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Aslan A, Ari Yuka S. Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives. Amino Acids 2024; 56:37. [PMID: 38822212 PMCID: PMC11143054 DOI: 10.1007/s00726-024-03397-3] [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: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
Abstract
Many drug formulations containing small active molecules are used for the treatment of coronary artery disease, which affects a significant part of the world's population. However, the inadequate profile of these molecules in terms of therapeutic efficacy has led to the therapeutic use of protein and peptide-based biomolecules with superior properties, such as target-specific affinity and low immunogenicity, in critical diseases. Protein‒protein interactions, as a consequence of advances in molecular techniques with strategies involving the combined use of in silico methods, have enabled the design of therapeutic peptides to reach an advanced dimension. In particular, with the advantages provided by protein/peptide structural modeling, molecular docking for the study of their interactions, molecular dynamics simulations for their interactions under physiological conditions and machine learning techniques that can work in combination with all these, significant progress has been made in approaches to developing therapeutic peptides that can modulate the development and progression of coronary artery diseases. In this scope, this review discusses in silico methods for the development of peptide therapeutics for the treatment of coronary artery disease and strategies for identifying the molecular mechanisms that can be modulated by these designs and provides a comprehensive perspective for future studies.
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Affiliation(s)
- Ayca Aslan
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey
| | - Selcen Ari Yuka
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey.
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2
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Lin J, Wang S, Wen L, Ye H, Shang S, Li J, Shu J, Zhou P. Targeting peptide-mediated interactions in omics. Proteomics 2023; 23:e2200175. [PMID: 36461811 DOI: 10.1002/pmic.202200175] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Peptide-mediated interactions (PMIs) play a crucial role in cell signaling network, which are responsible for about half of cellular protein-protein associations in the human interactome and have recently been recognized as a new kind of promising druggable target for drug development and disease therapy. In this article, we give a systematic review regarding the proteome-wide discovery of PMIs and targeting druggable PMIs (dPMIs) with chemical drugs, self-inhibitory peptides (SIPs) and protein agents, particularly focusing on their implications and applications for therapeutic purpose in omics. We also introduce computational peptidology strategies used to model, analyze, and design PMI-targeted molecular entities and further extend the concepts of protein context, direct/indirect readout, and enthalpy/entropy effect involved in PMIs. Current issues and future perspective on this topic are discussed. There is still a long way to go before establishment of efficient therapeutic strategies to target PMIs on the omics scale.
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Affiliation(s)
- Jing Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Shaozhou Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Li Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Haiyang Ye
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Shuyong Shang
- Institute of Ecological Environment Protection, Chengdu Normal University, Chengdu, China
| | - Juelin Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Jianping Shu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
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Ford KM, Panwala R, Chen DH, Portell A, Palmer N, Mali P. Peptide-tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors. Cell Syst 2021; 12:716-732.e7. [PMID: 34051140 PMCID: PMC8298269 DOI: 10.1016/j.cels.2021.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 02/09/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Gene fragments derived from structural domains mediating physical interactions can modulate biological functions. Utilizing this, we developed lentiviral overexpression libraries of peptides comprehensively tiling high-confidence cancer driver genes. Toward inhibiting cancer growth, we assayed ~66,000 peptides, tiling 65 cancer drivers and 579 mutant alleles. Pooled fitness screens in two breast cancer cell lines revealed peptides, which selectively reduced cellular proliferation, implicating oncogenic protein domains important for cell fitness. Coupling of cell-penetrating motifs to these peptides enabled drug-like function, with peptides derived from EGFR and RAF1 inhibiting cell growth at IC50s of 27-63 μM. We anticipate that this peptide-tiling (PepTile) approach will enable rapid de novo mapping of bioactive protein domains and associated interfering peptides.
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Affiliation(s)
- Kyle M Ford
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Dai-Hua Chen
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Andrew Portell
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Nathan Palmer
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
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Yang K, Yang JQ, Luo SH, Mei WJ, Lin JY, Zhan JQ, Wang ZY. Synthesis of N-2(5H)-furanonyl sulfonyl hydrazone derivatives and their biological evaluation in vitro and in vivo activity against MCF-7 breast cancer cells. Bioorg Chem 2020; 107:104518. [PMID: 33303210 DOI: 10.1016/j.bioorg.2020.104518] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/23/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023]
Abstract
A series of (E)-N-2(5H)-furanonyl sulfonyl hydrazone derivatives have been rationally designed and efficiently synthesized by one-pot reaction with good yields for the first time. This green approach with wide substrate range and good selectivity can be achieved at room temperature in a short time in the presence of metal-free catalyst. The cytotoxic activities against three human cancer cell lines of all newly obtained compounds have been evaluated by MTT assay. Among them, compound 5 k exhibits high cytotoxic activity against MCF-7 human breast cancer cells with an IC50 value of 14.35 μM. The cytotoxic mechanism may involve G2/M phase arrest pathway, which is probably caused by activating DNA damage. Comet test and immunofluorescence results show that compound 5 k can induce DNA damage in time- and dose-dependent manner. Importantly, 5 k also can effectively inhibit the proliferation of MCF-7 cells and angiogenesis in the zebrafish xenograft model. It is potential to further develop N-2(5H)-furanonyl sulfonyl hydrazone derivatives as potent drugs for breast cancer treatment with higher cytotoxic activity by modifying the structure of the compound.
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Affiliation(s)
- Kai Yang
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou, Guangdong, 510006, PR China; College of Pharmacy, Gannan Medical University, Ganzhou, Jiangxi 341000, PR China
| | - Jian-Qiong Yang
- Department of Clinical Research Center, the First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, PR China
| | - Shi-He Luo
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou, Guangdong, 510006, PR China.
| | - Wen-Jie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, PR China.
| | - Jian-Yun Lin
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou, Guangdong, 510006, PR China
| | - Jia-Qi Zhan
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou, Guangdong, 510006, PR China
| | - Zhao-Yang Wang
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou, Guangdong, 510006, PR China.
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Ntarakas N, Ermilova I, Lyubartsev AP. Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:813-824. [PMID: 31655893 PMCID: PMC6853862 DOI: 10.1007/s00249-019-01407-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/02/2019] [Accepted: 10/13/2019] [Indexed: 12/05/2022]
Abstract
Aggregation of amyloid-\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β (Aβ) peptides, cleaved from the amyloid precursor protein, is known as a precursor of the Alzheimer’s disease (AD). It is also known that Alzheimer’s disease is characterized by a substantial decrease of the amount of polyunsaturated lipids in the neuronal membranes of the frontal gray matter. To get insight into possible interconnection of these phenomena, we have carried out molecular dynamics simulations of two fragments of A\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β peptide, A\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β\documentclass[12pt]{minimal}
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\begin{document}$$_{1-28}$$\end{document}1-28 and A\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β\documentclass[12pt]{minimal}
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\begin{document}$$_{26-40}$$\end{document}26-40, in four different lipid bilayers: two monocomponent ones (14:0-14:0 PC, 18:0-22:6 PC), and two bilayers containing mixtures of 18:0-18:0 PE, 22:6-22:6 PE, 16:0-16:0 PC and 18:1-18:1 PC lipids of composition mimicking neuronal membranes in a “healthy” and “AD” brain. The simulations showed that the presence of lipids with highly unsaturated 22:6cis fatty acids chains strongly affects the interaction of amyloid-\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β peptides with lipid membranes. The polyunsaturated lipids cause stronger adsorption of A\documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β-peptides by the membrane and lead to weaker binding between peptides when the latter form aggregates. This difference in the behaviour observed in monocomponent bilayers is propagated in a similar fashion to the mixed membranes mimicking composition of neuronal membranes in “healthy” and “AD” brains, with “healthy” membrane having higher fraction of polyunsaturated lipids. Our simulations give strong indication that it can be physical–chemical background of the interconnection between amyloid fibrillization causing Alzheimer’s disease, and content of polyunsaturated lipids in the neuronal membranes.
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Affiliation(s)
- Nikolaos Ntarakas
- Department of Materials and Environmental Chemistry, Stockholm's University, 10691, Stockholm, Sweden
| | - Inna Ermilova
- Department of Materials and Environmental Chemistry, Stockholm's University, 10691, Stockholm, Sweden
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm's University, 10691, Stockholm, Sweden.
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Zhu J, Wei S, Huang L, Zhao Q, Zhu H, Zhang A. Molecular modeling and rational design of hydrocarbon-stapled/halogenated helical peptides targeting CETP self-binding site: Therapeutic implication for atherosclerosis. J Mol Graph Model 2019; 94:107455. [PMID: 31586754 DOI: 10.1016/j.jmgm.2019.107455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/04/2019] [Accepted: 09/24/2019] [Indexed: 11/28/2022]
Abstract
The human plasma cholesteryl ester transfer protein (CETP) collects triglycerides from very-/low-density lipoproteins (V/LDL) and exchanges them for cholesteryl esters from high-density lipoproteins (HDL), which has recognized as an important therapeutic target for atherosclerosis. The protein has a C-terminal amphipathic α-helix that serves as self-binding peptide to fulfill biological function by dynamically binding to/unbinding from its cognate site (termed self-binding site) in the same protein. Previously, we successfully derived and halogenated the helical peptide to competitively disrupt the self-binding behavior of CETP C-terminal tail. However, the halogenated peptides have only a limited affinity increase as compared to native helical peptide (∼3-fold), thus exhibiting only a moderate competitive potency. Here, instead of optimizing the direct intermolecular interaction of peptide with CETP self-binding site we attempt to further improve the peptide competitive potency by reducing its conformational flexibility with hydrocarbon-stapling technique. Computational analysis reveals that the helical peptide has large intrinsic disorder in unbound free state, which would incur a considerable entropy penalty upon rebinding to the self-binding site. All-hydrocarbon bridge is designed and optimized on native and halogenated peptides in terms of the helical pattern and binding mode of self-binding peptide. Dynamics simulation and circular dichroism indicate that the stapling can considerably reduce peptide disorder in free state. Energetics calculation and fluorescence assay conform that the binding affinity of stapled/halogenated peptides is improved substantially (by > 5-fold), thus exhibiting an effective competition potency with native peptide for the self-binding site. Structural examination suggests that the binding modes and nonbonded interactions of native and halogenated peptides are not influenced essentially due to the stapling.
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Affiliation(s)
- Jian Zhu
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
| | - Sen Wei
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China.
| | - Linchen Huang
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
| | - Qi Zhao
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
| | - Haichao Zhu
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
| | - Anwei Zhang
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
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Ding X, Zheng RC, Tang XL, Zheng YG. Engineering of Talaromyces thermophilus lipase by altering its crevice-like binding site for highly efficient biocatalytic synthesis of chiral intermediate of Pregablin. Bioorg Chem 2018; 77:330-338. [DOI: 10.1016/j.bioorg.2018.01.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 02/02/2023]
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8
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The σ and π Holes. The Halogen and Tetrel Bondings: Their Nature, Importance and Chemical, Biological and Medicinal Implications. ChemistrySelect 2017. [DOI: 10.1002/slct.201701676] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Yu J, Wang S, Yu J, Liu C, Xu F, Wang S, Yi Y, Yin Y. Structure-based rational design of self-inhibitory peptides to disrupt the intermolecular interaction between the troponin subunits C and I in neuropathic pain. Bioorg Chem 2017; 73:10-15. [PMID: 28525735 DOI: 10.1016/j.bioorg.2017.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/08/2017] [Accepted: 05/01/2017] [Indexed: 11/26/2022]
Abstract
The troponin (Tn) is a ternary complex consisting of three subunits TnC, TnI and TnT; molecular disruption of the Tn complex has been recognized as an attractive strategy against neuropathic pain. Here, a self-inhibitory peptide is stripped from the switch region of TnI interaction interface with TnC, which is considered as a lead molecular entity and then used to generate potential peptide disruptors of TnC-TnI interaction based on a rational molecular design protocol. The region is a helical peptide segment capped by N- and C-terminal disorders. Molecular dynamics simulation and binding free energy analysis suggests that the switch peptide can interact with TnC in a structurally and energetically independent manner. Terminal truncation of the peptide results in a number of potent TnC binders with considerably simplified structure and moderately decreased activity relative to the native switch. We also employ fluorescence polarization assays to substantiate the computational findings; it is found that the rationally designed peptides exhibit moderate or high affinity to TnC with dissociation constants KD at micromolar level.
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Affiliation(s)
- Junmin Yu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Shilei Wang
- Department of Anesthesiology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Junjie Yu
- Chinese Traditional Patent Medicine Dispensary, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Chuansheng Liu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Fenghe Xu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Shijie Wang
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yusheng Yi
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yanwei Yin
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
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Dong C, Yan P, Wang J, Mu H, Wang S, Guo F. Rational identification of natural organic compounds to target the intermolecular interaction between Foxm and DNA in colorectal cancer. Bioorg Chem 2017; 70:12-16. [DOI: 10.1016/j.bioorg.2016.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 11/06/2016] [Accepted: 11/08/2016] [Indexed: 10/20/2022]
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Zhang YL, Han ZF. Rational design of an orthogonal noncovalent interaction system at the MUPP1 PDZ11 complex interface with CaMKIIα-derived peptides in human fertilization. MOLECULAR BIOSYSTEMS 2017; 13:2145-2151. [PMID: 28832060 DOI: 10.1039/c7mb00379j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An orthogonal noncovalent interaction (ONI) system between a native hydrogen bond and a designed halogen bond across the complex interface of the MUPP1 PDZ11 domain with the CaMKIIαsia[Asn-1Phe] peptide mutant is introduced using a structure-based rational approach.
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Affiliation(s)
- Yi-Le Zhang
- Reproductive Medical Center
- the First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
| | - Zhao-Feng Han
- Department of Burn and Reconstruction Surgery
- the First Affiliated Hospital of Zhengzhou University
- Zhengzhou 450052
- China
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