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Li D, Jiang K, Teng D, Wu Z, Li W, Tang Y, Wang R, Liu G. Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking. J Chem Inf Model 2022; 62:486-497. [PMID: 35041411 DOI: 10.1021/acs.jcim.1c00662] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Estrogen-related receptor α (ERRα), a member of nuclear receptors (NRs), plays a role in the regulation of cellular energy metabolism and is reported to be a novel potential target for type 2 diabetes therapy. To date, only a few agonists of ERRα have been identified to improve insulin sensitivity and decrease blood glucose levels. Herein, the discovery of novel potent agonists of ERRα determined using a combined virtual screening approach is described. Molecular dynamics (MD) simulations were used to obtain structural ensembles that can consider receptor flexibility. Then, an efficient virtual screening strategy with a combination of similarity search and ensemble docking was performed against the Enamine, SPECS, and Drugbank databases to identify potent ERRα agonists. Finally, a total of 66 compounds were purchased for experimental testing. Biological investigation of promising candidates identified seven compounds that have activity against ERRα with EC50 values ranging from 1.11 to 21.70 μM, with novel scaffolds different from known ERRα agonists until now. Additionally, the molecule GX66 showed micromolar inverse activity against ERRα with an IC50 of 0.82 μM. The predicted binding modes showed that these compounds were anchored in ERRα-LBP via interactions with several residues of ERRα. Overall, this study not only identified the novel potent ERRα agonists or an inverse agonist that would be the promising starting point for further exploration but also demonstrated a successful molecular dynamics-guided approach applicable in virtual screening for ERRα agonists.
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Affiliation(s)
- Dongping Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Kexin Jiang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Dan Teng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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Magwenyane AM, Lawal MM, Amoako DG, Somboro AM, Agoni C, Khan RB, Mhlongo NN, Kumalo HM. Exploring the inhibitory mechanism of resorcinylic isoxazole amine NVP-AUY922 towards the discovery of potential heat shock protein 90 (Hsp90) inhibitors. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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3
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Bonanni D, Citarella A, Moi D, Pinzi L, Bergamini E, Rastelli G. Dual Targeting Strategies On Histone Deacetylase 6 (HDAC6) And Heat Shock Protein 90 (Hsp90). Curr Med Chem 2021; 29:1474-1502. [PMID: 34477503 DOI: 10.2174/0929867328666210902145102] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/08/2021] [Accepted: 07/23/2021] [Indexed: 11/22/2022]
Abstract
The design of multi-target drugs acting simultaneously on multiple signaling pathways is a growing field in medicinal chemistry, especially for the treatment of complex diseases such as cancer. Histone deacetylase 6 (HDAC6) is an established anticancer drug target involved in tumor cells transformation. Being an epigenetic enzyme at the interplay of many biological processes, HDAC6 has become an attractive target for polypharmacology studies aimed at improving therapeutic efficacy of anticancer drugs. For example, the molecular chaperone Heat shock protein 90 (Hsp90) is a substrate of HDAC6 deacetylation, and several lines of evidence demonstrate that simultaneous inhibition of HDAC6 and Hsp90 promote synergistic antitumor effects on different cancer cell lines, highlighting the potential benefits of developing a single molecule endowed with multi-target activity. This review will summarize the complex interplay between HDAC6 and Hsp90, providing also useful hints for multi-target drug design and discovery approaches in this field. To this end, crystallographic structures of HDAC6 and Hsp90 complexes will be extensively reviewed in the light of discussing binding pockets features and pharmacophore requirements and providing useful guidelines for the design of dual inhibitors. The few examples of multi-target inhibitors obtained so far, mostly based on chimeric approaches, will be summarized and put into context. Finally, the main features of HDAC6 and Hsp90 inhibitors will be compared, and ligand- and structure-based strategies potentially useful for the development of small molecular weight dual inhibitors will be proposed and discussed.
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Affiliation(s)
- Davide Bonanni
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Andrea Citarella
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Davide Moi
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Elisa Bergamini
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia Via Campi 183, 41125 Modena, Italy
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Coşkun KA, Koca İ, Gümüş M, Tutar Y. Designing Specific HSP70 Substrate Binding Domain Inhibitor for Perturbing Protein Folding Pathways to Inhibit Cancer Mechanism. Anticancer Agents Med Chem 2021; 21:1472-1480. [PMID: 32951578 DOI: 10.2174/1871520620666200918103509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND HSP70 is a survival factor for tumor cells in transformation and in tumor progression as well as in anti-apoptotic response. OBJECTIVE Several inhibitors targeting HSP70 ATPase function displayed off-target effects, but PES, which targets the HSP70 substrate binding domain, prevents tumor cell survival prominently. However, PES may not bind HSP70 in the absence of nucleotide. This research aimed to design a unique inhibitor molecule that works both in the presence and absence of nucleotides to amplify inhibition. METHODS A set of chimeric coumarine-pyrazole derivatives were determined by in silico techniques and synthesized to elucidate their inhibitory effects. Cell viability experiments displayed KBR1307 as the most efficient inhibitor. A set of characterization experiments were performed, and the results were compared to that of PES agent. Binding constant, ATP hydrolysis rate, and percent aggregation were determined in the presence and absence of inhibitors. RESULTS In silico docking experiments showed that only KBR1307 binds the HSP70 substrate binding domain and interacts with cochaperone interface. Binding experiments indicated that KBR1307 binds HSP70 both in the presence and absence of nucleotides, but PES does not. Both inhibitors significantly lower HSP70 ATPase activity and substrate protein disaggregation activity. However, KBR1307 displays a lower IC50 value at the MCF-7 cell line compared to PES. Both inhibitors do not alter HSP70 secondary structure composition and overall stability. CONCLUSION KBR1307 effectively inhibits HSP70 compared to PES and provides a promising template for novel anticancer drug development.
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Affiliation(s)
- Kübra A Coşkun
- Department of Basic Pharmaceutical Sciences, Division of Biochemistry, Faculty of Pharmacy, Cumhuriyet University, Sivas, Turkey
| | - İrfan Koca
- Bozok University, Faculty of Science, Department of Chemistry, Yozgat, Turkey
| | - Mehmet Gümüş
- Bozok University, Akdagmadeni Vocational School, Yozgat, Turkey
| | - Yusuf Tutar
- Department of Basic Pharmaceutical Sciences, Division of Biochemistry, Faculty of Pharmacy, Cumhuriyet University, Sivas, Turkey
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Leung E, Ayine-Tora DM, Santos-Ledo A, Korolchuk VI, Reynisson J. Identification of novel Atg3-Atg8 inhibitors using virtual screening for autophagy modulation. Bioorg Chem 2021; 114:105092. [PMID: 34147881 DOI: 10.1016/j.bioorg.2021.105092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/28/2021] [Accepted: 06/10/2021] [Indexed: 12/30/2022]
Abstract
A collection of 9050 natural products, their derivatives, and mimetics, was virtually screened against the human Atg3-Atg8 (Atg - autophagy) binding scaffold. By blocking this interaction, the lipidation of Atg8 does not occur and the formation of autophagosomes is inhibited. Forty-three (43) potential ligands were tested using enhanced Green Fluorescent Protein (eGFP) tagged LC3, the human ortholog of Atg8, in MCF7 breast cancer cells. Three hits showed single digit µM IC50 values with AT110, an isoflavone derivative, being the best at 1.2 ± 0.6 µM. Molecular modelling against Atg8 in conjunction with structural activity relationship (SAR) strongly supports the binding to this target. Testing in a panel of cancer cell lines showed little cytotoxic effect as compared to chloroquine. However, same concentration of AT110 was shown to be toxic to young zebrafish embryos. This can be explained in terms of the autophagy process being very active in the zebrafish embryos rendering them susceptible to AT110 whereas in the cancer cells tested the autophagy is not usually active. Nevertheless, AT110 blocks autophagy flux in the zebrafish confirming that the ligand is modulating autophagy. A small molecule non-cytotoxic autophagy inhibitor would open the door for adjunct therapies to bolster many established anticancer drugs, reducing their efficacious concentration thus limiting undesirable site effects. In addition, since many cancer types rely on the autophagy mechanism to survive a therapeutic regime, recurrence can potentially be reduced. The discovery of AT110 is an important step in establishing such an adjunct therapy.
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Affiliation(s)
- Euphemia Leung
- Auckland Cancer Society Research Centre, University of Auckland, New Zealand
| | | | - Adrián Santos-Ledo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Viktor I Korolchuk
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Newcastle under Lyme, Staffordshire ST5 5BG, United Kingdom.
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Banerjee M, Hatial I, Keegan BM, Blagg BSJ. Assay design and development strategies for finding Hsp90 inhibitors and their role in human diseases. Pharmacol Ther 2021; 221:107747. [PMID: 33245994 PMCID: PMC8744950 DOI: 10.1016/j.pharmthera.2020.107747] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/30/2022]
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone that facilitates the maturation of its client proteins including protein kinases, transcription factors, and steroid hormone receptors which are structurally and functionally diverse. These client proteins are involved in various cellular signaling pathways, and Hsp90 is implicated in various human diseases including cancer, inflammation, and diseases associated with protein misfolding; thus making Hsp90 a promising target for drug discovery. Some of its client proteins are well-known cancer targets. Instead of targeting these client proteins individually, however, targeting Hsp90 is more practical for cancer drug development. Efforts have been invested in recognizing potential drugs for clinical use that inhibit Hsp90 activity and result in the prevention of Hsp90 client maturation and dampening of subsequent signaling cascades. Here, we discuss current assays and technologies used to find and characterize Hsp90 inhibitors that include biophysical, biochemical, cell-based assays and computational modeling. This review highlights recent discoveries that N-terminal isoform-selective compounds and inhibitors that target the Hsp90 C-terminus that may offer the potential to overcome some of the detriments observed with pan Hsp90 inhibitors. The tools and assays summarized in this review should be used to develop Hsp90-targeting drugs with high specificity, potency, and drug-like properties that may prove immensely useful in the clinic.
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Affiliation(s)
- Monimoy Banerjee
- Department of Chemistry & Biochemistry, Warren Family Research Center for Drug Discovery and Development, 305 McCourtney Hall, University of Norte Dame, Norte Dame, IN 46656, USA
| | - Ishita Hatial
- Department of Chemistry & Biochemistry, Warren Family Research Center for Drug Discovery and Development, 305 McCourtney Hall, University of Norte Dame, Norte Dame, IN 46656, USA
| | - Bradley M Keegan
- Department of Chemistry & Biochemistry, Warren Family Research Center for Drug Discovery and Development, 305 McCourtney Hall, University of Norte Dame, Norte Dame, IN 46656, USA
| | - Brian S J Blagg
- Department of Chemistry & Biochemistry, Warren Family Research Center for Drug Discovery and Development, 305 McCourtney Hall, University of Norte Dame, Norte Dame, IN 46656, USA.
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7
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Mak OW, Sharma N, Reynisson J, Leung IKH. Discovery of novel Hsp90 C-terminal domain inhibitors that disrupt co-chaperone binding. Bioorg Med Chem Lett 2021; 38:127857. [PMID: 33609661 DOI: 10.1016/j.bmcl.2021.127857] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 12/20/2022]
Abstract
Heat shock protein 90 (Hsp90) is an essential molecular chaperone that performs vital stress-related and housekeeping functions in cells and is a current therapeutic target for diseases such as cancers. Particularly, the development of Hsp90 C-terminal domain (CTD) inhibitors is highly desirable as inhibitors that target the N-terminal nucleotide-binding domain may cause unwanted biological effects. Herein, we report on the discovery of two drug-like novel Hsp90 CTD inhibitors by using virtual screening and intrinsic protein fluorescence quenching binding assays, paving the way for future development of new therapies that employ molecular chaperone inhibitors.
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Affiliation(s)
- Oi Wei Mak
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Pharmacy and Bioengineering, Hornbeam Building, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom.
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
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8
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Hoxie RS, Street TO. Hsp90 chaperones have an energetic hot-spot for binding inhibitors. Protein Sci 2020; 29:2101-2111. [PMID: 32812680 PMCID: PMC7513732 DOI: 10.1002/pro.3933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/16/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022]
Abstract
Although Hsp90-family chaperones have been extensively targeted with ATP-competitive inhibitors, it is unknown whether high affinity is achieved from a few highly stabilizing contacts or from many weaker contacts within the ATP-binding pocket. A large-scale analysis of Hsp90α:inhibitor structures shows that inhibitor hydrogen-bonding to a conserved aspartate (D93 in Hsp90α) stands out as most universal among Hsp90 inhibitors. Here we show that the D93 region makes a dominant energetic contribution to inhibitor binding for both cytosolic and organelle-specific Hsp90 paralogs. For inhibitors in the resorcinol family, the D93:inhibitor hydrogen-bond is pH-dependent because the associated inhibitor hydroxyl group is titratable, rationalizing a linked-protonation event previously observed by the Matulis group. The inhibitor hydroxyl group pKa associated with the D93 hydrogen-bond is therefore critical for optimizing the affinity of resorcinol derivatives, and we demonstrate that spectrophotometric measurements can determine this pKa value. Quantifying the energetic contribution of the D93 hotspot is best achieved with the mitochondrial Hsp90 paralog, yielding 3-6 kcal/mol of stabilization (35-60% of the total binding energy) for a diverse set of inhibitors. The Hsp90 Asp93➔Asn substitution has long been known to abolish nucleotide binding, yet puzzlingly, native sequences of structurally similar ATPases, such as Topoisomerasese II, have an asparagine at this same crucial site. While aspartate and asparagine sidechains can both act as hydrogen bond acceptors, we show that a steric clash prevents the Hsp90 Asp93➔Asn sidechain from adopting the necessary rotamer, whereas this steric restriction is absent in Topoisomerasese II.
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Affiliation(s)
- Reyal S. Hoxie
- Department of BiochemistryBrandeis UniversityWalthamMassachusettsUSA
| | - Timothy O. Street
- Department of BiochemistryBrandeis UniversityWalthamMassachusettsUSA
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Eurtivong C, Pilkington LI, van Rensburg M, White RM, Brar HK, Rees S, Paulin EK, Xu CS, Sharma N, Leung IK, Leung E, Barker D, Reynisson J. Discovery of novel phosphatidylcholine-specific phospholipase C drug-like inhibitors as potential anticancer agents. Eur J Med Chem 2020; 187:111919. [DOI: 10.1016/j.ejmech.2019.111919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/11/2019] [Accepted: 11/26/2019] [Indexed: 01/09/2023]
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10
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Mamontova EM, Zakharenko AL, Zakharova OD, Dyrkheeva NS, Volcho KP, Reynisson J, Arabshahi HJ, Salakhutdinov NF, Lavrik OI. Identification of novel inhibitors for the tyrosyl-DNA-phosphodiesterase 1 (Tdp1) mutant SCAN1 using virtual screening. Bioorg Med Chem 2019; 28:115234. [PMID: 31831297 DOI: 10.1016/j.bmc.2019.115234] [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] [Received: 07/19/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
Abstract
Spinocerebellar ataxia syndrome with axonal neuropathy (SCAN1) is a debilitating neurological disease that is caused by the mutation the Tyrosyl-DNA phosphodiesterase 1 (TDP1) DNA repair enzyme. The crucial His493 in TDP1's binding site is replaced with an arginine amino acid residue rendering the enzyme dysfunctional. A virtual screen was performed against the homology model of SCAN1 and seventeen compounds were identified and tested in a novel SCAN1 specific biochemical assay. Six compounds showed activity with IC50 values between 3.5 and 25.1 µM. The most active ligand 5 (3.5 µM) is a dicoumarin followed by a close structural analogue 6 at 6.0 µM. A less potent series of β-carbolines (14 and 15) was found with potency in the mid-teens. According to molecular modelling an excellent fit for the active ligands into the binding pocket is predicted. To the best of our knowledge, data on inhibitors of the mutant form of TDP1 has not been reported previously. The virtual hits were also tested for wild type TDP1 activity and all six SCAN1 inhibitors are potent for the former, e.g., ligand 5 has a measured IC50 at 99 nM. In the last decade, TDP1 is considered as a promising target for adjuvant therapy against cancer in combination with Topoisomerase 1 poisons. The active ligands are mostly non-toxic to cancer cell lines A-549, T98G and MCF-7 as well as the immortalized WI-38 human fetal lung cells. Furthermore, ligands 5 and 7, show promising synergy in conjunction with topotecan, a clinically used topoisomerase 1 anticancer drug. The active ligands 5, 7, 14 and 15 have a good balance of the physicochemical properties required for oral bioavailability making the excellent candidates for further development.
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Affiliation(s)
- E M Mamontova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
| | - A L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - O D Zakharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - N S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - K P Volcho
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation; N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - J Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, United Kingdom
| | - H J Arabshahi
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - N F Salakhutdinov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation; N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation.
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Identification of Isoform-Selective Ligands for the Middle Domain of Heat Shock Protein 90 (Hsp90). Int J Mol Sci 2019; 20:ijms20215333. [PMID: 31717777 PMCID: PMC6862331 DOI: 10.3390/ijms20215333] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/01/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
The molecular chaperone heat shock protein 90 (Hsp90) is a current inhibition target for the treatment of diseases, including cancer. In humans, there are two major cytosolic isoforms of Hsp90 (Hsp90α and Hsp90β). Hsp90α is inducible and Hsp90β is constitutively expressed. Most Hsp90 inhibitors are pan-inhibitors that target both cytosolic isoforms of Hsp90. The development of isoform-selective inhibitors of Hsp90 may enable better clinical outcomes. Herein, by using virtual screening and binding studies, we report our work in the identification and characterisation of novel isoform-selective ligands for the middle domain of Hsp90β. Our results pave the way for further development of isoform-selective Hsp90 inhibitors.
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12
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The Development of Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. Combination of Monoterpene and Adamantine Moieties via Amide or Thioamide Bridges. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9132767] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eleven amide and thioamide derivatives with monoterpene and adamantine substituents were synthesised. They were tested for their activity against the tyrosyl-DNA phosphodiesterase 1 DNA (Tdp1) repair enzyme with the most potent compound 47a, having an IC50 value of 0.64 M. When tested in the A-549 lung adenocarcinoma cell line, no or very limited cytotoxic effect was observed for the ligands. However, in conjunction with topotecan, a well-established Topoisomerase 1 (Top1) poison in clinical use against cancer, derivative 46a was very cytotoxic at 5 M concentration, displaying strong synergism. This effect was only seen for 46a (IC50—3.3 M) albeit some other ligands had better IC50 values. Molecular modelling into the catalytic site of Tdp1 predicted plausible binding mode of 46a, effectively blocking access to the catalytic site.
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Bergsdorf C, Wright SK. A Guide to Run Affinity Screens Using Differential Scanning Fluorimetry and Surface Plasmon Resonance Assays. Methods Enzymol 2018; 610:135-165. [PMID: 30390797 DOI: 10.1016/bs.mie.2018.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past 30 years, drug discovery has evolved from a pure phenotypic approach to an integrated target-based strategy. The implementation of high-throughput biochemical and cellular assays has enabled the screening of large compound libraries which has become an important and often times the main source of new chemical matter that serve as starting point for medicinal chemistry efforts. In addition, biophysical methods measuring the physical interaction (affinity) between a low molecular weight ligand and a target protein became an integral part of hit validation/optimization to rule out false positives due to assay artifacts. Recent advances in throughput, robustness, and sensitivity of biophysical affinity screening methods have broadened their application in hit identification and validation such that they can now complement classical functional readouts. As a result, new target classes can be accessed that have not been amenable to functional assays. In this chapter, two affinity screening methods, differential scanning fluorimetry and surface plasmon resonance, which are broadly utilized in both academia and pharmaceutical industry are discussed in respect to their use in hit identification and validation. These methods exemplify how assays which differ in complexity, throughput, and information content can support the hit identification/validation process. This chapter focuses on the practical aspects and caveats of these techniques in order to enable the reader to establish their own affinity-based screens in both formats.
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Affiliation(s)
| | - S Kirk Wright
- Novartis Institutes for BioMedical Research, Cambridge, MA, United States
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14
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Bell EW, Zheng EJ, Ryno LM. Identification of inhibitors of the E. coli chaperone SurA using in silico and in vitro techniques. Bioorg Med Chem Lett 2018; 28:3540-3548. [PMID: 30301675 DOI: 10.1016/j.bmcl.2018.09.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 09/27/2018] [Indexed: 11/15/2022]
Abstract
SurA is a gram-negative, periplasmic chaperone protein involved in the proper folding of outer membrane porins (OMPs), which protect bacteria against toxins in the extracellular environment by selectively regulating the passage of nutrients into the cell. Previous studies demonstrated that deletion of SurA renders bacteria more sensitive to toxins that compromise the integrity of the outer membrane. Inhibitors of SurA will perturb the folding of OMPs, leading to disruption of the outer membrane barrier and making the cell more vulnerable to toxic insults. The discovery of novel SurA inhibitors is therefore of great importance for developing alternative strategies to overcome antibiotic resistance. Our laboratory has screened over 10,000,000 compoundsin silicoby computationally docking these compounds onto the crystal structure of SurA. Through this screen and a screen of fragment compounds (molecular weight less than 250 g/mol), we found twelve commercially readily available candidate compounds that bind to the putative client binding site of SurA. We confirmed binding to SurA by developing and employing a competitive fluorescence anisotropy-based binding assay. Our results show that one of these compounds, Fmoc-β-(2-quinolyl)-d-alanine, binds the client binding site with high micromolar affinity. Using this compound as a lead, we also discovered that Fmoc-l-tryptophan and Fmoc-l-phenylalanine, but not Fmoc-l-tyrosine, bind SurA with similar micromolar affinity. To our knowledge, this is the first report of a competitive fluorescence anisotropy assay developed for the identification of inhibitors of the chaperone SurA, and the identification of three small molecules that bind SurA at its client binding site.
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Affiliation(s)
- Eric W Bell
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland St. A263, Oberlin, OH 44074, United States
| | - Erica J Zheng
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland St. A263, Oberlin, OH 44074, United States
| | - Lisa M Ryno
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland St. A263, Oberlin, OH 44074, United States.
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Olotu F, Adeniji E, Agoni C, Bjij I, Khan S, Elrashedy A, Soliman M. An update on the discovery and development of selective heat shock protein inhibitors as anti-cancer therapy. Expert Opin Drug Discov 2018; 13:903-918. [PMID: 30207185 DOI: 10.1080/17460441.2018.1516035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Over the years, not a single HSP inhibitor has progressed into the post-market phase of drug development despite the success recorded in various pre-clinical and clinical studies. The inability of existing drugs to specifically target oncogenic HSPs has majorly accounted for these setbacks. Recent combinatorial strategies that incorporated computer-aided drug design (CADD) techniques are geared towards the development of highly specific HSP inhibitors with increased activities and minimal toxicities. Areas covered: In this review, strategic therapeutic approaches that have recently aided the development of selective HSP inhibitors were highlighted. Also, the significant contributions of CADD techniques over the years were discussed in detail. This article further describes promising computational paradigms and their applications towards the discovery of highly specific inhibitors of oncogenic HSPs. Expert opinion: The recent shift towards highly selective and specific HSP inhibition has shown great promise as evidenced by the development of paralog/isoform-selective HSP drugs. It could be further augmented with computer-aided drug design strategies, which incorporate reliable methods that would greatly enhance the design and optimization of novel inhibitors with improved activities and minimal toxicities.
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Affiliation(s)
- Fisayo Olotu
- a Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences , University of KwaZulu-Natal , Durban , South Africa
| | - Emmanuel Adeniji
- a Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences , University of KwaZulu-Natal , Durban , South Africa
| | - Clement Agoni
- a Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences , University of KwaZulu-Natal , Durban , South Africa
| | - Imane Bjij
- a Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences , University of KwaZulu-Natal , Durban , South Africa
| | - Shama Khan
- a Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences , University of KwaZulu-Natal , Durban , South Africa
| | | | - Mahmoud Soliman
- a Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences , University of KwaZulu-Natal , Durban , South Africa
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16
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Sepehri B, Rezaei M, Ghavami R. The in silico identification of potent anti-cancer agents by targeting the ATP binding site of the N-domain of HSP90. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:551-565. [PMID: 30058412 DOI: 10.1080/1062936x.2018.1494626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Indexed: 06/08/2023]
Abstract
To identify new HSP90 inhibitors, the ATP binding site of the N-domain of HSP90 was targeted by molecular docking of a library of 23,129,083 compounds (from the ZINC database) to the ATP binding site of the N-domain of HSP90. Structure-based virtual screen (SBVS) was performed using idock software on the istar web platform. Based on idock binding energies, 40 molecules were considered as HSP90 inhibitors. In the next step, the 40 molecules and the compound AT13387 (Onalespib) were docked to the XJX binding site using AutoDock Vina software. By comparing the binding energies of the 40 molecules selected with compound AT13387, 26 molecules were selected. By applying the rule of five, eight molecules were selected as hit compounds. The interactions of these eight compounds with the XJX binding site were obtained and investigated, and two-dimensional interaction maps were provided for the others. Finally, computing the toxicity of these compounds with the ProTox-II webserver shows that three compounds, namely ZINC89453765, ZINC23918431 and ZINC12414793, can be considered as good HSP90 inhibitors. These compounds are inactive for nuclear receptor signalling and stress response pathways including heat shock response, so do not have the limitations of common HSP90 inhibitors. They are also inactive for hepatotoxicity, carcinogenicity, immunotoxicity, mutagenicity and cytotoxicity.
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Affiliation(s)
- B Sepehri
- a Department of Chemistry, Faculty of Science , University of Kurdistan , Sanandaj , Iran
| | - M Rezaei
- a Department of Chemistry, Faculty of Science , University of Kurdistan , Sanandaj , Iran
| | - R Ghavami
- a Department of Chemistry, Faculty of Science , University of Kurdistan , Sanandaj , Iran
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17
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Kim HH, Hyun JS, Choi J, Choi KE, Jee JG, Park SJ. Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain. Sci Rep 2018; 8:368. [PMID: 29321504 PMCID: PMC5762686 DOI: 10.1038/s41598-017-18332-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/08/2017] [Indexed: 12/17/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is one of the most abundant cellular proteins and plays a substantial role in the folding of client proteins. The inhibition of Hsp90 has been regarded as an attractive therapeutic strategy for treating cancer because many oncogenic kinases are Hsp90 client proteins. In this study, we report new inhibitors that directly bind to N-terminal ATP-binding pocket of Hsp90. Optimized structure-based virtual screening predicted candidate molecules, which was followed by confirmation using biophysical and cell-based assays. Among the reported crystal structures, we chose the two structures that show the most favourable early enrichments of true-positives in the receiver operating characteristic curve. Four molecules showed significant changes in the signals of 2D [1H, 15N] correlation NMR spectroscopy. Differential scanning calorimetry analysis supported the results indicating direct binding. Quantified dissociation constant values of the molecules, determined by a series of 2D NMR experiments, lie in the range of 0.1–33 μM. Growth inhibition assay with breast and lung cancer cells confirmed the cellular activities of the molecules. Cheminformatics revealed that the molecules share limited chemical similarities with known inhibitors. Molecular dynamics simulations detailed the putative binding modes of the inhibitors.
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Affiliation(s)
- Hyun-Hwi Kim
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Republic of Korea
| | - Ja-Shil Hyun
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Republic of Korea
| | - Joonhyeok Choi
- Research Institute of Pharmaceutical Researches, College of Pharmacy, Kyungpook, National University, Daegu, 41566, Republic of Korea
| | - Kwang-Eun Choi
- Research Institute of Pharmaceutical Researches, College of Pharmacy, Kyungpook, National University, Daegu, 41566, Republic of Korea
| | - Jun-Goo Jee
- Research Institute of Pharmaceutical Researches, College of Pharmacy, Kyungpook, National University, Daegu, 41566, Republic of Korea.
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Republic of Korea.
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Li Y, Zafar A, Kilmartin PA, Reynisson J, Leung IKH. Development and Application of an NMR-Based Assay for Polyphenol Oxidases. ChemistrySelect 2017. [DOI: 10.1002/slct.201702144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yu Li
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| | - Ayesha Zafar
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| | - Paul A. Kilmartin
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
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19
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Bhusal RP, Patel K, Kwai BXC, Swartjes A, Bashiri G, Reynisson J, Sperry J, Leung IKH. Development of NMR and thermal shift assays for the evaluation of Mycobacterium tuberculosis isocitrate lyase inhibitors. MEDCHEMCOMM 2017; 8:2155-2163. [PMID: 30108733 PMCID: PMC6072051 DOI: 10.1039/c7md00456g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/16/2017] [Indexed: 12/17/2022]
Abstract
The enzymes isocitrate lyase (ICL) isoforms 1 and 2 are essential for Mycobacterium tuberculosis survival within macrophages during latent tuberculosis (TB). As such, ICLs are attractive therapeutic targets for the treatment of tuberculosis. However, there are few biophysical assays that are available for accurate kinetic and inhibition studies of ICL in vitro. Herein we report the development of a combined NMR spectroscopy and thermal shift assay to study ICL inhibitors for both screening and inhibition constant (IC50) measurement. Operating this new assay in tandem with virtual high-throughput screening has led to the discovery of several new ICL1 inhibitors.
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Affiliation(s)
- Ram Prasad Bhusal
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Krunal Patel
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Brooke X C Kwai
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Anne Swartjes
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
- Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ , Nijmegen , The Netherlands
| | - Ghader Bashiri
- School of Biological Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Jonathan Sperry
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Ivanhoe K H Leung
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
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