1
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Butterfield ER, Obado SO, Scutts SR, Zhang W, Chait BT, Rout MP, Field MC. A lineage-specific protein network at the trypanosome nuclear envelope. Nucleus 2024; 15:2310452. [PMID: 38605598 PMCID: PMC11018031 DOI: 10.1080/19491034.2024.2310452] [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: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
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Affiliation(s)
| | - Samson O. Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Simon R. Scutts
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
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2
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Wang X, Gao X, Fan X, Huai Z, Zhang G, Yao M, Wang T, Huang X, Lai L. WUREN: Whole-modal union representation for epitope prediction. Comput Struct Biotechnol J 2024; 23:2122-2131. [PMID: 38817963 PMCID: PMC11137340 DOI: 10.1016/j.csbj.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
B-cell epitope identification plays a vital role in the development of vaccines, therapies, and diagnostic tools. Currently, molecular docking tools in B-cell epitope prediction are heavily influenced by empirical parameters and require significant computational resources, rendering a great challenge to meet large-scale prediction demands. When predicting epitopes from antigen-antibody complex, current artificial intelligence algorithms cannot accurately implement the prediction due to insufficient protein feature representations, indicating novel algorithm is desperately needed for efficient protein information extraction. In this paper, we introduce a multimodal model called WUREN (Whole-modal Union Representation for Epitope predictioN), which effectively combines sequence, graph, and structural features. It achieved AUC-PR scores of 0.213 and 0.193 on the solved structures and AlphaFold-generated structures, respectively, for the independent test proteins selected from DiscoTope3 benchmark. Our findings indicate that WUREN is an efficient feature extraction model for protein complexes, with the generalizable application potential in the development of protein-based drugs. Moreover, the streamlined framework of WUREN could be readily extended to model similar biomolecules, such as nucleic acids, carbohydrates, and lipids.
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Affiliation(s)
| | | | - Xuezhe Fan
- XtalPi Innovation Center, Beijing, China
| | - Zhe Huai
- XtalPi Innovation Center, Beijing, China
| | | | | | | | | | - Lipeng Lai
- XtalPi Innovation Center, Beijing, China
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3
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Voziyan P, Brown KL, Uppuganti S, Leser M, Rose KL, Nyman JS. A map of glycation and glycoxidation sites in collagen I of human cortical bone: Effects of sex and type 2 diabetes. Bone 2024; 187:117209. [PMID: 39047900 DOI: 10.1016/j.bone.2024.117209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
Complications of diabetes is a major health problem affecting multiple organs including bone, where the chronic disease increases the risk of fragility fractures. One hypothesis suggests a pathogenic role for hyperglycemia-induced modification of proteins, a.k.a. advanced glycation end products (AGEs), resulting in structural and functional damage to bone extracellular matrix (ECM). Evidence supporting this hypothesis has been limited by the lack of comprehensive information about the location of AGEs that accumulate in vivo at specific sites within the proteins of bone ECM. Analyzing extracts from cortical bone of cadaveric femurs by liquid chromatography tandem mass spectrometry, we generated a quantitative AGE map of human collagen I for male and female adult donors with and without diabetes. The map describes the chemical nature, sequence position, and levels of four major physiological AGEs, e.g. carboxymethyllysine, and an AGE precursor fructosyllysine within the collagen I triple-helical region. The important features of the map are: 1) high map reproducibility in the individual bone extracts, i.e. 20 male and 20 female donors; 2) localization of modifications to distinct clusters: 10 clusters containing 34 AGE sites in male donors and 9 clusters containing 28 sites in female donors; 3) significant increases in modification levels in diabetes at multiple sites: 26 out of 34 sites in males and in 17 out of 28 sites in females; and 4) generally higher modification levels in male vs. female donors. Moreover, the AGE levels at multiple individual sites correlated with total bone pentosidine levels in male but not in female donors. Molecular dynamics simulations and molecular modeling predicted significant impact of modifications on solvent exposure, charge distribution, and hydrophobicity of the triple helix as well as disruptions to the structure of collagen I fibril. In summary, the AGE map of collagen I revealed diabetes-induced, sex-specific non-enzymatic modifications at distinct triple helical sites that can disrupt collagen structure, thus proposing a specific mechanism of AGE contribution to diabetic complications in human bone.
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Affiliation(s)
- Paul Voziyan
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
| | - Kyle L Brown
- Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Sasidhar Uppuganti
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Micheal Leser
- Department of Biochemistry and Proteomics Core, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Kristie Lindsey Rose
- Department of Biochemistry and Proteomics Core, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffry S Nyman
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA.
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4
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Samantaray M, Pattabiraman R, Murthy TPK, Ramaswamy A, Murahari M, Krishna S, Kumar SB. Structure-based virtual screening of natural compounds against wild and mutant (R1155K, A1156T and D1168A) NS3-4A protease of Hepatitis C virus. J Biomol Struct Dyn 2024; 42:8505-8522. [PMID: 37646701 DOI: 10.1080/07391102.2023.2246583] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
NS3-4A, a serine protease, is a primary target for drug development against Hepatitis C Virus (HCV). However, the effectiveness of potent next-generation protease inhibitors is limited by the emergence of mutations and resulting drug resistance. To address this, in this study a structure-based drug design approach is employed to screen a large library of 7320 natural compounds against both wild-type and mutant variants of NS3-4A protease. Telaprevir, a widely used protease inhibitor, was recruited as the control drug. The top 10 compounds with favorable binding affinities underwent drug-likeness evaluation. Based on ADMET studies, complexes of NP_024762 and NP_006776 were selected for molecular dynamic simulations. Principal component analysis (PCA) was employed to explore the conformational space and protein dynamics of the protein-ligand complex using a Free Energy Landscape (FEL) approach. The cosine values obtained from FEL analysis ranged from 0 to 1, and eigenvectors with cosine values below 0.2 were chosen for further analysis. To forecast binding free energies and evaluate energy contributions per residue, the MM-PBSA method was employed. The results highlighted the crucial role of amino acids in the catalytic domain for the binding of the protease with phytochemicals. Stable associations between the top compounds and the target protease were confirmed by the formation of hydrogen bonds in the binding pocket involving residues: His1057, Gly1137, Ser1139, and Ala1157. These findings suggest the potential of these compounds for further validation through biological evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahesh Samantaray
- Department of Bioinformatics, Pondicherry University, Pondicherry, India
| | - Ramya Pattabiraman
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - T P Krishna Murthy
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Amutha Ramaswamy
- Department of Bioinformatics, Pondicherry University, Pondicherry, India
| | - Manikanta Murahari
- Department of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Swati Krishna
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - S Birendra Kumar
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, Karnataka, India
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5
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Ojha MD, Yadav A, Kongkham B, Prabhakaran D, Gholap S, Kumar V, Inampudi KK, Hariprasad P. Polyphasic approaches to identify and understand α-glucosidase inhibitory potential of secondary metabolites of Withania coagulans fruit. Int J Biol Macromol 2024; 280:135718. [PMID: 39293614 DOI: 10.1016/j.ijbiomac.2024.135718] [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: 04/18/2024] [Revised: 09/12/2024] [Accepted: 09/14/2024] [Indexed: 09/20/2024]
Abstract
Withania coagulans (WC) is used in traditional and Ayurveda medicine to treat various ailments, including diabetes. Our investigation found that WC fruit hexane extract effectively suppresses α-glucosidase activity (IC50 = 0.013 mg/ml, Ki = 0.012 mg/ml). The purified molecule has an IC50 of 0.004 mg/ml and Ki of 0.0037 mg/ml. FTIR examination indicates distinctive peaks at 3500, 2900, 1770, and 1500 cm-1 corresponding to functional groups OH bending, CH stretching, CO stretching, and CO stretching. GCMS analysis reveals plant secondary metabolites (PSM) such as n-hexadecenoic acid and methyl 9,10-octadecadienoate. NMR confirms the existence of olefinic fatty acids. The bioactive fraction recorded a non-competitive mode of inhibition of α-glucosidase activity. The cytotoxicity exhibited against HELA cell was IC50 0.4 mg/ml and found positive in inhibiting the growth of Bacillus cereus, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Pseudomonas aeruginosa. Additionally, ensemble docking and molecular dynamic simulation showed that, out of the four PSMs examined, methyl 12,13-tetradecadienoate interacted with the α-glucosidase enzyme's allosteric site (BE -128.78 kJ/mol) and changed the configurations of the catalytic sites, as demonstrated by the enzyme's decreased affinity for isomaltose. The study found that PSMs from WC fruit may inhibit α-glucosidase, making them viable candidates for antidiabetic medication development.
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Affiliation(s)
- Monu Dinesh Ojha
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Ajay Yadav
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Bhani Kongkham
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Duraivadivel Prabhakaran
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shivajirao Gholap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Vikas Kumar
- Department of Biophysics, All Indian Institute of Medical Science, New Delhi 110016, India
| | - Krishna K Inampudi
- Department of Biophysics, All Indian Institute of Medical Science, New Delhi 110016, India
| | - P Hariprasad
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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6
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Yang P, Wang W, Hu Y, Wang Y, Xu Z, Liao X. Exploring high hydrostatic pressure effects on anthocyanin binding to serum albumin and food-derived transferrins. Food Chem 2024; 452:139544. [PMID: 38723571 DOI: 10.1016/j.foodchem.2024.139544] [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: 02/18/2024] [Revised: 04/20/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
This study investigated the effects of high hydrostatic pressure (HHP) on the binding interactions of cyanindin-3-O-glucoside (C3G) to bovine serum albumin, human serum albumin (HSA), bovine lactoferrin, and ovotransferrin. Fluorescence quenching revealed that HHP reduced C3G-binding affinity to HSA, while having a largely unaffected role for the other proteins. Notably, pretreating HSA at 500 MPa significantly increased its dissociation constant with C3G from 24.7 to 34.3 μM. Spectroscopic techniques suggested that HSA underwent relatively pronounced tertiary structural alterations after HHP treatments. The C3G-HSA binding mechanisms under pressure were further analyzed through molecular dynamics simulation. The localized structural changes in HSA under pressure might weaken its interaction with C3G, particularly polar interactions such as hydrogen bonds and electrostatic forces, consequently leading to a decreased binding affinity. Overall, the importance of pressure-induced structural alterations in proteins influencing their binding with anthocyanins was highlighted, contributing to optimizing HHP processing for anthocyanin-based products.
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Affiliation(s)
- Peiqing Yang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Wenxin Wang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yichen Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China.
| | - Yongtao Wang
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Zhenzhen Xu
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaojun Liao
- Beijing Key Laboratory for Food Non-thermal processing, Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Fruit & Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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7
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Franco Cairo JPL, Almeida DV, Andrade VB, Terrasan CRF, Telfer A, Gonçalves TA, Diaz DE, Figueiredo FL, Brenelli LB, Walton PH, Damasio A, Garcia W, Squina FM. Biochemical and structural insights of a recombinant AA16 LPMO from the marine and sponge-symbiont Peniophora sp. Int J Biol Macromol 2024; 280:135596. [PMID: 39276894 DOI: 10.1016/j.ijbiomac.2024.135596] [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: 07/13/2024] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that oxidize polysaccharides, leading to their cleavage. LPMOs are classified into eight CAZy families (AA9-11, AA13-17), with the functionality of AA16 being poorly characterized. This study presents biochemical and structural data for an AA16 LPMO (PnAA16) from the marine sponge symbiont Peniophora sp. Phylogenetic analysis revealed that PnAA16 clusters separately from previously characterized AA16s. However, the structural modelling of PnAA16 showed the characteristic immunoglobulin-like fold of LPMOs, with a conserved his-brace motif coordinating a copper ion. The copper-bound PnAA16 showed greater thermal stability than its apo-form, highlighting copper's role in enzyme stability. Functionally, PnAA16 demonstrated oxidase activity, producing 5 μM H₂O₂ after 30 min, but showed 20 times lower peroxidase activity (0.27 U/g) compared to a fungal AA9. Specific activity assays indicated that PnAA16 acts only on cellohexaose, generating native celloligosaccharides (C3 to C5) and oxidized products with regioselective oxidation at C1 and C4 positions. Finally, PnAA16 boosted the activity of a cellulolytic cocktail for cellulose saccharification in the presence of ascorbic acid, hydrogen peroxide, or both. In conclusion, the present work provides insights into the AA16 family, expanding the understanding of their structural and functional relationships and biotechnological potential.
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Affiliation(s)
- João Paulo L Franco Cairo
- Laboratório de Ciências Moleculares (LACIMO), Universidade de Sorocaba (UNISO), Sorocaba, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil; Department of Chemistry, University of York, York, United Kingdom
| | - Dnane V Almeida
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Viviane B Andrade
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - César R F Terrasan
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Abbey Telfer
- Department of Chemistry, University of York, York, United Kingdom
| | - Thiago A Gonçalves
- Laboratório de Ciências Moleculares (LACIMO), Universidade de Sorocaba (UNISO), Sorocaba, Brazil
| | - Daniel E Diaz
- Department of Chemistry, University of York, York, United Kingdom
| | - Fernanda L Figueiredo
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Livia B Brenelli
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Paul H Walton
- Department of Chemistry, University of York, York, United Kingdom
| | - André Damasio
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fabio M Squina
- Laboratório de Ciências Moleculares (LACIMO), Universidade de Sorocaba (UNISO), Sorocaba, Brazil.
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8
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Tirehdast A, Sheikhi-Mohammareh S, Sabet-Sarvestani H, Organ MG, Semeniuchenko V, Shiri A. Design and synthesis of novel main protease inhibitors of COVID-19: quinoxalino[2,1- b]quinazolin-12-ones. RSC Adv 2024; 14:29122-29133. [PMID: 39282064 PMCID: PMC11393744 DOI: 10.1039/d4ra06025c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 09/05/2024] [Indexed: 09/18/2024] Open
Abstract
The COVID-19 pandemic represents a substantial global challenge, being a significant cause of mortality in numerous countries. Thus, it is imperative to conduct research to develop effective therapies to combat COVID-19. The primary aim of this study is to employ a two-step tandem reaction involving 2,3-dichloroquinoxaline and 2-amino-N-substituted benzamides in alkaline media/DMF at an elevated temperature to design and synthesize a series of polycyclic derivatives endowed with quinoxalino[2,1-b]quinazolin-12-one framework. Following synthesis, the newly synthesized heterocycles were evaluated for their potential as inhibitors of the main protease of SARS-CoV-2 by means of molecular docking and dynamic simulation techniques. The in silico investigation demonstrated that all tested compounds effectively establish stable binding interactions, primarily through multiple hydrogen bonding and hydrophobic interactions, at the active site of the enzyme. These findings offer crucial structural insights that can be employed in future endeavors toward designing potent inhibitors targeting the main protease (Mpro). Among the investigated compounds, the p-tolylamino-substituted quinoxalino[2,1-b]quinazolinone derivative exhibited the most promise as an inhibitor of the main protease in COVID-19. Consequently, it warrants further investigation both in vitro and in vivo to identify it as a prospective candidate for anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Atefeh Tirehdast
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad Mashhad Iran
| | | | | | - Michael G Organ
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa Ottawa Canada
| | - Volodymyr Semeniuchenko
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa Ottawa Canada
| | - Ali Shiri
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad Mashhad Iran
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9
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Natarajan V, Satalkar V, Gumbart JC, Torres M. Molecular Dynamics Reveals Altered Interactions between Belzutifan and HIF-2 with Natural Variant G323E or Proximal Phosphorylation at T324. ACS OMEGA 2024; 9:37843-37855. [PMID: 39281922 PMCID: PMC11391435 DOI: 10.1021/acsomega.4c03777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/11/2024] [Accepted: 08/16/2024] [Indexed: 09/18/2024]
Abstract
In patients with von-Hippel Lindau (VHL) disease, hypoxia-independent accumulation of HIF-2α leads to increased transcriptional activity of HIF-2α:ARNT that drives cancers such as renal cell carcinoma. Belzutifan, a recently FDA-approved drug, is designed to prevent the transcriptional activity of HIF-2α:ARNT, thereby overcoming the consequences of its unnatural accumulation in VHL-dependent cancers. Emerging evidence suggests that the naturally occurring variant G323E located in the HIF-2α drug binding pocket prevents inhibitory activity of belzutifan analogs, though the mechanism of inhibition remains unclear. Interestingly, proximal phosphorylation at neighboring T324, previously shown to regulate HIF-2 protein interactions, has also been proposed to affect HIF-2 drug binding. Here, we used molecular dynamics (MD) simulations to understand and compare the molecular-level effects of G323E and phospho-T324 (pT324) on the belzutifan bound-HIF-2α:ARNT complex. We find that both G323E and pT324 increase structural flexibility within the drug binding site and reduce the apparent binding affinity for belzutifan. Whereas the effects of G323E are concentrated in the binding pocket Fα helix within the HIF-2α PAS-B domain, pT324 decreased the belzutifan binding affinity and stabilized the HIF-2 heterodimer through an alternate mechanism involving polar interactions between the HIF-2α PAS-B and PAS-A domains. Further analysis via ensemble machine learning uncovered important and distinct interchain residue interactions modified by G323E and pT324. These findings reveal a molecular mechanism of G323E-induced drug resistance and suggest that pT324 may also affect the efficacy of HIF-2 drug binding interactions via allosteric effects.
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Affiliation(s)
- Vishva Natarajan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vardhan Satalkar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Matthew Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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10
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Parashara P, Medina-Pritchard B, Abad MA, Sotelo-Parrilla P, Thamkachy R, Grundei D, Zou J, Spanos C, Kumar CN, Basquin C, Das V, Yan Z, Al-Murtadha AA, Kelly DA, McHugh T, Imhof A, Rappsilber J, Jeyaprakash AA. PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance. Science 2024; 385:1098-1104. [PMID: 39236175 DOI: 10.1126/science.ado8270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/30/2024] [Indexed: 09/07/2024]
Abstract
Accurate chromosome segregation requires the attachment of microtubules to centromeres, epigenetically defined by the enrichment of CENP-A nucleosomes. During DNA replication, CENP-A nucleosomes undergo dilution. To preserve centromere identity, correct amounts of CENP-A must be restored in a cell cycle-controlled manner orchestrated by the Mis18 complex (Mis18α-Mis18β-Mis18BP1). We demonstrate here that PLK1 interacts with the Mis18 complex by recognizing self-primed phosphorylations of Mis18α (Ser54) and Mis18BP1 (Thr78 and Ser93) through its Polo-box domain. Disrupting these phosphorylations perturbed both centromere recruitment of the CENP-A chaperone HJURP and new CENP-A loading. Biochemical and functional analyses showed that phosphorylation of Mis18α and PLK1 binding were required to activate Mis18α-Mis18β and promote Mis18 complex-HJURP interaction. Thus, our study reveals key molecular events underpinning the licensing role of PLK1 in ensuring accurate centromere inheritance.
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Affiliation(s)
- Pragya Parashara
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Maria Alba Abad
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Reshma Thamkachy
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - David Grundei
- Gene Center Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Juan Zou
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chandni Natalia Kumar
- Protein Analysis Unit, Biomedical Centre Munich, Faculty of Medicine, Ludwig-Maximilians-University, 82152 Munich, Germany
| | - Claire Basquin
- Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Vimal Das
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Zhaoyue Yan
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - David A Kelly
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Toni McHugh
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Axel Imhof
- Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
- Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - A Arockia Jeyaprakash
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
- Gene Center Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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11
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Zhang J, Fan X, Wang P, Liang R, Wang D, Xu J, Zhang D, Xie Y, Liao Q, Jiao Z, Shi Y, Peng G. Identification of novel broad-spectrum antiviral drugs targeting the N-terminal domain of the FIPV nucleocapsid protein. Int J Biol Macromol 2024; 279:135352. [PMID: 39242012 DOI: 10.1016/j.ijbiomac.2024.135352] [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: 06/13/2024] [Revised: 08/25/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Coronaviruses pose serious threats to human and animal health worldwide, of which their structural nucleocapsid (N) proteins play multiple key roles in viral replication. However, the structures of animal coronavirus N proteins are poorly understood, posing challenges for research on their functions and pathogenic mechanisms as well as the development of N protein-based antiviral drugs. Therefore, N proteins must be further explored as potential antiviral targets. We determined the structure of the NNTD of feline infectious peritonitis virus (FIPV) and identified 3,6-dihydroxyflavone (3,6- DHF) as an effective N protein inhibitor. 3,6-DHF successfully inhibited FIPV replication in CRFK cells, showing broad-spectrum activity and effectiveness against drugresistant strains. Our study provides important insights for developing novel broadspectrum anti-coronavirus drugs and treating infections caused by drug-resistant mutant strains.
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Affiliation(s)
- Jintao Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Xinyu Fan
- Department of Biotechnology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Pengpeng Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Rui Liang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Donghan Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Juan Xu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Ding Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Yunfei Xie
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Qi Liao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Zhe Jiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China.
| | - Yuejun Shi
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China.
| | - Guiqing Peng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China.
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12
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Chen J, Xu Y, Yang X, Cang Z, Geng W, Wei GW. Poisson-Boltzmann-based machine learning model for electrostatic analysis. Biophys J 2024; 123:2807-2814. [PMID: 38356263 PMCID: PMC11393697 DOI: 10.1016/j.bpj.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic solvation free energies for macromolecules due to the nonlinearity, dielectric jumps, charge singularity, and geometric complexity associated with the PB equation. The present work introduces a PB-based machine learning (PBML) model for biomolecular electrostatic analysis. Trained with the second-order accurate MIBPB solver, the proposed PBML model is found to be more accurate and faster than several eminent PB solvers in electrostatic analysis. The proposed PBML model can provide highly accurate PB electrostatic solvation free energy of new biomolecules or new conformations generated by molecular dynamics with much reduced computational cost.
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Affiliation(s)
- Jiahui Chen
- Department of Mathematics, University of Arkansas, Fayetteville, Arkansas
| | | | - Xin Yang
- Department of Mathematics, Southern Methodist University, Dallas, Texas
| | - Zixuan Cang
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina
| | - Weihua Geng
- Department of Mathematics, Southern Methodist University, Dallas, Texas.
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, Michigan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.
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13
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Sarma M, Borkotoky S, Dubey VK. Structure-based drug designing against Leishmania donovani using docking and molecular dynamics simulation studies: exploring glutathione synthetase as a drug target. J Biomol Struct Dyn 2024; 42:7628-7636. [PMID: 37491862 DOI: 10.1080/07391102.2023.2240429] [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: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023]
Abstract
In the pursuit of developing novel anti-leishmanial agents, we conducted an extensive computational study to screen inhibitors from the FDA-approved ZINC database against Leishmania donovani glutathione synthetase. The three-dimensional structure of Leishmania donovani glutathione synthetase was constructed by homology modeling, using the crystallographic structure of Trypanosoma brucei glutathione synthetase as a template. Subsequently, molecular docking studies were carried out for a large number of compounds using AutoDock Vina. Among the screened compounds, we selected the top five with strong binding affinity to Leishmania donovani glutathione synthetase but having a very low affinity to its human homolog. Further investigations on protein-ligand complexes were done by conducting molecular dynamics (MD) simulation and MM/PBSA analysis. The results revealed that Olysio (Simeprevir) exhibited the lowest binding energy (-89.21 kcal/mol), followed by Telithromycin (-45.34 kcal/mol). These findings showed that these compounds have the potential to act as inhibitors of glutathione synthetase. Hence, our study provides valuable insights for the development of a novel therapeutic strategy against Leishmania donovani by targeting the glutathione synthetase enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manash Sarma
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Subhomoi Borkotoky
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
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14
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Soni U, Singh A, Soni R, Samanta SK, Varadwaj PK, Misra K. Identification of candidate target genes of oral squamous cell carcinoma using high-throughput RNA-Seq data and in silico studies of their interaction with naturally occurring bioactive compounds. J Biomol Struct Dyn 2024; 42:8024-8044. [PMID: 37526306 DOI: 10.1080/07391102.2023.2242515] [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: 02/13/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
Oral Squamous Cell Carcinoma (OSCC) accounts for more than 90% of all kinds of oral neoplasms that develop in the oral cavity. It is a type of malignancy that shows high morbidity and recurrence rate, but data on the disease's target genes and biomarkers is still insufficient. In this study, in silico studies have been performed to find out the novel target genes and their potential therapeutic inhibitors for the effective and efficient treatment of OSCC. The DESeq2 package of RStudio was used in the current investigation to screen and identify differentially expressed genes for OSCC. As a result of gene expression analysis, the top 10 novel genes were identified using the Cytohubba plugin of Cytoscape, and among them, the ubiquitin-conjugating enzyme (UBE2D1) was found to be upregulated and playing a significant role in the progression of human oral cancers. Following this, naturally occurring compounds were virtually evaluated and simulated against the discovered novel target as prospective drugs utilizing the Maestro, Schrodinger, and Gromacs software. In a simulated screening of naturally occurring potential inhibitors against the novel target UBE2D1, Epigallocatechin 3-gallate, Quercetin, Luteoline, Curcumin, and Baicalein were identified as potent inhibitors. Novel identified gene UBE2D1 has a significant role in the proliferation of human cancers through suppression of 'guardian of genome' p53 via ubiquitination dependent pathway. Therefore, the treatment of OSCC may benefit significantly from targeting this gene and its discovered naturally occurring inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Unnati Soni
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
| | - Anirudh Singh
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
| | - Ramendra Soni
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
| | - Krishna Misra
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
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15
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Hassan HA, Muhammed SS, Al-Khdhairawi A, Abdelwahab SF, Abdel-Rahman IM, Abdelhamid MM. Unraveling effective extracellular signal-regulated kinase 2 inhibitors: a de novo drug design strategy enhanced by in-depth in silico analyses. J Biomol Struct Dyn 2024; 42:7906-7916. [PMID: 37584104 DOI: 10.1080/07391102.2023.2246563] [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: 05/02/2023] [Accepted: 07/23/2023] [Indexed: 08/17/2023]
Abstract
Extracellular signal-regulated kinase 2 (ERK-2) is a serine/threonine protein kinase in eukaryotic cells and belongs to the mitogen-activated protein kinase (MAPK) family. An activated form of ERK-2 phosphorylates substrates in the nucleus or cytoplasm and causes specific proteins to be expressed or activated, regulating cell proliferation, differentiation and other functions. Caffeic acid (3,4 - dihydroxy cinnamic acid), as previously reported, directly interacts with ERK-2 and reduces its effects in vitro. It is also reported to have a variety of pharmacological effects, including anti-inflammatory, immunomodulatory, antioxidant and anticancer activities. In the current study, a deep-learning protocol was employed to develop effective 100 compounds by modifying the chemical structure of DHC to improve its inhibitory performance against ERK-2. Calculations of physicochemical properties for those compounds revealed that 20 compounds had drug scores better than DHC (≥ 80%). Following that, molecular docking calculations were performed on the selected compounds and DHC. The obtained data revealed that five compounds had docking scores better than DHC (≥ -5.9 kcal/mol). Moreover, data from molecular mechanics and the Poisson - Boltzmann surface area (MM/PBSA) binding energy over 200 ns MD simulation confirmed that Cmd-1 and Cmd-4 exhibited higher stability with ΔGbinding of -40.8 and -49.1 kcal/mol, respectively, which is better than DHC (-35.1 kcal/mol). Finally, various energetic and structural studies showed the high stability of the two generated compounds within the active site of ERK-2. This study highlights the potential use of Cmd-1 and Cmd-4 as promising anti-ERK-2 drug candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, Egypt
| | - Sara S Muhammed
- Faculty of Pharmacy for girls, AlAzhar University, Banha, Egypt
| | - Ahmad Al-Khdhairawi
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Sayed F Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Islam M Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New-Minia, Egypt
| | - Mahmoud M Abdelhamid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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16
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Lach M, Rütten M, Beck T. Tunable crystalline assemblies using surface-engineered protein cages. Protein Sci 2024; 33:e5153. [PMID: 39167037 PMCID: PMC11337932 DOI: 10.1002/pro.5153] [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: 02/19/2024] [Revised: 07/04/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
Assembly of nanoparticles into superlattices yields nanomaterials with novel properties. We have recently shown that engineered protein cages are excellent building blocks for the assembly of inorganic nanoparticles into highly structured hybrid materials, with unprecedented precision. In this study, we show that the protein matrix, composed of surface-charged protein cages, can be readily tuned to achieve a number of different crystalline assemblies. Simply by altering the assembly conditions, different types of crystalline structures were produced, without the need to further modify the cages. Future work can utilize these new protein scaffolds to create nanoparticle superlattices with various assembly geometries and thus tune the functionality of these hybrid materials.
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Affiliation(s)
- Marcel Lach
- Department of Chemistry, Institute of Physical ChemistryUniversity of HamburgHamburgGermany
| | - Michael Rütten
- Department of Chemistry, Institute of Physical ChemistryUniversity of HamburgHamburgGermany
| | - Tobias Beck
- Department of Chemistry, Institute of Physical ChemistryUniversity of HamburgHamburgGermany
- The Hamburg Centre for Ultrafast ImagingHamburgGermany
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17
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Gao J, Ma J, Yu P, Yang D. Identification and mechanism of wheat protein disulfide isomerase-promoted gluten network formation. PNAS NEXUS 2024; 3:pgae356. [PMID: 39238603 PMCID: PMC11376372 DOI: 10.1093/pnasnexus/pgae356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/13/2024] [Indexed: 09/07/2024]
Abstract
Formation of the gluten network depends on glutenin crosslinking via disulfide bonds, and wheat protein disulfide isomerase (wPDI) plays an important role in this process. Here, we identify a substrate gluten protein of wPDI and the mechanism underlying wPDI-promoted glutenin crosslinking. Farinographic, rheologic, and alveographic analysis unambiguously proves that wPDI improves gluten network formation, which is directly observed by 3D reconstruction of the gluten network. Protein analysis and LC-MS/MS reveal that glutenin subunit 1Dx5 is primarily recruited by wPDI to participate in gluten network formation, and its cysteine-containing N-terminal domain (1Dx5-NTD), which harbors three cysteine residues for crosslinking, is purified. 1Dx5-NTD interacts with wPDI in both redox states, possibly folded by reduced wPDI and then catalyzed by oxidized wPDI, as further evidenced by wPDI-promoted self-crosslinking. Consistent with macroscopic observations, our results suggest that wPDI folds 1Dx5-NTD into β-strand structure that favors disulfide bond formation.
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Affiliation(s)
- Jihui Gao
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jiayin Ma
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Peixuan Yu
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Dong Yang
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
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18
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Went SC, Picton DM, Morgan RD, Nelson A, Brady A, Mariano G, Dryden DTF, Smith DL, Wenner N, Hinton JCD, Blower TR. Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence. Nat Commun 2024; 15:7236. [PMID: 39174540 PMCID: PMC11341690 DOI: 10.1038/s41467-024-51629-7] [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: 12/20/2023] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognise and methylate 6 bp non-palindromic motifs within the host genome, and prevent replication of non-methylated phage DNA that encodes these same motifs. How BREX recognises cognate motifs has not been fully understood. In this study we characterise BREX from pathogenic Salmonella and present X-ray crystallographic structures of the conserved BREX protein, PglX. The PglX N-terminal domain encodes the methyltransferase, whereas the C-terminal domain is for motif recognition. We also present the structure of PglX bound to the phage-derived DNA mimic, Ocr, an inhibitor of BREX activity. Our analyses propose modes for DNA-binding by PglX and indicate that both methyltransferase activity and defence require larger BREX complexes. Through rational engineering of PglX we broaden both the range of phages targeted, and the host motif sequences that are methylated by BREX. Our data demonstrate that PglX is used to recognise specific DNA sequences for BREX activity, contributing to motif recognition for both phage defence and host methylation.
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Affiliation(s)
- Sam C Went
- Department of Biosciences, Durham University, South Road, Durham, UK
| | - David M Picton
- Department of Biosciences, Durham University, South Road, Durham, UK
| | | | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Aisling Brady
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Giuseppina Mariano
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - David T F Dryden
- Department of Biosciences, Durham University, South Road, Durham, UK
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham, UK.
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19
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Zheng CC, Chen YL, Dong HL, Zhang XH, Tan ZJ. Effect of ethanol on the elasticities of double-stranded RNA and DNA revealed by magnetic tweezers and simulations. J Chem Phys 2024; 161:075101. [PMID: 39145565 DOI: 10.1063/5.0211869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024] Open
Abstract
The elasticities of double-stranded (ds) DNA and RNA, which are critical to their biological functions and applications in materials science, can be significantly modulated by solution conditions such as ions and temperature. However, there is still a lack of a comprehensive understanding of the role of solvents in the elasticities of dsRNA and dsDNA in a comparative way. In this work, we explored the effect of ethanol solvent on the elasticities of dsRNA and dsDNA by magnetic tweezers and all-atom molecular dynamics simulations. We found that the bending persistence lengths and contour lengths of dsRNA and dsDNA decrease monotonically with the increase in ethanol concentration. Furthermore, the addition of ethanol weakens the positive twist-stretch coupling of dsRNA, while promotes the negative twist-stretch coupling of dsDNA. Counter-intuitively, the lower dielectric environment of ethanol causes a significant re-distribution of counterions and enhanced ion neutralization, which overwhelms the enhanced repulsion along dsRNA/dsDNA, ultimately leading to the softening in bending for dsRNA and dsDNA. Moreover, for dsRNA, ethanol causes slight ion-clamping across the major groove, which weakens the major groove-mediated twist-stretch coupling, while for dsDNA, ethanol promotes the stretch-radius correlation due to enhanced ion binding and consequently enhances the helical radius-mediated twist-stretch coupling.
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Affiliation(s)
- Chen-Chen Zheng
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yun-Long Chen
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hai-Long Dong
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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20
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Phulera S, Dickson CJ, Schwalen CJ, Khoshouei M, Cassell SJ, Sun Y, Condos T, Whicher J, Weihofen WA. Scorpion α-toxin LqhαIT specifically interacts with a glycan at the pore domain of voltage-gated sodium channels. Structure 2024:S0969-2126(24)00284-3. [PMID: 39181123 DOI: 10.1016/j.str.2024.07.021] [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: 02/12/2024] [Revised: 06/13/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024]
Abstract
Voltage-gated sodium (Nav) channels sense membrane potential and drive cellular electrical activity. The deathstalker scorpion α-toxin LqhαIT exerts a strong action potential prolonging effect on Nav channels. To elucidate the mechanism of action of LqhαIT, we determined a 3.9 Å cryoelectron microscopy (cryo-EM) structure of LqhαIT in complex with the Nav channel from Periplaneta americana (NavPas). We found that LqhαIT binds to voltage sensor domain 4 and traps it in an "S4 down" conformation. The functionally essential C-terminal epitope of LqhαIT forms an extensive interface with the glycan scaffold linked to Asn330 of NavPas that augments a small protein-protein interface between NavPas and LqhαIT. A combination of molecular dynamics simulations, structural comparisons, and prior mutagenesis experiments demonstrates the functional importance of this toxin-glycan interaction. These findings establish a structural basis for the specificity achieved by scorpion α-toxins and reveal the conserved glycan as an essential component of the toxin-binding epitope.
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Affiliation(s)
- Swastik Phulera
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Callum J Dickson
- Global Discovery Chemistry, Novartis Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Christopher J Schwalen
- Global Discovery Chemistry, Novartis Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Maryam Khoshouei
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Samantha J Cassell
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yishan Sun
- Neuroscience, Novartis Biomedical Research, 22 Windsor St, Cambridge, MA 02139, USA
| | - Tara Condos
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jonathan Whicher
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Wilhelm A Weihofen
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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21
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Cha M, Xu A, Williams AJ. Structural study of a light chain mispaired bispecific predicts mechanism of downstream separation. J Chromatogr A 2024; 1730:465117. [PMID: 38972252 DOI: 10.1016/j.chroma.2024.465117] [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: 04/06/2024] [Revised: 06/07/2024] [Accepted: 06/22/2024] [Indexed: 07/09/2024]
Abstract
Bispecific antibodies expressed and assembled from a single upstream culture require the correct balance and pairing of four different heavy and light chains (HC and LC). The increased potential for chain-mispaired species challenges the downstream purification of this new format. While clearance of HC-mispaired species, including homodimers and half-antibodies, has been assessed, removal of LC mispairs requires a more stringent approach. Here, we report two case studies in which separation is achieved, as well as the structural basis of these separations: (A) In the first case, a main species with a positively charged patch in the correctly formed variable fragment (Fv) is disrupted when paired with the wrong LC. This LC-mispaired variant binds more weakly to a cation exchange resin and can be washed off in a chromatography step. (B) A second molecule whose LC mispair introduces a negative-charge patch and hydrophobic patch in close proximity, presenting increased binding to a multimodal anion exchange resin. This LC-mispaired variant can be retained on the column under conditions in which the bispecific is recovered. In both case studies, the molecular structural analysis by protein surface properties models correlated well with the chromatography experiments. The comprehensive interpretation of experimental and computational results has provided a better understanding of strategies and potential applications for predicting the downstream purification of complex molecules.
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Affiliation(s)
- Minjeong Cha
- Department of Purification, Microbiology and Virology, Genentech, Inc, South San Francisco, CA, United States.
| | - Ankai Xu
- Department of Purification, Microbiology and Virology, Genentech, Inc, South San Francisco, CA, United States; Department of Cell & Gene Therapy E2E Value Chain, Genentech, Inc., South San Francisco, CA, United States
| | - Ambrose J Williams
- Department of Purification, Microbiology and Virology, Genentech, Inc, South San Francisco, CA, United States
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22
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De Filippis V, Acquasaliente L, Pierangelini A, Marin O. Chemical Synthesis and Structure-Activity Relationship Studies of the Coagulation Factor Xa Inhibitor Tick Anticoagulant Peptide from the Hematophagous Parasite Ornithodoros moubata. Biomimetics (Basel) 2024; 9:485. [PMID: 39194464 DOI: 10.3390/biomimetics9080485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024] Open
Abstract
Tick Anticoagulant Peptide (TAP), a 60-amino acid protein from the soft tick Ornithodoros moubata, inhibits activated coagulation factor X (fXa) with almost absolute specificity. Despite TAP and Bovine Pancreatic Trypsin Inhibitor (BPTI) (i.e., the prototype of the Kunitz-type protease inhibitors) sharing a similar 3D fold and disulphide bond topology, they have remarkably different amino acid sequence (only ~24% sequence identity), thermal stability, folding pathways, protease specificity, and even mechanism of protease inhibition. Here, fully active and correctly folded TAP was produced in reasonably high yields (~20%) by solid-phase peptide chemical synthesis and thoroughly characterised with respect to its chemical identity, disulphide pairing, folding kinetics, conformational dynamics, and fXa inhibition. The versatility of the chemical synthesis was exploited to perform structure-activity relationship studies on TAP by incorporating non-coded amino acids at positions 1 and 3 of the inhibitor. Using Hydrogen-Deuterium Exchange Mass Spectrometry, we found that TAP has a remarkably higher conformational flexibility compared to BPTI, and propose that these different dynamics could impact the different folding pathway and inhibition mechanisms of TAP and BPTI. Hence, the TAP/BPTI pair represents a nice example of divergent evolution, while the relative facility of TAP synthesis could represent a good starting point to design novel synthetic analogues with improved pharmacological profiles.
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Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry & Molecular Haematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo 5, 35131 Padua, Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry & Molecular Haematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo 5, 35131 Padua, Italy
| | - Andrea Pierangelini
- Laboratory of Protein Chemistry & Molecular Haematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo 5, 35131 Padua, Italy
| | - Oriano Marin
- Department of Biomedical Sciences, School of Medicine, University of Padova, Via Trieste 75, 35121 Padua, Italy
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23
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Silverman I, Gerber M, Shaykevich A, Stein Y, Siegman A, Goel S, Maitra R. Structural modifications and kinetic effects of KRAS interactions with HRAS and NRAS: an in silico comparative analysis of KRAS mutants. Front Mol Biosci 2024; 11:1436976. [PMID: 39184150 PMCID: PMC11342451 DOI: 10.3389/fmolb.2024.1436976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/25/2024] [Indexed: 08/27/2024] Open
Abstract
The RAS genes which code for KRAS, HRAS, and NRAS are three of the most frequently mutated oncogenes responsible for cancer deaths. Tumorigenesis is one of the most significant outcomes of deregulation of RAS GTPases. Although the structures have been extensively studied, there is still more to be discovered about the actual binding conformations of the three isoforms, especially when mutated, to design an inhibitory drug. Recent studies have identified important interactions between the three isoforms that affect the oncogenic strength of the others when they are mutated. In this study, we utilize molecular dynamics simulations to examine the modifications of the structural property, mechanism, and kinetic energy of KRAS when interacting individually and with HRAS and NRAS. Notably, we found that WT-KRAS' orientation when bound to WT-HRAS vs. WT-NRAS is rotated 180°, with mutants demonstrating a similar binding pattern. The binding sites of the isoforms with KRAS share similarities with those involved in the GDP/GTP active site and site of KRAS dimerization. Thus, the isoform interaction can serve as an inhibitory method of KRAS actions. This study advances the understanding of inhibiting RAS-driven cancers through a novel isoform interaction approach only recently discovered, which has been proven to be an effective alternate therapeutic approach. We developed a blueprint of the interaction which would be beneficial in the development of KRAS mutant-specific and pan-KRAS mutant inhibitory drugs that mimic the isoform interactions. Our results support the direct interaction inhibition mechanism of mutant KRAS when bound to WT-HRAS and WT-NRAS by the isoforms' hypervariable region binding to the G-domain of KRAS. Furthermore, our results support the approach of reducing the effects of oncogenic KRAS by altering the concentration of the isoforms or a drug alternative based on the overall structural and kinetic stability, as well as the binding strength of the mutant-isoform complexes.
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Affiliation(s)
- Isaac Silverman
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Michael Gerber
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Aaron Shaykevich
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Yitzchak Stein
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Alexander Siegman
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Sanjay Goel
- Department of Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Radhashree Maitra
- Department of Biology, Yeshiva University, New York, NY, United States
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24
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Garg A, On KF, Xiao Y, Elkayam E, Cifani P, David Y, Joshua-Tor L. The molecular basis of Human FN3K mediated phosphorylation of glycated substrate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606604. [PMID: 39149269 PMCID: PMC11326186 DOI: 10.1101/2024.08.05.606604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Glycation, a non-enzymatic post-translational modification occurring on proteins, can be actively reversed via site-specific phosphorylation of the fructose-lysine moiety by FN3K kinase, to impact the cellular function of target protein. A regulatory axis between FN3K and glycated protein targets has been associated with conditions like diabetes and cancer. However the molecular basis of this relationship has not been explored so far. Here, we determined a series of crystal structures of HsFN3K in apo-state, and in complex with different nucleotide analogs together with a sugar substrate mimic to reveal the features important for its kinase activity and substrate recognition. Additionally, the dynamics in sugar substrate binding during the kinase catalytic cycle provide important mechanistic insights into HsFN3K function. Our structural work provides the molecular basis for rationale small molecule design targeting FN3K.
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Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, 11724 USA
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Kin Fan On
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, 11724 USA
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Yang Xiao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Elad Elkayam
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, 11724 USA
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, 11724 USA
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
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25
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ElSawy KM. Competitive Interaction of the SGFRKMAF Peptide with 3CLpro Dimerization Intermediates: A Brownian Dynamics Investigation. J Phys Chem B 2024; 128:7313-7321. [PMID: 39028939 DOI: 10.1021/acs.jpcb.4c01938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
The SGFRKMAF peptide is known to inhibit the dimerization of 3CLpro monomers, which is essential for SARS-CoV-2 replication. The mechanism behind this, however, is largely unknown. In this work, we used Brownian dynamics simulations to compare and contrast 3CLpro monomer-monomer interactions and 3CLpro monomer-SGFRKMAF peptide interactions. We found that formation of the 3CLpro wild-type dimer could potentially involve formation of three intermediates that are primarily stabilized by G11-G124, S1-S301, and T118-G278 interactions. Analysis of 3CLpro monomer interaction with the SGFRKMAF peptide, however, revealed the presence of eight basins of interactions where the peptide assumes the highest local densities at the 3CLPro monomer surface. The second highest-density basin was found to coincide with the interface region of the wild-type 3CLpro dimer, thereby directly blocking the 3CLpro dimer-dimer interactions. The other basins, however, were found to lie far from the interface region. Notably, we found that only 6% of the BD trajectories end up directly into the basin at the interface region and ∼39% of the trajectories end up into those basins lying away from the interface region, indicating a greater role for peptide binding at sites away from the dimer interface region. Importantly, the locations of the basins lying away from the interface were found to coincide with the 3CLpro residues involved in stabilization of the 3CLpro monomer-monomer intermediates. Given that the rate constant of the peptide reaching the monomer surface was found to be almost an order of magnitude higher than the rate constant of monomer-monomer association, the SGFRKMAF peptide has the potential to inhibit dimerization of 3CLpro monomers not only through blocking the interface region but also through blocking the formation of the intermediates involved in the dimerization process. This could potentially open new avenues for 3CLpro dimerization inhibitors that transcend traditional X-ray-based discovery approaches.
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Affiliation(s)
- Karim M ElSawy
- Department of Chemistry, College of Science, Qassim University, Buraydah 52571, Saudi Arabia
- York Cross-disciplinary Centre for Systems Analysis (YCCSA), University of York, York YO10 5GE, United Kingdom
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26
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Li K, Barrett K, Agger JW, Zeuner B, Meyer AS. Bioinformatics-based identification of GH12 endoxyloglucanases in citrus-pathogenic Penicillium spp. Enzyme Microb Technol 2024; 178:110441. [PMID: 38574421 DOI: 10.1016/j.enzmictec.2024.110441] [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: 12/21/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Millions of tons of citrus peel waste are produced every year as a byproduct of the juice industry. Citrus peel is rich in pectin and xyloglucan, but while the pectin is extracted for use in the food industry, the xyloglucan is currently not valorized. To target hydrolytic degradation of citrus peel xyloglucan into oligosaccharides, we have used bioinformatics to identify three glycoside hydrolase 12 (GH12) endoxyloglucanases (EC 3.2.1.151) from the citrus fruit pathogens Penicillium italicum GL-Gan1 and Penicillium digitatum Pd1 and characterized them on xyloglucan obtained by alkaline extraction from citrus peel. The enzymes displayed pH-temperature optima of pH 4.6-5.3 and 35-37°C. PdGH12 from P. digitatum and PiGH12A from P. italicum share 84% sequence identity and displayed similar kinetics, although kcat was highest for PdGH12. In contrast, PiGH12B from P. italicum, which has the otherwise conserved Trp in subsite -4 replaced with a Tyr, displayed a 3 times higher KM and a 4 times lower kcat/KM than PiGH12A, but was the most thermostable enzyme of the three Penicillium-derived endoxyloglucanases. The benchmark enzyme AnGH12 from Aspergillus nidulans was more thermally stable and had a higher pH-temperature optimum than the enzymes from Penicillum spp. The difference in structure of the xyloglucan oligosaccharides extracted from citrus peel xyloglucan and tamarind xyloglucan by the new endoxyloglucanases was determined by LC-MS. The inclusion of citrus peel xyloglucan demonstrated that the endoxyloglucanases liberated fucosylated xyloglucan oligomers, implying that these enzymes have the potential to upgrade citrus peel residues to produce oligomers useful as intermediates or bioactive compounds.
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Affiliation(s)
- Kai Li
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Kristian Barrett
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Jane W Agger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Birgitte Zeuner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark.
| | - Anne S Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
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27
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Polverini E, Squeri P, Gherardi V. Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study. Int J Biol Macromol 2024; 275:133663. [PMID: 38969036 DOI: 10.1016/j.ijbiomac.2024.133663] [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: 03/14/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Spinal muscular atrophy (SMA) is a disease that results from mutations in the Survival of Motor Neuron (SMN) gene 1, leading to muscle atrophy due to motor neurons degeneration. SMN plays a crucial role in the assembly of spliceosomal small nuclear ribonucleoprotein complexes via binding to the arginine-glycine rich C-terminal tails of Sm proteins recognized by SMN Tudor domain. E134K Tudor mutation, cause of the more severe type I SMA, compromises the SMN-Sm interaction without a perturbation of the domain fold. By molecular dynamics simulations, we investigated the mechanism of Tudor-SmD1 interaction, and the effects on it of E134K mutation. It was observed that E134 is crucial to catch the positive dimethylated arginines (DMRs) of the SmD1 tail that, wrapping around the acidic Tudor surface, enters a central DMR into an aromatic cage. The flexible cage residue Y130 must be blocked from the wrapped tail to assure a stable binding. The charge inversion in E134K mutation causes the loss of a critical anchor point, disfavoring the tail wrapping and leaving Y130 free to swing, leading to DMR detachments and exposition of the C-terminal region of the tail. This could suggest new hypotheses regarding a possible autoimmune response by anti-Sm autoantibodies.
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Affiliation(s)
- Eugenia Polverini
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
| | - Pietro Squeri
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Valeria Gherardi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
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28
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Thamkachy R, Medina-Pritchard B, Park SH, Chiodi CG, Zou J, de la Torre-Barranco M, Shimanaka K, Abad MA, Gallego Páramo C, Feederle R, Ruksenaite E, Heun P, Davies OR, Rappsilber J, Schneidman-Duhovny D, Cho US, Jeyaprakash AA. Structural basis for Mis18 complex assembly and its implications for centromere maintenance. EMBO Rep 2024; 25:3348-3372. [PMID: 38951710 PMCID: PMC11315898 DOI: 10.1038/s44319-024-00183-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: 03/22/2024] [Revised: 05/06/2024] [Accepted: 06/06/2024] [Indexed: 07/03/2024] Open
Abstract
The centromere, defined by the enrichment of CENP-A (a Histone H3 variant) containing nucleosomes, is a specialised chromosomal locus that acts as a microtubule attachment site. To preserve centromere identity, CENP-A levels must be maintained through active CENP-A loading during the cell cycle. A central player mediating this process is the Mis18 complex (Mis18α, Mis18β and Mis18BP1), which recruits the CENP-A-specific chaperone HJURP to centromeres for CENP-A deposition. Here, using a multi-pronged approach, we characterise the structure of the Mis18 complex and show that multiple hetero- and homo-oligomeric interfaces facilitate the hetero-octameric Mis18 complex assembly composed of 4 Mis18α, 2 Mis18β and 2 Mis18BP1. Evaluation of structure-guided/separation-of-function mutants reveals structural determinants essential for cell cycle controlled Mis18 complex assembly and centromere maintenance. Our results provide new mechanistic insights on centromere maintenance, highlighting that while Mis18α can associate with centromeres and deposit CENP-A independently of Mis18β, the latter is indispensable for the optimal level of CENP-A loading required for preserving the centromere identity.
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Affiliation(s)
- Reshma Thamkachy
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | | | - Sang Ho Park
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carla G Chiodi
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Juan Zou
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | | | - Kazuma Shimanaka
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maria Alba Abad
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | | | - Regina Feederle
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany
| | - Emilija Ruksenaite
- Institute Novo Nordisk Foundation Centre for Protein Research, Copenhagen, Denmark
| | - Patrick Heun
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Owen R Davies
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - A Arockia Jeyaprakash
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
- Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany.
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29
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El-Assaad AM, Hamieh T. SARS-CoV-2: Prediction of critical ionic amino acid mutations. Comput Biol Med 2024; 178:108688. [PMID: 38870723 DOI: 10.1016/j.compbiomed.2024.108688] [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: 10/31/2023] [Revised: 05/26/2024] [Accepted: 06/01/2024] [Indexed: 06/15/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that caused coronavirus disease 2019 (COVID-19), has been studied thoroughly, and several variants are revealed across the world with their corresponding mutations. Studies and vaccines development focus on the genetic mutations of the S protein due to its vital role in allowing the virus attach and fuse with the membrane of a host cell. In this perspective, we study the effects of all ionic amino acid mutations of the SARS-CoV-2 viral spike protein S1 when bound to Antibody CC12.1 within the SARS-CoV-2:CC12.1 complex model. Binding free energy calculations between SARS-CoV-2 and antibody CC12.1 are based on the Analysis of Electrostatic Similarities of Proteins (AESOP) framework, where the electrostatic potentials are calculated using Adaptive Poisson-Boltzmann Solver (APBS). The atomic radii and charges that feed into the APBS calculations are calculated using the PDB2PQR software. Our results are the first to propose in silico potential life-threatening mutations of SARS-CoV-2 beyond the present mutations found in the five common variants worldwide. We find each of the following mutations: K378A, R408A, K424A, R454A, R457A, K458A, and K462A, to play significant roles in the binding to Antibody CC12.1, since they are turned into strong inhibitors on both chains of the S1 protein, whereas the mutations D405A, D420A, and D427A, show to play important roles in this binding, as they are turned into mild inhibitors on both chains of the S1 protein.
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Affiliation(s)
- Atlal M El-Assaad
- Department of Electrical Engineering & Computer Science, University of Toledo (UT), Toledo OH 43606, USA; Department of Computer Science, Lebanese International University (LIU), Bekaa, Lebanon.
| | - Tayssir Hamieh
- Faculty of Science and Engineering, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands; Laboratory of Materials, Catalysis, Environment and Analytical Methods (MCEMA), Faculty of Sciences, Lebanese University, Hadath, Lebanon.
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30
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Legen J, Lenzen B, Kachariya N, Feltgen S, Gao Y, Mergenthal S, Weber W, Klotzsch E, Zoschke R, Sattler M, Schmitz-Linneweber C. A prion-like domain is required for phase separation and chloroplast RNA processing during cold acclimation in Arabidopsis. THE PLANT CELL 2024; 36:2851-2872. [PMID: 38723165 PMCID: PMC11289645 DOI: 10.1093/plcell/koae145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/06/2024] [Indexed: 08/02/2024]
Abstract
Arabidopsis (Arabidopsis thaliana) plants can produce photosynthetic tissue with active chloroplasts at temperatures as low as 4°C, and this process depends on the presence of the nuclear-encoded, chloroplast-localized RNA-binding protein CP29A. In this study, we demonstrate that CP29A undergoes phase separation in vitro and in vivo in a temperature-dependent manner, which is mediated by a prion-like domain (PLD) located between the two RNA recognition motif domains of CP29A. The resulting droplets display liquid-like properties and are found near chloroplast nucleoids. The PLD is required to support chloroplast RNA splicing and translation in cold-treated tissue. Together, our findings suggest that plant chloroplast gene expression is compartmentalized by inducible condensation of CP29A at low temperatures, a mechanism that could play a crucial role in plant cold resistance.
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Affiliation(s)
- Julia Legen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Benjamin Lenzen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Nitin Kachariya
- Helmholtz Munich, Institute of Structural Biology, Ingolstädter Landstrasse 1, Munich 85764, Germany
- Department of Bioscience, Bavarian NMR Center, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
| | - Stephanie Feltgen
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany
| | - Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Simon Mergenthal
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Willi Weber
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Enrico Klotzsch
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt-Universität zu Berlin, Invalidenstrasse 42, Berlin 10115, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Michael Sattler
- Helmholtz Munich, Institute of Structural Biology, Ingolstädter Landstrasse 1, Munich 85764, Germany
- Department of Bioscience, Bavarian NMR Center, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, Garching 85747, Germany
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31
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Yu B, Bolik-Coulon N, Rangadurai AK, Kay LE, Iwahara J. Gadolinium-Based NMR Spin Relaxation Measurements of Near-Surface Electrostatic Potentials of Biomolecules. J Am Chem Soc 2024; 146:20788-20801. [PMID: 39028837 PMCID: PMC11295196 DOI: 10.1021/jacs.4c04433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/09/2024] [Accepted: 06/28/2024] [Indexed: 07/21/2024]
Abstract
NMR spectroscopy is an important tool for the measurement of the electrostatic properties of biomolecules. To this point, paramagnetic relaxation enhancements (PREs) of 1H nuclei arising from nitroxide cosolutes in biomolecular solutions have been used to measure effective near-surface electrostatic potentials (ϕENS) of proteins and nucleic acids. Here, we present a gadolinium (Gd)-based NMR method, exploiting Gd chelates with different net charges, for measuring ϕENS values and demonstrate its utility through applications to a number of biomolecular systems. The use of Gd-based cosolutes offers several advantages over nitroxides for ϕENS measurements. First, unlike nitroxide compounds, Gd chelates enable electrostatic potential measurements on oxidation-sensitive proteins that require reducing agents. Second, the large electron spin quantum number of Gd (7/2) results in notably larger PREs for Gd chelates when used at the same concentrations as nitroxide radicals. Thus, it is possible to measure ϕENS values exclusively from + and - charged compounds even for highly charged biomolecules, avoiding the use of neutral cosolutes that, as we further establish here, limits the accuracy of the measured electrostatic potentials. In addition, the smaller concentrations of cosolutes required minimize potential binding to sites on macromolecules. Fourth, the closer proximity of the paramagnetic center and charged groups within Gd chelates, in comparison to the corresponding nitroxide compounds, enables more accurate predictions of ϕENS potentials for cross-validation of the experimental results. The Gd-based method described here, thus, broadens the applicability of studies of biomolecular electrostatics using solution NMR spectroscopy.
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Affiliation(s)
- Binhan Yu
- Department
of Biochemistry & Molecular Biology, Sealy Center for Structural
Biology & Molecular Biophysics, University
of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Nicolas Bolik-Coulon
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Atul K. Rangadurai
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Program
in Molecular Medicine, Hospital for Sick
Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Lewis E. Kay
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Program
in Molecular Medicine, Hospital for Sick
Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Junji Iwahara
- Department
of Biochemistry & Molecular Biology, Sealy Center for Structural
Biology & Molecular Biophysics, University
of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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32
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Nourisanami F, Sobol M, Li Z, Horvath M, Kowalska K, Kumar A, Vlasak J, Koupilova N, Luginbuhl DJ, Luo L, Rozbesky D. Molecular mechanisms of proteoglycan-mediated semaphorin signaling in axon guidance. Proc Natl Acad Sci U S A 2024; 121:e2402755121. [PMID: 39042673 PMCID: PMC11295036 DOI: 10.1073/pnas.2402755121] [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: 02/08/2024] [Accepted: 06/20/2024] [Indexed: 07/25/2024] Open
Abstract
The precise assembly of a functional nervous system relies on axon guidance cues. Beyond engaging their cognate receptors and initiating signaling cascades that modulate cytoskeletal dynamics, guidance cues also bind components of the extracellular matrix, notably proteoglycans, yet the role and mechanisms of these interactions remain poorly understood. We found that Drosophila secreted semaphorins bind specifically to glycosaminoglycan (GAG) chains of proteoglycans, showing a preference based on the degree of sulfation. Structural analysis of Sema2b unveiled multiple GAG-binding sites positioned outside canonical plexin-binding site, with the highest affinity binding site located at the C-terminal tail, characterized by a lysine-rich helical arrangement that appears to be conserved across secreted semaphorins. In vivo studies revealed a crucial role of the Sema2b C-terminal tail in specifying the trajectory of olfactory receptor neurons. We propose that secreted semaphorins tether to the cell surface through interactions with GAG chains of proteoglycans, facilitating their presentation to cognate receptors on passing axons.
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Affiliation(s)
- Farahdokht Nourisanami
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 43, Czechia
- Laboratory of Structural Neurobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague142 20, Czechia
| | - Margarita Sobol
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 43, Czechia
- Laboratory of Structural Neurobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague142 20, Czechia
| | - Zhuoran Li
- HHMI, Department of Biology, Stanford University, Stanford, CA94305
| | - Matej Horvath
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 43, Czechia
- Laboratory of Structural Neurobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague142 20, Czechia
| | - Karolina Kowalska
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 43, Czechia
- Laboratory of Structural Neurobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague142 20, Czechia
| | - Atul Kumar
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 43, Czechia
- Laboratory of Structural Neurobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague142 20, Czechia
| | - Jonas Vlasak
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 43, Czechia
- Laboratory of Structural Neurobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague142 20, Czechia
| | - Nicola Koupilova
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 43, Czechia
- Laboratory of Structural Neurobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague142 20, Czechia
| | | | - Liqun Luo
- HHMI, Department of Biology, Stanford University, Stanford, CA94305
| | - Daniel Rozbesky
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 43, Czechia
- Laboratory of Structural Neurobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague142 20, Czechia
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33
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Alrouji M, Yasmin S, Alhumaydhi FA, Sharaf SE, Shahwan M, Shamsi A. ROS1 kinase inhibition reimagined: identifying repurposed drug via virtual screening and molecular dynamics simulations for cancer therapeutics. Front Chem 2024; 12:1392650. [PMID: 39136033 PMCID: PMC11317403 DOI: 10.3389/fchem.2024.1392650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/01/2024] [Indexed: 08/15/2024] Open
Abstract
Precision medicine has revolutionized modern cancer therapeutic management by targeting specific molecular aberrations responsible for the onset and progression of tumorigenesis. ROS proto-oncogene 1 (ROS1) is a receptor tyrosine kinase (RTK) that can induce tumorigenesis through various signaling pathways, such as cell proliferation, survival, migration, and metastasis. It has emerged as a promising therapeutic target in various cancer types. However, there is very limited availability of specific ROS1 inhibitors for therapeutic purposes. Exploring repurposed drugs for rapid and effective treatment is a useful approach. In this study, we utilized an integrated approach of virtual screening and molecular dynamics (MD) simulations of repurposing existing drugs for ROS1 kinase inhibition. Using a curated library of 3648 FDA-approved drugs, virtual screening identified drugs capable of binding to ROS1 kinase domain. The results unveil two hits, Midostaurin and Alectinib with favorable binding profiles and stable interactions with the active site residues of ROS1. These hits were subjected to stability assessment through all-atom MD simulations for 200 ns. MD results showed that Midostaurin and Alectinib were stable with ROS1. Taken together, the study showed a rational framework for the selection of repurposed Midostaurin and Alectinib with ROS1 inhibitory potential for therapeutic management after further validation.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Sabina Yasmin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Sharaf E. Sharaf
- Pharmaceutical Sciences Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Moyad Shahwan
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
- Center of Medical and Bio-Allied Health Sciences Research (CMBHSR), Ajman University, Ajman, United Arab Emirates
| | - Anas Shamsi
- Center of Medical and Bio-Allied Health Sciences Research (CMBHSR), Ajman University, Ajman, United Arab Emirates
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34
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Yu J, Ramirez LM, Lin Q, Burz DS, Shekhtman A. Ribosome External Electric Field Regulates Metabolic Enzyme Activity: The RAMBO Effect. J Phys Chem B 2024; 128:7002-7021. [PMID: 39012038 DOI: 10.1021/acs.jpcb.4c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Ribosomes bind to many metabolic enzymes and change their activity. A general mechanism for ribosome-mediated amplification of metabolic enzyme activity, RAMBO, was formulated and elucidated for the glycolytic enzyme triosephosphate isomerase, TPI. The RAMBO effect results from a ribosome-dependent electric field-substrate dipole interaction energy that can increase or decrease the ground state of the reactant and product to regulate catalytic rates. NMR spectroscopy was used to determine the interaction surface of TPI binding to ribosomes and to measure the corresponding kinetic rates in the absence and presence of intact ribosome particles. Chemical cross-linking and mass spectrometry revealed potential ribosomal protein binding partners of TPI. Structural results and related changes in TPI energetics and activity show that the interaction between TPI and ribosomal protein L11 mediate the RAMBO effect.
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Affiliation(s)
- Jianchao Yu
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Lisa M Ramirez
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Qishan Lin
- RNA Epitranscriptomics & Proteomics Resource, University at Albany, State University of New York, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
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35
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Aguilar-Pineda J, González-Melchor M. Influence of the Water Model on the Structure and Interactions of the GPR40 Protein with the Lipid Membrane and the Solvent: Rigid versus Flexible Water Models. J Chem Theory Comput 2024; 20:6369-6387. [PMID: 38991114 PMCID: PMC11270832 DOI: 10.1021/acs.jctc.4c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024]
Abstract
G protein-coupled receptors (GPCR) are responsible for modulating various physiological functions and are thus related to the pathophysiology of different diseases. Being potential therapeutic targets, multiple computational methodologies have been developed to analyze their behavior and interactions with other species. The solvent, on the other hand, has received much less attention. In this work, we analyzed the effect of four explicit water models on the structure and interactions of the GPR40 receptor in its apo form. We employed the rigid SPC/E and TIP4P models, and their flexible versions, the FBA/ϵ and TIP4P/ϵflex. We explored the structural changes and their correlation with some bulk dynamic properties of water. Our results showed an adverse effect on the conservation of the secondary structure of the receptor with all the models due to the breaking of the intramolecular hydrogen bond network, being more evident for the TIP4P models. Notably, all four models brought the receptor to states similar to the active one, modifying the intracellular part of the TM5 and TM6 domains in a "hinge" type movement, allowing the opening of the structure. Regarding the dynamic properties, the rigid models showed results comparable to those obtained in other studies on membrane systems. However, flexible models exhibit disparities in the molecular representation of systems. Surprisingly, the FBA/ϵ model improves the molecular picture of several properties, even though their agreement with bulk diffusion is poorer. These findings reinforce our idea that exploring other water models or improving the current ones, to better represent the membrane interface, can lead to a positive impact on the description of the signal transduction mechanisms and the search of new drugs by targeting these receptors.
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Affiliation(s)
- Jorge
Alberto Aguilar-Pineda
- Instituto de Física
“Luis Rivera Terrazas”, Benemérita Universidad
Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal
J-48, Puebla 72570, México
| | - Minerva González-Melchor
- Instituto de Física
“Luis Rivera Terrazas”, Benemérita Universidad
Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal
J-48, Puebla 72570, México
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36
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Liu Z, Gui S, Lu B, Zhang L. An Unfitted Finite Element Poisson-Boltzmann Solver with Automatic Resolving of Curved Molecular Surface. J Phys Chem B 2024; 128:6463-6475. [PMID: 38949996 DOI: 10.1021/acs.jpcb.4c01894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
So far, the existing Poisson-Boltzmann (PB) solvers that accurately take into account the interface jump conditions need a pregenerated body-fitted mesh (molecular surface mesh). However, qualified biomolecular surface meshing and its implementation into numerical methods remains a challenging and laborious issue, which practically hinders the progress of further developments and applications of a bunch of numerical methods in this field. In addition, even with a molecular surface mesh, it is only a low-order approximation of the original curved surface. In this article, an interface-penalty finite element method (IPFEM), which is a typical unfitted finite element method, is proposed to solve the Poisson-Boltzmann equation (PBE) without requiring the user to generate a molecular surface mesh. The Gaussian molecular surface is used to represent the molecular surface and can be automatically resolved with a high-order approximation within our method. Theoretical convergence rates of the IPFEM for the linear PB equation have been provided and are well validated on a benchmark problem with an analytical solution (we also noticed from numerical examples that the IPFEM has similar convergence rates for the nonlinear PBE). Numerical results on a set of different-sized biomolecules demonstrate that the IPFEM is numerically stable and accurate in the calculation of biomolecular electrostatic solvation energy.
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Affiliation(s)
- Ziyang Liu
- ICMSEC, LSEC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng Gui
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems and Control, Institute of Systems Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Benzhuo Lu
- ICMSEC, LSEC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linbo Zhang
- ICMSEC, LSEC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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37
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Chakrabortty A, Mondal S, Bandyopadhyay S. Conformational Properties of Poly(A)-Binding Protein Complexed with Poly(A) RNA. J Phys Chem B 2024; 128:6449-6462. [PMID: 38941243 DOI: 10.1021/acs.jpcb.4c00704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Microscopic understanding of protein-RNA interactions is important for different biological activities, such as RNA transport, translation, splicing, silencing, etc. Polyadenine (Poly(A)) binding proteins (PABPs) make up a class of regulatory proteins that play critical roles in protecting the poly(A) tails of cellular mRNAs from nuclease degradation. In this work, we performed molecular dynamics simulations to investigate the conformational modifications of human PABP protein and poly(A) RNA that occur during complexation. It is demonstrated that the intermediate linker domain of the protein transforms from a disordered coil-like structure to a helical form during the recognition process, leading to the formation of the complex. On the other hand, disordered collapsed coil-like RNA on complexation has been found to transform into a rigid extended conformation. Importantly, the binding free energy calculation showed that the thermodynamic stability of the complex is primarily guided by favorable hydrophobic interactions between the protein and the RNA.
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Affiliation(s)
- Arun Chakrabortty
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
| | - Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
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38
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Rios T, Maximiano MR, Fernandes FC, Amorim GC, Porto WF, Buccini DF, Nieto Marín V, Feitosa GC, Freitas CDP, Barra JB, Alonso A, Grossi de Sá MF, Lião LM, Franco OL. Anti-Staphy Peptides Rationally Designed from Cry10Aa Bacterial Protein. ACS OMEGA 2024; 9:29159-29174. [PMID: 39005792 PMCID: PMC11238290 DOI: 10.1021/acsomega.3c07455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 07/16/2024]
Abstract
Bacterial infections pose a significant threat to human health, constituting a major challenge for healthcare systems. Antibiotic resistance is particularly concerning in the context of treating staphylococcal infections. In addressing this challenge, antimicrobial peptides (AMPs), characterized by their hydrophobic and cationic properties, unique mechanism of action, and remarkable bactericidal and immunomodulatory capabilities, emerge as promising alternatives to conventional antibiotics for tackling bacterial multidrug resistance. This study focuses on the Cry10Aa protein as a template for generating AMPs due to its membrane-penetrating ability. Leveraging the Joker algorithm, six peptide variants were derived from α-helix 3 of Cry10Aa, known for its interaction with lipid bilayers. In vitro, antimicrobial assays determined the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) required for inhibiting the growth of Staphylococcus aureus, Escherichia coli, Acinetobacter baummanii, Enterobacter cloacae, Enterococcus facallis, Klebsiella pneumonia, and Pseudomonas aeruginosa. Time-kill kinetics were performed using the parental peptide AMPCry10Aa, as well as AMPCry10Aa_1 and AMPCry10Aa_5, against E. coli ATCC, S. aureus 111 and S. aureus ATCC strains showing that AMPCry10Aa_1 and AMPCry10Aa_5 peptides can completely reduce the initial bacterial load with less than 2 h of incubation. AMPCry10Aa_1 and AMPCry 10Aa_5 present stability in human serum and activity maintenance up to 37 °C. Cytotoxicity assays, conducted using the MTT method, revealed that all of the tested peptides exhibited cell viability >50% (IC50). The study also encompassed evaluations of the structure and physical-chemical properties. The three-dimensional structures of AMPCry10Aa and AMPCry10Aa_5 were determined through nuclear magnetic resonance (NMR) spectroscopy, indicating the adoption of α-helical segments. Electron paramagnetic resonance (EPR) spectroscopy elucidated the mechanism of action, demonstrating that AMPCry10Aa_5 enters the outer membranes of E. coli and S. aureus, causing substantial increases in lipid fluidity, while AMPCry10Aa slightly increases lipid fluidity in E. coli. In conclusion, the results obtained underscore the potential of Cry10Aa as a source for developing antimicrobial peptides as alternatives to conventional antibiotics, offering a promising avenue in the battle against antibiotic resistance.
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Affiliation(s)
- Thuanny
Borba Rios
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
| | - Mariana Rocha Maximiano
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
| | - Fabiano Cavalcanti Fernandes
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
| | - Gabriella Cavalcante Amorim
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
- Embrapa
Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte—Asa Norte, Brasília, DF 70770-917, Brazil
| | | | - Danieli Fernanda Buccini
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
| | - Valentina Nieto Marín
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
| | - Gabriel Cidade Feitosa
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
- Pós-Graduação
em Patologia Molecular, Universidade de
Brasília, Campus
Darcy Ribeiro, Brasília, DF 70910-900, Brazil
| | | | - Juliana Bueno Barra
- Laboratório
de RMN, Instituto de Química, Universidade
Federal de Goiás, Goiânia, GO 74690-900, Brazil
| | - Antonio Alonso
- Instituto
de Física, Universidade Federal de
Goiás, Goiânia, GO 74690-900, Brazil
| | - Maria Fátima Grossi de Sá
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
- Embrapa
Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte—Asa Norte, Brasília, DF 70770-917, Brazil
| | - Luciano Morais Lião
- Laboratório
de RMN, Instituto de Química, Universidade
Federal de Goiás, Goiânia, GO 74690-900, Brazil
| | - Octávio Luiz Franco
- S-Inova
Biotech, Programa de Pós-Graduação
em Biotecnologia Universidade Católica Dom Bosco, Av. Tamandaré, 6000—Jardim
Seminario, Campo Grande, MS 79117-900, Brazil
- Centro
de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em
Ciências Genômicas e Biotecnologia Universidade Católica
de Brasília, St.
de Grandes Áreas Norte 916—Asa Norte, Brasília, DF 70790-160, Brazil
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39
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Zhao Y, Du SS, Zhao CY, Li TL, Tong SC, Zhao L. Mechanism of Abnormal Activation of MEK1 Induced by Dehydroalanine Modification. Int J Mol Sci 2024; 25:7482. [PMID: 39000589 PMCID: PMC11242638 DOI: 10.3390/ijms25137482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Mitogen-activated protein kinase kinase 1 (MAPK kinase 1, MEK1) is a key kinase in the mitogen-activated protein kinase (MAPK) signaling pathway. MEK1 mutations have been reported to lead to abnormal activation that is closely related to the malignant growth and spread of various tumors, making it an important target for cancer treatment. Targeting MEK1, four small-molecular drugs have been approved by the FDA, including Trametinib, Cobimetinib, Binimetinib, and Selumetinib. Recently, a study showed that modification with dehydroalanine (Dha) can also lead to abnormal activation of MEK1, which has the potential to promote tumor development. In this study, we used molecular dynamics simulations and metadynamics to explore the mechanism of abnormal activation of MEK1 caused by the Dha modification and predicted the inhibitory effects of four FDA-approved MEK1 inhibitors on the Dha-modified MEK1. The results showed that the mechanism of abnormal activation of MEK1 caused by the Dha modification is due to the movement of the active segment, which opens the active pocket and exposes the catalytic site, leading to sustained abnormal activation of MEK1. Among four FDA-approved inhibitors, only Selumetinib clearly blocks the active site by changing the secondary structure of the active segment from α-helix to disordered loop. Our study will help to explain the mechanism of abnormal activation of MEK1 caused by the Dha modification and provide clues for the development of corresponding inhibitors.
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Affiliation(s)
- Yue Zhao
- School of Life Sciences, Jilin University, Changchun 130118, China; (Y.Z.); (S.-S.D.); (C.-Y.Z.)
| | - Shan-Shan Du
- School of Life Sciences, Jilin University, Changchun 130118, China; (Y.Z.); (S.-S.D.); (C.-Y.Z.)
| | - Chao-Yue Zhao
- School of Life Sciences, Jilin University, Changchun 130118, China; (Y.Z.); (S.-S.D.); (C.-Y.Z.)
| | - Tian-Long Li
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China; (T.-L.L.); (S.-C.T.)
| | - Si-Cheng Tong
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, China; (T.-L.L.); (S.-C.T.)
| | - Li Zhao
- School of Life Sciences, Jilin University, Changchun 130118, China; (Y.Z.); (S.-S.D.); (C.-Y.Z.)
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40
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Jiang P, Zhang C, Wang H, Li P, Du X, Wang Y, Lyukmanova E, Lin C, Wang X. Nicotine Enantioselectively Targets Myeloid Differentiation Protein 2 and Inhibits the Toll-like Receptor 4 Signaling. J Chem Inf Model 2024; 64:5253-5261. [PMID: 38973303 DOI: 10.1021/acs.jcim.4c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Psychoactive substances, including morphine and methamphetamine, have been shown to interact with the classic innate immune receptor Toll-like receptor 4 (TLR4) and its partner protein myeloid differentiation protein 2 (MD2) in a nonenantioselective manner. (-)-Nicotine, the primary alkaloid in tobacco and a key component of highly addictive cigarettes, targets the TLR4/MD2, influencing TLR4 signaling pathways. Existing as two enantiomers, the stereoselective recognition of nicotine by TLR4/MD2 in the context of the innate immune response remains unclear. In this study, we synthesized (+)-nicotine and investigated its effects alongside (-)-nicotine on lipopolysaccharide (LPS)-induced TLR4 signaling. (-)-Nicotine dose-dependently inhibited proinflammatory factors such as tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), and cyclooxygenase-2 (COX-2). In contrast, (+)-nicotine showed no such inhibitory effects. Molecular dynamics simulations revealed that (-)-nicotine exhibited a stronger affinity with the TLR4 coreceptor MD2 than (+)-nicotine. Additionally, in silico simulations revealed that both nicotine enantiomers initially attach to the entrance of the MD2 cavity, creating a metastable state before they fully enter the cavity. In the metastable state, (-)-nicotine established more stable interactions with the surrounding residues at the entrance of the MD2 cavity compared to those of (+)-nicotine. This highlights the crucial role of the MD2 cavity entrance in the chiral recognition of nicotine. These findings provide valuable insights into the distinct interactions between nicotine enantiomers and the TLR4 coreceptor MD2, underscoring the enantioselective effect of nicotine on modulating TLR4 signaling.
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Affiliation(s)
- Pu Jiang
- Laboratory of Chemical Biology, , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Cong Zhang
- Laboratory of Chemical Biology, , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Hongshuang Wang
- Laboratory of Chemical Biology, , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Penghui Li
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiubo Du
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yibo Wang
- Laboratory of Chemical Biology, , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Ekaterina Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 119997, Russia
- Biological Department, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Cong Lin
- Laboratory of Chemical Biology, , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xiaohui Wang
- Laboratory of Chemical Biology, , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
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41
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Moqadam M, Gartan P, Talandashti R, Chiapparino A, Titeca K, Gavin AC, Reuter N. A Membrane-Assisted Mechanism for the Release of Ceramide from the CERT START Domain. J Phys Chem B 2024; 128:6338-6351. [PMID: 38903016 PMCID: PMC11228987 DOI: 10.1021/acs.jpcb.4c02398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/26/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Ceramide transfer protein CERT is the mediator of nonvesicular transfer of ceramide from the ER to Golgi. In CERT, START is the domain responsible for the binding and transport of ceramide. A wealth of structural data has revealed a helix-grip fold surrounding a large hydrophobic cavity holding the ceramide. Yet, little is known about the mechanisms by which START releases the ceramide through the polar region and into the packed environment of cellular membranes. As such events do not lend themselves easily to experimental investigations, we used multiple unbiased microsecond-long molecular simulations. We propose a membrane-assisted mechanism in which the membrane acts as an allosteric effector initiating the release of ceramide and where the passage of the ceramide acyl chains is facilitated by the intercalation of a single phosphatidylcholine lipid in the cavity, practically greasing the ceramide way out. We verify using free energy calculation and experimental lipidomics data that CERT forms stable complexes with phosphatidylcholine lipids, in addition to ceramide, thus providing validation for the proposed mechanism.
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Affiliation(s)
- Mahmoud Moqadam
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Parveen Gartan
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Reza Talandashti
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Antonella Chiapparino
- European
Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
| | - Kevin Titeca
- European
Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
- Department
of Cell Physiology and Metabolism, University
of Geneva, CMU Rue Michel-Servet 1, Genève 4 1211, Switzerland
| | - Anne-Claude Gavin
- Department
of Cell Physiology and Metabolism, University
of Geneva, CMU Rue Michel-Servet 1, Genève 4 1211, Switzerland
| | - Nathalie Reuter
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
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42
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Kang JM, Park JS, Lee JS, Jang JY, Han BW. Structural study for substrate recognition of human N-terminal glutamine amidohydrolase 1 in the arginine N-degron pathway. Protein Sci 2024; 33:e5067. [PMID: 38864716 PMCID: PMC11168063 DOI: 10.1002/pro.5067] [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: 01/02/2024] [Revised: 04/12/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024]
Abstract
The N-degron pathway determines the half-life of proteins by selectively destabilizing the proteins bearing N-degrons. N-terminal glutamine amidohydrolase 1 (NTAQ1) plays an essential role in the arginine N-degron (Arg/N-degron) pathway as an initializing enzyme via the deamidation of the N-terminal (Nt) glutamine (Gln). However, the Nt-serine-bound conformation of hNTAQ1 according to the previously identified crystal structure suggests the possibility of other factors influencing the recognition of Nt residues by hNTAQ1. Hence, in the current study, we aimed to further elucidate the substrate recognition of hNTAQ1; specifically, we explored 12 different substrate-binding conformations of hNTAQ1 depending on the subsequent residue of Nt-Gln. Results revealed that hNTAQ1 primarily interacts with the protein Nt backbone, instead of the side chain, for substrate recognition. Here, we report that the Nt backbone of proteins appears to be a key component of hNTAQ1 function and is the main determinant of substrate recognition. Moreover, not all second residues from Nt-Gln, but rather distinctive and charged residues, appeared to aid in detecting substrate recognition. These new findings define the substrate-recognition process of hNTAQ1 and emphasize the importance of the subsequent Gln residue in the Nt-Gln degradation system. Our extensive structural and biochemical analyses provide insights into the substrate specificity of the N-degron pathway and shed light on the mechanism underlying hNTAQ1 substrate recognition. An improved understanding of the protein degradation machinery could aid in developing therapies to promote overall health through enhanced protein regulation, such as targeted protein therapies.
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Affiliation(s)
- Jin Mo Kang
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Jae Seok Lee
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Jun Young Jang
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of PharmacySeoul National UniversitySeoulRepublic of Korea
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43
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Hsieh MC, Zhang J, Tang L, Huang CY, Shen Y, Matathia A, Qian J, Parekh BS. Characterization of the Charge Heterogeneity of a Monoclonal Antibody That Binds to Both Cation Exchange and Anion Exchange Columns under the Same Binding Conditions. Antibodies (Basel) 2024; 13:52. [PMID: 39051328 PMCID: PMC11270306 DOI: 10.3390/antib13030052] [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: 05/31/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Therapeutic antibodies play an important role in the public healthcare system to treat patients with a variety of diseases. Protein characterization using an array of analytical tools provides in-depth information for drug quality, safety, efficacy, and the further understanding of the molecule. A therapeutic antibody candidate MAB1 exhibits unique binding properties to both cation and anion exchange columns at neutral pH. This uniqueness disrupts standard purification processes and necessitates adjustments in manufacturing. This study identifies that the charge heterogeneity of MAB1 is primarily due to the N-terminal cyclization of glutamine to pyroglutamine and, to a lesser extent, succinimide intermediate, deamidation, and C-terminal lysine. Using three approaches, i.e., deferential chemical labeling, H/D exchange, and molecular modeling, the binding to anion exchange resins is attributed to negatively charged patches on the antibody's surface, involving specific carboxylic acid residues. The methodologies shown here can be extended to study protein binding orientation in column chromatography.
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Affiliation(s)
- Ming-Ching Hsieh
- Analytical Sciences, Eli Lilly and the Company, Branchburg, NJ 08876, USA
| | - Jingming Zhang
- Analytical Sciences, Eli Lilly and the Company, Branchburg, NJ 08876, USA
| | - Liangjie Tang
- Analytical Development, Eli Lilly and the Company, Indianapolis, IN 46221, USA
| | - Cheng-Yen Huang
- Analytical Sciences, Eli Lilly and the Company, Branchburg, NJ 08876, USA
| | - Yang Shen
- Antibody Technology, Eli Lilly and the Company, New York, NY 10016, USA
| | - Alice Matathia
- TS/MS Laboratories, Eli Lilly and the Company, Branchburg, NJ 08876, USA
| | - Jun Qian
- Analytical Development, Eli Lilly and the Company, Indianapolis, IN 46221, USA
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44
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Tolokh IS, Folescu DE, Onufriev AV. Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains. J Phys Chem B 2024; 128:5855-5873. [PMID: 38860842 PMCID: PMC11194828 DOI: 10.1021/acs.jpcb.4c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024]
Abstract
The current practical "workhorses" of the atomistic implicit solvation─the Poisson-Boltzmann (PB) and generalized Born (GB) models─face fundamental accuracy limitations. Here, we propose a computationally efficient implicit solvation framework, the Implicit Water Multipole GB (IWM-GB) model, that systematically incorporates the effects of multipole moments of water molecules in the first hydration shell of a solute, beyond the dipole water polarization already present at the PB/GB level. The framework explicitly accounts for coupling between polar and nonpolar contributions to the total solvation energy, which is missing from many implicit solvation models. An implementation of the framework, utilizing the GAFF force field and AM1-BCC atomic partial charges model, is parametrized and tested against the experimental hydration free energies of small molecules from the FreeSolv database. The resulting accuracy on the test set (RMSE ∼ 0.9 kcal/mol) is 12% better than that of the explicit solvation (TIP3P) treatment, which is orders of magnitude slower. We also find that the coupling between polar and nonpolar parts of the solvation free energy is essential to ensuring that several features of the IWM-GB model are physically meaningful, including the sign of the nonpolar contributions.
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Affiliation(s)
- Igor S. Tolokh
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Dan E. Folescu
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Mathematics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexey V. Onufriev
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center
for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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45
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Riepl D, Gamiz-Hernandez AP, Kovalova T, Król SM, Mader SL, Sjöstrand D, Högbom M, Brzezinski P, Kaila VRI. Long-range charge transfer mechanism of the III 2IV 2 mycobacterial supercomplex. Nat Commun 2024; 15:5276. [PMID: 38902248 PMCID: PMC11189923 DOI: 10.1038/s41467-024-49628-9] [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: 11/16/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
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Affiliation(s)
- Daniel Riepl
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Terezia Kovalova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sylwia M Król
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Dan Sjöstrand
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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46
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Muthukumaran R, Sankararamakrishnan R. Differences in the Membrane-Binding Properties of Flaviviral Nonstructural 1 (NS1) Protein: Comparative Simulations of Zika and Dengue Virus NS1 Proteins in Explicit Bilayers. ACS BIO & MED CHEM AU 2024; 4:137-153. [PMID: 38911907 PMCID: PMC11191575 DOI: 10.1021/acsbiomedchemau.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 06/25/2024]
Abstract
NS1 in flaviviruses is the only nonstructural protein that is secretory and interacts with different cellular components of the host cell membrane. NS1 is localized in the ER as a dimer to facilitate viral replication. Crystal structures of NS1 homologues from zika (ZIKV) and dengue (DENV) viruses have revealed the organization of different domains in NS1 dimers. The β-roll and the connector and intertwined loop regions of wing domains of NS1 have been shown to interact with the membranes. In this study, we have performed multiple molecular dynamics (MD) simulations of ZIKV and DENV NS1 systems in apo and in POPE bilayers with different cholesterol concentrations (0, 20 and 40%). The NS1 protein was placed just above the membrane surface, and for each NS1-membrane system two to three independent simulations with 600 ns production run were performed. At the end of the production runs, ZIKV NS1 inserts deeper inside the membrane compared to the DENV counterpart. Unlike ZIKV NS1, the orientation of DENV NS1 is asymmetric in which one of the chains in the dimer interacts with the membrane while the other is more exposed to the solvent. The β-roll region in ZIKV NS1 penetrates beyond the headgroup region and interacts with the lipid acyl chains while the C-terminal region barely interacts with the headgroup. Specific residues in the intertwined region deeply penetrate inside the membrane. The role of charged and aromatic residues of ZIKV NS1 in strongly interacting with the membrane components is revealed. The presence of cholesterol affects the extent of insertion in the membrane and interaction of individual residues. Overall, membrane-binding properties of ZIKV NS1 significantly differ from its counterpart in DENV. The differences found in the binding and insertion of NS1 can be used to design drugs and novel antibodies that can be flavivirus specific.
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Affiliation(s)
- Rajagopalan Muthukumaran
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Ramasubbu Sankararamakrishnan
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
- Mehta
Family Center for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur 208016, India
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47
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Salgado M, Márquez-Miranda V, Ferrada L, Rojas M, Poblete-Flores G, González-Nilo FD, Ardiles ÁO, Sáez JC. Ca 2+ permeation through C-terminal cleaved, but not full-length human Pannexin1 hemichannels, mediates cell death. Proc Natl Acad Sci U S A 2024; 121:e2405468121. [PMID: 38861601 PMCID: PMC11194574 DOI: 10.1073/pnas.2405468121] [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: 03/15/2024] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
Pannexin1 hemichannels (Panx1 HCs) are found in the membrane of most mammalian cells and communicate the intracellular and extracellular spaces, enabling the passive transfer of ions and small molecules. They are involved in physiological and pathophysiological conditions. During apoptosis, the C-terminal tail of Panx1 is proteolytically cleaved, but the permeability features of hemichannels and their role in cell death remain elusive. To address these topics, HeLa cells transfected with full-length human Panx1 (fl-hPanx1) or C-terminal truncated hPanx1 (Δ371hPanx1) were exposed to alkaline extracellular saline solution, increasing the activity of Panx1 HCs. The Δ371hPanx1 HC was permeable to DAPI and Etd+, but not to propidium iodide, whereas fl-hPanx1 HC was only permeable to DAPI. Furthermore, the cytoplasmic Ca2+ signal increased only in Δ371hPanx1 cells, which was supported by bioinformatics approaches. The influx of Ca2+ through Δ371hPanx1 HCs was necessary to promote cell death up to about 95% of cells, whereas the exposure to alkaline saline solution without Ca2+ failed to induce cell death, and the Ca2+ ionophore A23187 promoted more than 80% cell death even in fl-hPanx1 transfectants. Moreover, cell death was prevented with carbenoxolone or 10Panx1 in Δ371hPanx1 cells, whereas it was undetectable in HeLa Panx1-/- cells. Pretreatment with Ferrostatin-1 and necrostatin-1 did not prevent cell death, suggesting that ferroptosis or necroptosis was not involved. In comparison, zVAD-FMK, a pancaspase inhibitor, reduced death by ~60%, suggesting the involvement of apoptosis. Therefore, alkaline pH increases the activity of Δ371hPanx1HCs, leading to a critical intracellular free-Ca2+ overload that promotes cell death.
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Affiliation(s)
- Magdiel Salgado
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias, Universidad de Valparaíso, Valparaíso2381850, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago8370146, Chile
| | - Luciano Ferrada
- Centro de Microscopía Avanzada-Biobío, Universidad de Concepción, Concepción4070386, Chile
| | - Maximiliano Rojas
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago8370146, Chile
| | - Gonzalo Poblete-Flores
- Escuela de Medicina, Facultad de Medicina, Universidad de Valparaíso, Valparaíso2341386, Chile
| | - Fernando D. González-Nilo
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias, Universidad de Valparaíso, Valparaíso2381850, Chile
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago8370146, Chile
| | - Álvaro O. Ardiles
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias, Universidad de Valparaíso, Valparaíso2381850, Chile
- Escuela de Medicina, Facultad de Medicina, Universidad de Valparaíso, Valparaíso2341386, Chile
| | - Juan C. Sáez
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias, Universidad de Valparaíso, Valparaíso2381850, Chile
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48
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Bastos RS, de Aguiar CPO, Cruz JN, Ramos RS, Kimani NM, de Souza JSN, Chaves MH, de Freitas HF, Pita SSR, dos Santos CBR. Rational Approach toward COVID-19's Main Protease Inhibitors: A Hierarchical Biochemoinformatics Analysis. Int J Mol Sci 2024; 25:6715. [PMID: 38928422 PMCID: PMC11204165 DOI: 10.3390/ijms25126715] [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: 04/14/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
This study investigated the potential of selected compounds as inhibitors of SARS-CoV-2 Mpro through pharmacokinetic and toxicological analyses, molecular docking, and molecular dynamics simulations. In silico molecular docking simulations revealed promising ligands with favorable binding affinities for Mpro, ranging from -6.2 to -9.5 kcal/mol. Moreover, molecular dynamics simulations demonstrated the stability of protein-ligand complexes over 200 ns, maintaining protein secondary structures. MM-PBSA analysis revealed favorable interactions between ligands and Mpro, with negative binding energy values. Hydrogen bond formation capacity during molecular dynamics was confirmed, indicating consistent interactions with Mpro catalytic residues. Based on these findings, selected ligands show promise for future studies in developing COVID-19 treatments.
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Affiliation(s)
- Ruan S. Bastos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Christiane P. O. de Aguiar
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Ryan S. Ramos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Njogu M. Kimani
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya
- Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu P.O. Box 6-60100, Kenya
| | - João S. N. de Souza
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil
| | - Mariana H. Chaves
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil
| | - Humberto F. de Freitas
- Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Federal University of Bahia, Av. Barão de Jeremoabo, 147, Pharmacy College, Ondina, Salvador 40170-115, BA, Brazil; (H.F.d.F.); (S.S.R.P.)
| | - Samuel S. R. Pita
- Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Federal University of Bahia, Av. Barão de Jeremoabo, 147, Pharmacy College, Ondina, Salvador 40170-115, BA, Brazil; (H.F.d.F.); (S.S.R.P.)
| | - Cleydson B. R. dos Santos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
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49
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Boulaamane Y, Molina Panadero I, Hmadcha A, Atalaya Rey C, Baammi S, El Allali A, Maurady A, Smani Y. Antibiotic discovery with artificial intelligence for the treatment of Acinetobacter baumannii infections. mSystems 2024; 9:e0032524. [PMID: 38700330 PMCID: PMC11326114 DOI: 10.1128/msystems.00325-24] [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: 03/06/2024] [Accepted: 03/27/2024] [Indexed: 05/05/2024] Open
Abstract
Global challenges presented by multidrug-resistant Acinetobacter baumannii infections have stimulated the development of new treatment strategies. We reported that outer membrane protein W (OmpW) is a potential therapeutic target in A. baumannii. Here, a library of 11,648 natural compounds was subjected to a primary screening using quantitative structure-activity relationship (QSAR) models generated from a ChEMBL data set with >7,000 compounds with their reported minimal inhibitory concentration (MIC) values against A. baumannii followed by a structure-based virtual screening against OmpW. In silico pharmacokinetic evaluation was conducted to assess the drug-likeness of these compounds. The ten highest-ranking compounds were found to bind with an energy score ranging from -7.8 to -7.0 kcal/mol where most of them belonged to curcuminoids. To validate these findings, one lead compound exhibiting promising binding stability as well as favorable pharmacokinetics properties, namely demethoxycurcumin, was tested against a panel of A. baumannii strains to determine its antibacterial activity using microdilution and time-kill curve assays. To validate whether the compound binds to the selected target, an OmpW-deficient mutant was studied and compared with the wild type. Our results demonstrate that demethoxycurcumin in monotherapy and in combination with colistin is active against all A. baumannii strains. Finally, the compound was found to significantly reduce the A. baumannii interaction with host cells, suggesting its anti-virulence properties. Collectively, this study demonstrates machine learning as a promising strategy for the discovery of curcuminoids as antimicrobial agents for combating A. baumannii infections. IMPORTANCE Acinetobacter baumannii presents a severe global health threat, with alarming levels of antimicrobial resistance rates resulting in significant morbidity and mortality in the USA, ranging from 26% to 68%, as reported by the Centers for Disease Control and Prevention (CDC). To address this threat, novel strategies beyond traditional antibiotics are imperative. Computational approaches, such as QSAR models leverage molecular structures to predict biological effects, expediting drug discovery. We identified OmpW as a potential therapeutic target in A. baumannii and screened 11,648 natural compounds. We employed QSAR models from a ChEMBL bioactivity data set and conducted structure-based virtual screening against OmpW. Demethoxycurcumin, a lead compound, exhibited promising antibacterial activity against A. baumannii, including multidrug-resistant strains. Additionally, demethoxycurcumin demonstrated anti-virulence properties by reducing A. baumannii interaction with host cells. The findings highlight the potential of artificial intelligence in discovering curcuminoids as effective antimicrobial agents against A. baumannii infections, offering a promising strategy to address antibiotic resistance.
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Affiliation(s)
- Yassir Boulaamane
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Irene Molina Panadero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/Junta de Andalucía, Seville, Spain
| | - Abdelkrim Hmadcha
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
- Biosanitary Research Institute (IIB-VIU), Valencian International University (VIU), Valencia, Spain
| | - Celia Atalaya Rey
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/Junta de Andalucía, Seville, Spain
| | - Soukayna Baammi
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Amal Maurady
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
- Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Younes Smani
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/Junta de Andalucía, Seville, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
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50
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Mustapha T, B S, Zubair T, Patil RB, Bhongade BA, Sangshetti JN, Mali A, Babalola BJ, Moin AT, Islam T. In vitro and in silico investigation of effects of antimicrobial peptides from Solanaceae plants against rice sheath blight pathogen Rhizoctinia solani. PLoS One 2024; 19:e0302440. [PMID: 38870165 PMCID: PMC11175423 DOI: 10.1371/journal.pone.0302440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 04/01/2024] [Indexed: 06/15/2024] Open
Abstract
Rhizoctonia solani, the causative agent of sheath blight disease in rice, poses a significant threat to agricultural productivity. Traditional management approaches involving chemical fungicides have been effective but come with detrimental consequences for the ecosystem. This study aimed to investigate sustainable alternatives in the form of antifungal peptides derived from Solanaceous plant species as potential agents against R. solani. Peptide extracts were obtained using an optimized antimicrobial peptide (AMP) extraction method and desalted using the solid-phase extraction technique. The antifungal potential of peptide-rich extracts from Solanum tuberosum and Capsicum annum was assessed through in vitro tests employing the agar well diffusion method. Furthermore, peptide-protein docking analysis was performed on HPEPDOCK and HDOCK server; and molecular dynamics simulations (MDS) of 100 ns period were performed using the Gromacs 2020.4. The results demonstrated significant inhibition zones for both extracts at concentrations of 100 mg/mL. Additionally, the extracts of Solanum tuberosum and Capsicum annum had minimum inhibitory concentrations of 50 mg/mL and 25 mg/mL, respectively with minimum fungicidal concentrations of 25 mg/mL. Insights into the potential mechanisms of key peptides inhibiting R. solani targets were gleaned from in-silico studies. Notably, certain AMPs exhibited favorable free energy of binding against pathogenicity-related targets, including histone demethylase, sortin nexin, and squalene synthase, in protein-peptide docking simulations. Extended molecular dynamics simulations lasting 100 ns and MM-PBSA calculations were performed on select protein-peptide complexes. AMP10 displayed the most favorable binding free energy against all target proteins, with AMP3, AMP12b, AMP6, and AMP15 also exhibiting promising results against specific targets of R. solani. These findings underscore the potential of peptide extracts from S. tuberosum and C. annum as effective antifungal agents against rice sheath blight caused by R. solani.
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Affiliation(s)
- Tijjani Mustapha
- Department of Biological Sciences, Federal University, Dutse, Nigeria
| | - Shefin B
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Trivandrum, India
| | | | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Vadgaon (Bk), Pune, Maharashtra, India
| | - Bhoomendra A. Bhongade
- Department of Pharmaceutical Chemistry, RAK College of Pharmacy, RAK Medical & Health Sciences University, Ras Al Khaimah, United Arab Emirates
| | - Jaiprakash N. Sangshetti
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, (MS), India
| | - Aniket Mali
- Cancer Research Lab, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
| | | | - Abu Tayab Moin
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
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