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Huang Q, Peng Y, Peng Y, Lin H, Deng S, Feng S, Wei Y. Design, in silico evaluation, and in vitro verification of new bivalent Smac mimetics with pro-apoptotic activity. Methods 2024; 224:35-46. [PMID: 38373678 DOI: 10.1016/j.ymeth.2024.02.004] [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: 09/04/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
Bivalent Smac mimetics have been shown to possess binding affinity and pro-apoptotic activity similar to or more potent than that of native Smac, a protein dimer able to neutralize the anti-apoptotic activity of an inhibitor of caspase enzymes, XIAP, which endows cancer cells with resistance to anticancer drugs. We design five new bivalent Smac mimetics, which are formed by various linkers tethering two diazabicyclic cores being the IAP binding motifs. We built in silico models of the five mimetics by the TwistDock workflow and evaluated their conformational tendency, which suggests that compound 3, whose linker is n-hexylene, possess the highest binding potency among the five. After synthesis of these compounds, their ability in tumour cell growth inhibition and apoptosis induction displayed in experiments with SK-OV-3 and MDA-MB-231 cancer cell lines confirms our prediction. Among the five mimetics, compound 3 displays promising pro-apoptotic activity and deserves further optimization.
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Affiliation(s)
- Qingsheng Huang
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; School of Mathematics and Statistics, Hanshan Normal University, Chaozhou 521041, China
| | - Yin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, China
| | - Yuefeng Peng
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huijuan Lin
- Department of Ultrasound, Guangdong Women and Children Hospital, Guangzhou 510000, China
| | - Shiqi Deng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, China
| | - Shengzhong Feng
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Yanjie Wei
- Shenzhen Key Laboratory of Intelligent Bioinformatics & Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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Zhu H, Li Y, Liu Y, Han B. Bivalent SMAC Mimetics for Treating Cancer by Antagonizing Inhibitor of Apoptosis Proteins. ChemMedChem 2019; 14:1951-1962. [DOI: 10.1002/cmdc.201900410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/10/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Hongping Zhu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of PharmacyChengdu University of Traditional Chinese Medicine 1166 Liutai Avenue Chengdu 611137 China
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Huaguan Road Chengdu 610052 China
| | - Yi Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Huaguan Road Chengdu 610052 China
| | - Yue Liu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Huaguan Road Chengdu 610052 China
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of PharmacyChengdu University of Traditional Chinese Medicine 1166 Liutai Avenue Chengdu 611137 China
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3
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Huang Q, Peng Y, Peng Y, Wei D, Wei Y, Feng S. The TwistDock workflow for evaluation of bivalent Smac mimetics targeting XIAP. DRUG DESIGN DEVELOPMENT AND THERAPY 2019; 13:1373-1388. [PMID: 31118573 PMCID: PMC6499140 DOI: 10.2147/dddt.s194276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/05/2019] [Indexed: 01/13/2023]
Abstract
Purpose: Mimetics based on Smac, the native inhibitor of XIAP, are promising drug-candidates for the treatment of cancer. Bivalent Smac mimetics inhibit XIAP with even higher potency than monovalent mimetics, but how to optimize the linker that tethers the two monovalent binding motifs remains controversial. Methods: To construct an ensemble of bivalent complex structures for evaluating various linkers, we propose herein a workflow, named TwistDock, consisting of steps of monovalent docking and linker twisting, in which the degrees of freedom are sampled focusing on the rotation of single bonds of the linker. Results: The obtained conformations of bivalent complex distribute randomly in the conformational space with respect to two reaction coordinates introduced by the linker, which are the distance of the two binding motifs and the dihedral angle of the two planes through the linker and each of the binding motifs. Molecular dynamics starting from 10 conformations with the lowest enthalpy of every complex shows that the conformational tendency of the complex participated by compound 9, one of the compounds with the largest binding affinity, is distinct from others. By umbrella sampling of the complex, we find its global minimum of the free energy landscape. The structure shows that the linker favors a compact conformation, and the two BIR domains of XIAP encompass the ligand on the opposite sides. Conclusion: TwistDock can be used in fine-tuning of bivalent ligands targeting XIAP and similar receptors dimerized or oligomerized.
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Affiliation(s)
- Qingsheng Huang
- Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology and Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, People's Republic of China
| | - Yin Peng
- Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yuefeng Peng
- Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology and Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, People's Republic of China.,Center for Drug Evaluation and Research (CDER), Food and Drug Administration (FDA), Silver Spring, MD 20903, USA
| | - Dan Wei
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Yanjie Wei
- Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology and Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, People's Republic of China
| | - Shengzhong Feng
- Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology and Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, People's Republic of China
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Targeting the BIR Domains of Inhibitor of Apoptosis (IAP) Proteins in Cancer Treatment. Comput Struct Biotechnol J 2019; 17:142-150. [PMID: 30766663 PMCID: PMC6360406 DOI: 10.1016/j.csbj.2019.01.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 01/07/2023] Open
Abstract
Inhibitor of apoptosis (IAP) proteins are characterized by the presence of the conserved baculoviral IAP repeat (BIR) domain that is involved in protein-protein interactions. IAPs were initially thought to be mainly responsible for caspase inhibition, acting as negative regulators of apoptosis, but later works have shown that IAPs also control a plethora of other different cellular pathways. As X-linked IAP (XIAP), and other IAP, levels are often deregulated in cancer cells and have been shown to correlate with patients' prognosis, several approaches have been pursued to inhibit their activity in order to restore apoptosis. Many small molecules have been designed to target the BIR domains, the vast majority being inspired by the N-terminal tetrapeptide of Second Mitochondria-derived Activator of Caspases/Direct IAp Binding with Low pI (Smac/Diablo), which is the natural XIAP antagonist. These compounds are therefore usually referred to as Smac mimetics (SMs). Despite the fact that SMs were intended to specifically target XIAP, it has been shown that they also interact with cellular IAP-1 (cIAP1) and cIAP2, promoting their proteasome-dependent degradation. SMs have been tested in combination with several cytotoxic compounds and are now considered promising immune modulators which can be exploited in cancer therapy, especially in combination with immune checkpoint inhibitors. In this review, we give an overview of the structural hot-spots of BIRs, focusing on their fold and on the peculiar structural patches which characterize the diverse BIRs. These structures are exploited/exploitable for the development of specific and active IAP inhibitors.
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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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Ardecky RJ, Welsh K, Finlay D, Lee PS, González-López M, Ganji SR, Ravanan P, Mace PD, Riedl SJ, Vuori K, Reed JC, Cosford NDP. Design, synthesis and evaluation of inhibitor of apoptosis protein (IAP) antagonists that are highly selective for the BIR2 domain of XIAP. Bioorg Med Chem Lett 2013; 23:4253-7. [PMID: 23743278 DOI: 10.1016/j.bmcl.2013.04.096] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/22/2013] [Accepted: 04/29/2013] [Indexed: 01/02/2023]
Abstract
We recently reported the systematic ligand-based rational design and synthesis of monovalent Smac mimetics that bind preferentially to the BIR2 domain of the anti-apoptotic protein XIAP. Expanded structure-activity relationship (SAR) studies around these peptidomimetics led to compounds with significantly improved selectivity (>60-fold) for the BIR2 domain versus the BIR3 domain of XIAP. The potent and highly selective IAP antagonist 8q (ML183) sensitized TRAIL-resistant prostate cancer cells to apoptotic cell death, highlighting the merit of this probe compound as a valuable tool to investigate the biology of XIAP.
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Affiliation(s)
- Robert J Ardecky
- Program in Apoptosis and Cell Death, NCI-Designated Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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Kluczyk A, Cydzik M, Biernat M, Bąchor R, Pasikowski P, Stefanowicz P, Artym J, Zimecki M, Szewczuk Z. Dimeric analogs of immunosuppressive decapeptide fragment of ubiquitin. J Pept Sci 2012; 18:456-65. [PMID: 22628071 DOI: 10.1002/psc.2416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/30/2012] [Accepted: 03/30/2012] [Indexed: 11/12/2022]
Abstract
Our previous studies revealed that ubiquitin and its decapeptide fragment with the LEDGRTLSDY sequence, located on the exposed molecule loop, strongly suppressed the immune response. This suggested that the loop may serve as a functional epitope of ubiquitin molecule and that a possible mechanism of biological action of the synthesized peptides is associated with interfering in interactions of ubiquitin with other molecules. Ubiquitin is known to exist in oligomeric forms, which can interact with various oligomeric receptors. We designed and synthesized new dimeric analogs of the ubiquitin fragment, to probe whether dimeric peptides may have higher affinity towards the ubiquitin receptors responsible for immunosuppression, which are believed to form oligomeric structures. Three dimerization strategies, N-terminus to N-terminus, C-terminus to C-terminus, and N-terminus to C-terminus (head-to-tail) via PEG derivatives were used to synthesize the dimeric peptides on solid support. In the course of our research, we developed a new and straightforward procedure of dimerization where α-amino groups of the C-terminal lysine residues of two peptide fragments were linked by PEG spacer directly on solid support. The effect of dimeric analogs on the immunological response was tested in the AFC in vitro experiment. The immunological tests showed that the head-to-tail dimerization caused a more profound increase in the biological activity than other tested dimerization methods. Our results suggest that such orientation of peptide components may correspond to orientation of the hypothetic ubiquitin receptors responsible for the immunomodulatory activity.
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Affiliation(s)
- Alicja Kluczyk
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland
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