecules27030919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Accumulated preclinical and clinical data show that peripheral restricted opioids provide pain relief with reduced side effects. The peripherally acting opioid analgesic HS-731 is a potent dual μ-/δ-opioid receptor (MOR/DOR) full agonist, and a weak, partial agonist at the κ-opioid receptor (KOR). However, its binding mode at the opioid receptors remains elusive. Here, we present a comprehensive in silico evaluation of HS-731 binding at all opioid receptors. We provide insights into dynamic interaction patterns explaining the different binding and activity of HS-731 on the opioid receptors. For this purpose, we conducted docking, performed molecular dynamics (MD) simulations and generated dynamic pharmacophores (dynophores). Our results highlight two residues important for HS-731 recognition at the classical opioid receptors (MOR, DOR and KOR), particular the conserved residue 5.39 (K) and the non-conserved residue 6.58 (MOR: K, DOR: W and KOR: E). Furthermore, we assume a salt bridge between the transmembrane helices (TM) 5 and 6 via K2275.39 and E2976.58 to be responsible for the partial agonism of HS-731 at the KOR. Additionally, we experimentally demonstrated the absence of affinity of HS-731 to the nociceptin/orphanin FQ peptide (NOP) receptor. We consider the morphinan phenol Y1303.33 responsible for this affinity lack. Y1303.33 points deep into the NOP receptor binding pocket preventing HS-731 binding to the orthosteric binding pocket. These findings provide significant structural insights into HS-731 interaction pattern with the opioid receptors that are important for understanding the pharmacology of this peripheral opioid analgesic.
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Affiliation(s)
- Kristina Puls
- Department of Pharmaceutical Chemistry, Institute of Pharmcy, Freie Universität Berlin, Königin-Luise-Str. 2+4, D-14195 Berlin, Germany;
| | - Helmut Schmidhammer
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria;
| | - Gerhard Wolber
- Department of Pharmaceutical Chemistry, Institute of Pharmcy, Freie Universität Berlin, Königin-Luise-Str. 2+4, D-14195 Berlin, Germany;
| | - Mariana Spetea
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria;
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9
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Nayarisseri A. Experimental and Computational Approaches to Improve Binding Affinity in Chemical Biology and Drug Discovery. Curr Top Med Chem 2021; 20:1651-1660. [PMID: 32614747 DOI: 10.2174/156802662019200701164759] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug discovery is one of the most complicated processes and establishment of a single drug may require multidisciplinary attempts to design efficient and commercially viable drugs. The main purpose of drug design is to identify a chemical compound or inhibitor that can bind to an active site of a specific cavity on a target protein. The traditional drug design methods involved various experimental based approaches including random screening of chemicals found in nature or can be synthesized directly in chemical laboratories. Except for the long cycle design and time, high cost is also the major issue of concern. Modernized computer-based algorithm including structure-based drug design has accelerated the drug design and discovery process adequately. Surprisingly from the past decade remarkable progress has been made concerned with all area of drug design and discovery. CADD (Computer Aided Drug Designing) based tools shorten the conventional cycle size and also generate chemically more stable and worthy compounds and hence reduce the drug discovery cost. This special edition of editorial comprises the combination of seven research and review articles set emphasis especially on the computational approaches along with the experimental approaches using a chemical synthesizing for the binding affinity in chemical biology and discovery as a salient used in de-novo drug designing. This set of articles exfoliates the role that systems biology and the evaluation of ligand affinity in drug design and discovery for the future.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
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10
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Shen C, Weng G, Zhang X, Leung ELH, Yao X, Pang J, Chai X, Li D, Wang E, Cao D, Hou T. Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening? Brief Bioinform 2021; 22:6070382. [PMID: 33418562 DOI: 10.1093/bib/bbaa410] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/26/2020] [Accepted: 12/12/2020] [Indexed: 12/13/2022] Open
Abstract
Machine-learning (ML)-based scoring functions (MLSFs) have gradually emerged as a promising alternative for protein-ligand binding affinity prediction and structure-based virtual screening. However, clouds of doubts have still been raised against the benefits of this novel type of scoring functions (SFs). In this study, to benchmark the performance of target-specific MLSFs on a relatively unbiased dataset, the MLSFs trained from three representative protein-ligand interaction representations were assessed on the LIT-PCBA dataset, and the classical Glide SP SF and three types of ligand-based quantitative structure-activity relationship (QSAR) models were also utilized for comparison. Two major aspects in virtual screening campaigns, including prediction accuracy and hit novelty, were systematically explored. The calculation results illustrate that the tested target-specific MLSFs yielded generally superior performance over the classical Glide SP SF, but they could hardly outperform the 2D fingerprint-based QSAR models. Although substantial improvements could be achieved by integrating multiple types of protein-ligand interaction features, the MLSFs were still not sufficient to exceed MACCS-based QSAR models. In terms of the correlations between the hit ranks or the structures of the top-ranked hits, the MLSFs developed by different featurization strategies would have the ability to identify quite different hits. Nevertheless, it seems that target-specific MLSFs do not have the intrinsic attributes of a traditional SF and may not be a substitute for classical SFs. In contrast, MLSFs can be regarded as a new derivative of ligand-based QSAR models. It is expected that our study may provide valuable guidance for the assessment and further development of target-specific MLSFs.
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Affiliation(s)
- Chao Shen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Gaoqi Weng
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Xujun Zhang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China
| | - Jinping Pang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Xin Chai
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dan Li
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
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11
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Achary PGR. Applications of Quantitative Structure-Activity Relationships (QSAR) based Virtual Screening in Drug Design: A Review. Mini Rev Med Chem 2020; 20:1375-1388. [DOI: 10.2174/1389557520666200429102334] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022]
Abstract
The scientists, and the researchers around the globe generate tremendous amount of information
everyday; for instance, so far more than 74 million molecules are registered in Chemical
Abstract Services. According to a recent study, at present we have around 1060 molecules, which are
classified as new drug-like molecules. The library of such molecules is now considered as ‘dark chemical
space’ or ‘dark chemistry.’ Now, in order to explore such hidden molecules scientifically, a good
number of live and updated databases (protein, cell, tissues, structure, drugs, etc.) are available today.
The synchronization of the three different sciences: ‘genomics’, proteomics and ‘in-silico simulation’
will revolutionize the process of drug discovery. The screening of a sizable number of drugs like molecules
is a challenge and it must be treated in an efficient manner. Virtual screening (VS) is an important
computational tool in the drug discovery process; however, experimental verification of the
drugs also equally important for the drug development process. The quantitative structure-activity relationship
(QSAR) analysis is one of the machine learning technique, which is extensively used in VS
techniques. QSAR is well-known for its high and fast throughput screening with a satisfactory hit rate.
The QSAR model building involves (i) chemo-genomics data collection from a database or literature
(ii) Calculation of right descriptors from molecular representation (iii) establishing a relationship
(model) between biological activity and the selected descriptors (iv) application of QSAR model to
predict the biological property for the molecules. All the hits obtained by the VS technique needs to be
experimentally verified. The present mini-review highlights: the web-based machine learning tools, the
role of QSAR in VS techniques, successful applications of QSAR based VS leading to the drug discovery
and advantages and challenges of QSAR.
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Affiliation(s)
- Patnala Ganga Raju Achary
- Department of Chemistry, Faculty of Engineering & Technology (ITER), Siksha ‘O’ Anusandhan, Deemed to be University, Khandagiri Square, Bhubaneswar- 751030, India
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12
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Raschka S. Automated discovery of GPCR bioactive ligands. Curr Opin Struct Biol 2019; 55:17-24. [PMID: 30909105 DOI: 10.1016/j.sbi.2019.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/19/2019] [Indexed: 12/22/2022]
Abstract
While G-protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Because of the involvement of GPCRs in various signaling pathways and physiological roles, the identification of endogenous ligands as well as designing novel drugs is of high interest to the research and medical communities. Along with highlighting the recent advances in structure-based ligand discovery, including docking and molecular dynamics, this article focuses on the latest advances for automating the discovery of bioactive ligands using machine learning. Machine learning is centered around the development and applications of algorithms that can learn from data automatically. Such an approach offers immense opportunities for bioactivity prediction as well as quantitative structure-activity relationship studies. This review describes the most recent and successful applications of machine learning for bioactive ligand discovery, concluding with an outlook on deep learning methods that are capable of automatically extracting salient information from structural data as a promising future direction for rapid and efficient bioactive ligand discovery.
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Affiliation(s)
- Sebastian Raschka
- Department of Statistics, University of Wisconsin-Madison, 1300 Medical Sciences Center, Madison, WI 53706, USA.
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13
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Buendia R, Kogej T, Engkvist O, Carlsson L, Linusson H, Johansson U, Toccaceli P, Ahlberg E. Accurate Hit Estimation for Iterative Screening Using Venn-ABERS Predictors. J Chem Inf Model 2019; 59:1230-1237. [PMID: 30726080 DOI: 10.1021/acs.jcim.8b00724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Iterative screening has emerged as a promising approach to increase the efficiency of high-throughput screening (HTS) campaigns in drug discovery. By learning from a subset of the compound library, inferences on what compounds to screen next can be made by predictive models. One of the challenges of iterative screening is to decide how many iterations to perform. This is mainly related to difficulties in estimating the prospective hit rate in any given iteration. In this article, a novel method based on Venn-ABERS predictors is proposed. The method provides accurate estimates of the number of hits retrieved in any given iteration during an HTS campaign. The estimates provide the necessary information to support the decision on the number of iterations needed to maximize the screening outcome. Thus, this method offers a prospective screening strategy for early-stage drug discovery.
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Affiliation(s)
- Ruben Buendia
- Department of Information Technology , University of Borås , SE-501 90 Borås , Sweden
| | - Thierry Kogej
- Discovery Sciences , AstraZeneca IMED Biotech Unit , SE-431 83 Mölndal , Sweden
| | - Ola Engkvist
- Discovery Sciences , AstraZeneca IMED Biotech Unit , SE-431 83 Mölndal , Sweden
| | - Lars Carlsson
- Discovery Sciences , AstraZeneca IMED Biotech Unit , SE-431 83 Mölndal , Sweden.,Department of Computer Science, Royal Holloway , University of London , Egham , Surrey TW20 0EX , United Kingdom
| | - Henrik Linusson
- Department of Information Technology , University of Borås , SE-501 90 Borås , Sweden
| | - Ulf Johansson
- Department of Information Technology , University of Borås , SE-501 90 Borås , Sweden
| | - Paolo Toccaceli
- Department of Computer Science, Royal Holloway , University of London , Egham , Surrey TW20 0EX , United Kingdom
| | - Ernst Ahlberg
- Data Science and AI, Drug Safety & Metabolism , AstraZeneca IMED Biotech Unit , SE-431 83 Mölndal , Sweden
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14
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Seidel T, Schuetz DA, Garon A, Langer T. The Pharmacophore Concept and Its Applications in Computer-Aided Drug Design. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:99-141. [PMID: 31621012 DOI: 10.1007/978-3-030-14632-0_4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pharmacophore-based techniques currently are an integral part of many computer-aided drug design workflows and have been successfully and extensively applied for tasks such as virtual screening, de novo design, and lead optimization. Pharmacophore models can be derived both in a receptor-based and in a ligand-based manner, and provide an abstract description of essential non-bonded interactions that typically occur between small-molecule ligands and macromolecular targets. Due to their simplistic and abstract nature, pharmacophores are both perfectly suited for efficient computer processing and easy to comprehend by life and physical scientists. As a consequence, they have also proven to be a valuable tool for communicating between computational and medicinal chemists.This chapter aims to provide a short overview of the pharmacophore concept and its applications in modern computer-aided drug design. The chapter is divided into three distinct parts. The first section contains a brief introduction to the pharmacophore concept. The second section provides a description of the most common nonbonded interaction types and their representation as pharmacophoric features. Furthermore, it gives an overview of the various methods for pharmacophore generation and important pharmacophore-based techniques in drug design. This part concludes with examples for recent pharmacophore concept-related research and development. The last section is dedicated to a review of research in the field of natural product chemistry as carried out by employing pharmacophore-based drug design methods.
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Affiliation(s)
- Thomas Seidel
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria.
| | - Doris A Schuetz
- InteLigand GmbH, IRIC-Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, QC, Canada
| | - Arthur Garon
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
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15
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Duffy F, Maheshwari N, Buchete NV, Shields D. Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions. Methods Mol Biol 2019; 2001:73-95. [PMID: 31134568 DOI: 10.1007/978-1-4939-9504-2_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by cyclization. Accordingly, to mimic linear peptide interfaces with cyclic peptides, it can be beneficial to screen combinatorial cyclic peptide libraries. Computational methods have been developed to screen CPs, but face a number of challenges. Here, we review methods to develop in silico computational libraries, and the potential for screening naturally occurring libraries of CPs. The simplest and most rapid computational pharmacophore methods that estimate peptide three-dimensional structures to be screened versus targets are relatively easy to implement, and while the constraint on structure imposed by cyclization makes them more effective than the same approaches with linear peptides, there are a large number of limiting assumptions. In contrast, full molecular dynamics simulations of cyclic peptide structures not only are costly to implement, but also require careful attention to interpretation, so that not only is the computation time rate limiting, but the interpretation time is also rate limiting due to the analysis of the typically complex underlying conformational space of CPs. A challenge for the field of computational cyclic peptide screening is to bridge this gap effectively. Natural compound libraries of short cyclic peptides, and short cyclized regions of proteins, encoded in the genomes of many organisms present a potential treasure trove of novel functionality which may be screened via combined computational and experimental screening approaches.
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Affiliation(s)
- Fergal Duffy
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nikunj Maheshwari
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | | | - Denis Shields
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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16
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Kirchweger B, Kratz JM, Ladurner A, Grienke U, Langer T, Dirsch VM, Rollinger JM. In Silico Workflow for the Discovery of Natural Products Activating the G Protein-Coupled Bile Acid Receptor 1. Front Chem 2018; 6:242. [PMID: 30013964 PMCID: PMC6036132 DOI: 10.3389/fchem.2018.00242] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/06/2018] [Indexed: 12/16/2022] Open
Abstract
The G protein-coupled bile acid receptor (GPBAR1) has been recognized as a promising new target for the treatment of diverse diseases, including obesity, type 2 diabetes, fatty liver disease and atherosclerosis. The identification of novel and potent GPBAR1 agonists is highly relevant, as these diseases are on the rise and pharmacological unmet therapeutic needs are pervasive. Therefore, the aim of this study was to develop a proficient workflow for the in silico prediction of GPBAR1 activating compounds, primarily from natural sources. A protocol was set up, starting with a comprehensive collection of structural information of known ligands. This information was used to generate ligand-based pharmacophore models in LigandScout 4.08 Advanced. After theoretical validation, the two most promising models, namely BAMS22 and TTM8, were employed as queries for the virtual screening of natural product and synthetic small molecule databases. Virtual hits were progressed to shape matching experiments and physicochemical clustering. Out of 33 diverse virtual hits subjected to experimental testing using a reporter gene-based assay, two natural products, farnesiferol B (27) and microlobidene (28), were confirmed as GPBAR1 activators reaching more than 50% receptor activation at 20 μM with EC50s of 13.53 μM and 13.88 μM, respectively. This activity is comparable to that of the endogenous ligand lithocholic acid (1). Seven further virtual hits showed activity reaching at least 15% receptor activation either at 5 or 20 μM, including new scaffolds from natural and synthetic origin.
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Affiliation(s)
| | - Jadel M. Kratz
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Angela Ladurner
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Ulrike Grienke
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Verena M. Dirsch
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
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17
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Tripathi AC, Upadhyay S, Paliwal S, Saraf SK. Privileged scaffolds as MAO inhibitors: Retrospect and prospects. Eur J Med Chem 2018; 145:445-497. [PMID: 29335210 DOI: 10.1016/j.ejmech.2018.01.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/01/2017] [Accepted: 01/01/2018] [Indexed: 12/24/2022]
Abstract
This review aims to be a comprehensive, authoritative, critical, and readable review of general interest to the medicinal chemistry community because it focuses on the pharmacological, chemical, structural and computational aspects of diverse chemical categories as monoamine oxidase inhibitors (MAOIs). Monoamine oxidases (MAOs), namely MAO-A and MAO-B represent an enormously valuable class of neuronal enzymes embodying neurobiological origin and functions, serving as potential therapeutic target in neuronal pharmacotherapy, and hence we have coined the term "Neurozymes" which is being introduced for the first time ever. Nowadays, therapeutic attention on MAOIs engrosses two imperative categories; MAO-A inhibitors, in certain mental disorders such as depression and anxiety, and MAO-B inhibitors, in neurodegenerative disorders like Alzheimer's disease (AD) and Parkinson's disease (PD). The use of MAOIs declined due to some potential side effects, food and drug interactions, and introduction of other classes of drugs. However, curiosity in MAOIs is reviving and the recent developments of new generation of highly selective and reversible MAOIs, have renewed the therapeutic prospective of these compounds. The initial section of the review emphasizes on the detailed classification, structural and binding characteristics, therapeutic potential, current status and future challenges of the privileged pharmacophores. However, the chemical prospective of privileged scaffolds such as; aliphatic and aromatic amines, amides, hydrazines, azoles, diazoles, tetrazoles, indoles, azines, diazines, xanthenes, tricyclics, benzopyrones, and more interestingly natural products, along with their conclusive SARs have been discussed in the later segment of review. The last segment of the article encompasses some patents granted in the field of MAOIs, in a simplistic way.
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Affiliation(s)
- Avinash C Tripathi
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Babu Banarasi Das Northern India Institute of Technology, Lucknow 226028, UP, India
| | - Savita Upadhyay
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Babu Banarasi Das Northern India Institute of Technology, Lucknow 226028, UP, India
| | - Sarvesh Paliwal
- Pharmacy Department, Banasthali Vidyapith, Banasthali, Tonk 304022, Rajasthan, India
| | - Shailendra K Saraf
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Babu Banarasi Das Northern India Institute of Technology, Lucknow 226028, UP, India.
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18
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Kumar A, Sharma A. Computational Modeling of Multi-target-Directed Inhibitors Against Alzheimer’s Disease. NEUROMETHODS 2018. [DOI: 10.1007/978-1-4939-7404-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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19
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Synthesis, crystal structure, biological evaluation, and molecular docking studies of quinoline-arylpiperazine derivative as potent α1A-adrenoceptor antagonist. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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20
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Abstract
Molecular docking was earlier considered to predict the binding affinity of the receptor and ligand molecules. With the progress in computational power and developing approaches, new horizons are now opening for accurate prediction of molecular binding affinity. In the current book chapter, recent strategies for Computer-Aided Drug Designing (CADD) including virtual screening and molecular docking, encompassing molecular dynamics simulations, and binding free energy calculation methods are discussed. Brief overview of different binding free energy methods MMPBSA, MMGBSA, LIE and TI have also been given along with the recent Relaxed Complex Scheme protocol.
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Affiliation(s)
| | - Akhil Kumar
- CSIR-Central Institute of Medicinal and Aromatic Plants, India
| | | | - Ashok Sharma
- CSIR-Central Institute of Medicinal and Aromatic Plants, India
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21
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Kaczor AA, Silva AG, Loza MI, Kolb P, Castro M, Poso A. Structure-Based Virtual Screening for Dopamine D2Receptor Ligands as Potential Antipsychotics. ChemMedChem 2016; 11:718-29. [DOI: 10.1002/cmdc.201500599] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/06/2016] [Indexed: 02/04/2023]
Affiliation(s)
- Agnieszka A. Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Lab; Faculty of Pharmacy with Division for Medical Analytics; Medical University of Lublin; 4A Chodźki St. 20059 Lublin Poland
- School of Pharmacy; University of Eastern Finland; Yliopistonranta 1, P.O. Box 1627 70211 Kuopio Finland
| | - Andrea G. Silva
- Department of Pharmacology; Universidade de Santiago de Compostela; Center for Research in Molecular Medicine and Chronic Diseases (CIMUS); Avda de Barcelona 15782 Santiago de Compostela Spain
| | - María I. Loza
- Department of Pharmacology; Universidade de Santiago de Compostela; Center for Research in Molecular Medicine and Chronic Diseases (CIMUS); Avda de Barcelona 15782 Santiago de Compostela Spain
| | - Peter Kolb
- Department of Pharmaceutical Chemistry; Philipps University Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Marián Castro
- Department of Pharmacology; Universidade de Santiago de Compostela; Center for Research in Molecular Medicine and Chronic Diseases (CIMUS); Avda de Barcelona 15782 Santiago de Compostela Spain
| | - Antti Poso
- School of Pharmacy; University of Eastern Finland; Yliopistonranta 1, P.O. Box 1627 70211 Kuopio Finland
- University Hospital Tübingen; Department of Internal Medicine I; Division of Translational Gastrointestinal Oncology; Otfried-Müller-Strasse 10 72076 Tübingen Germany
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22
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Mehra R, Rani C, Mahajan P, Vishwakarma RA, Khan IA, Nargotra A. Computationally Guided Identification of Novel Mycobacterium tuberculosis GlmU Inhibitory Leads, Their Optimization, and in Vitro Validation. ACS COMBINATORIAL SCIENCE 2016; 18:100-16. [PMID: 26812086 DOI: 10.1021/acscombsci.5b00019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mycobacterium tuberculosis (Mtb) infections are causing serious health concerns worldwide. Antituberculosis drug resistance threatens the current therapies and causes further need to develop effective antituberculosis therapy. GlmU represents an interesting target for developing novel Mtb drug candidates. It is a bifunctional acetyltransferase/uridyltransferase enzyme that catalyzes the biosynthesis of UDP-N-acetyl-glucosamine (UDP-GlcNAc) from glucosamine-1-phosphate (GlcN-1-P). UDP-GlcNAc is a substrate for the biosynthesis of lipopolysaccharide and peptidoglycan that are constituents of the bacterial cell wall. In the current study, structure and ligand based computational models were developed and rationally applied to screen a drug-like compound repository of 20,000 compounds procured from ChemBridge DIVERSet database for the identification of probable inhibitors of Mtb GlmU. The in vitro evaluation of the in silico identified inhibitor candidates resulted in the identification of 15 inhibitory leads of this target. Literature search of these leads through SciFinder and their similarity analysis with the PubChem training data set (AID 1376) revealed the structural novelty of these hits with respect to Mtb GlmU. IC50 of the most potent identified inhibitory lead (5810599) was found to be 9.018 ± 0.04 μM. Molecular dynamics (MD) simulation of this inhibitory lead (5810599) in complex with protein affirms the stability of the lead within the binding pocket and also emphasizes on the key interactive residues for further designing. Binding site analysis of the acetyltransferase pocket with respect to the identified structural moieties provides a thorough analysis for carrying out the lead optimization studies.
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Affiliation(s)
- Rukmankesh Mehra
- Discovery
Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Chitra Rani
- Clinical
Microbiology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Priya Mahajan
- Discovery
Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Ram Ashrey Vishwakarma
- Discovery
Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Inshad Ali Khan
- Clinical
Microbiology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Amit Nargotra
- Discovery
Informatics, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- Academy
of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
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23
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Mehra R, Chib R, Munagala G, Yempalla KR, Khan IA, Singh PP, Khan FG, Nargotra A. Discovery of new Mycobacterium tuberculosis proteasome inhibitors using a knowledge-based computational screening approach. Mol Divers 2015; 19:1003-19. [PMID: 26232029 DOI: 10.1007/s11030-015-9624-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/19/2015] [Indexed: 12/22/2022]
Abstract
Mycobacterium tuberculosis bacteria cause deadly infections in patients [Corrected]. The rise of multidrug resistance associated with tuberculosis further makes the situation worse in treating the disease. M. tuberculosis proteasome is necessary for the pathogenesis of the bacterium validated as an anti-tubercular target, thus making it an attractive enzyme for designing Mtb inhibitors. In this study, a computational screening approach was applied to identify new proteasome inhibitor candidates from a library of 50,000 compounds. This chemical library was procured from the ChemBridge (20,000 compounds) and the ChemDiv (30,000 compounds) databases. After a detailed analysis of the computational screening results, 50 in silico hits were retrieved and tested in vitro finding 15 compounds with IC₅₀ values ranging from 35.32 to 64.15 μM on lysate. A structural analysis of these hits revealed that 14 of these compounds probably have non-covalent mode of binding to the target and have not reported for anti-tubercular or anti-proteasome activity. The binding interactions of all the 14 protein-inhibitor complexes were analyzed using molecular docking studies. Further, molecular dynamics simulations of the protein in complex with the two most promising hits were carried out so as to identify the key interactions and validate the structural stability.
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Affiliation(s)
- Rukmankesh Mehra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Reena Chib
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Gurunadham Munagala
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Kushalava Reddy Yempalla
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Parvinder Pal Singh
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Farrah Gul Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
| | - Amit Nargotra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India. .,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
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24
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Shin WH, Zhu X, Bures MG, Kihara D. Three-dimensional compound comparison methods and their application in drug discovery. Molecules 2015; 20:12841-62. [PMID: 26193243 PMCID: PMC5005041 DOI: 10.3390/molecules200712841] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/07/2015] [Accepted: 07/13/2015] [Indexed: 11/16/2022] Open
Abstract
Virtual screening has been widely used in the drug discovery process. Ligand-based virtual screening (LBVS) methods compare a library of compounds with a known active ligand. Two notable advantages of LBVS methods are that they do not require structural information of a target receptor and that they are faster than structure-based methods. LBVS methods can be classified based on the complexity of ligand structure information utilized: one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D). Unlike 1D and 2D methods, 3D methods can have enhanced performance since they treat the conformational flexibility of compounds. In this paper, a number of 3D methods will be reviewed. In addition, four representative 3D methods were benchmarked to understand their performance in virtual screening. Specifically, we tested overall performance in key aspects including the ability to find dissimilar active compounds, and computational speed.
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Affiliation(s)
- Woong-Hee Shin
- Department of Biological Science, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaolei Zhu
- School of Life Science, Anhui University, Hefei 230601, China.
| | - Mark Gregory Bures
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, IN 46285, USA.
| | - Daisuke Kihara
- Department of Biological Science, Purdue University, West Lafayette, IN 47907, USA.
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
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25
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Mehra R, Sharma R, Khan IA, Nargotra A. Identification and optimization of Escherichia coli GlmU inhibitors: An in silico approach with validation thereof. Eur J Med Chem 2015; 92:78-90. [DOI: 10.1016/j.ejmech.2014.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/21/2014] [Accepted: 12/18/2014] [Indexed: 12/25/2022]
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26
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Spielman SJ, Kumar K, Wilke CO. Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors. PeerJ 2015; 3:e773. [PMID: 25737813 PMCID: PMC4338800 DOI: 10.7717/peerj.773] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 01/29/2023] Open
Abstract
Biogenic amine receptors play critical roles in regulating behavior and physiology in both vertebrates and invertebrates, particularly within the central nervous system. Members of the G-protein coupled receptor (GPCR) family, these receptors interact with endogenous bioamine ligands such as dopamine, serotonin, and epinephrine, and are targeted by a wide array of pharmaceuticals. Despite the clear clinical and biological importance of these receptors, their evolutionary history remains poorly characterized. In particular, the relationships among biogenic amine receptors and any specific evolutionary constraints acting within distinct receptor subtypes are largely unknown. To advance and facilitate studies in this receptor family, we have constructed a comprehensive, high-quality sequence alignment of vertebrate biogenic amine receptors. In particular, we have integrated a traditional multiple sequence approach with robust structural domain predictions to ensure that alignment columns accurately capture the highly-conserved GPCR structural domains, and we demonstrate how ignoring structural information produces spurious inferences of homology. Using this alignment, we have constructed a structurally-partitioned maximum-likelihood phylogeny from which we deduce novel biogenic amine receptor relationships and uncover previously unrecognized lineage-specific receptor clades. Moreover, we find that roughly 1% of the 3039 sequences in our final alignment are either misannotated or unclassified, and we propose updated classifications for these receptors. We release our comprehensive alignment and its corresponding phylogeny as a resource for future research into the evolution and diversification of biogenic amine receptors.
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Affiliation(s)
| | - Keerthana Kumar
- Department of Integrative Biology, The University of Texas at Austin, Austin, USA
| | - Claus O. Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, USA
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27
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Duffy FJ, Devocelle M, Shields DC. Computational approaches to developing short cyclic peptide modulators of protein-protein interactions. Methods Mol Biol 2015; 1268:241-71. [PMID: 25555728 DOI: 10.1007/978-1-4939-2285-7_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclic peptides are a promising class of bioactive molecules potentially capable of modulating "difficult" targets, such as protein-protein interactions. Cyclic peptides have long been used as therapeutics derived from natural product derivatives, but remain an underexplored class of compounds from the perspective of rational drug design, possibly due to the known weaknesses of peptide drugs in general. While cyclic peptides are non"druglike" by the accepted empirical rules, their unique structure may lend itself to both membrane permeability and proteolytic resistance-the main barriers to oral delivery. The constrained shape of cyclic peptides also lends itself better to virtual screening approaches, and new tools and successes in this area have been recently noted. An increasing number of strategies are available, both to generate and screen cyclic peptide libraries, and best practises and current successes are described within. This chapter will describe various computational strategies for virtual screening cyclic peptides, along with known implementations and applications. We will explore the generation and screening of diverse combinatorial virtual libraries, incorporating a range of cyclization strategies and structural modifications. More advanced approaches covered include evolutionary algorithms designed to aid in screening large structural libraries, machine learning approaches, and harnessing bioinformatics resources to bias cyclic peptide virtual libraries towards known bioactive structures.
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Affiliation(s)
- Fergal J Duffy
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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28
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Cavasotto CN, Palomba D. Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. Chem Commun (Camb) 2015; 51:13576-94. [DOI: 10.1039/c5cc05050b] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We show the key role of structural homology models in GPCR structure-based lead discovery and optimization, highlighting methodological aspects, recent progress and future directions.
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Affiliation(s)
- Claudio N. Cavasotto
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
| | - Damián Palomba
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
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29
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Sato M, Hirokawa T. Extended Template-Based Modeling and Evaluation Method Using Consensus of Binding Mode of GPCRs for Virtual Screening. J Chem Inf Model 2014; 54:3153-61. [DOI: 10.1021/ci500499j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Miwa Sato
- Department
of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan
- Molecular
Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
- Mitsui Knowledge Industry Co., Ltd., Tokyo 105-6215, Japan
| | - Takatsugu Hirokawa
- Molecular
Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
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30
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31
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Rodríguez D, Ranganathan A, Carlsson J. Strategies for improved modeling of GPCR-drug complexes: blind predictions of serotonin receptors bound to ergotamine. J Chem Inf Model 2014; 54:2004-21. [PMID: 25030302 DOI: 10.1021/ci5002235] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The recent increase in the number of atomic-resolution structures of G protein-coupled receptors (GPCRs) has contributed to a deeper understanding of ligand binding to several important drug targets. However, reliable modeling of GPCR-ligand complexes for the vast majority of receptors with unknown structure remains to be one of the most challenging goals for computer-aided drug design. The GPCR Dock 2013 assessment, in which researchers were challenged to predict the crystallographic structures of serotonin 5-HT(1B) and 5-HT(2B) receptors bound to ergotamine, provided an excellent opportunity to benchmark the current state of this field. Our contributions to GPCR Dock 2013 accurately predicted the binding mode of ergotamine with RMSDs below 1.8 Å for both receptors, which included the best submissions for the 5-HT(1B) complex. Our models also had the most accurate description of the binding sites and receptor-ligand contacts. These results were obtained using a ligand-guided homology modeling approach, which combines extensive molecular docking screening with incorporation of information from multiple crystal structures and experimentally derived restraints. In this work, we retrospectively analyzed thousands of structures that were generated during the assessment to evaluate our modeling strategies. Major contributors to accuracy were found to be improved modeling of extracellular loop two in combination with the use of molecular docking to optimize the binding site for ligand recognition. Our results suggest that modeling of GPCR-drug complexes has reached a level of accuracy at which structure-based drug design could be applied to a large number of pharmaceutically relevant targets.
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Affiliation(s)
- David Rodríguez
- Science for Life Laboratory, Stockholm University , Box 1031, SE-171 21 Solna, Sweden
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32
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Chin SP, Buckle MJC, Chalmers DK, Yuriev E, Doughty SW. Toward activated homology models of the human M1 muscarinic acetylcholine receptor. J Mol Graph Model 2014; 49:91-8. [PMID: 24631873 DOI: 10.1016/j.jmgm.2014.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 10/25/2022]
Abstract
Structure-based virtual screening offers a good opportunity for the discovery of selective M1 muscarinic acetylcholine receptor (mAChR) agonists for the treatment of Alzheimer's disease. However, no 3-D structure of an M1 mAChR is yet available and the homology models that have been previously reported are only able to identify antagonists in virtual screening experiments. In this study, we generated a homology model of the human M1 mAChR, based on the crystal structure of an M3 mAChR as the template. This initial model was modified, using the agonist-bound crystal structure of a β2-adrenergic receptor as a guide, to give two possible activated structures. The T192 side chain was adjusted in both structures and one of the structures also had the whole of transmembrane (TM) 5 rotated and tilted toward the inner channel of the transmembrane region. The binding sites of all three structures were then refined by induced-fit docking (IFD) with acetylcholine. Virtual screening experiments showed that all three refined models could efficiently differentiate agonists from decoy molecules, with the TM5-modified models also giving good agonist/antagonist selectivity. The whole range of agonists and antagonists was observed to bind within the orthosteric site of the structure obtained by IFD refinement alone, implying that it has inactive state character. In contrast, the two TM5-modified structures were unable to accommodate the antagonists, supporting the proposition that they possess activated state character.
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Affiliation(s)
- Sek Peng Chin
- Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Michael J C Buckle
- Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Stephen W Doughty
- The School of Pharmacy, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
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33
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From Three-Dimensional GPCR Structure to Rational Ligand Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:129-57. [DOI: 10.1007/978-94-007-7423-0_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Yao S, Lu T, Zhou Z, Liu H, Yuan H, Ran T, Lu S, Zhang Y, Ke Z, Xu J, Xiong X, Chen Y. An efficient multistep ligand-based virtual screening approach for GPR40 agonists. Mol Divers 2013; 18:183-93. [PMID: 24307222 DOI: 10.1007/s11030-013-9493-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/11/2013] [Indexed: 10/25/2022]
Abstract
G protein-coupled receptor 40/free fatty acid receptor 1 (GPR40/FFAR1) is a member of the GPCR superfamily, and GPR40 agonists have therapeutic potential for type 2 diabetes. With the crystal structure of GPR40 currently unavailable, various ligand-based virtual screening approaches can be applied to identify novel agonists of GPR40. It is known that each ligand-based method has its own advantages and limitations. To improve the efficiency of individual ligand-based methods, an efficient multistep ligand-based virtual screening approach is presented in this study, including the pharmacophore-based screening, physicochemical property filtering, protein-ligand interaction fingerprint similarity analysis, and 2D-fingerprint structural similarity search. A focused decoy library was generated and used to evaluate the efficiency of this virtual screening protocol. This multistep workflow not only significantly improved the hit rate compared with each individual ligand-based method, but also identified diverse known actives from decoys. This protocol may serve as an efficient virtual screening tool for the targets without crystal structures available to discover novel active compounds.
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Affiliation(s)
- Sihui Yao
- Laboratory of Molecular Design and Drug Discovery, School of Basic Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
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35
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Vidler LR, Filippakopoulos P, Fedorov O, Picaud S, Martin S, Tomsett M, Woodward H, Brown N, Knapp S, Hoelder S. Discovery of novel small-molecule inhibitors of BRD4 using structure-based virtual screening. J Med Chem 2013; 56:8073-88. [PMID: 24090311 PMCID: PMC3807807 DOI: 10.1021/jm4011302] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Bromodomains
(BRDs) are epigenetic readers that recognize acetylated-lysine
(KAc) on proteins and are implicated in a number of diseases. We describe
a virtual screening approach to identify BRD inhibitors. Key elements
of this approach are the extensive design and use of substructure
queries to compile a set of commercially available compounds featuring
novel putative KAc mimetics and docking this set for final compound
selection. We describe the validation of this approach by applying
it to the first BRD of BRD4. The selection and testing of 143 compounds
lead to the discovery of six novel hits, including four unprecedented
KAc mimetics. We solved the crystal structure of four hits, determined
their binding mode, and improved their potency through synthesis and
the purchase of derivatives. This work provides a validated virtual
screening approach that is applicable to other BRDs and describes
novel KAc mimetics that can be further explored to design more potent
inhibitors.
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Affiliation(s)
- Lewis R Vidler
- Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , 15 Cotswold Road, Sutton, Surrey SM2 5NG, United Kingdom
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36
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Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK. Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem Biol 2013; 8:1018-26. [PMID: 23485065 PMCID: PMC3658555 DOI: 10.1021/cb400103f] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
A prospective,
large library virtual screen against an activated
β2-adrenergic receptor (β2AR) structure returned potent
agonists to the exclusion of inverse-agonists, providing the first
complement to the previous virtual screening campaigns against inverse-agonist-bound
G protein coupled receptor (GPCR) structures, which predicted only
inverse-agonists. In addition, two hits recapitulated the signaling
profile of the co-crystal ligand with respect to the G protein and
arrestin mediated signaling. This functional fidelity has important
implications in drug design, as the ability to predict ligands with
predefined signaling properties is highly desirable. However, the
agonist-bound state provides an uncertain template for modeling the
activated conformation of other GPCRs, as a dopamine D2 receptor (DRD2)
activated model templated on the activated β2AR structure returned
few hits of only marginal potency.
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Affiliation(s)
- Dahlia R. Weiss
- Department of Pharmaceutical
Chemistry, University of California San Francisco, San Francisco, California 94158-2550, United States
| | | | - Maria F. Sassano
- Department of Pharmacology
and
National Institute of Mental Health Psychoactive Drug Screening Program
School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | | | | | - Bryan L. Roth
- Department of Pharmacology
and
National Institute of Mental Health Psychoactive Drug Screening Program
School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | - Brian K. Shoichet
- Department of Pharmaceutical
Chemistry, University of California San Francisco, San Francisco, California 94158-2550, United States
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37
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Pala D, Beuming T, Sherman W, Lodola A, Rivara S, Mor M. Structure-based virtual screening of MT2 melatonin receptor: influence of template choice and structural refinement. J Chem Inf Model 2013; 53:821-35. [PMID: 23541165 DOI: 10.1021/ci4000147] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Developing GPCR homology models for structure-based virtual screening requires the choice of a suitable template and refinement of binding site residues. We explored this systematically for the MT2 melatonin receptor, with the aim to build a receptor homology model that is optimized for the enrichment of active melatoninergic ligands. A set of 12 MT2 melatonin receptor models was built using different GPCR X-ray structural templates and submitted to a virtual screening campaign on a set of compounds composed of 29 known melatonin receptor ligands and 2560 drug-like decoys. To evaluate the effect of including a priori information in receptor models, 12 representative melatonin receptor ligands were placed into the MT2 receptor models in poses consistent with known mutagenesis data and with assessed pharmacophore models. The receptor structures were then adapted to the ligands by induced-fit docking. Most of the 144 ligand-adapted MT2 receptor models showed significant improvements in screening enrichments compared to the unrefined homology models, with some template/refinement combinations giving excellent enrichment factors. The discriminating ability of the models was further tested on the 29 active ligands plus a set of 21 inactive or low-affinity compounds from the same chemical classes. Rotameric states of side chains for some residues, presumed to be involved in the binding process, were correlated with screening effectiveness, suggesting the existence of specific receptor conformations able to recognize active compounds. The top MT2 receptor model was able to identify 24 of 29 active ligands among the first 2% of the screened database. This work provides insights into the use of refined GPCR homology models for virtual screening.
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Affiliation(s)
- Daniele Pala
- Dipartimento di Farmacia, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
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38
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Target based virtual screening by docking into automatically generated GPCR models. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 914:255-70. [PMID: 22976033 DOI: 10.1007/978-1-62703-023-6_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Target based virtual screening (VS) combined with high-throughput measurements is an extremely useful tool to identify small molecule hits for proteins and in particular for G-protein coupled receptors (GPCRs). However, this is a quite difficult process for GPCRs due to the paucity of 3D structural information on these receptors. Therefore, the only possibility for target based VS is to build a structural model of the GPCR to be used for docking. However, GPCR model building is a very time consuming process, if the model should be able to explain all experimental findings and this investment is not always justified, if the model is only used for VS. Thus, a fully automated workflow is presented here, where a large number of GPCR models is built, and the best model is identified to be used for docking. The workflow leads to moderate enrichments with a very low effort. The inputs required are the sequence of the targeted GPCR, a reference ligand with experimental information and a database of small molecules to be used for docking. Manual intervention is recommended at various points, but it is strictly speaking not necessary.
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39
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Kooistra AJ, Roumen L, Leurs R, de Esch IJ, de Graaf C. From Heptahelical Bundle to Hits from the Haystack. Methods Enzymol 2013; 522:279-336. [DOI: 10.1016/b978-0-12-407865-9.00015-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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40
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Parrill AL. Computational Design and Experimental Characterization of GPCR Segment Models. Methods Enzymol 2013; 522:81-95. [DOI: 10.1016/b978-0-12-407865-9.00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Kouznetsov VV, Zacchino SA, Sortino M, Vargas Méndez LY, Gupta MP. Cytotoxic and Antifungal Activities of Diverse α-Naphthylamine Derivatives. Sci Pharm 2012; 80:867-77. [PMID: 23264936 PMCID: PMC3528049 DOI: 10.3797/scipharm.1209-03] [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: 09/10/2012] [Accepted: 10/23/2012] [Indexed: 11/29/2022] Open
Abstract
Diverse α-naphthylamine derivatives were easily prepared from corresponding aldimines derived from commercially available α-naphthaldehyde and anilines or isomeric pyridinecarboxyaldehydes and α-naphthylamine. The secondary amines obtained were tested as possible antifungal and cytotoxic agents. The diverse N-aryl-N-[1-(1-naphthyl)but-3-enyl]amines obtained were active (IC50 < 10 μg/mL) against breast (MCF-7), non-small cell lung (H-460), and central nervous system (SF-268) human cancer cell lines, while N-(pyridinylmethyl)-naphthalen-1-amines resulted in activity against (MIC 25–32 μg/mL) some human opportunistic pathogenic fungi including yeasts, hialohyphomycetes, and dermatophytes.
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Affiliation(s)
- Vladímir V Kouznetsov
- Laboratorio de Química Orgánica y Biomolecular, Escuela de Química, Universidad Industrial de Santander, A. A. 678, Bucaramanga, Colombia
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42
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Musafia B, Senderowitz H. Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design. Expert Opin Drug Discov 2012; 5:943-59. [PMID: 22823989 DOI: 10.1517/17460441.2010.513711] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD In silico or virtual screening has become a common practice in contemporary computer-aided drug discovery efforts and currently constitutes a reasonably mature paradigm. Application of ligand-based approaches to virtual screening requires the ability to identify the bioactive conformers of drug-like compounds as these conformers are expected to elicit the biological activity. However, given the complexity of the energy potential surfaces of such ligands and in particular those exhibiting some degree of flexibility and the limitation of contemporary energy functions, this is not an easy task. AREAS COVERED IN THIS REVIEW The current contribution provides an in-depth review of recent developments in the field of generating conformational ensembles of drug-like compounds with a particular emphasis of focusing such ensembles on bioactive conformers using both energy and structural criteria. The literature reviewed in this manuscript roughly covers the last decade. WHAT THE READER WILL GAIN Readers of this review will gain an appreciation for the complexity of identifying bioactive conformers of drug-like compounds and an exposure to the different computational methods which were developed in order to tackle this problem as well as to the remaining challenges in this field. TAKE HOME MESSAGE The identification of ensembles of bioactive conformers of drug-like compounds is far from being a solved problem. Recent research has advanced the field to the point where bioactive conformers could be readily identified from within conformational ensembles generated by contemporary computational tools. However, as such conformers are inevitably accompanied by many other non-relevant conformations, a focusing mechanism is required. New methods in this field are showing promise but more work is clearly needed. New research lines are proposed which are believed to enhance the performances and with it the usefulness of 3D ligand-based methods in drug discovery and development.
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43
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Molinski S, Eckford PDW, Pasyk S, Ahmadi S, Chin S, Bear CE. Functional Rescue of F508del-CFTR Using Small Molecule Correctors. Front Pharmacol 2012; 3:160. [PMID: 23055971 PMCID: PMC3458236 DOI: 10.3389/fphar.2012.00160] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 08/17/2012] [Indexed: 01/21/2023] Open
Abstract
High-throughput screens for small molecules that are effective in “correcting” the functional expression of F508del-CFTR have yielded several promising hits. Two such compounds are currently in clinical trial. Despite this success, it is clear that further advances will be required in order to restore 50% or greater of wild-type CFTR function to the airways of patients harboring the F508del-CFTR protein. Progress will be enhanced by our better understanding of the molecular and cellular defects caused by the F508del mutation, present in 90% of CF patients. The goal of this chapter is to review the current understanding of defects caused by F508del in the CFTR protein and in CFTR-mediated interactions important for its biosynthesis, trafficking, channel function, and stability at the cell surface. Finally, we will discuss the gaps in our knowledge regarding the mechanism of action of existing correctors, the unmet need to discover compounds which restore proper CFTR structure and function in CF affected tissues and new strategies for therapy development.
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Affiliation(s)
- Steven Molinski
- Programme in Molecular Structure and Function, Research Institute, Hospital for Sick Children Toronto, ON, Canada ; Department of Biochemistry, University of Toronto Toronto, ON, Canada
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44
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Nagarajan S, Skoufias DA, Kozielski F, Pae AN. Receptor–Ligand Interaction-Based Virtual Screening for Novel Eg5/Kinesin Spindle Protein Inhibitors. J Med Chem 2012; 55:2561-73. [DOI: 10.1021/jm201290v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shanthi Nagarajan
- Neuro-Medicine Center, Life
Sciences Division, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul 130-650, Republic of Korea
- School of Science, Korea University of Science and Technology, 52 Eoeun
dongYuseong-gu, Daejeon 305-333, Republic of Korea
| | - Dimitrios A. Skoufias
- Institute for Structural Biology (CEA-CNRS-UJF), 41 rue Jules Horowitz, 38027
Grenoble Cedex 1, France,
| | - Frank Kozielski
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road,
Bearsden, Glasgow, G61 1BD, Scotland, U.K
| | - Ae Nim Pae
- Neuro-Medicine Center, Life
Sciences Division, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul 130-650, Republic of Korea
- School of Science, Korea University of Science and Technology, 52 Eoeun
dongYuseong-gu, Daejeon 305-333, Republic of Korea
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45
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Sanders MPA, McGuire R, Roumen L, de Esch IJP, de Vlieg J, Klomp JPG, de Graaf C. From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00210d] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein structure-based pharmacophore (SBP) models derive the molecular features a ligand must contain to be biologically active by conversion of protein properties to reciprocal ligand space. SBPs improve molecular understanding of ligand–protein interactions and can be used as valuable tools for hit and lead optimization, compound library design, and target hopping.
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Affiliation(s)
- Marijn P. A. Sanders
- Computational Drug Discovery Group
- CMBI
- Radboud University Nijmegen
- Nijmegen
- The Netherlands
| | | | - Luc Roumen
- Division of Medicinal Chemistry
- LACDR
- VU University Amsterdam
- Amsterdam
- The Netherlands
| | - Iwan J. P. de Esch
- Division of Medicinal Chemistry
- LACDR
- VU University Amsterdam
- Amsterdam
- The Netherlands
| | - Jacob de Vlieg
- Computational Drug Discovery Group
- CMBI
- Radboud University Nijmegen
- Nijmegen
- The Netherlands
| | | | - Chris de Graaf
- Division of Medicinal Chemistry
- LACDR
- VU University Amsterdam
- Amsterdam
- The Netherlands
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46
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Kiss R, Sándor M, Gere A, Schmidt E, Balogh GT, Kiss B, Molnár L, Lemmen C, Keseru GM. Discovery of novel histamine H4 and serotonin transporter ligands using the topological feature tree descriptor. J Chem Inf Model 2011; 52:233-42. [PMID: 22168379 DOI: 10.1021/ci2004972] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligand-based approaches are particularly important in the hit identification process of drug discovery when no structural information on the target is available. Pharmacophore descriptors that use a topological representation of the ligands are usually fast enough to screen large compound libraries effectively when seeking novel lead candidates. One example of this kind is the Feature Tree descriptor, a reduced graph representation implemented in the FTrees software. In this study, we tested the screening efficiency of FTrees by both retrospective and prospective screens using known histamine H4 antagonists and serotonin transporter (SERT) inhibitors as query molecules. Our results demonstrate that FTrees can effectively find actives. Particularly when combined with a subsequent 2D fingerprint-based diversity selection, FTrees was found to be extremely effective at discovering a diverse set of scaffolds. Prospective screening of our in-house compound deck provided several novel H4 and SERT ligands that could serve as suitable starting points for further optimization.
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Affiliation(s)
- Róbert Kiss
- Gedeon Richter Plc, Gyömrői út 19-21, H-1103 Budapest, Hungary
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47
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Brunschweiger A, Hall J. A decade of the human genome sequence--how does the medicinal chemist benefit? ChemMedChem 2011; 7:194-203. [PMID: 22170741 DOI: 10.1002/cmdc.201100498] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Indexed: 12/11/2022]
Abstract
Many have claimed that the sequencing of the human genome has failed to deliver the promised new era of drug discovery and development. Here, we argue that in fact, the availability of the human genome sequence and the genomics technologies that resulted from those research efforts have had a major impact on drug discovery. Medicinal chemists are actively using the data gleaned from structural genomics projects over the past decade to design more selective and more effective drug candidates. For example, large superfamilies of related enzymes, such as the kinome, proteome, proteasome, transportome, identified because of the sequencing of the human genome represent a huge number of potential drug targets. Ten years on, we're able to design multitarget drugs where the selectivity for a certain subgroup of receptors can lead to increased efficacy rather than the side effects traditionally associated with "off-targets". New trends and discoveries in biomedical research are notoriously slow to show their value, and this is also true for genomics technologies. However, the examples we've selected show that these are firmly set in the drug-discovery process, and without the human genome sequence, a number of current clinical candidates and promising drug leads would not have been possible.
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Affiliation(s)
- Andreas Brunschweiger
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
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48
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Sanders MPA, Verhoeven S, de Graaf C, Roumen L, Vroling B, Nabuurs SB, de Vlieg J, Klomp JPG. Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs. J Chem Inf Model 2011; 51:2277-92. [PMID: 21866955 DOI: 10.1021/ci200088d] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
G-protein coupled receptors (GPCRs) are important drug targets for various diseases and of major interest to pharmaceutical companies. The function of individual members of this protein family can be modulated by the binding of small molecules at the extracellular side of the structurally conserved transmembrane (TM) domain. Here, we present Snooker, a structure-based approach to generate pharmacophore hypotheses for compounds binding to this extracellular side of the TM domain. Snooker does not require knowledge of ligands, is therefore suitable for apo-proteins, and can be applied to all receptors of the GPCR protein family. The method comprises the construction of a homology model of the TM domains and prioritization of residues on the probability of being ligand binding. Subsequently, protein properties are converted to ligand space, and pharmacophore features are generated at positions where protein ligand interactions are likely. Using this semiautomated knowledge-driven bioinformatics approach we have created pharmacophore hypotheses for 15 different GPCRs from several different subfamilies. For the beta-2-adrenergic receptor we show that ligand poses predicted by Snooker pharmacophore hypotheses reproduce literature supported binding modes for ∼75% of compounds fulfilling pharmacophore constraints. All 15 pharmacophore hypotheses represent interactions with essential residues for ligand binding as observed in mutagenesis experiments and compound selections based on these hypotheses are shown to be target specific. For 8 out of 15 targets enrichment factors above 10-fold are observed in the top 0.5% ranked compounds in a virtual screen. Additionally, prospectively predicted ligand binding poses in the human dopamine D3 receptor based on Snooker pharmacophores were ranked among the best models in the community wide GPCR dock 2010.
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Affiliation(s)
- Marijn P A Sanders
- Computational Drug Discovery Group, CMBI, Radboud University Nijmegen, Nijmegen, The Netherlands
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49
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Abstract
With the emerging new crystal structures of G-protein coupled receptors (GPCRs), the number of reported in silico receptor models vastly increases every year. The use of these models in lead optimization (LO) is investigated here. Although there are many studies where GPCR models are used to identify new chemotypes by virtual screening, the classical application in LO is rarely reported. The reason for this may be that the quality of a model, which is appropriate for atomistic modeling, must be very high, and the biology of GPCR ligand-dependent signaling is still not fully understood. However, the few reported studies show that GPCR models can be used efficiently in LO for various problems, such as affinity optimization or tuning of physicochemical parameters.
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Cai C, Gong J, Liu X, Jiang H, Gao D, Li H. A novel, customizable and optimizable parameter method using spherical harmonics for molecular shape similarity comparisons. J Mol Model 2011; 18:1597-610. [PMID: 21805132 DOI: 10.1007/s00894-011-1173-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 06/30/2011] [Indexed: 11/28/2022]
Abstract
A novel molecular shape similarity comparison method, namely SHeMS, derived from spherical harmonic (SH) expansion, is presented in this study. Through weight optimization using genetic algorithms for a customized reference set, the optimal combination of weights for the translationally and rotationally invariant (TRI) SH shape descriptor, which can specifically and effectively distinguish overall and detailed shape features according to the molecular surface, is obtained for each molecule. This method features two key aspects: firstly, the SH expansion coefficients from different bands are weighted to calculate similarity, leading to a distinct contribution of overall and detailed features to the final score, and thus can be better tailored for each specific system under consideration. Secondly, the reference set for optimization can be totally configured by the user, which produces great flexibility, allowing system-specific and customized comparisons. The directory of useful decoys (DUD) database was adopted to validate and test our method, and principal component analysis (PCA) reveals that SH descriptors for shape comparison preserve sufficient information to separate actives from decoys. The results of virtual screening indicate that the proposed method based on optimal SH descriptor weight combinations represents a great improvement in performance over original SH (OSH) and ultra-fast shape recognition (USR) methods, and is comparable to many other popular methods. Through combining efficient shape similarity comparison with SH expansion method, and other aspects such as chemical and pharmacophore features, SHeMS can play a significant role in this field and can be applied practically to virtual screening by means of similarity comparison with 3D shapes of known active compounds or the binding pockets of target proteins.
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Affiliation(s)
- Chaoqian Cai
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
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