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Wang Z, Fan F, Li Z, Ye F, Wang Q, Gao R, Qiu J, Lv Y, Lin M, Xu W, Luo C, Yu X. Structural insights into the functional mechanism of the ubiquitin ligase E6AP. Nat Commun 2024; 15:3531. [PMID: 38670961 PMCID: PMC11053172 DOI: 10.1038/s41467-024-47586-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
E6AP dysfunction is associated with Angelman syndrome and Autism spectrum disorder. Additionally, the host E6AP is hijacked by the high-risk HPV E6 to aberrantly ubiquitinate the tumor suppressor p53, which is linked with development of multiple types of cancer, including most cervical cancers. Here we show that E6AP and the E6AP/E6 complex exist, respectively, as a monomer and a dimer of the E6AP/E6 protomer. The short α1-helix of E6AP transforms into a longer helical structure when in complex with E6. The extended α1-helices of the dimer intersect symmetrically and contribute to the dimerization. The two protomers sway around the crossed region of the two α1-helices to promote the attachment and detachment of substrates to the catalytic C-lobe of E6AP, thus facilitating ubiquitin transfer. These findings, complemented by mutagenesis analysis, suggest that the α1-helix, through conformational transformations, controls the transition between the inactive monomer and the active dimer of E6AP.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Fengying Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihai Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Qingxia Wang
- Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Rongchao Gao
- Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiaxuan Qiu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixin Lv
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Min Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Wenwen Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528437, China.
- Department of Pharmacy, Guiyang University of Traditional Chinese Medicine, South Dong Qing Road, Huaxi District, Guizhou, 550025, China.
| | - Xuekui Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
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Zhou F, Li D, Hou Y, Cong Z, Li K, Gu X, Xiao G. Exploration of hypoglycemic peptides from porcine collagen based on network pharmacology and molecular docking. PLoS One 2024; 19:e0298674. [PMID: 38470866 DOI: 10.1371/journal.pone.0298674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/26/2024] [Indexed: 03/14/2024] Open
Abstract
In recent years, the extraction of hypoglycemic peptides from food proteins has gained increasing attention. Neuropeptides, hormone peptides, antimicrobial peptides, immune peptides, antioxidant peptides, hypoglycemic peptides and antihypertensive peptides have become research hotspots. In this study, bioinformatic methods were used to screen and predict the properties of pig collagen-derived hypoglycemic peptides, and their inhibitory effects on α-glucosidase were determined in vitro. Two peptides (RL and NWYR) were found to exhibit good water solubility, adequate ADMET (absorption, distribution, metabolism, elimination, and toxicity) properties, potentially high biological activity, and non-toxic. After synthesizing these peptides, NWYR showed the best inhibitory effect on α-glucosidase with IC50 = 0.200±0.040 mg/mL, and it can regulate a variety of biological processes, play a variety of molecular functions in different cellular components, and play a hypoglycemic role by participating in diabetic cardiomyopathy and IL-17 signaling pathway. Molecular docking results showed that NWYR had the best binding effect with the core target DPP4 (4n8d), with binding energy of -8.8 kcal/mol. NWYR mainly bonded with the target protein through hydrogen bonding, and bound with various amino acid residues such as Asp-729, Gln-731, Leu-765, etc., thus affecting the role of the target in each pathway. It is the best core target for adjuvant treatment of T2DM. In short, NWYR has the potential to reduce type 2 diabetes, providing a basis for further research or food applications as well as improved utilization of pig by-products. However, in subsequent studies, it is necessary to further verify the hypoglycemic ability of porcine collagen active peptide (NWYR), and explore the hypoglycemic mechanism of NWYR from multiple perspectives such as key target genes, protein expression levels and differences in metabolites in animal models of hyperglycemia, which will provide further theoretical support for its improvement in the treatment of T2DM.
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Affiliation(s)
- Fating Zhou
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Di Li
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Yakun Hou
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Zhihui Cong
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Kaifeng Li
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Xin Gu
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Guosheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
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Kumar YB, Kumar N, Vaikundamani S, Nagamani S, Mahanta HJ, Sastry GM, Sastry GN. Analyzing the aromatic-aromatic interactions in proteins: A 2ID 2.0. Int J Biol Macromol 2023; 253:127207. [PMID: 37797858 DOI: 10.1016/j.ijbiomac.2023.127207] [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: 06/30/2023] [Revised: 09/09/2023] [Accepted: 09/30/2023] [Indexed: 10/07/2023]
Abstract
The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (π-π) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a series of significant updates, leading to its current version, which focuses on the identification and analysis of 3,444,619 π-π networks from proteins. The geometrical parameters such as centroid-centroid distances (r) and interplanar angles (ϕ) were used to identify and characterize π-π networks. It was observed that among the 84,500 proteins with at least one aromatic π-π network, about 92.50 % of the instances are found to be either 2π (77.34 %) or 3π (15.23 %) networks. The analysis of interacting amino acid pairs in 2π networks indicated a dominance of PHE residues followed by TYR. The updated version of A2ID incorporates analysis of π-π networks based on SCOP2 and ECOD classifiers, in addition to the existing SCOP, CATH, and EC classifications. This expanded scope allows researchers to explore the characteristics and functional implications of π-π networks in protein structures from multiple perspectives. The current version of A2ID along with its extensive dataset and detailed geometric information is publicly accessible using https://acds.neist.res.in/a2idv2.
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Affiliation(s)
- Y Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - S Vaikundamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - G Madhavi Sastry
- Schrödinger Inc., HITEC City, Hyderabad, Telangana 500081, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India.
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Godinez J, Lee CY, Schwans JP. Synthesis and evaluation of Fmoc-amino esters and amides bearing a substrate like quaternary ammonium group as selective butyrylcholinesterase inhibitors. Bioorg Med Chem Lett 2023; 92:129392. [PMID: 37364726 DOI: 10.1016/j.bmcl.2023.129392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
The depletion of the neurotransmitter acetylcholine has been suggested to contribute to the reduced cognitive function observed in individuals suffering from neurodegenerative diseases such as Alzheimer's Disease (AD). For the two major cholinesterases, butyrylcholinesterase (BChE) and acetylcholinesterase (AChE), increased BChE activity observed in individuals with AD has been suggested to deplete acetylcholine levels. To reduce acetylcholine degradation and help restore the pool of the neurotransmitter, specific and potent BChE inhibitors are sought. Our previous findings have identified 9-fluorenylmethoxycarbonyl (Fmoc) amino acid-based inhibitors as effective BChE inhibitors. The amino acid-based compounds offered the opportunity to survey a range of structural features to enhance interactions with the enzyme active site. As enzymes interact with features of their substrates, incorporation of substrate-like features was predicted to lead to better inhibitors. Specifically, incorporation of a trimethylammonium moiety to mimic the cationic group of acetylcholine may lead to increased potency and selectivity. To test this model, a series of inhibitors bearing a cationic trimethylammonium group were synthesized, purified, and characterized. While the Fmoc-ester derivatives inhibited the enzyme, additional experiments showed the compounds acted as substrates and were enzymatically hydrolyzed. Inhibition studies with the Fmoc-amide derivatives showed that the compounds do not act as substrates and selectively inhibit BChE with IC50 values in the 0.06-10.0 µM range. Computational docking studies suggest that the inhibitors can interact with cholinyl binding site and peripheral site. Overall, the results suggest that introducing substrate-like characteristics within the Fmoc-amino acid-based background increases their potency. The versatile and ready access to amino acid-based compounds offers an attractive system to further our understanding of the relative importance of protein-small molecule interactions while guiding the development of better inhibitors.
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Affiliation(s)
- Jonathan Godinez
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840-9507, United States
| | - Catherine Y Lee
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840-9507, United States
| | - Jason P Schwans
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840-9507, United States.
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5
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Rosokha SV. Anion-π Interactions: What's in the Name? Chempluschem 2023; 88:e202300350. [PMID: 37526504 DOI: 10.1002/cplu.202300350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/02/2023]
Abstract
The studies of the anion-π interactions advanced during the last two decades from the discussion of the mere existence of this counter-intuitive bonding to its utilization for anion recognition and transport, catalysis, and other applications. Yet, there are substantial differences in the interpretation of nature and the driving forces of anion-π bonding. Most surprisingly, there are still different opinions about the meaning of this term (i. e., which associations can be considered anion-π complexes). After a brief overview of the studies in this area (including early examples of such complexes), we suggested that anion-π bonding occurs when there is evidence of a net attraction between a (close-shell) anion and the face of an electrophilic π-system. This definition encompasses fundamentally similar supramolecular complexes comprising diverse π-systems and anions and its general acceptance would facilitate a discussion of the nature and distinct driving forces of this fascinating interaction.
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Affiliation(s)
- Sergiy V Rosokha
- Chemistry Department, Ball State University, Muncie, IN 47306, USA
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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Chawla M, Kalra K, Cao Z, Cavallo L, Oliva R. Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules. Nucleic Acids Res 2022; 50:11455-11469. [PMID: 36416268 PMCID: PMC9723503 DOI: 10.1093/nar/gkac1081] [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: 05/13/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol-1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP-uracil and OP-guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.
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Affiliation(s)
- Mohit Chawla
- Correspondence may also be addressed to Mohit Chawla. ;
| | - Kanav Kalra
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Zhen Cao
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Correspondence may also be addressed to Luigi Cavallo. Tel: +966 02 8027566; Fax: +966 02 8021347;
| | - Romina Oliva
- To whom correspondence should be addressed. Tel: +39 081 5476541; Fax: +39 081 5476514;
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Hosseini-Hashemi Z, Eslami Moghadam M, Mirzaei M, Notash B. Biological Activity of Two Anticancer Pt Complexes with a Cyclohexylglycine Ligand against a Colon Cancer Cell Line: Theoretical and Experimental Study. ACS OMEGA 2022; 7:39794-39811. [PMID: 36385884 PMCID: PMC9648137 DOI: 10.1021/acsomega.2c03776] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/26/2022] [Indexed: 05/30/2023]
Abstract
Because of their extraordinary ability to disrupt the natural structure of nucleic acids, metal complexes could be used in cancer therapy. In this study, cyclohexylglycine (HL) as a ligand and two new Pt complexes, [Pt(NH3)2(L)]NO3 (1) and [Pt(bipy)(L)]NO3 (2), were synthesized and characterized by elemental analysis, LC-MS, UV-vis spectrometry, FT-IR, 1H NMR spectroscopy, 13C NMR spectroscopy, 195Pt NMR spectroscopy, HPLC analysis, and single-crystal X-ray diffraction. Complex 2 crystallized in the orthorhombic Pbca space group, and density functional theory (DFT) was used to describe its structural parameters were described in detail. These complexes can be classified as oral medications and drug-like molecules based on a comparison of their absorption, distribution, metabolism, and excretion assessment. Quantum chemical descriptors (QCDs) were determined using DFT calculations to predict the tendency of DNA to approach these complexes. During the determination of the function of the metallodrug in DNA binding, the fluorescence data indicated that static quenching took place for all ligands and complexes with higher DNA binding affinity. CD and isothermal absorption studies indicate the presence of electrostatic and groove binding for the amine derivative and that DNA binds with the bipy moiety via groove binding. Furthermore, the interaction modes were determined using molecular docking to investigate the binding of these compounds with the target DNA molecule. According to docking investigations, binding energies of -5.7, -11.56, and -10.00 kcal/mol for HL and complexes 1 and 2, respectively, indicate partially electrostatic and groove binding. The anticancer activities of the Pt(II) complexes were tested against the HCT116 human colon cancer cell line, with IC50 values of 35.51 and 51.33 μM for 1 and 2, respectively, after 72 h. These values show that the inhibitory effect of complex 1 was better than those of 2 and carboplatin (IC50 = 51.94 μM).
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Affiliation(s)
- Zahra Hosseini-Hashemi
- Department
of Chemistry, Faculty of Science, Ferdowsi
University of Mashhad, Mashhad, Razavi Khorasan9177948974, Iran
| | | | - Masoud Mirzaei
- Department
of Chemistry, Faculty of Science, Ferdowsi
University of Mashhad, Mashhad, Razavi Khorasan9177948974, Iran
- Khorasan
Science and Technology Park (KSTP), 12th km of Mashhad-Quchan Road, Mashhad, Razavi Khorasan9185173911, Iran
| | - Behrouz Notash
- Department
of Inorganic Chemistry and Catalysis, Shahid
Beheshti University, Tehran, Tehran1983969411, Iran
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