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Nakonieczna A, Topolska-Woś A, Łobocka M. New bacteriophage-derived lysins, LysJ and LysF, with the potential to control Bacillus anthracis. Appl Microbiol Biotechnol 2024; 108:76. [PMID: 38194144 PMCID: PMC10776502 DOI: 10.1007/s00253-023-12839-z] [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: 04/11/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/10/2024]
Abstract
Bacillus anthracis is an etiological agent of anthrax, a severe zoonotic disease that can be transmitted to people and cause high mortalities. Bacteriophages and their lytic enzymes, endolysins, have potential therapeutic value in treating infections caused by this bacterium as alternatives or complements to antibiotic therapy. They can also be used to identify and detect B. anthracis. Endolysins of two B. anthracis Wbetavirus phages, J5a and F16Ba which were described by us recently, differ significantly from the best-known B. anthracis phage endolysin PlyG from Wbetavirus genus bacteriophage Gamma and a few other Wbetavirus genus phages. They are larger than PlyG (351 vs. 233 amino acid residues), contain a signal peptide at their N-termini, and, by prediction, have a different fold of cell binding domain suggesting different structural basis of cell epitope recognition. We purified in a soluble form the modified versions of these endolysins, designated by us LysJ and LysF, respectively, and depleted of signal peptides. Both modified endolysins could lyse the B. anthracis cell wall in zymogram assays. Their activity against the living cells of B. anthracis and other species of Bacillus genus was tested by spotting on the layers of bacteria in soft agar and by assessing the reduction of optical density of bacterial suspensions. Both methods proved the effectiveness of LysJ and LysF in killing the anthrax bacilli, although the results obtained by each method differed. Additionally, the lytic efficiency of both proteins was different, which apparently correlates with differences in their amino acid sequence. KEY POINTS: • LysJ and LysF are B. anthracis-targeting lysins differing from lysins studied so far • LysJ and LysF could be overproduced in E. coli in soluble and active forms • LysJ and LysF are active in killing cells of B. anthracis virulent strains.
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Affiliation(s)
- Aleksandra Nakonieczna
- Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, 24-100, Puławy, Poland.
| | | | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
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Darvazi M, Ghorbani M, Ramazi S, Allahverdi A, Abdolmaleki P. A computational study of the R120G mutation in human αB-crystallin: implications for structural stability and functionality. J Biomol Struct Dyn 2024; 42:5788-5798. [PMID: 37354135 DOI: 10.1080/07391102.2023.2229434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
The eye is a vital organ in the visual system, which is composed of transparent vascular tissue. αB-crystallin, a significant protein found in the lens, plays a crucial role in our understanding of lens diseases. Mutations in the αB-crystallin protein can cause lens diseases, such as cataracts and myopathy. However, the molecular mechanism underlying the R120G mutation is not fully understood. In this study, we utilized molecular dynamics simulations to illustrate, in atomic detail, how the R120G mutation leads to the aggregation of αB-crystallin and scattering of light in the lens. Our findings show that the R120G mutation alters the dynamic and structural properties of the αB-crystallin protein. Specifically, this mutation causes the angle of the hairpin at the C-terminal to increase from 80° to 150°, while reducing the distance between the hydrophobic patches around residues 10 and 44-55 from 1.5 nm to 1 nm. In addition, our results showed that the mutation could disrupt the IPI motif - β4/β8 interaction. The disruption of this interaction could affect the αB-crystallin oligomerization and the chaperone activity of αB-crystallin protein. The exposed hydrophobic area at the IPI motif - β4/β8 could become the primary site for interprotein interactions, which are responsible for large-scale aggregation. We have demonstrated that, in wild-type αB-crystallin protein, salt bridges R120 and D109, R107 and D80 are formed. However, in the case of the R120G mutation, the salt bridges R120 and R109 are disrupted, and a new salt bridge with a different pattern is formed. In our study, it has been found that all of the changes associated with the R120G mutation are located at the interface of chains A and B, which could impact the multimerization of the αB-crystallin. Previous research on the K92-E99 residue has shown that a salt bridge in the dimer I can reduce the chaperone activity of the protein. Furthermore, the salt bridges R120 and D109, as well as R107 and D80 in dimer II, induce changes in the hydrophobic envelope of β-sheets in the α-crystallin domain (ACD). These changes could have an impact on the multimerization of the αB-crystallin, leading to disruption of the oligomer structure and aggregation. Moreover, the changes in the αB-crystallin resulting from the R120G mutation can lead to faulty interactions with other proteins, which can cause the aggregation of αB-crystallin with other proteins, such as desmin. These findings may provide new insights into the development of treatments for lens diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mona Darvazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Diniz EADS, da Silva DP, Ferreira SDS, Fernandes-Pedrosa MDF, Vieira DS. Temperature effect in the inhibition of PLA 2 activity of Bothrops brazili venom by Rosmarinic and Chlorogenic acids, experimental and computational approaches. J Biomol Struct Dyn 2024; 42:5238-5252. [PMID: 37378497 DOI: 10.1080/07391102.2023.2226912] [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: 03/28/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]
Abstract
Myotoxicity caused by snakebite envenoming emerges as one of the main problems of ophidic accidents as it is not well neutralized by the current serum therapy. A promising alternative is to search for efficient small molecule inhibitors that can act against multiple venom components. Phospholipase A2 (PLA2) is frequently found in snake venom and is usually associated with myotoxicity. Thus it represents an excellent target for the search of new treatments. This work reports the effect of temperature in the inhibition of catalytic properties of PLA2 from Bothrops brazili venom by Rosmarinic (RSM) and Chlorogenic (CHL) acids through experimental and computational approaches. Three temperatures were evaluated (25, 37 and 50 °C). In the experimental section, enzymatic assays showed that RSM is a better inhibitor in all three temperatures. At 50 °C, the inhibition efficiency decayed significantly for both acids. Docking studies revealed that both ligands bind to the hydrophobic channel of the protein dimer where the phospholipid binds in the catalytic process, interacting with several functional residues. In this context, RSM presents better interaction energies due to stronger interactions with chain B of the dimer. Molecular dynamics simulations showed that RSM can establish selective interactions with ARG112B of PLA2, which is located next to residues of the putative Membrane Disruption Site in PLA2-like structures. The affinity of RSM and CHL acids towards PLA2 is mainly driven by electrostatic interactions, especially salt bridge interactions established with residues ARG33B (for CHL) and ARG112B (RSM) and hydrogen bonds with residue ASP89A. The inability of CHL to establish a stable interaction with ARG112B was identified as the reason for its lower inhibition efficiency compared to RSM at the three temperatures. Furthermore, extensive structural analysis was performed to explain the lower inhibition efficiency at 50 °C for both ligands. The analysis performed in this work provides important information for the future design of new inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Diana Pontes da Silva
- Laboratory of Technology and Pharmaceutical Biotechnology (Tecbiofar), College of Pharmacy, Federal University of Rio Grande do Norte, Avenue General Gustavo Cordeiro de Farias, Petrópolis, Natal, Brazil
| | - Sarah de Sousa Ferreira
- Laboratory of Technology and Pharmaceutical Biotechnology (Tecbiofar), College of Pharmacy, Federal University of Rio Grande do Norte, Avenue General Gustavo Cordeiro de Farias, Petrópolis, Natal, Brazil
| | - Matheus de Freitas Fernandes-Pedrosa
- Laboratory of Technology and Pharmaceutical Biotechnology (Tecbiofar), College of Pharmacy, Federal University of Rio Grande do Norte, Avenue General Gustavo Cordeiro de Farias, Petrópolis, Natal, Brazil
| | - Davi Serradella Vieira
- Institute of Chemistry, Federal University of Rio Grande do Norte, Av Senador Salgado Filho, Natal-RN, Brazil
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Dousa KM, Shin E, Kurz SG, Plummer M, Nantongo M, Bethel CR, Taracila MA, Nguyen DC, Kreiswith BN, Daley CL, Remy KE, Holland SM, Bonomo RA. Synergistic effects of sulopenem in combination with cefuroxime or durlobactam against Mycobacterium abscessus. mBio 2024; 15:e0060924. [PMID: 38742824 DOI: 10.1128/mbio.00609-24] [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: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 05/16/2024] Open
Abstract
Mycobacterium abscessus (Mab) affects patients with immunosuppression or underlying structural lung diseases such as cystic fibrosis (CF). Additionally, Mab poses clinical challenges due to its resistance to multiple antibiotics. Herein, we investigated the synergistic effect of dual β-lactams [sulopenem and cefuroxime (CXM)] or the combination of sulopenem and CXM with β-lactamase inhibitors [BLIs-avibactam (AVI) or durlobactam (DUR)]. The sulopenem-CXM combination yielded low minimum inhibitory concentration (MIC) values for 54 clinical Mab isolates and ATCC19977 (MIC50 and MIC90 ≤0.25 µg/mL). Similar synergistic effects were observed in time-kill studies conducted at concentrations achievable in clinical settings. Sulopenem-CXM outperformed monotherapy, yielding ~1.5 Log10 CFU/mL reduction during 10 days. Addition of BLIs enhanced this antibacterial effect, resulting in an additional reduction of CFUs (~3 Log10 for sulopenem-CXM and AVI and ~4 Log10 for sulopenem-DUR). Exploration of the potential mechanisms of the synergy focused on their interactions with L,D-transpeptidases (Ldts; LdtMab1-LdtMab4), penicillin-binding-protein B (PBP B), and D,D-carboxypeptidase (DDC). Acyl complexes, identified via mass spectrometry analysis, demonstrated the binding of sulopenem with LdtMab2-LdtMab4, DDC, and PBP B and CXM with LdtMab2 and PBP B. Molecular docking and mass spectrometry data suggest the formation of a covalent adduct between sulopenem and LdtMab2 after the nucleophilic attack of the cysteine residue at the β-lactam carbonyl carbon, leading to the cleavage of the β-lactam ring and the establishment of a thioester bond linking the LdtMab2 with sulopenem. In conclusion, we demonstrated the biochemical basis of the synergy of sulopenem-CXM with or without BLIs. These findings potentially broaden the selection of oral therapeutic agents to combat Mab. IMPORTANCE Treating infections from Mycobacterium abscessus (Mab), particularly those resistant to common antibiotics like macrolides, is notoriously difficult, akin to a never-ending struggle for healthcare providers. The rate of treatment failure is even higher than that seen with multidrug-resistant tuberculosis. The role of combination β-lactams in inhibiting L,D-transpeptidation, the major peptidoglycan crosslink reaction in Mab, is an area of intense investigation, and clinicians have utilized this approach in the treatment of macrolide-resistant Mab, with reports showing clinical success. In our study, we found that cefuroxime and sulopenem, when used together, display a significant synergistic effect. If this promising result seen in lab settings, translates well into real-world clinical effectiveness, it could revolutionize current treatment methods. This combination could either replace the need for more complex intravenous medications or serve as a "step down" to an oral medication regimen. Such a shift would be much easier for patients to manage, enhancing their comfort and likelihood of sticking to the treatment plan, which could lead to better outcomes in tackling these tough infections. Our research delved into how these drugs inhibit cell wall synthesis, examined time-kill data and binding studies, and provided a scientific basis for the observed synergy in cell-based assays.
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Affiliation(s)
- Khalid M Dousa
- Louis Stokes Cleveland VA Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Eunjeong Shin
- Louis Stokes Cleveland VA Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Sebastian G Kurz
- Department of Medicine, University of Tübingen, Tübingen, Germany
| | - Mark Plummer
- Yale Center for Molecular Discovery, Yale University, New Haven, Connecticut, USA
| | - Mary Nantongo
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Christopher R Bethel
- Louis Stokes Cleveland VA Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Magdalena A Taracila
- Louis Stokes Cleveland VA Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - David C Nguyen
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Department of Internal Medicine, Division of Infectious Diseases, Rush Medical College, Chicago, Illinois, USA
| | - Barry N Kreiswith
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Charles L Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, Colorado, USA
| | - Kenneth E Remy
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert A Bonomo
- Louis Stokes Cleveland VA Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
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Acha-Sagredo A, Wilson CM, Garcia Bediaga N, Kalirai H, Davies MPA, Coupland SE, Field JK, Liloglou T. Novel Transcriptional and DNA Methylation Abnormalities of SORT1 Gene in Non-Small Cell Lung Cancer. Cancers (Basel) 2024; 16:2154. [PMID: 38893272 PMCID: PMC11171784 DOI: 10.3390/cancers16112154] [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: 05/09/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Sortilin is an important regulator with potential tumour-suppressor function by limiting EGFR signalling. In this study, we undertook a comprehensive expression analysis of sortilin transcript variants and the DNA methylation status of their corresponding promoters in human non-small cell carcinomas (NSCLCs). RNA/DNA was extracted from 81 NSCLC samples and paired normal tissue. mRNA expression was measured by qPCR and DNA methylation determined by pyrosequencing. BigDye-terminator sequencing was used to confirm exon-8 alternative splicing. Results demonstrated that both SORT1A and SORT1B variants were downregulated in lung tumours. The SORT1A/SORT1B expression ratio was higher in tumours compared to normal tissue. SORT1B promoter hypermethylation was detected in lung tumours compared to normal lung (median difference 14%, Mann-Whitney test p = 10-6). Interestingly, SORT1B is hypermethylated in white blood cells, but a small and very consistent drop in methylation (6%, p = 10-15) was observed in the lung cancer cases compared to control subjects. We demonstrate that the SORT1B exon-8 splice variation, reported in sequence databases, is also a feature of SORT1A. The significantly altered quantitative and qualitative characteristics of sortilin mRNA in NSCLC indicate a significant involvement in tumour pathogenesis and may have significant impact for its utility as a predictive marker in lung cancer management.
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Affiliation(s)
- Amelia Acha-Sagredo
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (A.A.-S.); (M.P.A.D.); (J.K.F.)
| | - Cornelia M. Wilson
- Life Sciences Industry Liaison Lab, School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, UK;
| | - Naiara Garcia Bediaga
- Adelaide Centre for Epigenetics, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia;
| | - Helen Kalirai
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L69 3BX, UK; (H.K.); (S.E.C.)
| | - Michael P. A. Davies
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (A.A.-S.); (M.P.A.D.); (J.K.F.)
| | - Sarah E. Coupland
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L69 3BX, UK; (H.K.); (S.E.C.)
| | - John K. Field
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (A.A.-S.); (M.P.A.D.); (J.K.F.)
| | - Triantafillos Liloglou
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (A.A.-S.); (M.P.A.D.); (J.K.F.)
- Medical School, Edge Hill University, St Helens Road, Ormskirk L39 4QP, UK
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Ma H, Kennard A, Mattson N, Khan AS. Characterization of Sf9 cell clones with differential susceptibilities to Sf-rhabdovirus X +3.7 and Sf-rhabdovirus X - replication. Virology 2024; 594:110038. [PMID: 38471199 DOI: 10.1016/j.virol.2024.110038] [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: 10/21/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Our laboratory previously discovered a novel rhabdovirus in the Spodoptera frugiperda Sf9 insect cell line that was designated as Sf-rhabdovirus. Using limiting dilution, this cell line was found to be a mixed population of cells infected by Sf-rhabdovirus variants containing either the full length X accessory gene with a 3.7 kb internal duplication (designated as Sf-rhabdovirus X+3.7) or lacking the duplication and part of the X gene (designated as Sf-rhabdovirus X-), and cells that were negative for Sf-rhabdovirus. In this paper, we found that the Sf-rhabdovirus negative cell clones had sub-populations with different susceptibilities to the replication of Sf-rhabdovirus X+3.7 and X- variants: cell clone Sf9-13F12 was more sensitive to replication by both virus variants compared to Sf9-3003; moreover, Sf9-3003 showed more resistance to X+3.7 replication than to X- replication. RNA-Seq analysis indicated significant differentially expressed genes in the Sf9-13F12 and Sf9-3003 cell clones further supporting that distinct sub-populations of virus-negative cells co-exist in the parent Sf9 cell line.
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Affiliation(s)
- Hailun Ma
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Andrea Kennard
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Nicholas Mattson
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Arifa S Khan
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
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Kapkaç HA, Arslanyolu M. Molecular Cloning, Expression and Enzymatic Characterization of Tetrahymena thermophila Glutathione-S-Transferase Mu 34. Protein J 2024; 43:613-626. [PMID: 38743189 DOI: 10.1007/s10930-024-10204-1] [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] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
Glutathione-S-transferase enzymes (GSTs) are essential components of the phase II detoxification system and protect organisms from oxidative stress induced by xenobiotics and harmful toxins such as 1-chloro-2,4-dinitrobenzene (CDNB). In Tetrahymena thermophila, the TtGSTm34 gene was previously reported to be one of the most responsive GST genes to CDNB treatment (LD50 = 0.079 mM). This study aimed to determine the kinetic features of recombinantly expressed and purified TtGSTm34 with CDNB and glutathione (GSH). TtGSTm34-8xHis was recombinantly produced in T. thermophila as a 25-kDa protein after the cloning of the 660-bp full-length ORF of TtGSTm34 into the pIGF-1 vector. A three-dimensional model of the TtGSTm34 protein constructed by the AlphaFold and PyMOL programs confirmed that it has structurally conserved and folded GST domains. The recombinant production of TtGSTm34-8xHis was confirmed by SDS‒PAGE and Western blot analysis. A dual-affinity chromatography strategy helped to purify TtGSTm34-8xHis approximately 3166-fold. The purified recombinant TtGSTm34-8xHis exhibited significantly high enzyme activity with CDNB (190 µmol/min/mg) as substrate. Enzyme kinetic analysis revealed Km values of 0.68 mM with GSH and 0.40 mM with CDNB as substrates, confirming its expected high affinity for CDNB. The optimum pH and temperature were determined to be 7.0 and 25 °C, respectively. Ethacrynic acid inhibited fully TtGSTm34-8xHis enzyme activity. These results imply that TtGSTm34 of T. thermophila plays a major role in the detoxification of xenobiotics, such as CDNB, as a first line of defense in aquatic protists against oxidative damage.
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Affiliation(s)
- Handan Açelya Kapkaç
- Department of Biology, Faculty of Sciences, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey
| | - Muhittin Arslanyolu
- Department of Biology, Faculty of Sciences, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey.
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Faiz Z, Parveen S, Saeed S, Tayyab M, Sultana M, Hussain M, Shafqat Z. Comparative genomic studies on the TGF-β superfamily in blue whale. Mamm Genome 2024; 35:228-240. [PMID: 38467865 DOI: 10.1007/s00335-024-10031-w] [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: 10/31/2023] [Accepted: 01/29/2024] [Indexed: 03/13/2024]
Abstract
TGF-β supergene family has a wide range of physiological functions including cell adhesion, motility, proliferation, apoptosis, and differentiation. We systematically analyzed and characterized the TGF-β gene superfamily from the whole blue whale (Balaenoptera musculus) genome, using comparative genomic and evolutionary analysis. We identified 30 TGF-β genes and were split into two subgroups, BMP-like and TGF-like. All TGF-β proteins demonstrating a basic nature, with the exception of BMP1, BMP2, BMP10, GDF2, MSTN, and NODAL modulator, had acidic characteristics. All the blue whale (B. musculus) TGF-β proteins, excluding BMP1, are thermostable based on aliphatic index. The instability index showed all proteins except the NODAL modulator was unstable. TGF-β proteins showed a hydrophilic character, with the exception of GDF1 and INHBC. Moreover, all the detected TGF-β genes showed evolutionary conserved nature. A segmental duplication was indicated by TGF-β gene family, and the Ka/Ks ratio showed that the duplicated gene pairs were subjected to selection pressure, indicating both purifying and positive selection pressure. Two possible recombination breakpoints were also predicted. This study provides insights into the genetic characterization and evolutionary aspects of the TGF-β superfamily in blue whales (B. musculus).
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Affiliation(s)
- Zunaira Faiz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
| | - Saba Saeed
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Mehwish Sultana
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Hussain
- Department of Veterinary and Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Zainab Shafqat
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
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Mirgaux M, Leherte L, Wouters J. Human indoleamine-2,3-dioxygenase 2 cofactor lability and low substrate affinity explained by homology modeling, molecular dynamics and molecular docking. J Biomol Struct Dyn 2024; 42:4475-4488. [PMID: 37301605 DOI: 10.1080/07391102.2023.2220830] [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: 03/07/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
The human indoleamine-2,3-dioxygenase 2 (hIDO2) protein is growing of interest as it is increasingly implicated in multiple diseases (cancer, autoimmune diseases, COVID-19). However, it is only poorly reported in the literature. Its mode of action remains unknown because it does not seem to catalyze the reaction for which it is attributed: the degradation of the L-Tryptophan into N-formyl-kynurenine. This contrasts with its paralog, the human indoleamine-2,3-dioxygenase 1 (hIDO1), which has been extensively studied in the literature and for which several inhibitors are already in clinical trials. Yet, the recent failure of one of the most advanced hIDO1 inhibitors, the Epacadostat, could be caused by a still unknown interaction between hIDO1 and hIDO2. In order to better understand the mechanism of hIDO2, and in the absence of experimental structural data, a computational study mixing homology modeling, Molecular Dynamics, and molecular docking was conducted. The present article highlights an exacerbated lability of the cofactor as well as an inadequate positioning of the substrate in the active site of hIDO2, which might bring part of an answer to its lack of activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manon Mirgaux
- Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Laurence Leherte
- Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Johan Wouters
- Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Namur, Belgium
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10
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Göttig L, Schreiner S. E4orf1: The triple agent of adenovirus - Unraveling its roles in oncogenesis, infectious obesity and immune responses in virus replication and vector therapy. Tumour Virus Res 2024; 17:200277. [PMID: 38428735 PMCID: PMC10937242 DOI: 10.1016/j.tvr.2024.200277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/03/2024] Open
Abstract
Human Adenoviruses (HAdV) are nearly ubiquitous pathogens comprising numerous sub-types that infect various tissues and organs. Among many encoded proteins that facilitate viral replication and subversion of host cellular processes, the viral E4orf1 protein has emerged as an intriguing yet under-investigated player in the complex interplay between the virus and its host. E4orf1 has gained attention as a metabolism activator and oncogenic agent, while recent research is showing that E4orf1 may play a more important role in modulating cellular pathways such as PI3K-Akt-mTOR, Ras, the immune response and further HAdV replication stages than previously anticipated. In this review, we aim to explore the structure, molecular mechanisms, and biological functions of E4orf1, shedding light on its potentially multifaceted roles during HAdV infection, including metabolic diseases and oncogenesis. Furthermore, we discuss the role of functional E4orf1 in biotechnological applications such as Adenovirus (AdV) vaccine vectors and oncolytic AdV. By dissecting the intricate relationships between HAdV types and E4orf1 proteins, this review provides valuable insights into viral pathogenesis and points to promising areas of future research.
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Affiliation(s)
- Lilian Göttig
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
| | - Sabrina Schreiner
- Institute of Virology, School of Medicine, Technical University of Munich, Germany; Institute of Virology, Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (Resolving Infection Susceptibility; EXC 2155), Hannover, Germany; Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.
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11
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Jermsutjarit P, Mebumroong S, Watcharavongtip P, Lin H, Tantituvanont A, Kaeoket K, Piñeyro P, Nilubol D. Evolution and virulence of porcine epidemic diarrhea virus following in vitro and in vivo propagation. Sci Rep 2024; 14:12279. [PMID: 38811677 PMCID: PMC11137156 DOI: 10.1038/s41598-024-62875-6] [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: 01/15/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024] Open
Abstract
Practice of inoculating porcine epidemic diarrhea virus (PEDV) in piglets generating feedback material might influence the genetic evolution and attenuation of PEDV. The study was conducted to evaluate evolutionary rate and attenuation following serial in vitro and in vivo propagation. In the study, PED-JPFP0-PJ, Passage 0 (P0), was isolated from infected pigs and serially passaged in Vero cells for 5 consecutive times, P1-P5. P0, P2 and P5 were then subjected to orally inoculate 3-day-old piglets. At 24 h post inoculation, intestines of each passage (F1), were collected, and subsequently sub-passaged in piglets for 2 additional passages (F2-F3). Virus titration, PEDV genomic copies number, VH:CD ratios, and immunohistochemistry were evaluated. S and ORF3 genes were characterized. The results of the study demonstrated that virus titer and virulence were negatively correlated with increased passages, both in vitro and in vivo. Increased substitution rate was observed in higher passages. The evolutionary rate of S gene was higher than that of ORF3. Seven aa changes at positions 223, 291, 317, 607, 694, 1114 and 1199, with reduced N-linked glycan were observed in P5F3. In conclusion, serial passage of PEDV, both in vitro and in vivo, influence the genetic development and the attenuation of PEDV.
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Affiliation(s)
- Patumporn Jermsutjarit
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Henry Dunant Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sunit Mebumroong
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Henry Dunant Road, Pathumwan, Bangkok, 10330, Thailand
| | - Parin Watcharavongtip
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Henry Dunant Road, Pathumwan, Bangkok, 10330, Thailand
| | - Hongyao Lin
- MSD Animal Health Innovation Pte Ltd, Singapore, Singapore
| | - Angkana Tantituvanont
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kampon Kaeoket
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhonpathom, Thailand
| | - Pablo Piñeyro
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Dachrit Nilubol
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Henry Dunant Road, Pathumwan, Bangkok, 10330, Thailand.
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12
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Cho SG, Kim JH, Lee JE, Choi IJ, Song M, Chuon K, Shim JG, Kang KW, Jung KH. Heliorhodopsin-mediated light-modulation of ABC transporter. Nat Commun 2024; 15:4306. [PMID: 38773114 PMCID: PMC11109279 DOI: 10.1038/s41467-024-48650-1] [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: 09/19/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Heliorhodopsins (HeRs) have been hypothesized to have widespread functions. Recently, the functions for few HeRs have been revealed; however, the hypothetical functions remain largely unknown. Herein, we investigate light-modulation of heterodimeric multidrug resistance ATP-binding cassette transporters (OmrDE) mediated by Omithinimicrobium cerasi HeR. In this study, we classifiy genes flanking the HeR-encoding genes and identify highly conservative residues for protein-protein interactions. Our results reveal that the interaction between OcHeR and OmrDE shows positive cooperatively sequential binding through thermodynamic parameters. Moreover, light-induced OcHeR upregulates OmrDE drug transportation. Hence, the binding may be crucial to drug resistance in O. cerasi as it survives in a drug-containing habitat. Overall, we unveil a function of HeR as regulatory rhodopsin for multidrug resistance. Our findings suggest potential applications in optogenetic technology.
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Affiliation(s)
- Shin-Gyu Cho
- Department of Life Science, Sogang University, Seoul, South Korea
- Research Institute for Basic Science, Sogang University, Seoul, South Korea
| | - Ji-Hyun Kim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Ji-Eun Lee
- Department of Life Science, Sogang University, Seoul, South Korea
| | - In-Jung Choi
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Myungchul Song
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kimleng Chuon
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Jin-Gon Shim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kun-Wook Kang
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kwang-Hwan Jung
- Department of Life Science, Sogang University, Seoul, South Korea.
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13
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Finke F, Hungerland J, Solov'yov IA, Schuhmann F. Different receptor models show differences in ligand binding strength and location: a computational drug screening for the tick-borne encephalitis virus. Mol Divers 2024:10.1007/s11030-024-10850-8. [PMID: 38739227 DOI: 10.1007/s11030-024-10850-8] [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: 02/09/2024] [Accepted: 03/16/2024] [Indexed: 05/14/2024]
Abstract
The tick-borne encephalitis virus (TBE) is a neurotrophic disease that has spread more rapidly throughout Europe and Asia in the past few years. At the same time, no cure or specific therapy is known to battle the illness apart from vaccination. To find a pharmacologically relevant drug, a computer-aided drug screening was initiated. Such a procedure probes a possible binding of a drug to the RNA Polymerase of TBE. The crystal structure of the receptor, however, includes missing and partially modeled regions, which rendered the structure incomplete and of questionable use for a thorough drug screening procedure. The quality of the receptor model was addressed by studying three putative structures created. We show that the choice of receptor models greatly influences the binding affinity of potential drug molecules and that the binding location could also be significantly impacted. We demonstrate that some drug candidates are unsuitable for one model but show decent results for another. Without any prejudice on the three employed receptor models, the study reveals the imperative need to investigate the receptor structure before drug binding is probed whether experimentally or computationally.
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Affiliation(s)
- Felicitas Finke
- Institute of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Jonathan Hungerland
- Institute of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany.
- Research Centre for Neurosensory Science, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany.
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany.
| | - Fabian Schuhmann
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.
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14
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Nantongo M, Nguyen DC, Bethel CR, Taracila MA, Li Q, Dousa KM, Shin E, Kurz SG, Nguyen L, Kreiswirth BN, Boom WH, Plummer MS, Bonomo RA. Durlobactam, a Diazabicyclooctane β-Lactamase Inhibitor, Inhibits BlaC and Peptidoglycan Transpeptidases of Mycobacterium tuberculosis. ACS Infect Dis 2024; 10:1767-1779. [PMID: 38619138 DOI: 10.1021/acsinfecdis.4c00119] [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] [Indexed: 04/16/2024]
Abstract
Peptidoglycan synthesis is an underutilized drug target in Mycobacterium tuberculosis (Mtb). Diazabicyclooctanes (DBOs) are a class of broad-spectrum β-lactamase inhibitors that also inhibit certain peptidoglycan transpeptidases that are important in mycobacterial cell wall synthesis. We evaluated the DBO durlobactam as an inhibitor of BlaC, the Mtb β-lactamase, and multiple Mtb peptidoglycan transpeptidases (PonA1, LdtMt1, LdtMt2, LdtMt3, and LdtMt5). Timed electrospray ionization mass spectrometry (ESI-MS) captured acyl-enzyme complexes with BlaC and all transpeptidases except LdtMt5. Inhibition kinetics demonstrated durlobactam was a potent and efficient DBO inhibitor of BlaC (KI app 9.2 ± 0.9 μM, k2/K 5600 ± 560 M-1 s-1) and similar to clavulanate (KI app 3.3 ± 0.6 μM, k2/K 8400 ± 840 M-1 s-1); however, durlobactam had a lower turnover number (tn = kcat/kinact) than clavulanate (1 and 8, respectively). KI app values with durlobactam and clavulanate were similar for peptidoglycan transpeptidases, but ESI-MS captured durlobactam complexes at more time points. Molecular docking and simulation demonstrated several productive interactions of durlobactam in the active sites of BlaC, PonA1, and LdtMt2. Antibiotic susceptibility testing was conducted on 11 Mtb isolates with amoxicillin, ceftriaxone, meropenem, imipenem, clavulanate, and durlobactam. Durlobactam had a minimum inhibitory concentration (MIC) range of 0.5-16 μg/mL, similar to the ranges for meropenem (1-32 μg/mL) and imipenem (0.5-64 μg/mL). In β-lactam + durlobactam combinations (1:1 mass/volume), MICs were lowered 4- to 64-fold for all isolates except one with meropenem-durlobactam. This work supports further exploration of novel β-lactamase inhibitors that target BlaC and Mtb peptidoglycan transpeptidases.
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Affiliation(s)
- Mary Nantongo
- Department of Molecular Biology and Microbiology, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - David C Nguyen
- Division of Infectious Diseases, Department of Pediatrics and Division of Infectious Diseases, and Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Christopher R Bethel
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Magdalena A Taracila
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
| | - Qing Li
- Department of Medicine, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
| | - Khalid M Dousa
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
- Medical Service, Veterans Affairs Northeast Ohio Healthcare System (VANEOHS), Cleveland, Ohio 44106, United States
| | - Eunjeong Shin
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
| | - Sebastian G Kurz
- Department of Internal Medicine VIII, Medical Oncology and Pneumology, University of Tübingen, 72076 Tübingen, Germany
| | - Liem Nguyen
- Department of Molecular Biology and Microbiology, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack, New Jersey 07110, United States
| | - W Henry Boom
- Department of Molecular Biology and Microbiology, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
| | - Mark S Plummer
- Biopharmaworks, Groton, Connecticut 06340, United States
| | - Robert A Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University (CWRU), Cleveland, Ohio 44106, United States
- Medical Service, Veterans Affairs Northeast Ohio Healthcare System (VANEOHS), Cleveland, Ohio 44106, United States
- CWRU-Cleveland VAMC Center for Antibiotic Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States
- Departments of Biochemistry, Pharmacology, and Proteomics and Bioinformatics, CWRU, Cleveland, Ohio 44106, United States
- Cleveland Geriatrics Research Education and Clinical Center (GRECC), VANEOHS, Cleveland, Ohio 44106, United States
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15
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Buzan MR, Grijincu M, Zbîrcea LE, Haidar L, Tamaș TP, Cotarcă MD, Tănasie G, Weber M, Babaev E, Stolz F, Valenta R, Păunescu V, Panaitescu C, Chen KW. Insect Cell-Expressed Major Ragweed Allergen Amb a 1.01 Exhibits Similar Allergenic Properties to Its Natural Counterpart from Common Ragweed Pollen. Int J Mol Sci 2024; 25:5175. [PMID: 38791214 PMCID: PMC11121294 DOI: 10.3390/ijms25105175] [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: 03/14/2024] [Revised: 04/29/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Common ragweed pollen allergy has become a health burden worldwide. One of the major allergens in ragweed allergy is Amb a 1, which is responsible for over 90% of the IgE response in ragweed-allergic patients. The major allergen isoform Amb a 1.01 is the most allergenic isoform in ragweed pollen. So far, no recombinant Amb a 1.01 with similar allergenic properties to its natural counterpart (nAmb a 1.01) has been produced. Hence, this study aimed to produce a recombinant Amb a 1.01 with similar properties to the natural isoform for improved ragweed allergy management. Amb a 1.01 was expressed in insect cells using a codon-optimized DNA construct with a removable N-terminal His-Tag (rAmb a 1.01). The recombinant protein was purified by affinity chromatography and physicochemically characterized. The rAmb a 1.01 was compared to nAmb a 1.01 in terms of the IgE binding (enzyme-linked immunosorbent assay (ELISA), immunoblot) and allergenic activity (mediator release assay) in well-characterized ragweed-allergic patients. The rAmb a 1.01 exhibited similar IgE reactivity to nAmb a 1.01 in different IgE-binding assays (i.e., IgE immunoblot, ELISA, quantitative ImmunoCAP inhibition measurements). Furthermore, the rAmb a 1.01 showed comparable dose-dependent allergenic activity to nAmb a 1.01 regarding basophil activation. Overall, the results showed the successful expression of an rAmb a 1.01 with comparable characteristics to the corresponding natural isoform. Our findings provide the basis for an improvement in ragweed allergy research, diagnosis, and immunotherapy.
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Affiliation(s)
- Maria-Roxana Buzan
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
- OncoGen Center, Pius Brinzeu County Clinical Emergency Hospital, 300723 Timisoara, Romania;
| | - Manuela Grijincu
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
- OncoGen Center, Pius Brinzeu County Clinical Emergency Hospital, 300723 Timisoara, Romania;
| | - Lauriana-Eunice Zbîrcea
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
- OncoGen Center, Pius Brinzeu County Clinical Emergency Hospital, 300723 Timisoara, Romania;
| | - Laura Haidar
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
| | - Tudor-Paul Tamaș
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
| | - Monica-Daniela Cotarcă
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
| | - Gabriela Tănasie
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
- OncoGen Center, Pius Brinzeu County Clinical Emergency Hospital, 300723 Timisoara, Romania;
| | - Milena Weber
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Elijahu Babaev
- Vienna Competence Center, Biomay AG, 1090 Vienna, Austria
| | - Frank Stolz
- Vienna Competence Center, Biomay AG, 1090 Vienna, Austria
| | - Rudolf Valenta
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090 Vienna, Austria
- Laboratory for Immunopathology, Department of Clinical Immunology and Allergology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Karl Landsteiner University of Health Sciences, 3500 Krems, Austria
- NRC Institute of Immunology FMBA of Russia, 115478 Moscow, Russia
| | - Virgil Păunescu
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
- OncoGen Center, Pius Brinzeu County Clinical Emergency Hospital, 300723 Timisoara, Romania;
| | - Carmen Panaitescu
- Center of Immuno-Physiology and Biotechnologies, Department of Functional Sciences, Victor Babes University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.-R.B.); (M.G.); (L.-E.Z.)
- OncoGen Center, Pius Brinzeu County Clinical Emergency Hospital, 300723 Timisoara, Romania;
| | - Kuan-Wei Chen
- OncoGen Center, Pius Brinzeu County Clinical Emergency Hospital, 300723 Timisoara, Romania;
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Gong Y, Zhou M, Zhu Y, Pan J, Zhou X, Jiang Y, Zeng H, Zheng H, Geng X, Huang D. PVALB Was Identified as an Independent Prognostic Factor for HCC Closely Related to Immunity, and Its Absence Accelerates Tumor Progression by Regulating NK Cell Infiltration. J Hepatocell Carcinoma 2024; 11:813-838. [PMID: 38737383 PMCID: PMC11088852 DOI: 10.2147/jhc.s450479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/23/2024] [Indexed: 05/14/2024] Open
Abstract
Purpose Hepatocellular carcinoma is the most common primary liver cancer, with poor prognosis. Complex immune microenvironment of the liver is linked to the development of HCC. PVALB is a calcium-binding protein which has been described as a cancer suppressor gene in thyroid cancer and glioma. Nevertheless, the role of PVALB in HCC is unknown. Materials and Methods We obtained data from TCGA and GSE54236 datasets. MCP-counter, WGCNA and LASSO model were applied to identify PVALB. With UALCAN, MethSurv, and other websites, we probed the expression, methylation and survival of PVALB. LinkedOmics and GSEA were adopted for functional analysis, while TIMER, TISIDB, Kaplan-Meier plotter, TIDE databases were utilized to evaluate the relevance of PVALB to the tumor immune microenvironment and predict immunotherapy efficacy. TargetScan, DIANA, LncRNASNP2 databases and relevant experiments were employed to construct ceRNA network. Finally, molecular docking and drug sensitivity of PVALB were characterized by GeneMANIA, CTD, and so on. Results PVALB was recognized as a gene associated with HCC and NK cell. Its expression was down-regulated in HCC tissue, which lead to adverse prognosis. Besides, the hypomethylation of PVALB was related to its reduced expression. Notably, PVALB was tightly linked to immune, and its reduced expression attenuated the anticancer effect of NK cells via the Fas/FasL pathway, leading to a adverse outcome. The lnc-YY1AP1-3/hsa-miR-6735-5p/PVALB axis may regulate the PVALB expression. Finally, we found immunotherapy might be a viable treatment option. Conclusion In a word, PVALB is a prognostic indicator, whose low expression facilitates HCC progression by impacting NK cell infiltration.
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Affiliation(s)
- Yiyang Gong
- Department of Thyroid Surgery; Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Yanting Zhu
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Hao Zheng
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Xitong Geng
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Da Huang
- Department of Thyroid Surgery; Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
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17
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Cosse M, Rehders T, Eirich J, Finkemeier I, Selinski J. Cysteine oxidation as a regulatory mechanism of Arabidopsis plastidial NAD-dependent malate dehydrogenase. PHYSIOLOGIA PLANTARUM 2024; 176:e14340. [PMID: 38741259 DOI: 10.1111/ppl.14340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Malate dehydrogenases (MDHs) catalyze a reversible NAD(P)-dependent-oxidoreductase reaction that plays an important role in central metabolism and redox homeostasis of plant cells. Recent studies suggest a moonlighting function of plastidial NAD-dependent MDH (plNAD-MDH; EC 1.1.1.37) in plastid biogenesis, independent of its enzyme activity. In this study, redox effects on activity and conformation of recombinant plNAD-MDH from Arabidopsis thaliana were investigated. We show that reduced plNAD-MDH is active while it is inhibited upon oxidation. Interestingly, the presence of its cofactors NAD+ and NADH could prevent oxidative inhibition of plNAD-MDH. In addition, a conformational change upon oxidation could be observed via non-reducing SDS-PAGE. Both effects, its inhibition and conformational change, were reversible by re-reduction. Further investigation of single cysteine substitutions and mass spectrometry revealed that oxidation of plNAD-MDH leads to oxidation of all four cysteine residues. However, cysteine oxidation of C129 leads to inhibition of plNAD-MDH activity and oxidation of C147 induces its conformational change. In contrast, oxidation of C190 and C333 does not affect plNAD-MDH activity or structure. Our results demonstrate that plNAD-MDH activity can be reversibly inhibited, but not inactivated, by cysteine oxidation and might be co-regulated by the availability of its cofactors in vivo.
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Affiliation(s)
- Maike Cosse
- Plant Cell Biology, Botanical Institute, Christian-Albrechts University, Kiel, Germany
| | - Tanja Rehders
- Plant Cell Biology, Botanical Institute, Christian-Albrechts University, Kiel, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany
| | - Jennifer Selinski
- Plant Cell Biology, Botanical Institute, Christian-Albrechts University, Kiel, Germany
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18
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Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, Hunter CN, Kang A, Brackenbrough E, Bera AK, Baek M, DiMaio F, Baker D. Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science 2024; 384:eadl2528. [PMID: 38452047 DOI: 10.1126/science.adl2528] [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: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.
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Affiliation(s)
- Rohith Krishna
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Jue Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Woody Ahern
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Pascal Sturmfels
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Indrek Kalvet
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | | | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ryan McHugh
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Dionne Vafeados
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | | | - Andrew Hitchcock
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Evans Brackenbrough
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Minkyung Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
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19
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Wahid M, Nazeer M, Qadir A, Azmi MB. Investigating the Protein-Based Therapeutic Relationship between Honey Protein SHP-60 and Bevacizumab on Angiogenesis: Exploring the Synergistic Effect through In Vitro and In Silico Analysis. ACS OMEGA 2024; 9:17143-17153. [PMID: 38645361 PMCID: PMC11024967 DOI: 10.1021/acsomega.3c09736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 04/23/2024]
Abstract
Honey is a natural product produced by honeybees, which has been used not only as food but also as a medicine by humans for thousands of years. In this study, 60 kDa protein was purified from Pakistani Sidr honey named as SHP-60 (Sidr Honey Protein-60), and its antioxidant potential and the effect of Bevacizumab with purified protein on in vitro angiogenesis using human umbilical vein endothelial cells (HUVEC) were investigated. We further validated the molecular protein-protein (SHP-60 with Bevacizumab) interactions through in silico analysis. It showed very promising antioxidant activity by reducing 2,2-diphenyl-1-picrylhydrazyl free radicals with a maximum of 83% inhibition at 50 μM and an IC50 of 26.45 μM statistically significant (**p < 0.01). Angiogenesis is considered a hallmark of cancer, and without it, the tumor cannot grow or metastasize. Bevacizumab, SHP-60, and both in combination were used to treat HUVEC, and the MTT assay was used to assess cell viability. To demonstrate in vitro angiogenesis, HUVEC was grown on Geltrex, and the formation of endotubes was examined using a tube formation assay. HUVEC viability was dose-dependently decreased by Bevacizumab, SHP-60, and both together. Bevacizumab and SHP-60 both inhibited angiogenesis in vitro, and their combination displayed levels of inhibition even higher than those of Bevacizumab alone. We investigated the protein-protein molecular docking interactions and molecular dynamics simulation analysis of MRJP3 (major royal jelly protein 3) similar to SHP-60 in molecular weight with both the heavy chain (HC) and light chain (LC) of Bevacizumab. We found significant interactions between the LC and MRJP3, indicating that ASN468, GLN470, and ASN473 of MRJP3 interact with SER156, SER159, and GLU161 of LC of Bevacizumab. The integration of experimental data and computational techniques is believed to improve the reliability of the findings and aid in future drug design.
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Affiliation(s)
- Mohsin Wahid
- Dow
Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi 74200, Pakistan
- Department
of Pathology, Dow International Medical College, Dow University of Health Sciences, Karachi 74200, Pakistan
| | - Meshal Nazeer
- Dow
Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi 74200, Pakistan
| | - Abdul Qadir
- Dow
Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi 74200, Pakistan
- Department
of Pharmacology, United Medical and Dental
College, Karachi 75190, Pakistan
| | - Muhammad Bilal Azmi
- Department
of Biochemistry, Dow Medical College, Dow
University of Health Sciences, Karachi 74200, Pakistan
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20
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Sun X, Ke Z, Zheng D, She M, Wu Z, Li QX, Zhang Z. Cloning, Expression, and Functional Characterization of Two Highly Efficient Flavonoid-di- O-glycosyltransferases ZmUGT84A1 and ZmUGT84A2 from Maize ( Zea mays L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7354-7363. [PMID: 38511857 DOI: 10.1021/acs.jafc.3c06327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The maize (Zea mays L.) glycosyltransferase family 1 comprises many uridine diphosphate glycosyltransferase (UGT) members. However, UGT activities and biochemical functions have seldom been revealed. In this study, the genes of two flavonoid di-O-glycosyltransferases ZmUGT84A1 and ZmUGT84A2 were cloned from maize plant and expressed in Escherichia coli. Phylogenetic analysis showed that the two enzymes were homologous to AtUGT84A1 and AtUGT84A3. The two recombinant enzymes showed a high conversion rate of luteolin to its glucosides, mainly 4',7-di-O-glucoside and minorly 3',7-di-O-glucoside in two-step glycosylation reactions in vitro. Moreover, the recombinant ZmUGT84A1 and ZmUGT84A2 had a broad substrate spectrum, converting eriodictyol, naringenin, apigenin, quercetin, and kaempferol to monoglucosides and diglucosides. The highly efficient ZmUGT84A1 and ZmUGT84A2 may be used as a tool for the effective synthesis of various flavonoid O-glycosides and as markers for crop breeding to increase O-glycosyl flavonoid content in food.
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Affiliation(s)
- Xiaorong Sun
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhao Ke
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 100096, China
| | - Dengyu Zheng
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Meng She
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- College of Agriculture, Yangtze University, Jingzhou, Hubei 434022, China
| | - Zhongyi Wu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, Hawaii 96822, United States
| | - Zhongbao Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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21
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Shang Y, Zhang Y, Wang R, Peng Y, Ding B, Liu Y, Li C, Feng L, Liu H, Yang C, Tang Y. Deciphering the molecular and functional basis of TMexCD1: the plasmid-encoded efflux pump of resistance-nodulation-division superfamily. Antimicrob Agents Chemother 2024; 68:e0167823. [PMID: 38477539 PMCID: PMC10989000 DOI: 10.1128/aac.01678-23] [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: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Horizontal gene transfer has been demonstrated to be an important driver for the emergency of multidrug-resistant pathogens. Recently, a transferable gene cluster tmexCD1-toprJ1 of the resistance-nodulation-division (RND) superfamily was identified in the plasmids of animal-derived Klebsiella pneumoniae strains, with a higher efflux capacity for various drugs than the Escherichia coli AcrAB-TolC homolog system. In this study, we focused on the differences in the inner membrane pump of these two systems and identified some key residues that contribute to the robust efflux activity of the TMexCD1 system. With the aid of homologous modeling and molecular docking, eight residues from the proximal binding pocket (PBP) and nine from the distal binding pocket (DBP) were selected and subjected to site-directed mutagenesis. Several of them, such as S134, I139, D181, and A290, were shown to be important for substrate binding in the DBP region, and all residues in PBP and DBP showed certain substrate preferences. Apart from the conservative switch loop (L613-623TMexD1) previously identified in the E. coli AcrB (EcAcrB), a relatively unconservative loop (L665-675TMexD1) at the bottom of PBP was proposed as a critical element for the robust activity of TMexD1, due to variations at sites E669, G670, N673, and S674 compared to EcAcrAB, and the significantly altered efflux activity due to their mutations. The conservation and flexibility of these key factors can contribute to the evolution of the RND efflux pumps and thus serve as potential targets for developing inhibitors to block the widespread of the TMexCD1 system.
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Affiliation(s)
- Yan Shang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ye Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ruimin Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yishu Peng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Bo Ding
- Shandong Institute for Food and Drug Control, Jinan, China
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Yuanxiang Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Chongzhou Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Luhua Feng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Honglei Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yajie Tang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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22
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Sunita, Singhvi N, Gupta V, Singh Y, Shukla P. Computational Approaches for the Structure-Based Identification of Novel Inhibitors Targeting Nucleoid-Associated Proteins in Mycobacterium Tuberculosis. Mol Biotechnol 2024; 66:814-823. [PMID: 36913083 DOI: 10.1007/s12033-023-00710-5] [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: 06/09/2022] [Accepted: 02/24/2023] [Indexed: 03/14/2023]
Abstract
Implementation of computational tools in the identification of novel drug targets for Tuberculosis (TB) has been a promising area of research. TB has been a chronic infectious disease caused by Mycobacterium tuberculosis (Mtb) localized primarily on the lungs and it has been one of the most successful pathogen in the history of mankind. Extensively arising drug resistivity in TB has made it a global challenge and need for new drugs has become utmost important.The involvement of Nucleoid-Associated Proteins (NAPs) in maintaining the structure of the genomic material and regulating various cellular processes like transcription, DNA replication, repair and recombination makes significant, has opened a new arena to find the drugs targeting Mtb. The current study aims to identify potential inhibitors of NAPs through a computational approach. In the present work we worked on the eight NAPs of Mtb, namely, Lsr2, EspR, HupB, HNS, NapA, mIHF and NapM. The structural modelling and analysis of these NAPs were carried out. Moreover, molecular interaction were checked and binding energy was identified for 2500 FDA-approved drugs that were selected for antagonist analysis to choose novel inhibitors targeting NAPs of Mtb. Drugs including Amikacin, streptomycin, kanamycin, and isoniazid along with eight FDA-approved molecules that were found to be potential novel targets for these mycobacterial NAPs and have an impact on their functions. The potentiality of several anti-tubercular drugs as therapeutic agents identified through computational modelling and simulation unlocks a new gateway for accomplishing the goal to treat TB.
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Affiliation(s)
- Sunita
- Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Nirjara Singhvi
- Department of Zoology, Hansraj College, University of Delhi, Delhi, 110007, India
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand, 248001, India
| | - Vipin Gupta
- Ministry of Environment, Forest and Climate Change, Government of India, Dehradun, Uttarakhand, 248001, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Pratyoosh Shukla
- Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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23
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Torres de Oliveira C, Alexandrino de Assis M, Lourenço Franco Cairo JP, Damasio A, Guimarães Pereira GA, Mazutti MA, de Oliveira D. Functional characterization and structural insights of three cutinases from the ascomycete Fusarium verticillioides. Protein Expr Purif 2024; 216:106415. [PMID: 38104791 DOI: 10.1016/j.pep.2023.106415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Cutinases are serine esterases that belong to the α/β hydrolases superfamily. The natural substrates for these enzymes are cutin and suberin, components of the plant cuticle, the first barrier in the defense system against pathogen invasion. It is well-reported that plant pathogens produce cutinases to facilitate infection. Fusarium verticillioides, one important corn pathogens, is an ascomycete upon which its cutinases are poorly explored. Consequently, the objective of this study was to perform the biochemical characterization of three precursor cutinases (FvCut1, FvCut2, and FvCut3) from F. verticillioides and to obtain structural insights about them. The cutinases were produced in Escherichia coli and purified. FvCut1, FvCut2, and FvCut3 presented optimal temperatures of 20, 40, and 35 °C, and optimal pH of 9, 7, and 8, respectively. Some chemicals stimulated the enzymatic activity. The kinetic parameters revealed that FvCut1 has higher catalytic efficiency (Kcat/Km) in the p-nitrophenyl-butyrate (p-NPB) substrate. Nevertheless, the enzymes were not able to hydrolyze polyethylene terephthalate (PET). Furthermore, the three-dimensional models of these enzymes showed structural differences among them, mainly FvCut1, which presented a narrower opening cleft to access the catalytic site. Therefore, our study contributes to exploring the diversity of fungal cutinases and their potential biotechnological applications.
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Affiliation(s)
- Caroline Torres de Oliveira
- Department of Chemical and Food Engineering, Technology Center, Federal University of Santa Catarina, UFSC, Florianópolis, Brazil
| | - Michelle Alexandrino de Assis
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, Brazil
| | | | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, Brazil
| | | | - Marcio Antonio Mazutti
- Department of Chemical Engineering, Technology Center, Federal University of Santa Maria, UFSM, Santa Maria, Brazil
| | - Débora de Oliveira
- Department of Chemical and Food Engineering, Technology Center, Federal University of Santa Catarina, UFSC, Florianópolis, Brazil.
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24
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Alavizargar A, Gass M, Krahn MP, Heuer A. Elucidating the Membrane Binding Process of a Disordered Protein: Dynamic Interplay of Anionic Lipids and the Polybasic Region. ACS PHYSICAL CHEMISTRY AU 2024; 4:167-179. [PMID: 38560754 PMCID: PMC10979486 DOI: 10.1021/acsphyschemau.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 04/04/2024]
Abstract
Intrinsically disordered regions of proteins are responsible for many biological processes such as in the case of liver kinase B1 (LKB1)-a serine/threonine kinase relevant for cell proliferation and cell polarity. LKB1 becomes fully activated upon recruitment to the plasma membrane by binding of its disordered C-terminal polybasic motif consisting of eight lysines/arginines to phospholipids. Here, we present extensive molecular dynamics (MD) simulations of the polybasic motif interacting with a model membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleyl phosphatidic acid (PA) and cell culture experiments. Protein-membrane binding effects are due to the electrostatic interactions between the polybasic amino acids and PAs. For significant binding, the first three lysines turn out to be dispensable, which was also recapitulated in cell culture using transfected GFP-LKB1 variants. LKB1-membrane binding results in nonmonotonous changes in the structure of the protein as well as the membrane, in particular, accumulation of PAs and reduced thickness at the protein-membrane contact area. The protein-lipid binding turns out to be highly dynamic due to an interplay of PA-PA repulsion and protein-PA attraction. The thermodynamics of this interplay is captured by a statistical fluctuation model, which allows the estimation of both energies. Quantification of the significance of each polar amino acid in the polybasic provides detailed insights into the molecular mechanism of protein-membrane binding of LKB1. These results can likely be transferred to other proteins, which interact by intrinsically disordered polybasic regions with anionic membranes.
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Affiliation(s)
- Azadeh Alavizargar
- Institute
of Physical Chemistry, University of Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Maximilian Gass
- Medical
Cell Biology, Medical Clinic D, University
Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149 Münster, Germany
| | - Michael P. Krahn
- Medical
Cell Biology, Medical Clinic D, University
Hospital of Münster, Albert-Schweitzer Campus 1-A14, 48149 Münster, Germany
| | - Andreas Heuer
- Institute
of Physical Chemistry, University of Münster, Corrensstr. 28/30, 48149 Münster, Germany
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25
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Rodriguez Galvan JJ, de Vries M, Belblidia S, Fisher A, Prescott RA, Crosse KM, Mangel WF, Duerr R, Dittmann M. In-silico docking platform with serine protease inhibitor (SERPIN) structures identifies host cysteine protease targets with significance for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.11.18.517133. [PMID: 36415456 PMCID: PMC9681043 DOI: 10.1101/2022.11.18.517133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Serine Protease Inhibitors (SERPINs) regulate protease activity in various physiological processes such as inflammation, cancer metastasis, angiogenesis, and neurodegenerative diseases. However, their potential in combating viral infections, where proteases are also crucial, remains underexplored. This is due to our limited understanding of SERPIN expression during viral-induced inflammation and of the SERPINs' full spectrum of target proteases. Here, we demonstrate widespread expression of human SERPINs in response to respiratory virus infections, both in vitro and in vivo , alongside classical antiviral effectors. Through comprehensive in-silico docking with full-length SERPIN and protease 3D structures, we confirm known inhibitors of specific proteases; more importantly, the results predict novel SERPIN-protease interactions. Experimentally, we validate the direct inhibition of key proteases essential for viral life cycles, including the SERPIN PAI-1's capability to inhibit select cysteine proteases such as cathepsin L, and the serine protease TMPRSS2. Consequently, PAI-1 suppresses spike maturation and multi-cycle SARS-CoV-2 replication. Our findings challenge conventional notions of SERPIN selectivity, underscore the power of in-silico docking for SERPIN target discovery, and offer potential therapeutic interventions targeting host proteolytic pathways to combat viruses with urgent unmet therapeutic needs. SIGNIFICANCE Serine protease inhibitors (SERPINs) play crucial roles in various physiological processes, including viral infections. However, our comprehension of the full array of proteases targeted by the SERPIN family has traditionally been limited, hindering a comprehensive understanding of their regulatory potential. We developed an in-silico docking platform to identify new SERPIN target proteases expressed in the respiratory tract, a critical viral entry portal. The platform confirmed known and predicted new targets for every SERPIN examined, shedding light on previously unrecognized patterns in SERPIN selectivity. Notably, both key proteases for SARS-CoV-2 maturation were among the newly predicted targets, which we validated experimentally. This underscores the platform's potential in uncovering targets with significance in viral infections, paving the way to define the full potential of the SERPIN family in infectious disease and beyond.
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26
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El-Sayed GM, Emam MTH, Hammad MA, Mahmoud SH. Gene Cloning, Heterologous Expression, and In Silico Analysis of Chitinase B from Serratia marcescens for Biocontrol of Spodoptera frugiperda Larvae Infesting Maize Crops. Molecules 2024; 29:1466. [PMID: 38611746 PMCID: PMC11012731 DOI: 10.3390/molecules29071466] [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: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Spodoptera frugiperda, the fall armyworm (FAW), is a highly invasive polyphagous insect pest that is considered a source of severe economic losses to agricultural production. Currently, the majority of chemical insecticides pose tremendous threats to humans and animals besides insect resistance. Thus, there is an urgent need to develop new pest management strategies with more specificity, efficiency, and sustainability. Chitin-degrading enzymes, including chitinases, are promising agents which may contribute to FAW control. Chitinase-producing microorganisms are reported normally in bacteria and fungi. In the present study, Serratia marcescens was successfully isolated and identified from the larvae of Spodoptera frugiperda. The bacterial strain NRC408 displayed the highest chitinase enzyme activity of 250 units per milligram of protein. Subsequently, the chitinase gene was cloned and heterologously expressed in E. coli BL21 (DE3). Recombinant chitinase B was overproduced to 2.5-fold, driven by the T7 expression system. Recombinant chitinase B was evaluated for its efficacy as an insecticidal bioagent against S. frugiperda larvae, which induced significant alteration in subsequent developmental stages and conspicuous malformations. Additionally, our study highlights that in silico analyses of the anticipated protein encoded by the chitinase gene (ChiB) offered improved predictions for enzyme binding and catalytic activity. The effectiveness of (ChiB) against S. frugiperda was evaluated in laboratory and controlled field conditions. The results indicated significant mortality, disturbed development, different induced malformations, and a reduction in larval populations. Thus, the current study consequently recommends chitinase B for the first time to control FAW.
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Affiliation(s)
- Ghada M. El-Sayed
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo 12622, Egypt
| | - Maha T. H. Emam
- Genetics & Cytology Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo 12622, Egypt;
| | - Maher A. Hammad
- Department of Plant Protection, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | - Shaymaa H. Mahmoud
- Zoology Department, Faculty of Science, Menoufia University, Shibin El Kom 32511, Egypt;
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27
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Khazaal MT, Faraag AHI, El-Hendawy HH. In vitro and in silico studies of enterobactin-inspired Ciprofloxacin and Fosfomycin first generation conjugates on the antibiotic resistant E. coli OQ866153. BMC Microbiol 2024; 24:95. [PMID: 38519885 PMCID: PMC10958948 DOI: 10.1186/s12866-024-03248-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 03/03/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The emergence of antimicrobial resistance in bacterial pathogens is a growing concern worldwide due to its impact on the treatment of bacterial infections. The "Trojan Horse" strategy has been proposed as a potential solution to overcome drug resistance caused by permeability issues. OBJECTIVE The objective of our research was to investigate the bactericidal activity and mechanism of action of the "Trojan Horse" strategy using enterobactin conjugated with Ciprofloxacin and Fosfomycin against the antibiotic-resistant Escherichia coli strain OQ866153. METHODOLOGY Enterobactin, a mixed ligand of E. coli OQ866153, was conjugated with Ciprofloxacin and Fosfomycin individually to aid active absorption via specific enterobactin binding proteins (FepABCDG). The effectiveness of the conjugates was assessed by measuring their bactericidal activity against E. coli OQ866153, as well as their ability to inhibit DNA gyrase enzyme and biofilm formation. RESULTS The Fe+3-enterobactin-Ciprofloxacin conjugate effectively inhibited the DNA gyrase enzyme (Docking score = -8.597 kcal/mol) and resulted in a lower concentration (25 μg/ml) required to eliminate supercoiled DNA plasmids compared to the parent drug (35 μg/ml; Docking score = -6.264 kcal/mol). The Fe+3-Enterobactin-Fosfomycin conjugate showed a higher inhibition percentage (100%) of biofilm formation compared to Fosfomycin (21.58%) at a concentration of 2 mg/ml, with docking scores of -5.481 and -3.756 kcal/mol against UDP-N acetylglucosamine 1-carboxyvinyltransferase MurA. CONCLUSION The findings of this study suggest that the "Trojan Horse" strategy using enterobactin conjugated with Ciprofloxacin and Fosfomycin can effectively overcome permeability issues caused by efflux proteins and enhance the bactericidal activity of these drugs against antibiotic-resistant strains of E. coli.
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Affiliation(s)
- Mohamed T Khazaal
- Botany and Microbiology Department, Faculty of Science, Helwan University, HelwanCairo, 11795, Egypt
| | - Ahmed H I Faraag
- Botany and Microbiology Department, Faculty of Science, Helwan University, HelwanCairo, 11795, Egypt.
- School of Biotechnology, Badr University in Cairo, Badr City, Cairo, 11829, Egypt.
| | - Hoda H El-Hendawy
- Botany and Microbiology Department, Faculty of Science, Helwan University, HelwanCairo, 11795, Egypt.
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Coppinger MN, Laramore K, Popham DL, Stabb EV. A prototrophic suppressor of a Vibrio fischeri D-glutamate auxotroph reveals a member of the periplasmic broad-spectrum racemase family (BsrF). J Bacteriol 2024; 206:e0033323. [PMID: 38411059 PMCID: PMC10955857 DOI: 10.1128/jb.00333-23] [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: 12/08/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Although bacterial peptidoglycan (PG) is highly conserved, some natural variations in PG biosynthesis and structure have evolved. Understanding the mechanisms and limits of such variation will inform our understanding of antibiotic resistance, innate immunity, and the evolution of bacteria. We have explored the constraints on PG evolution by blocking essential steps in PG biosynthesis in Vibrio fischeri and then selecting mutants with restored prototrophy. Here, we attempted to select prototrophic suppressors of a D-glutamate auxotrophic murI racD mutant. No suppressors were isolated on unsupplemented lysogeny broth salts (LBS), despite plating >1011 cells, nor were any suppressors generated through mutagenesis with ethyl methanesulfonate. A single suppressor was isolated on LBS supplemented with iso-D-gln, although the iso-D-gln subsequently appeared irrelevant. This suppressor has a genomic amplification formed by the creation of a novel junction that fuses proB to a gene encoding a putative broad-spectrum racemase of V. fischeri, bsrF. An engineered bsrF allele lacking the putative secretion signal (ΔSS-bsrF) also suppressed D-glu auxotrophy, resulting in PG that was indistinguishable from the wild type. The ΔSS-bsrF allele similarly suppressed the D-alanine auxotrophy of an alr mutant and restored prototrophy to a murI alr double mutant auxotrophic for both D-ala and D-glu. The ΔSS-bsrF allele increased resistance to D-cycloserine but had no effect on sensitivity to PG-targeting antibiotics penicillin, ampicillin, or vancomycin. Our work helps define constraints on PG evolution and reveals a periplasmic broad-spectrum racemase in V. fischeri that can be co-opted for PG biosynthesis, with concomitant D-cycloserine resistance. IMPORTANCE D-Amino acids are used and produced by organisms across all domains of life, but often, their origins and roles are not well understood. In bacteria, D-ala and D-glu are structural components of the canonical peptidoglycan cell wall and are generated by dedicated racemases Alr and MurI, respectively. The more recent discovery of additional bacterial racemases is broadening our view and deepening our understanding of D-amino acid metabolism. Here, while exploring alternative PG biosynthetic pathways in Vibrio fischeri, we unexpectedly shed light on an unusual racemase, BsrF. Our results illustrate a novel mechanism for the evolution of antibiotic resistance and provide a new avenue for exploring the roles of non-canonical racemases and D-amino acids in bacteria.
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Affiliation(s)
- Macey N. Coppinger
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Department of Biological Sciences, University of Illinois, Chicago, Illinois, USA
| | - Kathrin Laramore
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Eric V. Stabb
- Department of Biological Sciences, University of Illinois, Chicago, Illinois, USA
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Polanco EA, Opdam LV, Passerini L, Huber M, Bonnet S, Pandit A. An artificial metalloenzyme that can oxidize water photocatalytically: design, synthesis, and characterization. Chem Sci 2024; 15:3596-3609. [PMID: 38455019 PMCID: PMC10915814 DOI: 10.1039/d3sc05870k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
In nature, light-driven water oxidation (WO) catalysis is performed by photosystem II via the delicate interplay of different cofactors positioned in its protein scaffold. Artificial systems for homogeneous photocatalytic WO are based on small molecules that often have limited solubility in aqueous solutions. In this work, we alleviated this issue and present a cobalt-based WO-catalyst containing artificial metalloenzyme (ArM) that is active in light-driven, homogeneous WO catalysis in neutral-pH aqueous solutions. A haem-containing electron transfer protein, cytochrome B5 (CB5), served to host a first-row transition-metal-based WO catalyst, CoSalen (CoIISalen, where H2Salen = N,N'-bis(salicylidene)ethylenediamine), thus producing an ArM capable of driving photocatalytic WO. The CoSalen ArM formed a water-soluble pre-catalyst in the presence of [Ru(bpy)3](ClO4)2 as photosensitizer and Na2S2O8 as the sacrificial electron acceptor, with photocatalytic activity similar to that of free CoSalen. During photocatalysis, the CoSalen-protein interactions were destabilized, and the protein partially unfolded. Rather than forming tens of nanometer sized CoOx nanoparticles as free CoSalen does under photocatalytic WO conditions, the CB5 : CoSalen ArM showed limited protein cross-linking and remained soluble. We conclude that a weak, dynamic interaction between a soluble cobalt species and apoCB5 was formed, which generated a catalytically active adduct during photocatalysis. A detailed analysis was performed on protein stability and decomposition processes during the harsh oxidizing reaction conditions of WO, which will serve for the future design of WO ArMs with improved activity and stability.
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Affiliation(s)
- Ehider A Polanco
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Laura V Opdam
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Leonardo Passerini
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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Ma B, Shi S, Guo W, Zhang H, Zhao Z, An H. Liensinine, a Novel and Food-Derived Compound, Exerts Potent Antihepatoma Efficacy via Inhibiting the Kv10.1 Channel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4689-4702. [PMID: 38382537 DOI: 10.1021/acs.jafc.3c06142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Plant metabolites from natural product extracts offer unique advantages against carcinogenesis in the development of drugs. The target-based virtual screening from food-derived compounds represents a promising approach for tumor therapy. In this study, we performed virtual screening to target the presumed inhibitor-binding pocket and identified a highly potent Kv10.1 inhibitor, liensinine (Lien), which can inhibit the channel in a dose-dependent way with an IC50 of 0.24 ± 0.07 μM. Combining molecular dynamics simulations with mutagenesis experiments, our data show that Lien interacts with Kv10.1 by binding with Y539, T543, D551, E553, and H601 in the C-linker domain of Kv10.1. In addition, the interaction of sequence alignment and 3D structural modeling revealed differences between the C-linker domain of the Kv10.1 channel and the Kv11.1 channel. Furthermore, antitumor experiments revealed that Lien suppresses the proliferation and migration of HCC both in vitro and in vivo. In summary, the food-derived compound, Lien, may serve as a lead compound for antihepatoma therapeutic drugs targeting Kv10.1.
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Affiliation(s)
- Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Sai Shi
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Wei Guo
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailin Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Zhen Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
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Awuni E, Abdallah Musah R. Proposing lead compounds for the development of SARS-CoV-2 receptor-binding inhibitors. J Biomol Struct Dyn 2024; 42:2282-2297. [PMID: 37116068 DOI: 10.1080/07391102.2023.2204505] [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: 08/23/2022] [Accepted: 04/11/2023] [Indexed: 04/30/2023]
Abstract
The COVID-19 pandemic has had deleterious effects on the world and demands urgent measures to find therapeutic agents to combat the current and related future outbreaks. The entry of SARS-CoV-2 into the host's cell is facilitated by the interaction between the viral spike receptor-binding domain (sRBD) and the human angiotensin-converting enzyme 2 (hACE2). Although the interface of sRBD involved in the sRBD-hACE2 interaction has been projected as a primary vaccine and drug target, currently no small-molecule drugs have been approved for covid-19 treatment targeting sRBD. Herein structure-based virtual screening and molecular dynamics (MD) simulation strategies were applied to identify novel potential small-molecule binders of the SARS-CoV-2 sRBD from an sRBD-targeted compound library as leads for the development of anti-COVID-19 drugs. The library was initially screened against sRBD by using the GOLD docking program whereby 19 compounds were shortlisted based on docking scores after using a control compound to set the selection cutoff. The stability of each compound in MD simulations was used as a further standard to select four hits namely T4S1820, T4589, E634-1449, and K784-7078. Analyses of simulations data showed that the four compounds remained stably bound to sRBD for ≥ 80 ns with reasonable affinities and interacted with pharmacologically important amino acid residues. The compounds exhibited fair solubility, lipophilicity, and toxicity-propensity characteristics that could be improved through lead optimization regimes. The overall results suggest that the scaffolds of T4S1820, E634-1449, and K784-7078 could serve as seeds for developing potent small-molecule inhibitors of SARS-CoV-2 receptor binding and cell entry.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elvis Awuni
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
| | - Radiatu Abdallah Musah
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
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Yuan W, Rao X, Zhong B, Chen M, Ali H, Lv C, Niu C. Exploring the functional profiles of odorant binding proteins crucial for sensing key odorants in the new leaves of coconut palms in Rhynchophorus ferrugineus. Int J Biol Macromol 2024; 261:129852. [PMID: 38307432 DOI: 10.1016/j.ijbiomac.2024.129852] [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: 12/10/2023] [Revised: 01/28/2024] [Accepted: 01/28/2024] [Indexed: 02/04/2024]
Abstract
The red palm weevil (RPW), Rhynchophorus ferrugineus (Curculionidae: Coleoptera) is a highly destructive global pest of coconut trees, with a preference for laying its eggs on new leaves. Females can identify where to lay eggs by using their sense of smell to detect specific odorants found in new leaves. In this study, we focused on the two odorants commonly found in new leaves by GC-MS: trans, trans-2,4-nonadienal and trans-2-nonenal. Our behavioral assays demonstrated a significant attraction of females to both of these odorants, with their electrophysiological responses being dose-dependent. Furthermore, we examined the expression patterns induced by these odorants in eleven RferOBP genes. Among them, RferOBP3 and RferOBP1768 exhibited the most significant and simultaneous upregulation. To further understand the role of these two genes, we conducted experiments with females injected with OBP-dsRNA. This resulted in a significant decrease in the expression of RferOBP3 and RferOBP1768, as well as impaired the perception of the two odorants. A fluorescence competitive binding assay also showed that both RferOBPs strongly bound to the odorants. Additionally, sequence analysis revealed that these two RferOBPs belong to the Minus-C family and possess four conserved cysteines. Molecular docking simulations showed strong interactions between these two RferOBPs and the odorant molecules. Overall, our findings highlight the crucial role of RferOBP3 and RferOBP1768 in the olfactory perception of the key odorants in coconut palm new leaves. This knowledge significantly improves our understanding of how RPW females locate sites for oviposition and lays the foundation for future research on the development of environmentally friendly pest attractants.
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Affiliation(s)
- Weiqin Yuan
- Coconut Research Institute/Tropical Oil Crops Research Institute, Chinese Academy of Tropical Agriculture Sciences, Wenchang, Hainan 571300, China; College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xinjie Rao
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; New Horizon Health Co., Ltd., Hangzhou 310051, China
| | - Baozhu Zhong
- Coconut Research Institute/Tropical Oil Crops Research Institute, Chinese Academy of Tropical Agriculture Sciences, Wenchang, Hainan 571300, China
| | - Mengran Chen
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Habib Ali
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information technology, Rahim Yar Khan 64200, Pakistan
| | - Chaojun Lv
- Coconut Research Institute/Tropical Oil Crops Research Institute, Chinese Academy of Tropical Agriculture Sciences, Wenchang, Hainan 571300, China.
| | - Changying Niu
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Zhai T, Lan S, Xv L, Zhang X, Ma X, Li Z, Gao J, Chen Y, Lai Z, Lin Y. Genome-Wide Identification and Expression Analysis Reveal bZIP Transcription Factors Mediated Hormones That Functions during Early Somatic Embryogenesis in Dimocarpus longan. PLANTS (BASEL, SWITZERLAND) 2024; 13:662. [PMID: 38475508 DOI: 10.3390/plants13050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/14/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
The basic leucine zip (bZIP) transcription factors (TFs) are a group of highly conserved gene families that play important roles in plant growth and resistance to adversity stress. However, studies on hormonal regulatory pathways and functional analysis during somatic embryogenesis (SE) in Dimocarpus longan is still unavailable. In this study, a total of 51 bZIP family members were systematically identified in the whole genome of longan, a comprehensive bioinformatics analysis of DlbZIP (bZIP family members of D. longan) was performed, and subcellular localization and profiles patterns after transiently transformed DlbZIP60 were analyzed. The combined analysis of RNA-seq, ATAC-seq and ChIP-seq showed that four members have different H3K4me1 binding peaks in early SE and differentially expressed with increased chromatin accessibility. Comparative transcriptome analysis of bZIPs expression in early SE, different tissues and under 2,4-D treatment revealed that DlbZIP family might involved in growth and development during longan early SE. The qRT-PCR results implied that DlbZIP family were subjected to multiple hormonal responses and showed different degrees of up-regulated expression under indole-3-acetic acid (IAA), abscisic acid (ABA) and methyl jasmonate (MeJA) treatments, which indicated that they played an important role in the hormone synthesis pathways associated with the early SE of longan. Subcellular localization showed that DlbZIP60 was located in the nucleus, and the contents of endogenous IAA, MeJA and ABA were up-regulated in transiently DlbZIP60 overexpressed cell lines. These results suggest that DlbZIP60 may mediate hormones pathways that functions the development during early SE in longan.
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Affiliation(s)
- Tingkai Zhai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuoxian Lan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Luzhen Xv
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiangwei Ma
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuoyun Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Gao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Barraza-Flores P, Moghadaszadeh B, Lee W, Isaac B, Sun L, Troiano EC, Rockowitz S, Sliz P, Beggs AH. Zebrafish and cellular models of SELENON-Related Myopathy exhibit novel embryonic and metabolic phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.581979. [PMID: 38464009 PMCID: PMC10925121 DOI: 10.1101/2024.02.26.581979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
SELENON-Related Myopathy (SELENON-RM) is a rare congenital myopathy caused by mutations of the SELENON gene characterized by axial muscle weakness and progressive respiratory insufficiency. Muscle histopathology commonly includes multiminicores or a dystrophic pattern but is often non-specific. The SELENON gene encodes selenoprotein N (SelN), a selenocysteine-containing redox enzyme located in the endo/sarcoplasmic reticulum membrane where it colocalizes with mitochondria-associated membranes. However, the molecular mechanism(s) by which SelN deficiency causes SELENON-RM are undetermined. A hurdle is the lack of cellular and animal models that show assayable phenotypes. Here we report deep-phenotyping of SelN-deficient zebrafish and muscle cells. SelN-deficient zebrafish exhibit changes in embryonic muscle function and swimming activity in larvae. Analysis of single cell RNAseq data in a zebrafish embryo-atlas revealed coexpression between selenon and genes involved in glutathione redox pathway. SelN-deficient zebrafish and mouse myoblasts exhibit changes in glutathione and redox homeostasis, suggesting a direct relationship with SelN function. We report changes in metabolic function abnormalities in SelN-null myotubes when compared to WT. These results suggest that SelN has functional roles during zebrafish early development and myoblast metabolism.
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Affiliation(s)
- Pamela Barraza-Flores
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Behzad Moghadaszadeh
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Won Lee
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Biju Isaac
- Research Computing, Information Technology Department, Boston Children’s Hospital, Boston, MA, USA
| | - Liang Sun
- Research Computing, Information Technology Department, Boston Children’s Hospital, Boston, MA, USA
| | - Emily C. Troiano
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Shira Rockowitz
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Research Computing, Information Technology Department, Boston Children’s Hospital, Boston, MA, USA
| | - Piotr Sliz
- Research Computing, Information Technology Department, Boston Children’s Hospital, Boston, MA, USA
- Division of Molecular Medicine, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alan H. Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
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Amini R, Moradi S, Najafi R, Mazdeh M, Taherkhani A. BACE1 Inhibition Utilizing Organic Compounds Holds Promise as a Potential Treatment for Alzheimer's and Parkinson's Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2024; 2024:6654606. [PMID: 38425997 PMCID: PMC10904208 DOI: 10.1155/2024/6654606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/14/2023] [Accepted: 11/08/2023] [Indexed: 03/02/2024]
Abstract
Background Neurological disorders like Alzheimer's disease (AD) and Parkinson's disease (PD) manifest through gradually deteriorating cognitive functions. An encouraging strategy for addressing these disorders involves the inhibition of precursor-cleaving enzyme 1 (BACE1). Objectives In the current research, a virtual screening technique was employed to identify potential BACE1 inhibitors among selected herbal isolates. Methods This study evaluated 79 flavonoids, anthraquinones (AQs), and cinnamic acid derivatives for their potential blood-brain barrier (BBB) permeability. Using the AutoDock 4.0 tool, molecular docking analysis was conducted to determine the binding affinity of BBB permeable compounds to the BACE1 active site. Molecular dynamics (MD) simulations were performed to assess the stability of the docked poses of the most potent inhibitors. The interactions between the most effective plant-based inhibitors and the residues within the BACE1 catalytic site were examined before and after MD simulations. Results Ponciretin, danthron, chrysophanol, and N-p-coumaroyltyramine were among the highest-ranking BACE1 inhibitors, with inhibition constant values calculated in the nanomolar range. Furthermore, during 10 ns simulations, the docked poses of these ligands were observed to be stable. Conclusion The findings propose that ponciretin, danthron, chrysophanol, and N-p-coumaroyltyramine might serve as potential choices for the treatment of AD and PD, laying the groundwork for the creation of innovative BACE1 inhibitors.
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Affiliation(s)
- Razieh Amini
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shadi Moradi
- Department of Medical Immunology, School of Medicine, Hamadan University of Medical Science, Hamadan, Iran
| | - Rezvan Najafi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mehrdokht Mazdeh
- Hearing Disorders Research Cerner, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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Gao B, Li P, Zhu S. Single Deletion Unmasks Hidden Anti-Gram-Negative Bacterial Activity of an Insect Defensin-Derived Peptide. J Med Chem 2024; 67:2512-2528. [PMID: 38335999 DOI: 10.1021/acs.jmedchem.3c01584] [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: 02/12/2024]
Abstract
Insect defensins are a large family of antimicrobial peptides primarily active against Gram-positive bacteria. Here, we explore their hidden anti-Gram-negative bacterial potential via a nature-guided strategy inspired by natural deletion variants of Drosophila defensins. Referring to these variants, we deleted the equivalent region of an insect defensin with the first cysteine-containing N-terminus, and the last three cysteine-containing C-terminal regions remained. This 15-mer peptide exhibits low solubility and specifically targets Gram-positive bacteria. Further deletion of alanine-9 remarkably improves its solubility, unmasks its hidden anti-Gram-negative bacterial activity, and alters its states in different environments. Intriguingly, compared with the oxidized form, the 14-mer reduced peptide shows increased activity on Gram-positive and Gram-negative bacteria through a membrane-disruptive mechanism. The broad-spectrum activity and tolerance to high-salt environments and human serum, together with no toxicity to mammalian or human cells, make it a promising candidate for the design of new peptide antibiotics against Gram-negative bacterial infections.
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Affiliation(s)
- Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Ping Li
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), National Center for Nanoscience and Technology, No.11 ZhongGuanCun BeiYiTiao, Haidian District, Beijing 100190, China
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
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37
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Giacobbi NS, Mullapudi S, Nabors H, Pyeon D. The Chemokine CXCL14 as a Potential Immunotherapeutic Agent for Cancer Therapy. Viruses 2024; 16:302. [PMID: 38400076 PMCID: PMC10892169 DOI: 10.3390/v16020302] [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: 01/08/2024] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
There is great enthusiasm toward the development of novel immunotherapies for the treatment of cancer, and given their roles in immune system regulation, chemokines stand out as promising candidates for use in new cancer therapies. Many previous studies have shown how chemokine signaling pathways could be targeted to halt cancer progression. We and others have revealed that the chemokine CXCL14 promotes antitumor immune responses, suggesting that CXCL14 may be effective for cancer immunotherapy. However, it is still unknown what mechanism governs CXCL14-mediated antitumor activity, how to deliver CXCL14, what dose to apply, and what combinations with existing therapy may boost antitumor immune responses in cancer patients. Here, we provide updates on the role of CXCL14 in cancer progression and discuss the potential development and application of CXCL14 as an immunotherapeutic agent.
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Affiliation(s)
| | | | | | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (N.S.G.); (S.M.); (H.N.)
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38
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Tan C, Li S, Song J, Zheng X, Zheng H, Xu W, Wan C, Zhang T, Bian Q, Men S. 3,4-Dichlorophenylacetic acid acts as an auxin analog and induces beneficial effects in various crops. Commun Biol 2024; 7:161. [PMID: 38332111 PMCID: PMC10853179 DOI: 10.1038/s42003-024-05848-9] [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: 04/25/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Auxins and their analogs are widely used to promote root growth, flower and fruit development, and yield in crops. The action characteristics and application scope of various auxins are different. To overcome the limitations of existing auxins, expand the scope of applications, and reduce side effects, it is necessary to screen new auxin analogs. Here, we identified 3,4-dichlorophenylacetic acid (Dcaa) as having auxin-like activity and acting through the auxin signaling pathway in plants. At the physiological level, Dcaa promotes the elongation of oat coleoptile segments, the generation of adventitious roots, and the growth of crop roots. At the molecular level, Dcaa induces the expression of auxin-responsive genes and acts through auxin receptors. Molecular docking results showed that Dcaa can bind to auxin receptors, among which TIR1 has the highest binding activity. Application of Dcaa at the root tip of the DR5:GUS auxin-responsive reporter induces GUS expression in the root hair zone, which requires the PIN2 auxin efflux carrier. Dcaa also inhibits the endocytosis of PIN proteins like other auxins. These results provide a basis for the application of Dcaa in agricultural practices.
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Affiliation(s)
- Chao Tan
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Suxin Li
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Jia Song
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Xianfu Zheng
- Zhengzhou ZhengShi Chemical Co., Ltd, 450000, Zhengzhou, China
| | - Hao Zheng
- Zhengzhou ZhengShi Chemical Co., Ltd, 450000, Zhengzhou, China
| | - Weichang Xu
- Zhengzhou ZhengShi Chemical Co., Ltd, 450000, Zhengzhou, China
| | - Cui Wan
- Zhengzhou ZhengShi Chemical Co., Ltd, 450000, Zhengzhou, China
| | - Tan Zhang
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Qiang Bian
- National Pesticide Engineering Research Center (Tianjin), College of Chemistry, Nankai University, 300071, Tianjin, China.
| | - Shuzhen Men
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, China.
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39
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Wang X, Cun J, Li S, Shi Y, Liu Y, Wei H, Zhang Y, Cong R, Yang T, Wang W, Xiao J, Song Y, Yan D, Yang Q, Sun Q, Ji T. Genotype F of Echovirus 25 with multiple recombination pattern have been persistently and extensively circulating in Chinese mainland. Sci Rep 2024; 14:3212. [PMID: 38332009 PMCID: PMC10853551 DOI: 10.1038/s41598-024-53513-2] [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: 10/18/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
Echovirus 25 (E25), a member of the Enterovirus B (EV-B) species, can cause aseptic meningitis (AM), viral meningitis (VM), and acute flaccid paralysis (AFP). However, systematic studies on the molecular epidemiology of E25, especially those concerning its evolution and recombination, are lacking. In this study, 18 strains of E25, isolated from seven provinces of China between 2009 and 2018, were collected based on the Chinese hand, foot, and mouth disease (HFMD) surveillance network, and 95 sequences downloaded from GenBank were also screened. Based on the phylogenetic analysis of 113 full-length VP1 sequences worldwide, globally occurring E25 strains were classified into 9 genotypes (A-I), and genotype F was the dominant genotype in the Chinese mainland. The average nucleotide substitution rate of E25 was 6.08 × 10-3 substitutions/site/year, and six important transmission routes were identified worldwide. Seventeen recombination patterns were determined, of which genotype F can be divided into 9 recombination patterns. A positive selector site was found in the capsid protein region of genotype F. Recombination analysis and pressure selection analysis for genotype F showed multiple recombination patterns and evolution characteristics, which may be responsible for it being the dominant genotype in the Chinese mainland. This study provides a theoretical basis for the subsequent prevention and control of E25.
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Affiliation(s)
- Xiaoyi Wang
- Medical School, Anhui University of Science and Technology, Huainan, 232001, China
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jianping Cun
- Yunnan Center for Disease Control and Prevention, Kunming, 650100, China
| | - Shikang Li
- Hunan Center for Disease Control and Prevention, Changsha, 410005, China
| | - Yong Shi
- Jiangxi Center for Disease Control and Prevention, Nanchang, 330006, China
| | - Yingying Liu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, 050000, China
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou, 450000, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ruyi Cong
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Tingting Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Wenhui Wang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qiang Sun
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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40
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Dodd-O J, Roy A, Siddiqui Z, Jafari R, Coppola F, Ramasamy S, Kolloli A, Kumar D, Kaundal S, Zhao B, Kumar R, Robang AS, Li J, Azizogli AR, Pai V, Acevedo-Jake A, Heffernan C, Lucas A, McShan AC, Paravastu AK, Prasad BVV, Subbian S, Král P, Kumar V. Antiviral fibrils of self-assembled peptides with tunable compositions. Nat Commun 2024; 15:1142. [PMID: 38326301 PMCID: PMC10850501 DOI: 10.1038/s41467-024-45193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
The lasting threat of viral pandemics necessitates the development of tailorable first-response antivirals with specific but adaptive architectures for treatment of novel viral infections. Here, such an antiviral platform has been developed based on a mixture of hetero-peptides self-assembled into functionalized β-sheets capable of specific multivalent binding to viral protein complexes. One domain of each hetero-peptide is designed to specifically bind to certain viral proteins, while another domain self-assembles into fibrils with epitope binding characteristics determined by the types of peptides and their molar fractions. The self-assembled fibrils maintain enhanced binding to viral protein complexes and retain high resilience to viral mutations. This method is experimentally and computationally tested using short peptides that specifically bind to Spike proteins of SARS-CoV-2. This platform is efficacious, inexpensive, and stable with excellent tolerability.
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Affiliation(s)
- Joseph Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Abhishek Roy
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Santhamani Ramasamy
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Afsal Kolloli
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Dilip Kumar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Soni Kaundal
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Boyang Zhao
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ranjeet Kumar
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jeffrey Li
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Abdul-Rahman Azizogli
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Varun Pai
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Amanda Acevedo-Jake
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
- SAPHTx Inc, Newark, NJ, 07104, USA
| | - Alexandra Lucas
- Center for Personalized Diagnostics and Center for Immunotherapy Vaccines and Virotherapy, Biodesign Institute, Arizona State University, 727 E, Tempe, AZ, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Vivek Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- SAPHTx Inc, Newark, NJ, 07104, USA.
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA.
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41
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Ambrose AJ, Zerio CJ, Sivinski J, Zhu X, Godek J, Sanchez JL, Khanna M, Khanna R, Lairson L, Zhang DD, Chapman E. Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins. Biochemistry 2024; 63:251-263. [PMID: 38243804 DOI: 10.1021/acs.biochem.3c00531] [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: 01/22/2024]
Abstract
The 13 Hsp70 proteins in humans act on unique sets of substrates with diversity often being attributed to J-domain-containing protein (Hsp40 or JDP) cofactors. We were therefore surprised to find drastically different binding affinities for Hsp70-peptide substrates, leading us to probe substrate specificity among the 8 canonical Hsp70s from humans. We used peptide arrays to characterize Hsp70 binding and then mined these data using machine learning to develop an algorithm for isoform-specific prediction of Hsp70 binding sequences. The results of this algorithm revealed recognition patterns not predicted based on local sequence alignments. We then showed that none of the human isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s consisting of the human nucleotide-binding domain and the substrate-binding domain of DnaK complement during heat shock, providing further evidence in vivo of the divergent function of the Hsp70 substrate-binding domains. We also demonstrated that the differences in heat shock complementation among the chimeras are not due to loss of DnaJ binding. Although we do not exclude JDPs as additional specificity factors, our data demonstrate substrate specificity among the Hsp70s, which has important implications for inhibitor development in cancer and neurodegeneration.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher J Zerio
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Xiaoyi Zhu
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack Godek
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jonathan L Sanchez
- Department of Pharmacology, College of Medicine, The University of Arizona Health Sciences, Tucson, Arizona 85424, United States
| | - May Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Luke Lairson
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
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42
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Qu P, Xu K, Faraone JN, Goodarzi N, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Gumina RJ, Liu SL. Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants. Cell 2024; 187:585-595.e6. [PMID: 38194968 PMCID: PMC10872432 DOI: 10.1016/j.cell.2023.12.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/11/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose-vaccinated and bivalent-vaccinated healthcare workers, XBB.1.5-wave-infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially different conformational stability of BA.2.86 spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.
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Affiliation(s)
- Panke Qu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Kai Xu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Julia N Faraone
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Negin Goodarzi
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Yi-Min Zheng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Claire Carlin
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph S Bednash
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Jeffrey C Horowitz
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Rama K Mallampalli
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Linda J Saif
- Center for Food Animal Health, Animal Sciences Department, OARDC, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; Veterinary Preventive Medicine Department, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Daniel Jones
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Richard J Gumina
- Department of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA.
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43
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Fonseca-González I, Velasquez-Agudelo E, Londoño-Mesa MH, Álvarez JC. De novo transcriptome sequencing and annotation of the Antarctic polychaete Microspio moorei (Spionidae) with its characterization of the heat stress-related proteins (HSP, SOD & CAT). Mar Genomics 2024; 73:101085. [PMID: 38301367 DOI: 10.1016/j.margen.2024.101085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
We present a de novo transcriptome assembly for the non-model Antarctic polychaete worm Microspio moorei (Spionidae) collected during Antarctic field expedition in Fildes Bay, King George Island, Antarctic Peninsula, in 2017. Here, we report the first transcriptome reference array for Microspio spp. The gene sequences of the spionid worm were annotated from a wide range of functions (i.e., biological, and metabolic processes, catalytic processes, and catalytic activity). HSP70, HSP90 SOD and CAT families were compared to reported annelid transcriptomes and proteomes. The phylogenetic analysis using COI, 16S, and 18S markers effectively clusters the species within the family. However, it also casts uncertainty on the monophyletic nature of the Microspio genera, indicating the necessity for additional data and potentially requiring a reevaluation of its grouping. Within these protein families, 3D model software was used to create one representative of their protein structures. Structural predictions were compared with related reported annelids living at different temperatures and a human X-ray reference. We found structural differences (RMSE >1.8) between the human HSP proteins but no significant differences between the polychaete-predicted proteins (RMSE <1.2). These results encourage further research of heat stress-related proteins, the development of genetic markers for climate change-induced temperature stress, and the study of the underlying mechanisms of the heat response. Moreover, these results motivate the extension of these findings to congeneric species.
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Affiliation(s)
- Idalyd Fonseca-González
- LimnoBasE & Biotamar Research Group, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Esteban Velasquez-Agudelo
- Research Group in Biodiversity, Evolution and Conservation (BEC), EAFIT University, Medellín 050022, Colombia
| | - Mario H Londoño-Mesa
- LimnoBasE & Biotamar Research Group, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Javier C Álvarez
- Research Group in Biodiversity, Evolution and Conservation (BEC), EAFIT University, Medellín 050022, Colombia.
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44
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Gisriel CJ, Shen G, Brudvig GW, Bryant DA. Structure of the antenna complex expressed during far-red light photoacclimation in Synechococcus sp. PCC 7335. J Biol Chem 2024; 300:105590. [PMID: 38141759 PMCID: PMC10810746 DOI: 10.1016/j.jbc.2023.105590] [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: 10/22/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 12/25/2023] Open
Abstract
Far-red light photoacclimation, or FaRLiP, is a facultative response exhibited by some cyanobacteria that allows them to absorb and utilize lower energy light (700-800 nm) than the wavelengths typically used for oxygenic photosynthesis (400-700 nm). During this process, three essential components of the photosynthetic apparatus are altered: photosystem I, photosystem II, and the phycobilisome. In all three cases, at least some of the chromophores found in these pigment-protein complexes are replaced by chromophores that have red-shifted absorbance relative to the analogous complexes produced in visible light. Recent structural and spectroscopic studies have elucidated important features of the two photosystems when altered to absorb and utilize far-red light, but much less is understood about the modified phycobiliproteins made during FaRLiP. We used single-particle, cryo-EM to determine the molecular structure of a phycobiliprotein core complex comprising allophycocyanin variants that absorb far-red light during FaRLiP in the marine cyanobacterium Synechococcus sp. PCC 7335. The structure reveals the arrangement of the numerous red-shifted allophycocyanin variants and the probable locations of the chromophores that serve as the terminal emitters in this complex. It also suggests how energy is transferred to the photosystem II complexes produced during FaRLiP. The structure additionally allows comparisons with other previously studied allophycocyanins to gain insights into how phycocyanobilin chromophores can be tuned to absorb far-red light. These studies provide new insights into how far-red light is harvested and utilized during FaRLiP, a widespread cyanobacterial photoacclimation mechanism.
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Affiliation(s)
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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Iturrieta-González I, Chahin C, Cabrera J, Concha C, Olivares-Ferretti P, Briones J, Vega F, Bustos-Medina L, Fonseca-Salamanca F. Molecular Study of Pneumocystis jirovecii in Respiratory Samples of HIV Patients in Chile. J Fungi (Basel) 2024; 10:117. [PMID: 38392789 PMCID: PMC10889964 DOI: 10.3390/jof10020117] [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: 08/31/2023] [Revised: 10/01/2023] [Accepted: 10/06/2023] [Indexed: 02/24/2024] Open
Abstract
Pneumocystis is an opportunistic fungus that causes potentially fatal pneumonia (PCP) in immunocompromised patients. The objective of this study was to determine the prevalence of P. jirovecii in HIV patients through phenotypic and molecular study, to investigate the genetic polymorphisms of P. jirovecii at the mitochondrial gene mtLSU and at the nuclear dihydropteroate synthase gene (DHPS), and by analysis of molecular docking to study the effect of DHPS mutations on the enzymatic affinity for sulfamethoxazole. A PCP prevalence of 28.3% was detected, with mtLSU rRNA genotypes 3 (33.3%) and 2 (26.6%) being the most common. A prevalence of 6.7% (1/15) mutations in the DHPS gene was detected, specifically at codon 55 of the amino acid sequence of dihydropteroate synthase. Molecular docking analysis showed that the combination of mutations at 55 and 98 codons is required to significantly reduce the affinity of the enzyme for sulfamethoxazole. We observed a low rate of mutations in the DHPS gene, and molecular docking analysis showed that at least two mutations in the DHPS gene are required to significantly reduce the affinity of dihydropteroate synthase for sulfamethoxazole.
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Affiliation(s)
- Isabel Iturrieta-González
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectology and Clinical Immunology, Center of Excellence in Translational Medicine-Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
- Jeffrey Modell Foundation for Diagnosis and Research in Primary Immunodeficiencies, Center of Excellence in Translational Medicine, Medicine Faculty, Universidad de La Frontera, Temuco 4810296, Chile
| | - Carolina Chahin
- Infectology Unit, Hospital Dr. Hernán Henríquez Aravena, Temuco 4781151, Chile
| | - Johanna Cabrera
- Infectology Unit, Hospital Dr. Hernán Henríquez Aravena, Temuco 4781151, Chile
| | - Carla Concha
- Infectology Unit, Hospital Dr. Hernán Henríquez Aravena, Temuco 4781151, Chile
| | | | - Javier Briones
- Infectology Unit, Hospital Dr. Hernán Henríquez Aravena, Temuco 4781151, Chile
| | - Fernando Vega
- Critical Patient Unit, Hospital Dr. Hernán Henríquez Aravena, Temuco 4781151, Chile
| | - Luis Bustos-Medina
- Department of Public Health and CIGES, Faculty of Medicine, Universidad de La Frontera, Temuco 4781176, Chile
| | - Flery Fonseca-Salamanca
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Molecular Immunoparasitology, Center of Excellence in Translational Medicine-Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
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Bayat Z, Mazaheri T, Farhadifard H, Taherkhani A. Mechanisms Involved in Therapeutic Effects of Scutellaria baicalensis Georgi in Oral Squamous Cell Carcinoma Based on Systems Biology and Structural Bioinformatics Approaches. BIOMED RESEARCH INTERNATIONAL 2024; 2024:1236910. [PMID: 38322303 PMCID: PMC10846925 DOI: 10.1155/2024/1236910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 11/30/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Objective Oral squamous cell carcinoma (OSCC) is the most frequent oral cancer, constituting more than 90% of all oral carcinomas. The 5-year survival rate of OSCC patients is not satisfactory, and therefore, there is an urgent need for new practical therapeutic approaches besides the current therapies to overcome OSCC. Scutellaria baicalensis Georgi (SBG) is a plant of the family Lamiaceae with several pharmaceutical properties such as antioxidant, anti-inflammatory, and anticancer effects. Previous studies have demonstrated the curative effects of SBG in OSCC. Methods A systems biology approach was conducted to identify differentially expressed miRNAs (DEMs) in OSCC patients with a dismal prognosis compared to OSCC patients with a favorable prognosis. A protein interaction map (PIM) was built based on DEMs targets, and the hub genes within the PIM were indicated. Subsequently, the prognostic role of the hubs was studied using Kaplan-Meier curves. Next, the binding affinity of SBG's main components, including baicalein, wogonin, oroxylin-A, salvigenin, and norwogonin, to the prognostic markers in OSCC was evaluated using molecular docking analysis. Results Survival analysis showed that overexpression of CAV1, SERPINE1, ACTB, SMAD3, HMGA2, MYC, EIF2S1, HSPA4, HSPA5, and IL6 was significantly related to a poor prognosis in OSCC. Besides, molecular docking analysis demonstrated the ΔGbinding and inhibition constant values between SBG's main components and SERPINE1, ACTB, HMGA2, EIF2S1, HSPA4, and HSPA5 were as <-8.00 kcal/mol and nanomolar concentration, respectively. The most salient binding affinity was observed between wogonin and SERPINE1 with a criterion of ΔGbinding < -10.02 kcal/mol. Conclusion The present results unraveled potential mechanisms involved in therapeutic effects of SBG in OSCC based on systems biology and structural bioinformatics analyses.
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Affiliation(s)
- Zeynab Bayat
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Tina Mazaheri
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Homa Farhadifard
- Department of Orthodontics, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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Samuchiwal S, Sahu A, Selvaraju K, Singh S, Malik A. Unveiling the azo-reductase mechanism in Pseudomonas putida for efficient decolorization of textile Reactive dyes: an in-silico study. J Biomol Struct Dyn 2024:1-14. [PMID: 38284378 DOI: 10.1080/07391102.2024.2308768] [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: 08/16/2023] [Accepted: 01/14/2024] [Indexed: 01/30/2024]
Abstract
The textile industry utilizing affordable azo dyes is a high threat to aquatic life and causes environmental problems due to their toxicity. Biodegradation of azo dyes employing microbes and enzymes has proved to be an efficient method for treating industrial effluent. This study used the novel microbial consortium to decolorize reactive azo dyes (Reactive Red 120; Reactive Black 5 and Reactive Blue 13), and its azo-reductase activity was evaluated. The metagenomic analysis of the consortium identified azo-reductase-producing bacterial species. The molecular docking revealed that PpAzoR from Pseudomonas putida had the highest binding affinities for all the three dyes such as Reactive Black 5 (-9.3 kcal/mol), Reactive Blue 13 (-9.8 kcal/mol) and Reactive Red 120 (-10.7 kcal/mol). The structural rigidity and stability of the docked complex were confirmed through MD simulations evaluated across multiple descriptors from the simulation trajectories. Further, MMPBSA analysis validated the results that binding of the ligands, i.e. dye molecules Reactive Black (RB5), Reactive Blue (RB13) and Reactive Red (RR120) binding with the Azoreductase (PpAzoR) to the screened Azo-dyes was spontaneous. Based on molecular dynamics simulations for 100 ns, RR 120 showed the highest binding affinity (-411.336 ± 46.799 KJ/mol), followed by RB5 (-288.012 ± 33.371 KJ/mol). The dyes (RR120 and RB5) exhibited stable interactions with the target azoreductase (PpAzoR). The present study provides insights that PpAzoR shows the highest decolorization potency, which could be interpreted as a potential dye-degrading protein based on dye-degrading assay findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saurabh Samuchiwal
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Delhi, India
| | - Abhishek Sahu
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Delhi, India
| | - Koushalya Selvaraju
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Delhi, India
| | - Shubha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - Anushree Malik
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Delhi, India
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Beierlein F, Horn AHC, Sticht H, Mokhir A, Imhof P. In Silico Study of Camptothecin-Based Pro-Drugs Binding to Human Carboxylesterase 2. Biomolecules 2024; 14:153. [PMID: 38397391 PMCID: PMC10886758 DOI: 10.3390/biom14020153] [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: 12/29/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Pro-drugs, which ideally release their active compound only at the site of action, i.e., in a cancer cell, are a promising approach towards an increased specificity and hence reduced side effects in chemotherapy. A popular form of pro-drugs is esters, which are activated upon their hydrolysis. Since carboxylesterases that catalyse such a hydrolysis reaction are also abundant in normal tissue, it is of great interest whether a putative pro-drug is a probable substrate of such an enzyme and hence bears the danger of being activated not just in the target environment, i.e., in cancer cells. In this work, we study the binding mode of carboxylesters of the drug molecule camptothecin, which is an inhibitor of topoisomerase I, of varying size to human carboxylesterase 2 (HCE2) by molecular docking and molecular dynamics simulations. A comparison to irinotecan, known to be a substrate of HCE2, shows that all three pro-drugs analysed in this work can bind to the HCE2 protein, but not in a pose that is well suited for subsequent hydrolysis. Our data suggest, moreover, that for the irinotecan substrate, a reactant-competent pose is stabilised once the initial proton transfer from the putative nucleophile Ser202 to the His431 of the catalytic triad has already occurred. Our simulation work also shows that it is important to go beyond the static models obtained from molecular docking and include the flexibility of enzyme-ligand complexes in solvents and at a finite temperature. Under such conditions, the pro-drugs studied in this work are unlikely to be hydrolysed by the HCE2 enzyme, indicating a low risk of undesired drug release in normal tissue.
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Affiliation(s)
- Frank Beierlein
- Department for Chemistry and Pharmacy, Computer Chemistry Center, Friedrich-Alexander University Erlangen Nürnberg (FAU), Nägelsbachstraße 25, 91052 Erlangen, Germany;
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander University Erlangen Nürnberg (FAU), Martensstraße 1, 91058 Erlangen, Germany;
| | - Anselm H. C. Horn
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander University Erlangen Nürnberg (FAU), Martensstraße 1, 91058 Erlangen, Germany;
- Institute of Biochemistry, Friedrich-Alexander University Erlangen Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany;
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander University Erlangen Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany;
| | - Andriy Mokhir
- Department for Chemistry and Pharmacy, Institute for Organic Chemistry, Friedrich-Alexander University Erlangen Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany;
| | - Petra Imhof
- Department for Chemistry and Pharmacy, Computer Chemistry Center, Friedrich-Alexander University Erlangen Nürnberg (FAU), Nägelsbachstraße 25, 91052 Erlangen, Germany;
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Yu S, Wang Z, Li Q, Wang T, Zhao W. Innovative application of a novel di-D-fructofuranose 1,2':2,3'-dianhydride hydrolase (DFA-IIIase) from Duffyella gerundensis A4 to burdock root to improve nutrition. Food Funct 2024; 15:1021-1030. [PMID: 38180053 DOI: 10.1039/d3fo03277a] [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: 01/06/2024]
Abstract
Burdock is native to Europe and Asia and rich in many functional ingredients, including biomacromolecule polysaccharide inulin. The prebiotic fructan inulin can provide energy to organisms via several pathways. One pathway is that inulin fructotransferase (IFTase) first converts inulin to III-type difructose anhydride (DFA-III), which has many beneficial physiological functions. Then, DFA-III is hydrolyzed to inulobiose, which is a Fn-type prebiotic fructo-oligosaccharide, via difructose anhydride hydrolase (DFA-IIIase). However, there has been no study on the application of IFTase or DFA-IIIase to process burdock to increase DFA-III or inulobiose. Moreover, only five DFA-IIIases have been reported to date and all of them are from the Arthrobacter genus. Whether other microbes except for the Arthrobacter genus can utilize DFA-III through DFA-IIIase is unknown. In this work, a DFA-IIIase from Duffyella gerundensis A4 (D. gerundensis A4), abbreviated as DgDFA-IIIase, was identified and characterized in detail. DgDFA-IIIase is a bifunctional enzyme, that is, besides its hydrolytic ability to DFA-III, it has the same catalytic ability as IFTase to inulin. The enzyme was applied to the burdock root aiming at inulin and DFA-III, and inulobiose was produced with an increase in Gn-type fructo-oligosaccharide. The work verifies that microorganisms of the non-Arthrobacter genus also have the potential ability to use DFA-III by DFA-IIIase, and DFA-IIIase is feasible to increase functional substances of burdock root instead of IFTase and endo-inulinase, which paves the way for the production of functional food utilizing the polysaccharide inulin to improve nutrition and health.
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Affiliation(s)
- Shuhuai Yu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhenlong Wang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Qiting Li
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Tong Wang
- Microsoft Research AI4Science, Beijing 100080, China
| | - Wei Zhao
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, School of Internet of Things Engineering, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
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50
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Takarada JE, Cunha MR, Almeida VM, Vasconcelos SNS, Santiago AS, Godoi PH, Salmazo A, Ramos PZ, Fala AM, de Souza LR, Da Silva IEP, Bengtson MH, Massirer KB, Couñago RM. Discovery of pyrazolo[3,4-d]pyrimidines as novel mitogen-activated protein kinase kinase 3 (MKK3) inhibitors. Bioorg Med Chem 2024; 98:117561. [PMID: 38157838 DOI: 10.1016/j.bmc.2023.117561] [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: 10/14/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
The dual-specificity protein kinase MKK3 has been implicated in tumor cell proliferation and survival, yet its precise role in cancer remains inconclusive. A critical step in elucidating the kinase's involvement in disease biology is the identification of potent, cell-permeable kinase inhibitors. Presently, MKK3 lacks a dedicated tool compound for these purposes, along with validated methods for the facile screening, identification, and optimization of inhibitors. In this study, we have developed a TR-FRET-based enzymatic assay for the detection of MKK3 activity in vitro and a BRET-based assay to assess ligand binding to this enzyme within intact human cells. These assays were instrumental in identifying hit compounds against MKK3 that share a common chemical scaffold, sourced from a library of bioactive kinase inhibitors. Initial hits were subsequently expanded through the synthesis of novel analogs. The resulting structure-activity relationship (SAR) was rationalized using molecular dynamics simulations against a homology model of MKK3. We expect our findings to expedite the development of novel, potent, selective, and bioactive inhibitors, thus facilitating investigations into MKK3's role in various cancers.
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Affiliation(s)
- Jéssica E Takarada
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Micael R Cunha
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Vitor M Almeida
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Stanley N S Vasconcelos
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - André S Santiago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Paulo H Godoi
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Anita Salmazo
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Priscila Z Ramos
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Angela M Fala
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Lucas R de Souza
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Italo E P Da Silva
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Mario H Bengtson
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Katlin B Massirer
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Rafael M Couñago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States.
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