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Su X, Dohle W, Mills SJ, Watt JM, Rossi AM, Taylor CW, Potter BVL. Inositol Adenophostin: Convergent Synthesis of a Potent Agonist of d- myo-Inositol 1,4,5-Trisphosphate Receptors. ACS OMEGA 2020; 5:28793-28811. [PMID: 33195933 PMCID: PMC7659177 DOI: 10.1021/acsomega.0c04145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
d-myo-Inositol 1,4,5-trisphosphate receptors (IP3Rs) are Ca2+ channels activated by the intracellular messenger inositol 1,4,5-trisphosphate (IP3, 1). The glyconucleotide adenophostin A (AdA, 2) is a potent agonist of IP3Rs. A recent synthesis of d-chiro-inositol adenophostin (InsAdA, 5) employed suitably protected chiral building blocks and replaced the d-glucose core by d-chiro-inositol. An alternative approach to fully chiral material is now reported using intrinsic sugar chirality to avoid early isomer resolution, involving the coupling of a protected and activated racemic myo-inositol derivative to a d-ribose derivative. Diastereoisomer separation was achieved after trans-isopropylidene group removal and the absolute ribose-inositol conjugate stereochemistry assigned with reference to the earlier synthesis. Optimization of stannylene-mediated regiospecific benzylation was explored using the model 1,2-O-isopropylidene-3,6-di-O-benzyl-myo-inositol and conditions successfully transferred to one conjugate diastereoisomer with 3:1 selectivity. However, only roughly 1:1 regiospecificity was achieved on the required diastereoisomer. The conjugate regioisomers of benzyl derivatives 39 and 40 were successfully separated and 39 was transformed subsequently to InsAdA after amination, pan-phosphorylation, and deprotection. InsAdA from this synthetic route bound with greater affinity than AdA to IP3R1 and was more potent in releasing Ca2+ from intracellular stores through IP3Rs. It is the most potent full agonist of IP3R1 known and .equipotent with material from the fully chiral synthetic route.
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Affiliation(s)
- Xiangdong Su
- Medicinal
Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Wolfgang Dohle
- Medicinal
Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Stephen J. Mills
- Medicinal
Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Joanna M. Watt
- Medicinal
Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
- Wolfson
Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
| | - Ana M. Rossi
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K.
| | - Colin W. Taylor
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K.
| | - Barry V. L. Potter
- Medicinal
Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
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Inhibiting two cellular mutant epidermal growth factor receptor tyrosine kinases by addressing computationally assessed crystal ligand pockets. Future Med Chem 2019; 11:833-846. [PMID: 30724109 DOI: 10.4155/fmc-2018-0525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: Blocking receptor tyrosine kinases is a useful strategy for inhibiting the overexpression of EGFR. However, the quality of crystal pocket is an essential issue for virtually identifying new leads for surviving resistance cancer cells. Results: With the examinating crystal pocket quality by the self-docking root-mean-square deviation (RMSD) calculation, we used the two best kinase pockets of mutant EGFR kinases, T790M/L858R and G719S, for virtual screening. After sorting all the docking poses of the 57,177 library compounds by consensus scores, three evidently blocked cellular EGFR phosphorylation in the H1975 and SW48 cell lines. Conclusion: The computationally assessed qualities of crystal pockets of crystal EGFR kinases can help identify new cellular active and target-specific ligands rapidly and at low cost.
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Gunaratne GS, Johns ME, Hintz HM, Walseth TF, Marchant JS. A screening campaign in sea urchin egg homogenate as a platform for discovering modulators of NAADP-dependent Ca 2+ signaling in human cells. Cell Calcium 2018; 75:42-52. [PMID: 30145428 PMCID: PMC6286156 DOI: 10.1016/j.ceca.2018.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 12/16/2022]
Abstract
The Ca2+ mobilizing second messenger nicotinic acid adenine dinucleotide phosphate (NAADP) regulates intracellular trafficking events, including translocation of certain enveloped viruses through the endolysosomal system. Targeting NAADP-evoked Ca2+ signaling may therefore be an effective strategy for discovering novel antivirals as well as therapeutics for other disorders. To aid discovery of novel scaffolds that modulate NAADP-evoked Ca2+ signaling in human cells, we have investigated the potential of using the sea urchin egg homogenate system for a screening campaign. Known pharmacological inhibitors of NAADP-evoked Ca2+ release (but not cADPR- or IP3-evoked Ca2+ release) in this invertebrate system strongly correlated with inhibition of MERS-pseudovirus infectivity in a human cell line. A primary screen of 1534 compounds yielded eighteen 'hits' exhibiting >80% inhibition of NAADP-evoked Ca2+ release. A validation pipeline for these candidates yielded seven drugs that inhibited NAADP-evoked Ca2+ release without depleting acidic Ca2+ stores in a human cell line. These candidates displayed a similar penetrance of inhibition in both the sea urchin system and the human cell line, and the extent of inhibition of NAADP-evoked Ca2+ signals correlated well with observed inhibition of infectivity of a Middle East Respiratory syndrome coronavirus (MERS-CoV) pseudovirus. These experiments support the potential of this simple, homogenate system for screening campaigns to discover modulators of NAADP, cADPR and IP3-dependent Ca2+ signaling with potential therapeutic value.
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Affiliation(s)
- Gihan S Gunaratne
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, USA
| | - Malcolm E Johns
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, USA
| | - Hallie M Hintz
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, USA
| | - Timothy F Walseth
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, USA
| | - Jonathan S Marchant
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee WI 53226, USA.
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Kumar A, Zhang KYJ. Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Front Chem 2018; 6:315. [PMID: 30090808 PMCID: PMC6068280 DOI: 10.3389/fchem.2018.00315] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Affiliation(s)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
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Abstract
This chapter describes two powerful 3D ligand-based shape similarity and scoring methods called ROCS and EON, their basic operation and selected validation data. The steps required to prepare a database of molecules for successful use with ROCS and EON are described and selected examples of their application in prospective lead discovery experiments are summarized.
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Affiliation(s)
- Paul C D Hawkins
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM, 87508, USA
| | - Gunther Stahl
- OpenEye Scientific Software, Josephstr. 29, 50678, Köln, Germany.
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Matsuoka M, Kumar A, Muddassar M, Matsuyama A, Yoshida M, Zhang KYJ. Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum. J Chem Inf Model 2017; 57:203-213. [DOI: 10.1021/acs.jcim.6b00649] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Masaki Matsuoka
- Chemical
Genomics Research Group, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ashutosh Kumar
- Structural
Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Muhammad Muddassar
- Structural
Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akihisa Matsuyama
- Chemical
Genomics Research Group, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Chemical
Genomics Research Group, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- CREST Research
Project, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kam Y. J. Zhang
- Structural
Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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7
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A pose prediction approach based on ligand 3D shape similarity. J Comput Aided Mol Des 2016; 30:457-69. [DOI: 10.1007/s10822-016-9923-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/01/2016] [Indexed: 11/27/2022]
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Kumar A, Zhang KYJ. Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise. J Chem Inf Model 2015; 56:965-73. [PMID: 26247231 DOI: 10.1021/acs.jcim.5b00279] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
To evaluate the applicability of shape similarity in docking-based pose selection and virtual screening, we participated in the CSARdock2014 benchmark exercise for identifying the correct docking pose of inhibitors targeting factor XA, spleen tyrosine kinase, and tRNA methyltransferase. This exercise provides a valuable opportunity for researchers to test their docking programs, methods, and protocols in a blind testing environment. In the CSARdock2014 benchmark exercise, we have implemented an approach that uses ligand 3D shape similarity to facilitate docking-based pose selection and virtual screening. We showed here that ligand 3D shape similarity between bound poses could be used to identify the native-like pose from an ensemble of docking-generated poses. Our method correctly identified the native pose as the top-ranking pose for 73% of test cases in a blind testing environment. Moreover, the pose selection results also revealed an excellent correlation between ligand 3D shape similarity scores and RMSD to X-ray crystal structure ligand. In the virtual screening exercise, the average RMSD for our pose prediction was found to be 1.02 Å, and it was one of the top performances achieved in CSARdock2014 benchmark exercise. Furthermore, the inclusion of shape similarity improved virtual screening performance of docking-based scoring and ranking. The coefficient of determination (r(2)) between experimental activities and docking scores for 276 spleen tyrosine kinase inhibitors was found to be 0.365 but reached 0.614 when the ligand 3D shape similarity was included.
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Affiliation(s)
- Ashutosh Kumar
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN , 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN , 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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