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Shivani, Abdul Rahaman TA, Chaudhary S. Targeting cancer using scaffold-hopping approaches: illuminating SAR to improve drug design. Drug Discov Today 2024; 29:104115. [PMID: 39067613 DOI: 10.1016/j.drudis.2024.104115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Scaffold hopping is a design approach involving alterations to the core structure of an already bioactive scaffold to generate novel molecules to discover bioactive hit compounds with innovative core structures. Scaffold hopping enhances selectivity and potency while maintaining physicochemical, pharmacodynamic (PD), and pharmacokinetic (PK) properties, including toxicity parameters. Numerous molecules have been designed based on a scaffold-hopping strategy that showed potent inhibition activity against multiple targets for the diverse types of malignancy. In this review, we critically discuss recent applications of scaffold hopping along with essential components of medicinal chemistry, such as structure-activity relationship (SAR) profiles. Moreover, we shed light on the limitations and challenges associated with scaffold hopping-based anticancer drug discovery.
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Affiliation(s)
- Shivani
- Laboratory of Bioactive Heterocycles and Catalysis (BHC lab), Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli (Transit Campus), Bijnor-Sisendi Road, Near CRPF Base Camp, Sarojini Nagar, Lucknow 226002, India
| | - T A Abdul Rahaman
- Laboratory of Bioactive Heterocycles and Catalysis (BHC lab), Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli (Transit Campus), Bijnor-Sisendi Road, Near CRPF Base Camp, Sarojini Nagar, Lucknow 226002, India
| | - Sandeep Chaudhary
- Laboratory of Bioactive Heterocycles and Catalysis (BHC lab), Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli (Transit Campus), Bijnor-Sisendi Road, Near CRPF Base Camp, Sarojini Nagar, Lucknow 226002, India.
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2
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Michaelides IN, Collie GW. E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology. J Med Chem 2023; 66:3173-3194. [PMID: 36821822 PMCID: PMC10009759 DOI: 10.1021/acs.jmedchem.2c01882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 02/25/2023]
Abstract
Ubiquitination is a key post-translational modification of proteins, affecting the regulation of multiple cellular processes. Cells are equipped with over 600 ubiquitin orchestrators, called E3 ubiquitin ligases, responsible for directing the covalent attachment of ubiquitin to substrate proteins. Due to their regulatory role in cells, significant efforts have been made to discover ligands for E3 ligases. The recent emergence of the proteolysis targeting chimera (PROTAC) and molecular glue degrader (MGD) modalities has further increased interest in E3 ligases as drug targets. This perspective focuses on how fragment based lead discovery (FBLD) methods have been used to discover new ligands for this important target class. In some cases these efforts have led to clinical candidates; in others, they have provided tools for deepening our understanding of E3 ligase biology. Recently, FBLD-derived ligands have inspired the design of PROTACs that are able to artificially modulate protein levels in cells.
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Affiliation(s)
- Iacovos N. Michaelides
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
| | - Gavin W. Collie
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
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3
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Abdellattif MH, Elkamhawy A, Hagar M, Hadda TB, Shehab WS, Mansy W, Belal A, Arief MMH, Hussien MA. Novel saccharin analogs as promising antibacterial and anticancer agents: synthesis, DFT, POM analysis, molecular docking, molecular dynamic simulations, and cell-based assay. Front Pharmacol 2022; 13:958379. [PMID: 36267293 PMCID: PMC9577234 DOI: 10.3389/fphar.2022.958379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022] Open
Abstract
Saccharine is a pharmacologically significant active scaffold for various biological activities, including antibacterial and anticancer activities. Herein, saccharinyl hydrazide (1) was synthesized and converted into 2-[(2Z)-2-(1,1-dioxo-1,2-dihydro-3H-1λ6,2- benzothiazole-3-ylidene) hydrazinyl] acetohydrazide (5), which was employed as a key precursor for synthesizing a novel series of small molecules bearing different moieties of monosaccharides, aldehydes, and anhydrides. Potent biological activities were found against Staphylococcus and Escherichia coli, and the results indicated that compounds 6c and 10a were the most active analogs with an inhibition zone diameter of 30–35 mm. In cell-based anticancer assay over Ovcar-3 and M-14 cell lines, compound 10a was the most potent analog with IC50 values of 7.64 ± 0.01 and 8.66 ± 0.01 µM, respectively. The Petra Orisis Molinspiration (POM) theoretical method was used to calculate the drug score of tested compounds and compare them with their experimental screening data. Theoretical DFT calculations were carried out in a gas phase in a set of B3LYP 6-311G (d,p). Molecular docking studies utilizing the MOE indicated the best binding mode with the highest energy interaction within the binding sites. The molecular docking for Ovcar-3 was carried out on the ovarian cancer protein (3W2S), while the molecular docking for M-14 melanoma was carried out on the melanoma cancer protein (2OPZ). The MD performed about 2ns simulations to validate selected compounds’ theoretical studies.
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Affiliation(s)
- Magda H. Abdellattif
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
- *Correspondence: Magda H. Abdellattif, ; M. M. H. Arief,
| | - Ahmed Elkamhawy
- College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mohamed Hagar
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Wesam S. Shehab
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Wael Mansy
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amany Belal
- Department of Pharmaceutical Chemistry, College of Pharmacy Taif University, Taif, Saudi Arabia
| | - M. M. H. Arief
- Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
- *Correspondence: Magda H. Abdellattif, ; M. M. H. Arief,
| | - Mostafa A. Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
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4
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Sen N, Madhusudhan MS. A structural database of chain–chain and domain–domain interfaces of proteins. Protein Sci 2022. [DOI: 10.1002/pro.4406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Neeladri Sen
- Indian Institute of Science Education and Research Pune India
- Institute of Structural and Molecular Biology University College London London UK
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5
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Shimizu H, Renslo A. Systematic Exploration of Passive Permeability in Tetrapeptides with Hydrogen---Bond Accepting Amino Acid Side Chains. ChemMedChem 2022; 17:e202200204. [PMID: 35696654 DOI: 10.1002/cmdc.202200204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/10/2022] [Indexed: 11/08/2022]
Abstract
We synthesized and experimentally tested the passive permeability of more than thirty tetrapeptides mimicking the N -terminus of the pro-apoptotic protein Smac (Second mitochondria-derived activator of caspases). Each peptide bore one or two unnatural Hydrogen Bond Acceptor-bearing Amino Acid (HBA-AA) residues, such that intramolecular hydrogen bonding with proximal backbone amide N-H donors is feasible. Passive permeability of the synthetic peptides was determined using the parallel artificial membrane permeability assay (PAMPA). Experimental permeability values were found to span three orders of magnitude, providing useful empirical guidance for the design of more permeable Smac mimetics specifically, and peptidic ligands generally.
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Affiliation(s)
- Hiroki Shimizu
- Daiichi Sankyo Pharma Development, Medicinal Chemistry, JAPAN
| | - Adam Renslo
- University of California San Francisco School of Pharmacy, Pharmaceutical Chemistry, 600 16th Street, Genentech Hall N572B, 94143, San Francisco, UNITED STATES
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6
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Shultis D, Mitra P, Huang X, Johnson J, Khattak NA, Gray F, Piper C, Czajka J, Hansen L, Wan B, Chinnaswamy K, Liu L, Wang M, Pan J, Stuckey J, Cierpicki T, Borchers CH, Wang S, Lei M, Zhang Y. Changing the Apoptosis Pathway through Evolutionary Protein Design. J Mol Biol 2019; 431:825-841. [PMID: 30625288 DOI: 10.1016/j.jmb.2018.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/12/2018] [Accepted: 12/28/2018] [Indexed: 11/30/2022]
Abstract
One obstacle in de novo protein design is the vast sequence space that needs to be searched through to obtain functional proteins. We developed a new method using structural profiles created from evolutionarily related proteins to constrain the simulation search process, with functions specified by atomic-level ligand-protein binding interactions. The approach was applied to redesigning the BIR3 domain of the X-linked inhibitor of apoptosis protein (XIAP), whose primary function is to suppress the cell death by inhibiting caspase-9 activity; however, the function of the wild-type XIAP can be eliminated by the binding of Smac peptides. Isothermal calorimetry and luminescence assay reveal that the designed XIAP domains can bind strongly with the Smac peptides but do not significantly inhibit the caspase-9 proteolytic activity in vitro compared with the wild-type XIAP protein. Detailed mutation assay experiments suggest that the binding specificity in the designs is essentially determined by the interplay of structural profile and physical interactions, which demonstrates the potential to modify apoptosis pathways through computational design.
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Affiliation(s)
- David Shultis
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Pralay Mitra
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Jarrett Johnson
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Naureen Aslam Khattak
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Felicia Gray
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Clint Piper
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Jeff Czajka
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Logan Hansen
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Bingbing Wan
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | | | - Liu Liu
- Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Mi Wang
- Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jingxi Pan
- Department of Biochemistry & Microbiology, The University of Victoria-Genome BC Proteomics Centre, Victoria, BC, Canada V8Z 7X8
| | - Jeanne Stuckey
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Christoph H Borchers
- Department of Biochemistry & Microbiology, The University of Victoria-Genome BC Proteomics Centre, Victoria, BC, Canada V8Z 7X8
| | - Shaomeng Wang
- Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ming Lei
- Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.
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7
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Xu D, Si Y, Meroueh SO. A Computational Investigation of Small-Molecule Engagement of Hot Spots at Protein-Protein Interaction Interfaces. J Chem Inf Model 2017; 57:2250-2272. [PMID: 28766941 DOI: 10.1021/acs.jcim.7b00181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The binding affinity of a protein-protein interaction is concentrated at amino acids known as hot spots. It has been suggested that small molecules disrupt protein-protein interactions by either (i) engaging receptor protein hot spots or (ii) mimicking hot spots of the protein ligand. Yet, no systematic studies have been done to explore how effectively existing small-molecule protein-protein interaction inhibitors mimic or engage hot spots at protein interfaces. Here, we employ explicit-solvent molecular dynamics simulations and end-point MM-GBSA free energy calculations to explore this question. We select 36 compounds for which high-quality binding affinity and cocrystal structures are available. Five complexes that belong to three classes of protein-protein interactions (primary, secondary, and tertiary) were considered, namely, BRD4•H4, XIAP•Smac, MDM2•p53, Bcl-xL•Bak, and IL-2•IL-2Rα. Computational alanine scanning using MM-GBSA identified hot-spot residues at the interface of these protein interactions. Decomposition energies compared the interaction of small molecules with individual receptor hot spots to those of the native protein ligand. Pharmacophore analysis was used to investigate how effectively small molecules mimic the position of hot spots of the protein ligand. Finally, we study whether small molecules mimic the effects of the native protein ligand on the receptor dynamics. Our results show that, in general, existing small-molecule inhibitors of protein-protein interactions do not optimally mimic protein-ligand hot spots, nor do they effectively engage protein receptor hot spots. The more effective use of hot spots in future drug design efforts may result in smaller compounds with higher ligand efficiencies that may lead to greater success in clinical trials.
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Affiliation(s)
- David Xu
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing , Indianapolis, Indiana 46202, United States
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Kim KS, Zhang L, Williams D, Perez HL, Stang E, Borzilleri RM, Posy S, Lei M, Chaudhry C, Emanuel S, Talbott R. Discovery of tetrahydroisoquinoline-based bivalent heterodimeric IAP antagonists. Bioorg Med Chem Lett 2014; 24:5022-9. [DOI: 10.1016/j.bmcl.2014.09.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/04/2014] [Accepted: 09/08/2014] [Indexed: 11/16/2022]
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9
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Seiter MA, Salcher S, Rupp M, Hagenbuchner J, Kiechl-Kohlendorfer U, Mortier J, Wolber G, Rollinger JM, Obexer P, Ausserlechner MJ. Discovery of Sanggenon G as a natural cell-permeable small-molecular weight inhibitor of X-linked inhibitor of apoptosis protein (XIAP). FEBS Open Bio 2014; 4:659-71. [PMID: 25161875 PMCID: PMC4141193 DOI: 10.1016/j.fob.2014.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 06/10/2014] [Accepted: 07/01/2014] [Indexed: 01/29/2023] Open
Abstract
Discovery of a novel XIAP-inhibitory natural compound from Morus root bark (Sanggenon G). Sanggenon G binds specific to the BIR3 domain of XIAP in a low μM range. Sanggenon G interferes with XIAP-BIR3-substrate binding in living cells. Sanggenon G acts as chemosensitizer in tumor cell lines with high XIAP expression.
Defects in the regulation of apoptosis are one main cause of cancer development and may result from overexpression of anti-apoptotic proteins such as the X-linked inhibitor of apoptosis protein (XIAP). XIAP is frequently overexpressed in human leukemia and prostate and breast tumors. Inhibition of apoptosis by XIAP is mainly coordinated through direct binding to the initiator caspase-9 via its baculovirus-IAP-repeat-3 (BIR3) domain. XIAP inhibits caspases directly making it to an attractive target for anti-cancer therapy. In the search for novel, non-peptidic XIAP inhibitors in this study we focused on the chemical constituents of sāng bái pí (mulberry root bark). Most promising candidates of this plant were tested biochemically in vitro by a fluorescence polarization (FP) assay and in vivo via protein fragment complementation analysis (PCA). We identified the Diels Alder adduct Sanggenon G (SG1) as a novel, small-molecular weight inhibitor of XIAP. As shown by FP and PCA analyses, SG1 binds specifically to the BIR3 domain of XIAP with a binding affinity of 34.26 μM. Treatment of the transgenic leukemia cell line Molt3/XIAP with SG1 enhances caspase-8, -3 and -9 cleavage, displaces caspase-9 from XIAP as determined by immunoprecipitation experiments and sensitizes these cells to etoposide-induced apoptosis. SG1 not only sensitizes the XIAP-overexpressing leukemia cell line Molt3/XIAP to etoposide treatment but also different neuroblastoma cell lines endogenously expressing high XIAP levels. Taken together, Sanggenon G (SG1) is a novel, natural, non-peptidic, small-molecular inhibitor of XIAP that can serve as a starting point to develop a new class of improved XIAP inhibitors.
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Key Words
- (FP-) assay, fluorescence polarization assay
- ARPF-FAM, ARPF-K(5-Fam)-NH2-peptide
- BIR-3, baculovirus-IAP-repeat-3
- CC, column chromatography
- Cell permeable
- Kd, dissociation constant
- Ki, binding affinity
- MAC, methanol crude extract of mulberry root bark
- Natural
- PCA, protein fragment complementation analysis
- RLU, relative luminescence units
- SG1, sanggenon G
- Sanggenon G
- Small-molecular weight
- XIAP inhibitor
- XIAP, X-linked inhibitor of apoptosis protein
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Affiliation(s)
- Maximilian A Seiter
- Department of Pediatrics I, Medical University Innsbruck, Anichstraße 35, A-6020 Innsbruck, Austria ; Tyrolean Cancer Research Institute, Innrain 66, A-6020 Innsbruck, Austria
| | - Stefan Salcher
- Department of Pediatrics II, Medical University Innsbruck, Anichstraße 35, A-6020 Innsbruck, Austria ; Tyrolean Cancer Research Institute, Innrain 66, A-6020 Innsbruck, Austria
| | - Martina Rupp
- Department of Pediatrics II, Medical University Innsbruck, Anichstraße 35, A-6020 Innsbruck, Austria ; Tyrolean Cancer Research Institute, Innrain 66, A-6020 Innsbruck, Austria
| | - Judith Hagenbuchner
- Department of Pediatrics II, Medical University Innsbruck, Anichstraße 35, A-6020 Innsbruck, Austria ; Tyrolean Cancer Research Institute, Innrain 66, A-6020 Innsbruck, Austria
| | | | - Jérémie Mortier
- Freie Universität Berlin, Institute of Pharmacy, Department Pharmaceutical & Medicinal Chemistry, Koenigin-Luise-Straße 2, 14195 Berlin, Germany
| | - Gerhard Wolber
- Freie Universität Berlin, Institute of Pharmacy, Department Pharmaceutical & Medicinal Chemistry, Koenigin-Luise-Straße 2, 14195 Berlin, Germany
| | - Judith M Rollinger
- Institutes of Pharmacy/Pharmacognosy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Petra Obexer
- Department of Pediatrics II, Medical University Innsbruck, Anichstraße 35, A-6020 Innsbruck, Austria ; Tyrolean Cancer Research Institute, Innrain 66, A-6020 Innsbruck, Austria
| | - Michael J Ausserlechner
- Department of Pediatrics I, Medical University Innsbruck, Anichstraße 35, A-6020 Innsbruck, Austria ; Tyrolean Cancer Research Institute, Innrain 66, A-6020 Innsbruck, Austria
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10
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Obexer P, Ausserlechner MJ. X-linked inhibitor of apoptosis protein - a critical death resistance regulator and therapeutic target for personalized cancer therapy. Front Oncol 2014; 4:197. [PMID: 25120954 PMCID: PMC4112792 DOI: 10.3389/fonc.2014.00197] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/14/2014] [Indexed: 01/01/2023] Open
Abstract
Defects in apoptosis regulation are one main cause of cancer development and may result from overexpression of anti-apoptotic proteins such as inhibitor of apoptosis proteins (IAPs). IAPs are cell death regulators that, among other functions, bind caspases, and interfere with apoptotic signaling via death receptors or intrinsic cell death pathways. All IAPs share one to three common structures, the so called baculovirus-IAP-repeat (BIR)-domains that allow them to bind caspases and other proteins. X-linked inhibitor of apoptosis protein (XIAP) is the most potent and best-defined anti-apoptotic IAP family member that directly neutralizes caspase-9 via its BIR3 domain and the effector caspases-3 and -7 via its BIR2 domain. A natural inhibitor of XIAP is SMAC/Diablo, which is released from mitochondria in apoptotic cells and displaces bound caspases from the BIR2/BIR3 domains of XIAP thereby reactivating cell death execution. The central apoptosis-inhibitory function of XIAP and its overexpression in many different types of advanced cancers have led to significant efforts to identify therapeutics that neutralize its anti-apoptotic effect. Most of these drugs are chemical derivatives of the N-terminal part of SMAC/Diablo. These “SMAC-mimetics” either specifically induce apoptosis in cancer cells or act as drug-sensitizers. Several “SMAC-mimetics” are currently tested by the pharmaceutical industry in Phase I and Phase II trials. In this review, we will discuss recent advances in understanding the function of IAPs in normal and malignant cells and focus on approaches to specifically neutralize XIAP in cancer cells.
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Affiliation(s)
- Petra Obexer
- Department of Pediatrics II, Medical University Innsbruck , Innsbruck , Austria ; Tyrolean Cancer Research Institute , Innsbruck , Austria
| | - Michael J Ausserlechner
- Tyrolean Cancer Research Institute , Innsbruck , Austria ; Department of Pediatrics I, Medical University Innsbruck , Innsbruck , Austria
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11
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Singh N, D'Souza A, Cholleti A, Sastry GM, Bose K. Dual regulatory switch confers tighter control on HtrA2 proteolytic activity. FEBS J 2014; 281:2456-70. [DOI: 10.1111/febs.12799] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 02/03/2023]
Affiliation(s)
- Nitu Singh
- Advanced Centre for Treatment; Research and Education in Cancer (ACTREC); Tata Memorial Centre; Kharghar Navi Mumbai India
| | - Areetha D'Souza
- Advanced Centre for Treatment; Research and Education in Cancer (ACTREC); Tata Memorial Centre; Kharghar Navi Mumbai India
| | | | | | - Kakoli Bose
- Advanced Centre for Treatment; Research and Education in Cancer (ACTREC); Tata Memorial Centre; Kharghar Navi Mumbai India
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12
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Elsawy MA, Martin L, Tikhonova IG, Walker B. Solid phase synthesis of Smac/DIABLO-derived peptides using a ‘Safety-Catch’ resin: Identification of potent XIAP BIR3 antagonists. Bioorg Med Chem 2013; 21:5004-11. [DOI: 10.1016/j.bmc.2013.06.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 06/20/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
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13
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Lukacs C, Belunis C, Crowther R, Danho W, Gao L, Goggin B, Janson CA, Li S, Remiszewski S, Schutt A, Thakur MK, Singh SK, Swaminathan S, Pandey R, Tyagi R, Gosu R, Kamath AV, Kuglstatter A. The structure of XIAP BIR2: understanding the selectivity of the BIR domains. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1717-25. [PMID: 23999295 PMCID: PMC3760131 DOI: 10.1107/s0907444913016284] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/11/2013] [Indexed: 11/11/2022]
Abstract
XIAP, a member of the inhibitor of apoptosis family of proteins, is a critical regulator of apoptosis. Inhibition of the BIR domain-caspase interaction is a promising approach towards treating cancer. Previous work has been directed towards inhibiting the BIR3-caspase-9 interaction, which blocks the intrinsic apoptotic pathway; selectively inhibiting the BIR2-caspase-3 interaction would also block the extrinsic pathway. The BIR2 domain of XIAP has successfully been crystallized; peptides and small-molecule inhibitors can be soaked into these crystals, which diffract to high resolution. Here, the BIR2 apo crystal structure and the structures of five BIR2-tetrapeptide complexes are described. The structural flexibility observed on comparing these structures, along with a comparison with XIAP BIR3, affords an understanding of the structural elements that drive selectivity between BIR2 and BIR3 and which can be used to design BIR2-selective inhibitors.
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Affiliation(s)
- Christine Lukacs
- Discovery Technologies, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Charles Belunis
- Discovery Technologies, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Robert Crowther
- Discovery Technologies, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Waleed Danho
- Medicinal Chemistry, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Lin Gao
- Discovery Technologies, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Barry Goggin
- Discovery Oncology, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Cheryl A. Janson
- Discovery Technologies, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Shirley Li
- Discovery Technologies, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Stacy Remiszewski
- Medicinal Chemistry, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Andrew Schutt
- Discovery Oncology, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
| | | | - Saroj K. Singh
- Structural Biology, Jubilant Biosys Ltd, Bangalore, India
| | | | - Rajat Pandey
- Structural Biology, Jubilant Biosys Ltd, Bangalore, India
| | - Rajiv Tyagi
- Structural Biology, Jubilant Biosys Ltd, Bangalore, India
| | | | | | - Andreas Kuglstatter
- Discovery Technologies, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA
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Sun H, Tawa G, Wallqvist A. Classification of scaffold-hopping approaches. Drug Discov Today 2012; 17:310-24. [PMID: 22056715 PMCID: PMC3328312 DOI: 10.1016/j.drudis.2011.10.024] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 10/15/2022]
Abstract
The general goal of drug discovery is to identify novel compounds that are active against a preselected biological target with acceptable pharmacological properties defined by marketed drugs. Scaffold hopping has been widely applied by medicinal chemists to discover equipotent compounds with novel backbones that have improved properties. In this article we classify scaffold hopping into four major categories, namely heterocycle replacements, ring opening or closure, peptidomimetics and topology-based hopping. We review the structural diversity of original and final scaffolds with respect to each category. We discuss the advantages and limitations of small, medium and large-step scaffold hopping. Finally, we summarize software that is frequently used to facilitate different kinds of scaffold-hopping methods.
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Affiliation(s)
- Hongmao Sun
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Frederick, MD 21702, USA.
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LING BAOPING, ZHANG RUI, WANG ZHIGUO, LIU YONGJUN, LIU CHENGBU. STUDY ON THE INTERACTIONS OF Smac MIMETICS WITH XIAP-BIR3 DOMAIN BY DOCKING AND MOLECULAR DYNAMICS SIMULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610005980] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Upon receiving an apoptotic stimulus, the mature mitochondrial protein second mitochondria-derived activator of caspases (Smac)/direct IAP-binding protein with low PI (DIABLO), which could be released from mitochondria into the cytosol together with cytochrome C , specifically binds to inhibitor of apoptosis proteins (IAPs) and relieves the inhibitory effect of caspase, thus promotes cell death. Some artificial small molecules (called Smac mimetics) can mimic the N-terminal four residues Ala1-Val2-Pro3-Ile4 (AVPI) sequence of mitochondrial protein Smac, and competitively bind to X-linked inhibitor of apoptosis protein baculoviral IAP repeats (XIAP-BIR3) domain with caspase-9, which leads to the removal of the inhibition of caspase-9 by XIAP and induce apoptosis. To gain an insight into the nature of XIAP-BIR3 domain recognizing Smac mimetics, we used docking and molecular dynamics simulations methods to study four representative Smac mimetics. The docking results show that the orientations of these backbones of ligands are identical with that of AVPI in the binding pocket. Each ligand corresponds to two competitive conformations, which are called extended and bended conformations. The results of molecular dynamics simulations show that the extended conformation is more stable, and the calculations of energy decomposition reveal that the residue Thr308 makes the strongest interaction with XIAP-BIR3. In addition, Asp309, Glu314, and Trp323 are indispensable for XIAP-BIR3 recognizing and binding Smac mimetics.
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Affiliation(s)
- BAOPING LING
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
| | - RUI ZHANG
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, P. R. China
| | - ZHIGUO WANG
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, P. R. China
| | - YONGJUN LIU
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, P. R. China
| | - CHENGBU LIU
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
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16
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Transient pockets on XIAP-BIR2: toward the characterization of putative binding sites of small-molecule XIAP inhibitors. J Mol Model 2011; 18:2031-42. [DOI: 10.1007/s00894-011-1217-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 08/09/2011] [Indexed: 10/17/2022]
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17
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Monfardini I, Huang JW, Beck B, Cellitti JF, Pellecchia M, Dömling A. Screening Multicomponent Reactions for X-Linked Inhibitor of Apoptosis-Baculoviral Inhibitor of Apoptosis Protein Repeats Domain Binder. J Med Chem 2011; 54:890-900. [DOI: 10.1021/jm101341m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ilaria Monfardini
- University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Jui-Wen Huang
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Barbara Beck
- University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Jason F. Cellitti
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maurizio Pellecchia
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alexander Dömling
- University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
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18
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Andersson IE, Batsalova T, Dzhambazov B, Edvinsson L, Holmdahl R, Kihlberg J, Linusson A. Oxazole-modified glycopeptides that target arthritis-associated class II MHC A(q) and DR4 proteins. Org Biomol Chem 2010; 8:2931-40. [PMID: 20485848 DOI: 10.1039/c003640d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The glycopeptide CII259-273, a fragment from type II collagen (CII), can induce tolerance in mice susceptible to collagen-induced arthritis (CIA), which is a validated disease model for rheumatoid arthritis (RA). Here, we describe the design and synthesis of a small series of modified CII259-273 glycopeptides with oxazole heterocycles replacing three potentially labile peptide bonds. These glycopeptidomimetics were evaluated for binding to murine CIA-associated A(q) and human RA-associated DR4 class II major histocompatibility complex (MHC) proteins. The oxazole modifications drastically reduced or completely abolished binding to A(q). Two of the glycopeptidomimetics were, however, well tolerated in binding to DR4 and they also induced strong responses by one or two DR4-restricted T-cell hybridomas. This work contributes to the development of an altered glycopeptide for inducing immunological tolerance in CIA, with the long-term goal of developing a therapeutic vaccine for treatment of RA.
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Affiliation(s)
- Ida E Andersson
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
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19
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Abstract
The recent discovery of Smac and the elucidation of its structure and function have led to the rapid development of Smac mimetics, comprising Smac derivative and mimicking molecules, for use in cancer treatment. Smac is an endogenous proapoptotic protein that resides in the mitochondria and is released when a cell is triggered to undergo programmed cell death. One of the mechanisms by which Smac promotes apoptosis is through its ability to inhibit inhibitors of apoptosis (IAPs), by direct inhibition and/or proteasomal degradation of some members of the IAP family, and therefore disinhibit caspases. Thus, the use of Smac mimetics as anticancer agents follows a rational approach in cancer therapeutics. This approach directly targets dysregulated, neoplastic cells that overexpress IAPs or underexpress Smac. Although Smac mimetics are able to elicit an anticancer response when used alone, these molecules can also function effectively and synergistically when combined with other therapeutic agents. A variety of Smac mimetic types comprising peptides, polynucleotides, and compounds have been studied both in vitro and in vivo. This discussion addresses the current status of Smac mimetics in cancer research.
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Crisóstomo FRP, Feng Y, Zhu X, Welsh K, An J, Reed JC, Huang Z. Design and synthesis of a simplified inhibitor for XIAP-BIR3 domain. Bioorg Med Chem Lett 2009; 19:6413-8. [PMID: 19819692 DOI: 10.1016/j.bmcl.2009.09.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 09/04/2009] [Accepted: 09/14/2009] [Indexed: 11/28/2022]
Abstract
Based on tetrapeptide AVPI, we were able to design and synthesize a new simplified scaffold to inhibit the BIR3 domain of the XIAP protein at low micromolar range. The uncomplicated synthesis and the binding activity of the molecule disclosed here represent an attractive alternative to develop new compounds targeting the protein-protein interaction of XIAP/caspase9.
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21
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Structural Basis for Bivalent Smac-Mimetics Recognition in the IAP Protein Family. J Mol Biol 2009; 392:630-44. [DOI: 10.1016/j.jmb.2009.04.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 04/15/2009] [Accepted: 04/16/2009] [Indexed: 01/22/2023]
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Moore CD, Wu H, Bolaños B, Bergqvist S, Brooun A, Pauly T, Nowlin D. Structural and Biophysical Characterization of XIAP BIR3 G306E Mutant: Insights in Protein Dynamics and Application for Fragment-Based Drug Design. Chem Biol Drug Des 2009; 74:212-23. [DOI: 10.1111/j.1747-0285.2009.00862.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Cytotoxic approaches to killing tumor cells, such as chemotherapeutic agents, gamma-irradiation, suicide genes or immunotherapy, have been shown to induce cell death through apoptosis. The intrinsic apoptotic pathway is activated following treatment with cytotoxic drugs, and these reactions ultimately lead to the activation of caspases, which promote cell death in tumor cells. In addition, activation of the extrinsic apoptotic pathway with death-inducing ligands leads to an increased sensitivity of tumor cells toward cytotoxic stimuli, illustrating the interplay between the two cell death pathways. In contrast, tumor resistance to cytotoxic stimuli may be due to defects in apoptotic signaling. As a result of their importance in killing cancer cells, a number of apoptotic molecules are implicated in cancer therapy. The knowledge gleaned from basic research into apoptotic pathways from cell biological, structural, biochemical, and biophysical approaches can be used in strategies to develop novel compounds that eradicate tumor cells. In addition to current drug targets, research into molecules that activate procaspase-3 directly may show the direct activation of the executioner caspase to be a powerful therapeutic strategy in the treatment of many cancers.
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Affiliation(s)
- Sarah H. MacKenzie
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - A. Clay Clark
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
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