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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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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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Panchal J, Prajapati J, Dabhi M, Patel A, Patel S, Rawal R, Saraf M, Goswami D. Comprehensive computational investigation for ligand recognition and binding dynamics of SdiA: a degenerate LuxR -type receptor in Klebsiella pneumoniae. Mol Divers 2024:10.1007/s11030-023-10785-6. [PMID: 38212453 DOI: 10.1007/s11030-023-10785-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/26/2023] [Indexed: 01/13/2024]
Abstract
SdiA is a LuxR-type receptor that controls the virulence of Klebsiella pneumoniae, a Gram-negative bacterium that causes various infections in humans. SdiA senses exogenous acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2), two types of quorum sensing signals produced by other bacterial species. However, the molecular details of how SdiA recognizes and binds to different ligands and how this affects its function and regulation in K. pneumoniae still need to be better understood. This study uses computational methods to explore the protein-ligand binding dynamics of SdiA with 11 AHLs and 2 AI-2 ligands. The 3D structure of SdiA was predicted through homology modeling, followed by molecular docking with AHLs and AI-2 ligands. Binding affinities were quantified using MM-GBSA, and complex stability was assessed via Molecular Dynamics (MD) simulations. Results demonstrated that SdiA in Klebsiella pneumoniae exhibits a degenerate binding nature, capable of interacting with multiple AHLs and AI-2. Specific ligands, namely C10-HSL, C8-HSL, 3-oxo-C8-HSL, and 3-oxo-C10-HSL, were found to have high binding affinities and formed critical hydrogen bonds with key amino acid residues of SdiA. This finding aligns with the observed preference of SdiA for AHLs having 8 to 10 carbon-length acyl chains and lacking hydroxyl groups. In contrast, THMF and HMF demonstrated poor binding properties. Furthermore, AI-2 exhibited a low affinity, corroborating the inference that SdiA is not the primary receptor for AI-2 in K. pneumoniae. These findings provide insights into the protein-ligand binding dynamics of SdiA and its role in quorum sensing and virulence of K. pneumoniae.
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Affiliation(s)
- Janki Panchal
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Jignesh Prajapati
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Milan Dabhi
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Arun Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Kamdhenu University, Sardarkrushinagar 385505, Gujarat, India
| | - Sandip Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Kamdhenu University, Sardarkrushinagar 385505, Gujarat, India
| | - Rakesh Rawal
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Meenu Saraf
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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Arora H, Choudhir G, Sengupta A, Sharma A, Sharma S. Bioactive metabolites of licorice and thyme as potential inhibitors of Cox1 enzyme of phytopathogens of Capsicum annuum L.: In-silico approaches. J Biomol Struct Dyn 2024:1-18. [PMID: 38217280 DOI: 10.1080/07391102.2024.2303603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Cytochrome c oxidase subunit 1 (Cox1), a key enzyme, has a crucial role in cellular respiration in eukaryotes and prokaryotes. Generally, respiratory inhibitors are considered one of the types of chemical pesticides. Thyme oil and licorice aqueous extract have been reported to have antifungal activities against fungal phytopathogens of Capsicum annuum L., i.e., Colletotrichum capsici, Fusarium oxysporum, and Pythium aphanidermatum. The present study focuses on identifying the key bioactive molecules of thyme and licorice botanicals inhibiting the activity of the Cox1 enzymes of the above mentioned phytopathogens, employing the in-silico approach. From a wide range of bioactive molecules screened, the molecular docking indicated trans-carveol, carvacrol, kaempferol 3-rhamnoside 7-xyloside, kaempferitrin, and astragalin 7-rhamnoside as the potential inhibitors for Cox1 of C. capsici, β-Caryophyllene, Caryophyllene acetate, hispaglabridin A, kaempferol 3-rhamnoside 7-xyloside and licorice glycoside A for Cox1 of F. oxysporum and (+)-Longifolen, Caryophyllene acetate, Hispaglabridin A, Neoliquiritin 2''-apioside and Licorice-saponin A3 for Cox1 of P. aphanidermatum. Most of the top-scoring bioactive molecules exhibited higher binding affinity with the targets than the chemical compound, i.e., carbendazim. Density functional theory (DFT) analysis confirmed the reactivity of the top-docked compounds. Molecular dynamic simulations confirmed the stability of docked complexes when evaluated through multiple descriptors. Additionally, MM/PBSA analysis supported the findings, indicating the spontaneous binding of the enzymes to the screened ligands. ADMET analysis revealed the safety of the selected bioactive compounds. The present findings could be useful in developing biopesticidal formulations as efficient and sustainable alternatives to chemical pesticides.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Himanshu Arora
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi, India
| | - Gourav Choudhir
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi, India
| | - Arunava Sengupta
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | - Abhishek Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida, India
| | - Satyawati Sharma
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi, India
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Arias-Orozco P, Zhou L, Yi Y, Cebrián R, Kuipers OP. Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains. Microbiol Spectr 2024; 12:e0361123. [PMID: 38088546 PMCID: PMC10783134 DOI: 10.1128/spectrum.03611-23] [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: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Genome mining studies have revealed the remarkable combinatorial diversity of ribosomally synthesized and post-translationally modified peptides (RiPPs) in marine bacteria, including prochlorosins. However, mining strategies also prove valuable in investigating the genomic landscape of associated genes within biosynthetic gene cluster (BGC) specific to targeted RiPPs of interest. Our study contributes to the enrichment of knowledge regarding prochlorosin diversity. It offers insights into potential mechanisms involved in their biosynthesis and modification, such as hyper-modification, which may give rise to active lantibiotics. Additionally, our study uncovers putative novel promiscuous post-translational enzymes, thereby expanding the chemical space explored within the Synechococcus genus. Moreover, this research extends the applications of mining techniques beyond the discovery of new RiPP-like clusters, allowing for a deeper understanding of genomics and diversity. Furthermore, it holds the potential to reveal previously unknown functions within the intriguing RiPP families, particularly in the case of prochlorosins.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs.GRANADA, San Cecilio University Hospital, Granada, Spain
- CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
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Gutmann M, Reinhardt D, Seidensticker C, Raschig M, Hahn L, Moscaroli A, Behe M, Meinel L, Lühmann T. Matrix Metalloproteinase-Responsive Delivery of PEGylated Fibroblast Growth Factor 2. ACS Biomater Sci Eng 2024; 10:156-165. [PMID: 37988287 DOI: 10.1021/acsbiomaterials.3c01511] [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] [Indexed: 11/23/2023]
Abstract
Attachment of polyethylene glycol (PEG) chains is a common, well-studied, and Food and Drug Administration-approved method to address the pharmacokinetic challenges of therapeutic proteins. Occasionally, PEGylation impairs the activity of pharmacodynamics (PD). To overcome this problem, disease-relevant cleavable linkers between the polymer and the therapeutic protein can unleash full PD by de-PEGylating the protein at its target site. In this study, we engineered a matrix metalloproteinase (MMP)-responsive fibroblast growth factor 2 (FGF-2) mutant that was site-specifically extended with a PEG polymer chain. Using bioinspired strategies, the bioconjugate was designed to release the native protein at the desired structure/environment with preservation of the proliferative capacity in vitro on NIH3T3 cells. In vivo, hepatic exposure was diminished but not its renal distribution over time compared to unconjugated FGF-2. By releasing the growth factor from the PEG polymer in response to MMP cleavage, restored FGF-2 may enter hard-to-reach tissues and activate cell surface receptors or nuclear targets.
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Affiliation(s)
- Marcus Gutmann
- Institute of Pharmacy and Food Chemistry, University of Würzburg, DE-97074 Würzburg, Germany
| | - Debora Reinhardt
- Institute of Pharmacy and Food Chemistry, University of Würzburg, DE-97074 Würzburg, Germany
| | - Christian Seidensticker
- Medizinische Klinik und Poliklinik Für Innere Medizin II, Klinikum Rechts der Isar der TU München, Ismaninger Str. 22, 81675 Munich, Germany
| | - Martina Raschig
- Institute of Pharmacy and Food Chemistry, University of Würzburg, DE-97074 Würzburg, Germany
| | - Lukas Hahn
- Institute of Pharmacy and Food Chemistry, University of Würzburg, DE-97074 Würzburg, Germany
| | - Alessandra Moscaroli
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Martin Behe
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry, University of Würzburg, DE-97074 Würzburg, Germany
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), DE-97080 Würzburg, Germany
| | - Tessa Lühmann
- Institute of Pharmacy and Food Chemistry, University of Würzburg, DE-97074 Würzburg, Germany
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Mahdavi M, Mohsen-Pour N, Maleki M, Ghasemi S, Tabib A, Houshmand G, Naderi N, Masoumi T, Pouraliakbar H, Kalayinia S. Whole-exome sequencing reveals a likely pathogenic LMNA variant causing hypertrophic cardiomyopathy. Lab Med 2024; 55:62-70. [PMID: 37246508 DOI: 10.1093/labmed/lmad038] [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] [Indexed: 05/30/2023] Open
Abstract
OBJECTIVE We studied the clinical and molecular features of a family with hypertrophic cardiomyopathy (HCM). BACKGROUND A very heterogeneous disease affecting the heart muscle, HCM is mostly caused by variants in the proteins of sarcomeres. The detection of HCM pathogenic variants can affect the handling of patients and their families. METHODS Whole-exome sequencing (WES) was performed to assess the genetic cause(s) of HCM in a consanguineous Iranian family. RESULTS Missense likely pathogenic variant c.1279C>T (p.Arg427Cys) within exon 7 of the LMNA gene (NM_170707) was found. The segregations were confirmed by polymerase chain reaction-based Sanger sequencing. CONCLUSIONS Variant c.1279C>T (p.Arg427Cys) in the LMNA gene seemed to have been the cause of HCM in the family. A few LMNA gene variants related to HCM phenotypes have been recognized so far. Identifying HCM genetic basis confers significant opportunities to understand how the disease can develop and, by extension, how this progression can be arrested. Our study supports WES effectiveness for first-tier variant screening of HCM in a clinical setting.
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Affiliation(s)
- Mohammad Mahdavi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Mohsen-Pour
- Department of Genetics and Molecular Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Serwa Ghasemi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Avisa Tabib
- Heart Valve Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Golnaz Houshmand
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Niloofar Naderi
- Cardiogenetic Research Center and Iran University of Medical Sciences, Tehran, Iran
| | - Tannaz Masoumi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Pouraliakbar
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- Cardiogenetic Research Center and Iran University of Medical Sciences, Tehran, Iran
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Zhang Y, Nada B, Baker SE, Evans JE, Tian C, Benz JP, Tamayo E. Unveiling a classical mutant in the context of the GH3 β-glucosidase family in Neurospora crassa. AMB Express 2024; 14:4. [PMID: 38180602 PMCID: PMC10770018 DOI: 10.1186/s13568-023-01658-0] [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: 11/24/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024] Open
Abstract
Classical fungal mutant strains obtained by mutagenesis have helped to elucidate fundamental metabolic pathways in the past. In the filamentous fungus Neurospora crassa, the gluc-1 strain was isolated long ago and characterized by its low level of β-glucosidase activity, which is essential for the degradation of cellulose, the most abundant biopolymer on Earth and the main polymeric component of the plant cell wall. Based on genomic resequencing, we hypothesized that the causative mutation resides in the β-glucosidase gene gh3-3 (bgl6, NCU08755). In this work, growth patterns, enzymatic activities and sugar utilization rates were analyzed in several mutant and overexpression strains related to gluc-1 and gh3-3. In addition, different mutants affected in the degradation and transport of cellobiose were analyzed. While overexpression of gh3-3 led to the recovery of β-glucosidase activity in the gluc-1 mutant, as well as normal utilization of cellobiose, the full gene deletion strain Δgh3-3 was found to behave differently than gluc-1 with lower secreted β-glucosidase activity, indicating a dominant role of the amino acid substitution in the point mutated gh3-3 gene of gluc-1. Our results furthermore confirm that GH3-3 is the major extracellular β-glucosidase in N. crassa and demonstrate that the two cellodextrin transporters CDT-1 and CDT-2 are essential for growth on cellobiose when the three main N. crassa β-glucosidases are absent. Overall, these findings provide valuable insight into the mechanisms of cellulose utilization in filamentous fungi, being an essential step in the efficient production of biorefinable sugars from agricultural and forestry plant biomass.
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Affiliation(s)
- Yuxin Zhang
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Basant Nada
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Scott E Baker
- DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - James E Evans
- Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - J Philipp Benz
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Elisabeth Tamayo
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
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64
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Woellner-Santos D, Tahira AC, Malvezzi JVM, Mesel V, Morales-Vicente DA, Trentini MM, Marques-Neto LM, Matos IA, Kanno AI, Pereira ASA, Teixeira AAR, Giordano RJ, Leite LCC, Pereira CAB, DeMarco R, Amaral MS, Verjovski-Almeida S. Schistosoma mansoni vaccine candidates identified by unbiased phage display screening in self-cured rhesus macaques. NPJ Vaccines 2024; 9:5. [PMID: 38177171 PMCID: PMC10767053 DOI: 10.1038/s41541-023-00803-x] [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: 08/03/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Schistosomiasis, a challenging neglected tropical disease, affects millions of people worldwide. Developing a prophylactic vaccine against Schistosoma mansoni has been hindered by the parasite's biological complexity. In this study, we utilized the innovative phage-display immunoprecipitation followed by a sequencing approach (PhIP-Seq) to screen the immune response of 10 infected rhesus macaques during self-cure and challenge-resistant phases, identifying vaccine candidates. Our high-throughput S. mansoni synthetic DNA phage-display library encoded 99.6% of 119,747 58-mer peptides, providing comprehensive coverage of the parasite's proteome. Library screening with rhesus macaques' antibodies, from the early phase of establishment of parasite infection, identified significantly enriched epitopes of parasite extracellular proteins known to be expressed in the digestive tract, shifting towards intracellular proteins during the late phase of parasite clearance. Immunization of mice with a selected pool of PhIP-Seq-enriched phage-displayed peptides from MEG proteins, cathepsins B, and asparaginyl endopeptidase significantly reduced worm burden in a vaccination assay. These findings enhance our understanding of parasite-host immune responses and provide promising prospects for developing an effective schistosomiasis vaccine.
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Affiliation(s)
- Daisy Woellner-Santos
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana C Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - João V M Malvezzi
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
- Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Vinicius Mesel
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - David A Morales-Vicente
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Monalisa M Trentini
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
| | - Lázaro M Marques-Neto
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
| | - Isaac A Matos
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alex I Kanno
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
| | - Adriana S A Pereira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - André A R Teixeira
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Institute for Protein Innovation, Boston, MA, USA
| | | | - Luciana C C Leite
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
| | - Carlos A B Pereira
- Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ricardo DeMarco
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Murilo S Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil.
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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65
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Zheng W, Liu X. Modeling and Simulation of the NMDA Receptor at Coarse-Grained and Atomistic Levels. Methods Mol Biol 2024; 2799:269-280. [PMID: 38727913 DOI: 10.1007/978-1-0716-3830-9_15] [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] [Indexed: 06/01/2024]
Abstract
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. While high-resolution structures were solved for an allosterically inhibited form of functional NMDA receptor, other key functional states (particularly the active open-channel state) have not yet been resolved at atomic resolutions. To decrypt the molecular mechanism of the NMDA receptor activation, structural modeling and simulation are instrumental in providing detailed information about the dynamics and energetics of the receptor in various functional states. In this chapter, we describe coarse-grained modeling of the NMDA receptor using an elastic network model and related modeling/analysis tools (e.g., normal mode analysis, flexibility and hotspot analysis, cryo-EM flexible fitting, and transition pathway modeling) based on available structures. Additionally, we show how to build an atomistic model of the active-state receptor with targeted molecular dynamics (MD) simulation and explore its energetics and dynamics with conventional MD simulation. Taken together, these modeling and simulation can offer rich structural and dynamic information which will guide experimental studies of the activation of this key receptor.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, NY, USA.
| | - Xing Liu
- Department of Physics, State University of New York at Buffalo, Buffalo, NY, USA
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Behçet A, Taslimi P, Şen B, Taskın-Tok T, Aktaş A, Gök Y, Aygün M, Gülçin İ. New palladium complexes with N-heterocyclic carbene and morpholine ligands: Synthesis, characterization, crystal structure, molecular docking, and biological activities. J Biochem Mol Toxicol 2024; 38:e23554. [PMID: 37855258 DOI: 10.1002/jbt.23554] [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: 05/24/2023] [Revised: 07/12/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
This work includes the synthesis of a new series of palladium-based complexes containing both morpholine and N-heterocyclic carbene (NHC) ligands. The new complexes were characterized using NMR (1 H and 13 C), FTIR spectroscopic, and elemental analysis techniques. The crystal structure of complex 1b was obtained by utilizing the single-crystal X-ray diffraction method. X-ray studies show that the coordination environment of palladium atom is completed by the carbene carbon atom of the NHC ligand, the nitrogen atom of the morpholine ring, and a pair of bromide ligand, resulting in the formation of slightly distorted square planar geometry. All complexes were determined for some metabolic enzyme activities. Results indicated that all the synthetic complexes exhibited powerful inhibitory actions against all aims as compared to the control molecules. Ki values of new morpholine-liganded complexes bearing 4-hydroxyphenylethyl group 1a-e for hCA I, hCA II, AChE, BChE, and α-glycosidase enzymes were obtained in the ranges 0.93-2.14, 1.01-2.03, 4.58-10.27, 7.02-13.75, and 73.86-102.65 µM, respectively. Designing of reported complexes is impacted by molecular docking study, and interaction with the current enzymes also proclaimed that compounds 1e (-12.25 kcal/mol for AChE and -11.63 kcal/mol for BChE), 1c (-10.77 kcal/mol and -9.26 kcal/mol for α-Gly and hCA II, respectively), and 1a (-8.31 kcal/mol for hCA I) are showing binding affinity and interaction from the synthesized five novel complexes.
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Affiliation(s)
- Ayten Behçet
- Department of Chemistry, Faculty of Science and Arts, Inonu University, Malatya, Türkiye
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Türkiye
| | - Betül Şen
- Department of Physics, Faculty of Science, Dokuz Eylül University, Buca, Türkiye
| | - Tuğba Taskın-Tok
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, Gaziantep, Türkiye
- Institute of Health Sciences, Gaziantep University, Gaziantep, Türkiye
| | - Aydın Aktaş
- Vocational School of Health Service, Inonu University, Malatya, Türkiye
| | - Yetkin Gök
- Department of Chemistry, Faculty of Science and Arts, Inonu University, Malatya, Türkiye
| | - Muhittin Aygün
- Department of Physics, Faculty of Science, Dokuz Eylül University, Buca, Türkiye
| | - İlhami Gülçin
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Türkiye
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67
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Bains A, Fischer K, Guan W, LiWang PJ. The Antiviral Activity of the Lectin Griffithsin against SARS-CoV-2 Is Enhanced by the Presence of Structural Proteins. Viruses 2023; 15:2452. [PMID: 38140693 PMCID: PMC10747160 DOI: 10.3390/v15122452] [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: 10/14/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Although COVID-19 transmission has been reduced by the advent of vaccinations and a variety of rapid monitoring techniques, the SARS-CoV-2 virus itself has shown a remarkable ability to mutate and persist. With this long track record of immune escape, researchers are still exploring prophylactic treatments to curtail future SARS-CoV-2 variants. Specifically, much focus has been placed on the antiviral lectin Griffithsin in preventing spike protein-mediated infection via the hACE2 receptor (direct infection). However, an oft-overlooked aspect of SARS-CoV-2 infection is viral capture by attachment receptors such as DC-SIGN, which is thought to facilitate the initial stages of COVID-19 infection in the lung tissue (called trans-infection). In addition, while immune escape is dictated by mutations in the spike protein, coronaviral virions also incorporate M, N, and E structural proteins within the particle. In this paper, we explored how several structural facets of both the SARS-CoV-2 virion and the antiviral lectin Griffithsin can affect and attenuate the infectivity of SARS-CoV-2 pseudovirus. We found that Griffithsin was a better inhibitor of hACE2-mediated direct infection when the coronaviral M protein is present compared to when it is absent (possibly providing an explanation regarding why Griffithsin shows better inhibition against authentic SARS-CoV-2 as opposed to pseudotyped viruses, which generally do not contain M) and that Griffithsin was not an effective inhibitor of DC-SIGN-mediated trans-infection. Furthermore, we found that DC-SIGN appeared to mediate trans-infection exclusively via binding to the SARS-CoV-2 spike protein, with no significant effect observed when other viral proteins (M, N, and/or E) were present. These results provide etiological data that may help to direct the development of novel antiviral treatments, either by leveraging Griffithsin binding to the M protein as a novel strategy to prevent SARS-CoV-2 infection or by narrowing efforts to inhibit trans-infection to focus on DC-SIGN binding to SARS-CoV-2 spike protein.
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Affiliation(s)
- Arjan Bains
- Chemistry and Biochemistry, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Kathryn Fischer
- Quantitative and Systems Biology, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Wenyan Guan
- Materials and Biomaterials Science and Engineering, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA;
| | - Patricia J. LiWang
- Molecular Cell Biology, Health Sciences Research Institute, University of California Merced, 5200 North Lake Rd., Merced, CA 95343, USA
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Côco LZ, Aires R, Carvalho GR, Belisário EDS, Yap MKK, Amorim FG, Conde-Aranda J, Nogueira BV, Vasquez EC, Pereira TDMC, Campagnaro BP. Unravelling the Gastroprotective Potential of Kefir: Exploring Antioxidant Effects in Preventing Gastric Ulcers. Cells 2023; 12:2799. [PMID: 38132119 PMCID: PMC10742242 DOI: 10.3390/cells12242799] [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: 10/30/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The present study was conducted to evaluate the protective effect of milk kefir against NSAID-induced gastric ulcers. Male Swiss mice were divided into three groups: control (Vehicle; UHT milk at a dose of 0.3 mL/100 g), proton pump inhibitor (PPI; lansoprazole 30 mg/kg), and 4% milk kefir (Kefir; 0.3 mL/100 g). After 14 days of treatment, gastric ulcer was induced by oral administration of indomethacin (40 mg/kg). Reactive oxygen species (ROS), nitric oxide (NO), DNA content, cellular apoptosis, IL-10 and TNF-α levels, and myeloperoxidase (MPO) enzyme activity were determined. The interaction networks between NADPH oxidase 2 and kefir peptides 1-35 were determined using the Residue Interaction Network Generator (RING) webserver. Pretreatment with kefir for 14 days prevented gastric lesions. In addition, kefir administration reduced ROS production, DNA fragmentation, apoptosis, and TNF-α systemic levels. Simultaneously, kefir increased NO bioavailability in gastric cells and IL-10 systemic levels. A total of 35 kefir peptides showed affinity with NADPH oxidase 2. These findings suggest that the gastroprotective effect of kefir is due to its antioxidant and anti-inflammatory properties. Kefir could be a promising natural therapy for gastric ulcers, opening new perspectives for future research.
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Affiliation(s)
- Larissa Zambom Côco
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Rafaela Aires
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Glaucimeire Rocha Carvalho
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Eduarda de Souza Belisário
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | | | - Fernanda Gobbi Amorim
- Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, 4000 Liège, Belgium;
| | - Javier Conde-Aranda
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain;
| | - Breno Valentim Nogueira
- Department of Morphology, Health Sciences Center, Federal University of Espírito Santo (UFES), Vitoria 29047-105, ES, Brazil;
| | - Elisardo Corral Vasquez
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Thiago de Melo Costa Pereira
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Bianca Prandi Campagnaro
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
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Zhao Y, Zheng Z, Zhang Z, Xu Y, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Biashad SA, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle. Nat Commun 2023; 14:8054. [PMID: 38052795 PMCID: PMC10698142 DOI: 10.1038/s41467-023-43623-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
Hyaluronic acid is a major component of extracellular matrix which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (Heterocephalus glaber) contains abundant high-molecular-mass hyaluronic acid in its tissues, which contributes to this species' cancer resistance and possibly to its longevity. Here we report that abundant high-molecular-mass hyaluronic acid is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These subterranean mammalian species accumulate abundant high-molecular-mass hyaluronic acid by regulating the expression of genes involved in hyaluronic acid degradation and synthesis and contain unique mutations in these genes. The abundant high-molecular-mass hyaluronic acid may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic conditions. Our work suggests that high-molecular-mass hyaluronic acid has evolved with subterranean lifestyle.
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Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 301158, China
| | - Zhizhong Zheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Zhihui Zhang
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Yandong Xu
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 301158, China
| | - Eric Hillpot
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Yifei S Lin
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Frances T Zakusilo
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - J Yuyang Lu
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Seyed Ali Biashad
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Richard A Miller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY, 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY, 14627, USA.
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70
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Jantorn P, Tipmanee V, Wanna W, Prapasarakul N, Visutthi M, Sotthibandhu DS. Potential natural antimicrobial and antibiofilm properties of Piper betle L. against Staphylococcus pseudintermedius and methicillin-resistant strains. JOURNAL OF ETHNOPHARMACOLOGY 2023; 317:116820. [PMID: 37369337 DOI: 10.1016/j.jep.2023.116820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/08/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Piper betle L. has potent of antimicrobial activity and is widely used as a traditional remedy to treat skin infections. However, no clear evidence exists concerning antimicrobial and antibiofilm activity against Staphylococcus pseudintermedius and methicillin-resistant S. pseudintermedius (MRSP) opportunistic pathogens that cause wound infections and pyoderma in canines and zoonotic disease. AIM OF THE STUDY The antimicrobial and antibiofilm activities of P. betle extract were assessed against S. pseudintermedius and MRSP strains. MATERIALS AND METHODS Ethanol leaf extract of P. betle was investigated for its antibacterial effect on S. pseudintermedius and MRSP by broth microdilution and time-kill assays. Biofilm inhibition and production assays were performed to evaluate antibiofilm and biofilm eradication effects, respectively. Biofilm-associated gene expression was further studied using real-time polymerase chain reaction (PCR). The possible interaction between IcaA and major compounds in P. betle was analyzed by molecular docking. RESULTS The extract showed minimum inhibitory concentration (MIC) at 250 μg/mL. Growth inhibition of P. betle at 1 MIC against the bacteria was initially observed after treatment for 4 h. All isolates were completely killed after 18 h exposure to the extract. Minimum biofilm inhibitory concentrations (MBICs) of the extract against the tested isolates ranged 1/2 MIC to 1 MIC, while minimum biofilm eradication concentration (MBEC) of P. betle was initialed at 8 MIC. Quantitative inhibition and eradication effects were observed in representative strains. The extract at 1/2 MIC and 1 MIC values inhibited biofilm formation up to 100%, with bacterial biofilm removed at up to 94.21% by 4 MIC of the extract. The extract downregulated the expression of the icaA gene among biofilm-producing isolates. The most abundant compounds, 4-allyl-1,2-diacetoxybenzene and eugenol showed a strong affinity with IcaA protein at -5.65 and -5.31 kcal/mol, respectively. CONCLUSIONS P. betle extract demonstrated the antibacterial, antibiofilm, and biofilm-removal activity against S. pseudintermedius and MRSP. Downregulation of the icaA gene expression and protein interaction were possible modes of action of the extract that impacted biofilm production. This extract showed promise as an alternative treatment for S. pseudintermedius infection, especially drug-resistant and biofilm-associated cases.
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Affiliation(s)
- Pavarish Jantorn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Warapond Wanna
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Nuvee Prapasarakul
- Center of Excellence in Diagnosis and Monitoring of Animal Pathogens (DMAP), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Monton Visutthi
- Biology Program, Faculty of Science and Technology, Nakhon Ratchasima Rajabhat University, Nakhon Ratchasima 30000, Thailand
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71
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Kamli H, Shaikh A, Bappi MH, Raposo A, Ahmad MF, Sonia FA, Akbor MS, Prottay AAS, Gonçalves SA, Araújo IM, Coutinho HDM, Elbendary EY, Lho LH, Han H, Islam MT. Sclareol exerts synergistic antidepressant effects with quercetin and caffeine, possibly suppressing GABAergic transmission in chicks. Biomed Pharmacother 2023; 168:115768. [PMID: 37866001 DOI: 10.1016/j.biopha.2023.115768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023] Open
Abstract
This study evaluated the effects of sclareol (SCL) with or without caffeine (CAF) and quercetin (QUR) using in-vivo and in-silico studies. For this, 5-day-old chicks weighing between 45 and 48 g were randomly divided into five groups and treated accordingly. The chicks were monitored to compare the occurrence, latency, and duration of sleep as well as the loss and gain of righting reflex in response to SCL-10 mg/kg, CAF-10 mg/kg, and QUR-50 mg/kg using a thiopental sodium (TS)-induced sleeping model. Data were analyzed by one-way ANOVA followed by t-Student-Newman-Keuls' as a posthoc test at 95% confidence intervals with multiple comparisons. An in-silico study was also performed to investigate the possible antidepressant mechanisms of the test and/or standard drugs with different subunits of GABAA receptors. In comparison to the SCL, CAF, and QUR individual groups, SCL+CAF+QUR significantly increased the latency while decreasing the length of sleep. The incidence of loss and gain of the righting reflex was also modulated in the combination group. SCL showed better interaction with GABAA (α2 and α5) subunits than QUR with α2, α3, and α5. All these compounds showed stronger interactions with the GABAA receptor subunits than the standard CAF. Taken together, SCL, CAF, and QUR reduced the TS-induced righting reflex and sleeping time in the combination group more than in the individual treatments. SCL may show its antidepressant effects, possibly through interactions with GABAA receptor subunits.
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Affiliation(s)
- Hossam Kamli
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Ahmad Shaikh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Mehedi Hasan Bappi
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Md Faruque Ahmad
- Department of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Fatema Akter Sonia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md Showkoth Akbor
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Abdullah Al Shamsh Prottay
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Sheila Alves Gonçalves
- Department of Biological Chemistry, Laboratory of Microbiology and Molecular Biology, Program of Post-Graduation in Molecular Bioprospection, Regional University of Cariri, Crato, CE 63105-000, Brazil
| | - Isaac Moura Araújo
- Department of Biological Chemistry, Laboratory of Microbiology and Molecular Biology, Program of Post-Graduation in Molecular Bioprospection, Regional University of Cariri, Crato, CE 63105-000, Brazil
| | - Henrique Douglas Melo Coutinho
- Department of Biological Chemistry, Laboratory of Microbiology and Molecular Biology, Program of Post-Graduation in Molecular Bioprospection, Regional University of Cariri, Crato, CE 63105-000, Brazil
| | - Ehab Y Elbendary
- Department of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Linda Heejung Lho
- College of Business Division of Tourism and Hotel Management, Cheongju University, 298 Daesung-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28503, Republic of Korea.
| | - Heesup Han
- College of Hospitality and Tourism Management, Sejong University, 98 Gunja-Dong, Gwanjin-Gu, Seoul 143-747, Republic of Korea.
| | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh.
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Miyazaki M, Asakura M, Ide T, Hayakawa T. Random Mutational Analysis Targeting Residue K 155 within the Transmembrane β-Hairpin of the Mosquitocidal Mpp46Ab Toxin. BIOLOGY 2023; 12:1481. [PMID: 38132307 PMCID: PMC10741074 DOI: 10.3390/biology12121481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Mpp46Ab is a mosquito-larvicidal pore-forming toxin derived from Bacillus thuringiensis TK-E6. Pore formation is believed to be a central mode of Mpp46Ab action, and the cation selectivity of the channel pores, in particular, is closely related to its mosquito-larvicidal activity. In the present study, we constructed a mutant library in which residue K155 within the transmembrane β-hairpin was randomly replaced with other amino acid residues. Upon mutagenesis and following primary screening using Culex pipiens mosquito larvae, we obtained 15 mutants in addition to the wild-type toxin. Bioassays using purified proteins revealed that two mutants, K155E and K155I, exhibited toxicity significantly higher than that of the wild-type toxin. Although increased cation selectivity was previously reported for K155E channel pores, we demonstrated in the present study that the cation selectivity of K155I channel pores was also significantly increased. Considering the characteristics of the amino acids, the charge of residue 155 may not directly affect the cation selectivity of Mpp46Ab channel pores. Replacement of K155 with glutamic acid or isoleucine may induce a similar conformational change in the region associated with the ion selectivity of the Mpp46Ab channel pores. Mutagenesis targeting the transmembrane β-hairpin may be an effective strategy for enhancing the ion permeability of the channel pores and the resulting mosquito-larvicidal activity of Mpp46Ab.
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Affiliation(s)
| | | | | | - Tohru Hayakawa
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan; (M.M.); (M.A.); (T.I.)
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73
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Hessel SS, Dwivany FM, Zainuddin IM, Wikantika K, Celik I, Emran TB, Tallei TE. A computational simulation appraisal of banana lectin as a potential anti-SARS-CoV-2 candidate by targeting the receptor-binding domain. J Genet Eng Biotechnol 2023; 21:148. [PMID: 38015308 PMCID: PMC10684481 DOI: 10.1186/s43141-023-00569-8] [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: 12/10/2022] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND The ongoing concern surrounding coronavirus disease 2019 (COVID-19) primarily stems from continuous mutations in the genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), leading to the emergence of numerous variants. The receptor-binding domain (RBD) in the S1 subunit of the S protein of the virus plays a crucial role in recognizing the host's angiotensin-converting enzyme 2 (hACE2) receptor and facilitating cell membrane fusion processes, making it a potential target for preventing viral entrance into cells. This research aimed to determine the potential of banana lectin (BanLec) proteins to inhibit SARS-CoV-2 attachment to host cells by interacting with RBD through computational modeling. MATERIALS AND METHODS The BanLecs were selected through a sequence analysis process. Subsequently, the genes encoding BanLec proteins were retrieved from the Banana Genome Hub database. The FGENESH online tool was then employed to predict protein sequences, while web-based tools were utilized to assess the physicochemical properties, allergenicity, and toxicity of BanLecs. The RBDs of SARS-CoV-2 were modeled using the SWISS-MODEL in the following step. Molecular docking procedures were conducted with the aid of ClusPro 2.0 and HDOCK web servers. The three-dimensional structures of the docked complexes were visualized using PyMOL. Finally, molecular dynamics simulations were performed to investigate and validate the interactions of the complexes exhibiting the highest interactions, facilitating the simulation of their dynamic properties. RESULTS The BanLec proteins were successfully modeled based on the RNA sequences from two species of banana (Musa sp.). Moreover, an amino acid modification in the BanLec protein was made to reduce its mitogenicity. Theoretical allergenicity and toxicity predictions were conducted on the BanLecs, which suggested they were likely non-allergenic and contained no discernible toxic domains. Molecular docking analysis demonstrated that both altered and wild-type BanLecs exhibited strong affinity with the RBD of different SARS-CoV-2 variants. Further analysis of the molecular docking results showed that the BanLec proteins interacted with the active site of RBD, particularly the key amino acids residues responsible for RBD's binding to hACE2. Molecular dynamics simulation indicated a stable interaction between the Omicron RBD and BanLec, maintaining a root-mean-square deviation (RMSD) of approximately 0.2 nm for a duration of up to 100 ns. The individual proteins also had stable structural conformations, and the complex demonstrated a favorable binding-free energy (BFE) value. CONCLUSIONS These results confirm that the BanLec protein is a promising candidate for developing a potential therapeutic agent for combating COVID-19. Furthermore, the results suggest the possibility of BanLec as a broad-spectrum antiviral agent and highlight the need for further studies to examine the protein's safety and effectiveness as a potent antiviral agent.
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Affiliation(s)
- Sofia Safitri Hessel
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia
| | - Fenny Martha Dwivany
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia.
| | - Ima Mulyama Zainuddin
- Department of Biosystems, KU Leuven, Willem de Croylaan 42 box 2455, B-3001, Leuven, Belgium
| | - Ketut Wikantika
- Remote Sensing and Geographical Information Science Research Group, Faculty of Earth Science and Technology (FITB), Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38039, Kayseri, Turkey
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi, 95115, Indonesia.
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74
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Pacak P, Kluger C, Vogel V. Molecular dynamics of JUNO-IZUMO1 complexation suggests biologically relevant mechanisms in fertilization. Sci Rep 2023; 13:20342. [PMID: 37990051 PMCID: PMC10663542 DOI: 10.1038/s41598-023-46835-0] [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: 07/20/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023] Open
Abstract
JUNO-IZUMO1 binding is the first known physical link created between the sperm and egg membranes in fertilization, however, how this initiates sperm-egg fusion remains elusive. As advanced structural insights will help to combat the infertility crisis, or advance fertility control, we employed all-atom Molecular Dynamics (MD) to derive dynamic structural insights that are difficult to obtain experimentally. We found that the hydrated JUNO-IZUMO1 interface is composed of a large set of short-lived non-covalent interactions. The contact interface is destabilized by strategically located point mutations, as well as by Zn2+ ions, which shift IZUMO1 into the non-binding "boomerang" conformation. We hypothesize that the latter might explain how the transient zinc spark, as released after sperm entry into the oocyte, might contribute to block polyspermy. To address a second mystery, we performed another set of simulations, as it was previously suggested that JUNO in solution is unable to bind to folate despite it belonging to the folate receptor family. MD now suggests that JUNO complexation with IZUMO1 opens up the binding pocket thereby enabling folate insertion. Our MD simulations thus provide crucial new hypotheses how the dynamics of the JUNO-IZUMO1 complex upon solvation might regulate fertility.
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Affiliation(s)
- Paulina Pacak
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Carleen Kluger
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität, München, Munich, Germany
- Evotec München GmbH, Neuried, Germany
| | - Viola Vogel
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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75
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Härer L, Ernst L, Bechtner J, Wefers D, Ehrmann MA. Glycoside hydrolase family 32 enzymes from Bombella spp. catalyze the formation of high-molecular weight fructans from sucrose. J Appl Microbiol 2023; 134:lxad268. [PMID: 37974045 DOI: 10.1093/jambio/lxad268] [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: 08/30/2023] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
AIMS Acetic acid bacteria of the genus Bombella have not been reported to produce exopolysaccharides (EPS). In this study, the formation of fructans by B. apis TMW 2.1884 and B. mellum TMW 2.1889 was investigated. METHODS AND RESULTS Out of eight strains from four different Bombella species, only B. apis TMW 2.1884 and B. mellum TMW 2.1889 showed EPS formation with 50 g l-1 sucrose as substrate. Both EPS were identified as high-molecular weight (HMW) polymers (106-107 Da) by asymmetric flow field-flow fractionation coupled to multi angle laser light scattering and UV detecors (AF4-MALLS/UV) and high performance size exclusion chromatography coupled to MALLS and refractive index detectors (HPSEC-MALLS/RI) analyses. Monosaccharide analysis via trifluoroacetic acid hydrolysis showed that both EPS are fructans. Determination of glycosidic linkages by methylation analysis revealed mainly 2,6-linked fructofuranose (Fruf) units with additional 2,1-linked Fruf units (10%) and 2,1,6-Fruf branched units (7%). No glycoside hydrolase (GH) 68 family genes that are typically associated with the formation of HMW fructans in bacteria could be identified in the genomes. Through heterologous expression in Escherichia coli Top10, an enzyme of the GH32 family could be assigned to the catalysis of fructan formation. The identified fructosyltransferases could be clearly differentiated phylogenetically and structurally from other previously described bacterial fructosyltransferases. CONCLUSIONS The formation of HMW fructans by individual strains of the genus Bombella is catalyzed by enzymes of the GH32 family. Analysis of the fructans revealed an atypical structure consisting of 2,6-linked Fruf units as well as 2,1-linked Fruf units and 2,1,6-Fruf units.
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Affiliation(s)
- Luca Härer
- Chair of Microbiology, Technical University of Munich, Gregor-Mendel-Straße 4, 85354 Freising, Germany
| | - Luise Ernst
- Institute of Chemistry, Division of Food Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 2, 06120 Halle (Saale), Germany
| | - Julia Bechtner
- Department of Food Science-Food Technology, Aarhus University, Agro Food Park 48, 8200 Aarhus N, Denmark
| | - Daniel Wefers
- Institute of Chemistry, Division of Food Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 2, 06120 Halle (Saale), Germany
| | - Matthias A Ehrmann
- Chair of Microbiology, Technical University of Munich, Gregor-Mendel-Straße 4, 85354 Freising, Germany
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76
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Parrett GA, Brones PD, Jenkins GM, Mounts SM, Nguyen A, Risser DD. Identification of a morphogene required for tapered filament termini in filamentous cyanobacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37971486 DOI: 10.1099/mic.0.001416] [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: 11/19/2023]
Abstract
Although the photosynthetic cyanobacteria are monophyletic, they exhibit substantial morphological diversity across species, and even within an individual species due to phenotypic plasticity in response to life cycles and environmental signals. This is particularly prominent among the multicellular filamentous cyanobacteria. One example of this is the appearance of tapering at the filament termini. However, the morphogenes controlling this phenotype and the adaptive function of this morphology are not well defined. Here, using the model filamentous cyanobacterium Nostoc punctiforme ATCC29133 (PCC73102), we identify tftA, a morphogene required for the development of tapered filament termini. The tftA gene is specifically expressed in developing hormogonia, motile trichomes where the tapered filament morphology is observed, and encodes a protein containing putative amidase_3 and glucosaminidase domains, implying a function in peptidoglycan hydrolysis. Deletion of tftA abolished filament tapering inidcating that TftA plays a role in remodelling the cell wall to produce tapered filaments. Genomic conservation of tftA specifically in filamentous cyanobacteria indicates this is likely to be a conserved mechanism among these organisms. Finally, motility assays indicate that filaments with tapered termini migrate more efficiently through dense substratum, providing a plausible biological role for this morphology.
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Affiliation(s)
- Gabriel A Parrett
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Peyton D Brones
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Garrett M Jenkins
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Savanna M Mounts
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Alicia Nguyen
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Douglas D Risser
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
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Wiedmann F, Paasche A, Nietfeld J, Kraft M, Meyer AL, Warnecke G, Karck M, Frey N, Schmidt C. Activation of neurokinin-III receptors modulates human atrial TASK-1 currents. J Mol Cell Cardiol 2023; 184:26-36. [PMID: 37793594 DOI: 10.1016/j.yjmcc.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
RATIONALE The neurokinin-III receptor was recently shown to regulate atrial cardiomyocyte excitability by inhibiting atrial background potassium currents. TASK-1 (hK2P3.1) two-pore-domain potassium channels, which are expressed atrial-specifically in the human heart, contribute significantly to atrial background potassium currents. As TASK-1 channels are regulated by a variety of intracellular signalling cascades, they represent a promising candidate for mediating the electrophysiological effects of the Gq-coupled neurokinin-III receptor. OBJECTIVE To investigate whether TASK-1 channels mediate the neurokinin-III receptor activation induced effects on atrial electrophysiology. METHODS AND RESULTS In Xenopus laevis oocytes, heterologously expressing neurokinin-III receptor and TASK-1, administration of the endogenous neurokinin-III receptor ligands substance P or neurokinin B resulted in a strong TASK-1 current inhibition. This could be reproduced by application of the high affinity neurokinin-III receptor agonist senktide. Moreover, preincubation with the neurokinin-III receptor antagonist osanetant blunted the effect of senktide. Mutagenesis studies employing TASK-1 channel constructs which lack either protein kinase C (PKC) phosphorylation sites or the domain which is regulating the diacyl glycerol (DAG) sensitivity domain of TASK-1 revealed a protein kinase C independent mechanism of TASK-1 current inhibition: upon neurokinin-III receptor activation TASK-1 channels are blocked in a DAG-dependent fashion. Finally, effects of senktide on atrial TASK-1 currents could be reproduced in patch-clamp measurements, performed on isolated human atrial cardiomyocytes. CONCLUSIONS Heterologously expressed human TASK-1 channels are inhibited by neurokinin-III receptor activation in a DAG dependent fashion. Patch-clamp measurements, performed on human atrial cardiomyocytes suggest that the atrial-specific effects of neurokinin-III receptor activation on cardiac excitability are predominantly mediated via TASK-1 currents.
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Affiliation(s)
- Felix Wiedmann
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg /Mannheim, University of Heidelberg, Heidelberg, Germany; HCR, Heidelberg Center for Heart Rhythm Disorders, University Hospital Heidelberg, Heidelberg, Germany
| | - Amelie Paasche
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg /Mannheim, University of Heidelberg, Heidelberg, Germany; HCR, Heidelberg Center for Heart Rhythm Disorders, University Hospital Heidelberg, Heidelberg, Germany
| | - Jendrik Nietfeld
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Manuel Kraft
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg /Mannheim, University of Heidelberg, Heidelberg, Germany; HCR, Heidelberg Center for Heart Rhythm Disorders, University Hospital Heidelberg, Heidelberg, Germany
| | - Anna L Meyer
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Gregor Warnecke
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Karck
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Norbert Frey
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg /Mannheim, University of Heidelberg, Heidelberg, Germany; HCR, Heidelberg Center for Heart Rhythm Disorders, University Hospital Heidelberg, Heidelberg, Germany
| | - Constanze Schmidt
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg /Mannheim, University of Heidelberg, Heidelberg, Germany; HCR, Heidelberg Center for Heart Rhythm Disorders, University Hospital Heidelberg, Heidelberg, Germany.
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78
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Rane AS, Nair VS, Joshi RS, Giri AP. Domain Shuffling and Site-Saturation Mutagenesis for the Enhanced Inhibitory Potential of Amaranthaceae α-Amylase Inhibitors. Protein J 2023; 42:519-532. [PMID: 37598128 DOI: 10.1007/s10930-023-10148-y] [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] [Accepted: 07/31/2023] [Indexed: 08/21/2023]
Abstract
Amaranthaceae α-amylase inhibitors (AAIs) are knottin-type proteins with selective inhibitory potential against coleopteran α-amylases. Their small size and remarkable stability make them exciting molecules for protein engineering to achieve superior selectivity and efficacy. In this report, we have designed a set of AAI pro- and mature peptides chimeras. Based on in silico analysis, stable AAI chimeras having a stronger affinity with target amylases were selected for characterization. In vitro studies validated that chimera of the propeptide from Chenopodium quinoa α-AI and mature peptide from Beta vulgaris α-AI possess 3, 7.6, and 4.26 fold higher inhibition potential than parental counterparts. Importantly, recombinant AAI chimera retained specificity towards target coleopteran α-amylases. In addition, to improve the inhibitory potential of AAI, we performed in silico site-saturation mutagenesis. Computational analysis followed by experimental data showed that substituting Asparagine at the 6th position with Methionine had a remarkable increase in the specific inhibition potential of Amaranthus hypochondriacus α-AI. These results provide structural-functional insights into the vitality of AAI propeptide and a potential hotspot for mutagenesis to enhance the AAI activity. Our investigation will be a toolkit for AAI's optimization and functional differentiation for future biotechnological applications.
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Affiliation(s)
- Ashwini S Rane
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vineetkumar S Nair
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra, 411008, India
| | - Rakesh S Joshi
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Ashok P Giri
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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Budagaga Y, Sabet Z, Zhang Y, Novotná E, Hanke I, Rozkoš T, Hofman J. Tazemetostat synergistically combats multidrug resistance by the unique triple inhibition of ABCB1, ABCC1, and ABCG2 efflux transporters in vitro and ex vivo. Biochem Pharmacol 2023; 216:115769. [PMID: 37634597 DOI: 10.1016/j.bcp.2023.115769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
ATP-binding cassette (ABC) drug efflux transporters and drug metabolizing enzymes play crucial roles in pharmacokinetic drug-drug interactions and multidrug tumor resistance (MDR). Tazemetostat (EPZ-6438, Tazverik) is a novel epigenetic drug that has been recently approved for the therapy of advanced epithelioid sarcoma and follicular lymphoma. Additionally, this medication is currently being clinically tested to treat several other cancers such as non-small cell lung cancer (NSCLC). This study aimed to investigate the inhibitory effects of tazemetostat on selected ABC transporters/cytochrome P450 3A4 (CYP3A4) enzyme to comprehensively explore its role in MDR. First, our accumulation and molecular docking studies showed that tazemetostat is a unique triple inhibitor of ABCB1, ABCC1, and ABCG2 transporters. In contrast, tazemetostat exhibited only low level of interaction with the CYP3A4 isozyme. Drug combination assays confirmed that tazemetostat is a multipotent MDR modulator able to synergize with various conventional chemotherapeutics in vitro. Subsequent caspase activity assays and microscopic staining of apoptotic nuclei proved that the effective induction of apoptosis is behind the observed synergies. Notably, a potent MDR-modulatory capacity of tazemetostat was recorded in primary ex vivo NSCLC explants generated from patients' biopsies. On the contrary, its possible position of pharmacokinetic MDR's victim was excluded in comparative proliferation assays. Finally, tested drug has not been identified as an inducer of resistant phenotype in NSCLC cell lines. In conclusion, we demonstrated that tazemetostat is a unique multispecific chemosensitizer, which has strong potential to overcome limitations seen in the era of traditional MDR modulators.
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Affiliation(s)
- Youssif Budagaga
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Králové, Czech Republic
| | - Ziba Sabet
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Králové, Czech Republic
| | - Yu Zhang
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Králové, Czech Republic
| | - Eva Novotná
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Králové, Czech Republic
| | - Ivo Hanke
- Department of Cardiac Surgery, Faculty of Medicine, Charles University in Hradec Králové and University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Tomáš Rozkoš
- The Fingerland Department of Pathology, Charles University, Faculty of Medicine and University Hospital in Hradec Králové, Czech Republic, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Jakub Hofman
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Králové, Czech Republic.
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Ma S, Xiao G, Deng X, Tong M, Huang J, Li Q, Zhang Y. CovidShiny: An Integrated Web Tool for SARS-CoV-2 Mutation Profiling and Molecular Diagnosis Assay Evaluation In Silico. Viruses 2023; 15:2017. [PMID: 37896794 PMCID: PMC10611021 DOI: 10.3390/v15102017] [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: 08/24/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuing to evolve and accumulate mutations. While various bioinformatics tools have been developed for SARS-CoV-2, a well-curated mutation-tracking database integrated with in silico evaluation for molecular diagnostic assays is currently unavailable. To address this, we introduce CovidShiny, a web tool that integrates mutation profiling, in silico evaluation, and data download capabilities for genomic sequence-based SARS-CoV-2 assays and data download. It offers a feasible framework for surveilling the mutation of SARS-CoV-2 and evaluating the coverage of the molecular diagnostic assay for SARS-CoV-2. With CovidShiny, we examined the dynamic mutation pattern of SARS-CoV-2 and evaluated the coverage of commonly used assays on a large scale. Based on our in silico analysis, we stress the importance of using multiple target molecular diagnostic assays for SARS-CoV-2 to avoid potential false-negative results caused by viral mutations. Overall, CovidShiny is a valuable tool for SARS-CoV-2 mutation surveillance and in silico assay design and evaluation.
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Affiliation(s)
- Shaoqian Ma
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Gezhi Xiao
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Xusheng Deng
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Mengsha Tong
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Jialiang Huang
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Qingge Li
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Yongyou Zhang
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361100, China
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81
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Rodriguez Moncivais OJ, Chavez SA, Estrada Jimenez VH, Sun S, Li L, Kirken RA, Rodriguez G. Structural Analysis of Janus Tyrosine Kinase Variants in Hematological Malignancies: Implications for Drug Development and Opportunities for Novel Therapeutic Strategies. Int J Mol Sci 2023; 24:14573. [PMID: 37834019 PMCID: PMC10572942 DOI: 10.3390/ijms241914573] [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: 08/19/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Janus tyrosine kinase (JAK) variants are known drivers for hematological disorders. With the full-length structure of mouse JAK1 being recently resolved, new observations on the localization of variants within closed, open, and dimerized JAK structures are possible. Full-length homology models of human wild-type JAK family members were developed using the Glassman et al. reported mouse JAK1 containing the V658F structure as a template. Many mutational sites related to proliferative hematological disorders reside in the JH2 pseudokinase domains facing the region important in dimerization of JAKs in both closed and open states. More than half of all JAK gain of function (GoF) variants are changes in polarity, while only 1.2% are associated with a change in charge. Within a JAK1-JAK3 homodimer model, IFNLR1 (PDB ID7T6F) and the IL-2 common gamma chain subunit (IL2Rγc) were aligned with the respective dimer implementing SWISS-MODEL coupled with ChimeraX. JAK3 variants were observed to encircle the catalytic site of the kinase domain, while mutations in the pseudokinase domain align along the JAK-JAK dimerization axis. FERM domains of JAK1 and JAK3 are identified as a hot spot for hematologic malignancies. Herein, we propose new allosteric surfaces for targeting hyperactive JAK dimers.
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Affiliation(s)
- Omar J. Rodriguez Moncivais
- Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
| | - Stephanie A. Chavez
- Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
| | - Victor H. Estrada Jimenez
- Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
| | - Shengjie Sun
- Department of Physics, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
- Computational Sciences Program, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
| | - Lin Li
- Department of Physics, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
- Computational Sciences Program, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
| | - Robert A. Kirken
- Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
| | - Georgialina Rodriguez
- Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79902, USA
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82
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Leasure CS, Grunenwald CM, Choby JE, Sauer JD, Skaar EP. Maintenance of heme homeostasis in Staphylococcus aureus through post-translational regulation of glutamyl-tRNA reductase. J Bacteriol 2023; 205:e0017123. [PMID: 37655914 PMCID: PMC10521356 DOI: 10.1128/jb.00171-23] [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: 06/01/2023] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
Staphylococcus aureus is an important human pathogen responsible for a variety of infections including skin and soft tissue infections, endocarditis, and sepsis. The combination of increasing antibiotic resistance in this pathogen and the lack of an efficacious vaccine underscores the importance of understanding how S. aureus maintains metabolic homeostasis in a variety of environments, particularly during infection. Within the host, S. aureus must regulate cellular levels of the cofactor heme to support enzymatic activities without encountering heme toxicity. Glutamyl tRNA reductase (GtrR), the enzyme catalyzing the first committed step in heme synthesis, is an important regulatory node of heme synthesis in Bacteria, Archaea, and Plantae. In many organisms, heme status negatively regulates the abundance of GtrR, controlling flux through the heme synthesis pathway. We identified two residues within GtrR, H32 and R214, that are important for GtrR-heme binding. However, in strains expressing either GtrRH32A or GtrRR214A, heme homeostasis was not perturbed, suggesting an alternative mechanism of heme synthesis regulation occurs in S. aureus. In this regard, we report that heme synthesis is regulated through phosphorylation and dephosphorylation of GtrR by the serine/threonine kinase Stk1 and the phosphatase Stp1, respectively. Taken together, these results suggest that the mechanisms governing staphylococcal heme synthesis integrate both the availability of heme and the growth status of the cell. IMPORTANCE Staphylococcus aureus represents a significant threat to human health. Heme is an iron-containing enzymatic cofactor that can be toxic at elevated levels. During infection, S. aureus must control heme levels to replicate and survive within the hostile host environment. We identified residues within a heme biosynthetic enzyme that are critical for heme binding in vitro; however, abrogation of heme binding is not sufficient to perturb heme homeostasis within S. aureus. This marks a divergence from previously reported mechanisms of heme-dependent regulation of the highly conserved enzyme glutamyl tRNA reductase (GtrR). Additionally, we link cell growth arrest to the modulation of heme levels through the post-translational regulation of GtrR by the kinase Stk1 and the phosphatase Stp1.
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Affiliation(s)
- Catherine S. Leasure
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Caroline M. Grunenwald
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jacob E. Choby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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83
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Liu K, Guo F, Ma Y, Yu X, Fu X, Li W, Han W. Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes. Int J Mol Sci 2023; 24:14471. [PMID: 37833919 PMCID: PMC10572755 DOI: 10.3390/ijms241914471] [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: 08/13/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The disease of SARS-CoV-2 has caused considerable morbidity and mortality globally. Spike proteins on the surface of SARS-CoV-2 allow it to bind with human cells, leading to infection. Fullerenes and their derivatives are promising SARS-CoV-2 inhibitors and drug-delivery vehicles. In this study, Gaussian accelerated molecular dynamics simulations and the Markov state model were employed to delve into the inhibitory mechanism of Fullerene-linear-polyglycerol-b-amine sulfate (F-LGPS) on spike proteins. During the study, it was discovered that fullerene derivatives can operate at the interface of the receptor-binding domain (RBD) and the N-terminal domain (NTD), keeping structural domains in a downward conformation. It was also observed that F-LGPS demonstrated superior inhibitory effects on the XBB variant in comparison to the wild-type variant. This study yielded invaluable insights for the potential development of efficient therapeutics targeting the spike protein of SARS-CoV-2.
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Affiliation(s)
- Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (K.L.); (Y.M.)
| | - Fangfang Guo
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (F.G.); (X.Y.); (X.F.)
| | - Yingying Ma
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (K.L.); (Y.M.)
| | - Xiangyu Yu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (F.G.); (X.Y.); (X.F.)
| | - Xueqi Fu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (F.G.); (X.Y.); (X.F.)
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (F.G.); (X.Y.); (X.F.)
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (K.L.); (Y.M.)
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Arivuselvam R, Dera AA, Parween Ali S, Alraey Y, Saif A, Hani U, Arumugam Ramakrishnan S, Azeeze MSTA, Rajeshkumar R, Susil A, Harindranath H, Kumar BRP. Isolation, Identification, and Antibacterial Properties of Prodigiosin, a Bioactive Product Produced by a New Serratia marcescens JSSCPM1 Strain: Exploring the Biosynthetic Gene Clusters of Serratia Species for Biological Applications. Antibiotics (Basel) 2023; 12:1466. [PMID: 37760761 PMCID: PMC10526024 DOI: 10.3390/antibiotics12091466] [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: 08/27/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Prodigiosin pigment has high medicinal value, so exploring this compound is a top priority. This report presents a prodigiosin bioactive compound isolated from Serratia marcescens JSSCPM1, a new strain. The purification process of this compound involves the application of different chromatographic methods, including UV-visible spectroscopy, high-performance liquid chromatography (HPLC), and liquid chromatography-mass spectrometry (LC/MS). Subsequent analysis was performed using nuclear magnetic resonance (NMR) to achieve a deeper understanding of the compound's structure. Finally, through a comprehensive review of the existing literature, the structural composition of the isolated bioactive compound was found to correspond to that of the well-known compound prodigiosin. The isolated prodigiosin compound was screened for antibacterial activity against both Gram-positive and Gram-negative bacteria. The compound inhibited the growth of Gram-negative bacterial strains compared with Gram-positive bacterial strains. It showed a maximum minimum inhibitory concentration against Escherichia coli NCIM 2065 at a 15.9 ± 0.31 μg/mL concentration. The potential binding capabilities between prodigiosin and the OmpF porin proteins (4GCS, 4GCP, and 4GCQ) were determined using in silico studies, which are generally the primary targets of different antibiotics. Comparative molecular docking analysis indicated that prodigiosin exhibits a good binding affinity toward these selected drug targets.
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Affiliation(s)
- Rajaguru Arivuselvam
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty 643001, TN, India; (R.A.); (S.A.R.)
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India
| | - Ayed A. Dera
- Department of Clinical Laboratory Sciences, Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia; (A.A.D.); (S.P.A.); (Y.A.)
| | - Syed Parween Ali
- Department of Clinical Laboratory Sciences, Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia; (A.A.D.); (S.P.A.); (Y.A.)
| | - Yasser Alraey
- Department of Clinical Laboratory Sciences, Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia; (A.A.D.); (S.P.A.); (Y.A.)
| | - Ahmed Saif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia;
| | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Guraiger, Abha 62529, Saudi Arabia;
| | - Sivaa Arumugam Ramakrishnan
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty 643001, TN, India; (R.A.); (S.A.R.)
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India
| | | | - Raman Rajeshkumar
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty 643001, TN, India; (R.A.); (S.A.R.)
| | - Aishwarya Susil
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India (H.H.)
| | - Haritha Harindranath
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India (H.H.)
| | - B. R. Prashantha Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagar, Mysore 570015, KA, India (H.H.)
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Saksena S, Forbes K, Rajan N, Giles D. Phylogenetic investigation of Gammaproteobacteria proteins involved in exogenous long-chain fatty acid acquisition and assimilation. Biochem Biophys Rep 2023; 35:101504. [PMID: 37601446 PMCID: PMC10439403 DOI: 10.1016/j.bbrep.2023.101504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 08/22/2023] Open
Abstract
Background The incorporation of exogenous fatty acids into the cell membrane yields structural modifications that directly influence membrane phospholipid composition and indirectly contribute to virulence. FadL and FadD are responsible for importing and activating exogenous fatty acids, while acyltransferases (PlsB, PlsC, PlsX, PlsY) incorporate fatty acids into the cell membrane. Many Gammaproteobacteria species possess multiple homologs of these proteins involved in exogenous fatty acid metabolism, suggesting the evolutionary acquisition and maintenance of this transport pathway. Methods This study developed phylogenetic trees based on amino acid and nucleotide sequences of homologs of FadL, FadD, PlsB, PlsC, PlsX, and PlsY via Mr. Bayes and RAxML algorithms. We also explored the operon arrangement of genes encoding for FadL. Additionally, FadL homologs were modeled via SWISS-MODEL, validated and refined by SAVES, Galaxy Refine, and GROMACS, and docked with fatty acids via AutoDock Vina. Resulting affinities were analyzed by 2-way ANOVA test and Tukey's post-hoc test. Results Our phylogenetic trees revealed grouping based on operon structure, original homolog blasted from, and order of the homolog, suggesting a more ancestral origin of the multiple homolog phenomena. Our molecular docking simulations indicated a similar binding pattern for the fatty acids between the different FadL homologs. General significance Our study is the first to illustrate the phylogeny of these proteins and to investigate the binding of various FadL homologs across orders with fatty acids. This study helps unravel the mystery surrounding these proteins and presents topics for future research.
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Affiliation(s)
- Saksham Saksena
- College of Arts and Sciences, Vanderbilt University, 2201 West End Ave., Nashville, TN, 37235, USA
| | - Kwame Forbes
- College of Science and Mathematics, The University of the Virgin Islands, 2 John Brewers Bay, St. Thomas, USVI, 00802-9990, USA
| | - Nipun Rajan
- East Hamilton High School, 2015 Ooltewah Ringgold Road, Ootlewah, TN, 37363, USA
| | - David Giles
- Department of Biology, Geology and Environmental Science, The University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN, 37403, USA
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86
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Olivares-Ferretti P, Beltrán JF, Salazar LA, Fonseca-Salamanca F. Protein Modelling and Molecular Docking Analysis of Fasciola hepatica β-Tubulin's Interaction Sites, with Triclabendazole, Triclabendazole Sulphoxide and Triclabendazole Sulphone. Acta Parasitol 2023; 68:535-547. [PMID: 37330945 DOI: 10.1007/s11686-023-00692-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: 06/16/2022] [Accepted: 05/29/2023] [Indexed: 06/20/2023]
Abstract
PURPOSE Fasciola hepatica is a globally distributed trematode that causes significant economic losses. Triclabendazole is the primary pharmacological treatment for this parasite. However, the increasing resistance to triclabendazole limits its efficacy. Previous pharmacodynamics studies suggested that triclabendazole acts by interacting mainly with the β monomer of tubulin. METHODS We used a high-quality method to model the six isotypes of F. hepatica β-tubulin in the absence of three-dimensional structures. Molecular dockings were conducted to evaluate the destabilization regions in the molecule against the ligands triclabendazole, triclabendazole sulphoxide and triclabendazole sulphone. RESULTS The nucleotide binding site demonstrates higher affinity than the binding sites of colchicine, albendazole, the T7 loop and pβVII (p < 0.05). We suggest that the binding of the ligands to the polymerization site of β-tubulin can lead a microtubule disruption. Furthermore, we found that triclabendazole sulphone exhibited significantly higher binding affinity than other ligands (p < 0.05) across all isotypes of β-tubulin. CONCLUSIONS Our investigation has yielded new insight on the mechanism of action of triclabendazole and its sulphometabolites on F. hepatica β-tubulin through computational tools. These findings have significant implications for ongoing scientific research ongoing towards the discovery of novel therapeutics to treat F. hepatica infections.
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Affiliation(s)
- Pamela Olivares-Ferretti
- Laboratory of Molecular Immunoparasitology, Center of Excellence in Translational Medicine-Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Temuco, Chile
| | - Jorge F Beltrán
- Chemical Engineering Department, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Luis A Salazar
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, 4811230, Temuco, Chile
| | - Flery Fonseca-Salamanca
- Laboratory of Molecular Immunoparasitology, Center of Excellence in Translational Medicine-Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Temuco, Chile.
- Preclinical Sciences Department, Faculty of Medicine, Universidad de La Frontera, Temuco, Chile.
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87
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Davies-Bolorunduro OF, Jaemsai B, Ruangchai W, Phumiphanjarphak W, Aiewsakun P, Palittapongarnpim P. Analysis of whiB7 in Mycobacterium tuberculosis reveals novel AT-hook deletion mutations. Sci Rep 2023; 13:13324. [PMID: 37587174 PMCID: PMC10432532 DOI: 10.1038/s41598-023-40152-2] [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: 04/11/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023] Open
Abstract
Mutations in whiB7 have been associated with both hypersusceptibility and resistance to various antibiotics in Mycobacterium tuberculosis (Mtb). Unlocking the secrets of antibiotic resistance in the bacterium, we examined mutations in the coding sequences of whiB7 of over 40,000 diverse Mtb isolates. Our results unveil the dominant c.191delG (Gly64delG) mutation, present in all members of the lineage L1.2.2 and its impact on WhiB7's conserved GVWGG-motif, causing conformational changes and deletion of the C-terminal AT-hook. Excitingly, we discovered six unique mutations associated with partial or total deletion of the AT-hook, specific to certain sublineages. Our findings suggest the selective pressures driving these mutations, underlining the potential of genomics to advance our understanding of Mtb's antibiotic resistance. As tuberculosis remains a global health threat, our study offers valuable insights into the diverse nature and functional consequences of whiB7 mutations, paving the way for the development of novel therapeutic interventions.
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Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Center for Tuberculosis Research, Microbiology Department, Nigerian Institute of Medical Research, 6 Edmund Crescent, P.M.B 2013, Yaba, 101012, Lagos, Nigeria
| | - Bharkbhoom Jaemsai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
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88
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Lester A, Sandman M, Herring C, Girard C, Dixon B, Ramsdell H, Reber C, Poulos J, Mitchell A, Spinney A, Henager ME, Evans CN, Turlington M, Johnson QR. Computational Exploration of Potential CFTR Binding Sites for Type I Corrector Drugs. Biochemistry 2023; 62:2503-2515. [PMID: 37437308 PMCID: PMC10433520 DOI: 10.1021/acs.biochem.3c00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/22/2023] [Indexed: 07/14/2023]
Abstract
Cystic fibrosis (CF) is a recessive genetic disease that is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The recent development of a class of drugs called "correctors", which repair the structure and function of mutant CFTR, has greatly enhanced the life expectancy of CF patients. These correctors target the most common disease causing CFTR mutant F508del and are exemplified by the FDA-approved VX-809. While one binding site of VX-809 to CFTR was recently elucidated by cryo-electron microscopy, four additional binding sites have been proposed in the literature and it has been theorized that VX-809 and structurally similar correctors may engage multiple CFTR binding sites. To explore these five binding sites, ensemble docking was performed on wild-type CFTR and the F508del mutant using a large library of structurally similar corrector drugs, including VX-809 (lumacaftor), VX-661 (tezacaftor), ABBV-2222 (galicaftor), and a host of other structurally related molecules. For wild-type CFTR, we find that only one site, located in membrane spanning domain 1 (MSD1), binds favorably to our ligand library. While this MSD1 site also binds our ligand library for F508del-CFTR, the F508del mutation also opens a binding site in nucleotide binding domain 1 (NBD1), which enables strong binding of our ligand library to this site. This NBD1 site in F508del-CFTR exhibits the strongest overall binding affinity for our library of corrector drugs. This data may serve to better understand the structural changes induced by mutation of CFTR and how correctors bind to the protein. Additionally, it may aid in the design of new, more effective CFTR corrector drugs.
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Affiliation(s)
- Anna Lester
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Madeline Sandman
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Caitlin Herring
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Christian Girard
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Brandon Dixon
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Havanna Ramsdell
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Callista Reber
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Jack Poulos
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Alexis Mitchell
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Allison Spinney
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Marissa E. Henager
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Claudia N. Evans
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Mark Turlington
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
| | - Quentin R. Johnson
- Berry College Department
of Chemistry and Biochemistry, Mount Berry, Georgia 30149, United States
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89
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O'Connor MS, Bragg ZT, Dearworth JR, Hendrickson HP. Quantum Mechanics/Molecular mechanics calculations predict A1, not A2, is present in melanopsin (Opn4m) of red-eared slider turtles (Trachemys scripta elegans). Vision Res 2023; 209:108245. [PMID: 37290221 DOI: 10.1016/j.visres.2023.108245] [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: 01/12/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 06/10/2023]
Abstract
Melanopsin is a photopigment that plays a role in non-visual, light-driven, cellular processes such as modulation of circadian rhythms, retinal vascular development, and the pupillary light reflex (PLR). In this study, computational methods were used to understand which chromophore is harbored by melanopsin in red-eared slider turtles (Trachemys scripta elegans). In mammals, the vitamin A derivative 11-cis-retinal (A1) is the chromophore, which provides functionality for melanopsin. However, in red-eared slider turtles, a member of the reptilian class, the identity of the chromophore remains unclear. Red-eared slider turtles, similar to other freshwater vertebrates, possess visual pigments that harbor a different vitamin A derivative, 11-cis-3,4-didehydroretinal (A2), making their pigments more sensitive to red-light than blue-light, therefore, suggesting the chromophore to be the A2 derivative instead of the A1. To help resolve the chromophore identity, in this work, computational homology models of melanopsin in red-eared slider turtles were first constructed. Next, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to compare how A1 and A2 derivatives bind to melanopsin. Time dependent density functional theory (TDDFT) calculations were then used to determine the excitation energy of the pigments. Lastly, calculated excitation energies were compared to experimental spectral sensitivity data from responses by the irises of red-eared sliders. Contrary to what was expected, our results suggest that melanopsin in red-eared slider turtles is more likely to harbor the A1 chromophore than the A2. Furthermore, a glutamine (Q622.56) and tyrosine (Y853.28) residue in the chromophore binding pocket are shown to play a role in the spectral tuning of the chromophore.
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Affiliation(s)
- Michael S O'Connor
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States
| | - Zoey T Bragg
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States
| | - James R Dearworth
- Department of Biology, Lafayette College, Easton, PA 18042, United States
| | - Heidi P Hendrickson
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States.
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90
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Dutta Gupta O, Karbat I, Pal K. Understanding the Molecular Regulation of Serotonin Receptor 5-HTR 1B-β-Arrestin1 Complex in Stress and Anxiety Disorders. J Mol Neurosci 2023; 73:664-677. [PMID: 37580644 DOI: 10.1007/s12031-023-02146-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
The serotonin receptor subtype 5-HTR1B is widely distributed in the brain with an important role in various behavioral implications including neurological conditions and psychiatric disorders. The neuromodulatory action of 5-HTR1B largely depends upon its arrestin mediated signaling pathway. In this study, we tried to investigate the role of unusually long intracellular loop 3 (ICL3) region of the serotonin receptor 5-HTR1B in interaction with β-arrestin1 (Arr2) to compensate for the absence of the long cytoplasmic tail. Molecular modeling and docking tools were employed to obtain a suitable molecular conformation of the ICL3 region in complex with Arr2 which dictates the specific complex formation of 5-HTR1B with Arr2. This reveals the novel molecular mechanism of phosphorylated ICL3 mediated GPCR-arrestin interaction in the absence of the long cytoplasmic tail. The in-cell disulfide cross-linking experiments and molecular dynamics simulations of the complex further validate the model of 5-HTR1B-ICL3-Arr2 complex. Two serine residues (Ser281 and Ser295) within the 5-HTR1B-ICL3 region were found to be occupying the electropositive pocket of Arr2 in our model and might be crucial for phosphorylation and specific Arr2 binding. The alignment studies of these residues showed them to be conserved only across 5-HTR1B mammalian species. Thus, our studies were able to predict a molecular conformation of 5-HTR1B-Arr2 and identify the role of long ICL3 in the signaling process which might be crucial in designing targeted drugs (biased agonists) that promote GPCR-Arr2 signaling to deter the effects of stress and anxiety-like disorders.
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Affiliation(s)
- Oindrilla Dutta Gupta
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, 700126, Kolkata, West Bengal, India
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Kuntal Pal
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, 700126, Kolkata, West Bengal, India.
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, 632014, Vellore, Tamil Nadu, India.
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91
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Hetmann M, Langner C, Durmaz V, Cespugli M, Köchl K, Krassnigg A, Blaschitz K, Groiss S, Loibner M, Ruau D, Zatloukal K, Gruber K, Steinkellner G, Gruber CC. Identification and validation of fusidic acid and flufenamic acid as inhibitors of SARS-CoV-2 replication using DrugSolver CavitomiX. Sci Rep 2023; 13:11783. [PMID: 37479788 PMCID: PMC10362000 DOI: 10.1038/s41598-023-39071-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023] Open
Abstract
In this work, we present DrugSolver CavitomiX, a novel computational pipeline for drug repurposing and identifying ligands and inhibitors of target enzymes. The pipeline is based on cavity point clouds representing physico-chemical properties of the cavity induced solely by the protein. To test the pipeline's ability to identify inhibitors, we chose enzymes essential for SARS-CoV-2 replication as a test system. The active-site cavities of the viral enzymes main protease (Mpro) and papain-like protease (Plpro), as well as of the human transmembrane serine protease 2 (TMPRSS2), were selected as target cavities. Using active-site point-cloud comparisons, it was possible to identify two compounds-flufenamic acid and fusidic acid-which show strong inhibition of viral replication. The complexes from which fusidic acid and flufenamic acid were derived would not have been identified using classical sequence- and structure-based methods as they show very little structural (TM-score: 0.1 and 0.09, respectively) and very low sequence (~ 5%) identity to Mpro and TMPRSS2, respectively. Furthermore, a cavity-based off-target screening was performed using acetylcholinesterase (AChE) as an example. Using cavity comparisons, the human carboxylesterase was successfully identified, which is a described off-target for AChE inhibitors.
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Affiliation(s)
- M Hetmann
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - C Langner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - V Durmaz
- Innophore, San Francisco, CA, USA
| | | | - K Köchl
- Innophore, San Francisco, CA, USA
| | | | | | - S Groiss
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - M Loibner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - D Ruau
- NVIDIA, Santa Clara, CA, USA
| | - K Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - K Gruber
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - G Steinkellner
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - C C Gruber
- Innophore, San Francisco, CA, USA.
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- Austrian Centre of Industrial Biotechnology, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
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92
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Oppenheim T, Radzinski M, Braitbard M, Brielle ES, Yogev O, Goldberger E, Yesharim Y, Ravid T, Schneidman-Duhovny D, Reichmann D. The Cdc48 N-terminal domain has a molecular switch that mediates the Npl4-Ufd1-Cdc48 complex formation. Structure 2023; 31:764-779.e8. [PMID: 37311459 DOI: 10.1016/j.str.2023.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 02/28/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023]
Abstract
Cdc48 (VCP/p97) is a major AAA-ATPase involved in protein quality control, along with its canonical cofactors Ufd1 and Npl4 (UN). Here, we present novel structural insights into the interactions within the Cdc48-Npl4-Ufd1 ternary complex. Using integrative modeling, we combine subunit structures with crosslinking mass spectrometry (XL-MS) to map the interaction between Npl4 and Ufd1, alone and in complex with Cdc48. We describe the stabilization of the UN assembly upon binding with the N-terminal-domain (NTD) of Cdc48 and identify a highly conserved cysteine, C115, at the Cdc48-Npl4-binding interface which is central to the stability of the Cdc48-Npl4-Ufd1 complex. Mutation of Cys115 to serine disrupts the interaction between Cdc48-NTD and Npl4-Ufd1 and leads to a moderate decrease in cellular growth and protein quality control in yeast. Our results provide structural insight into the architecture of the Cdc48-Npl4-Ufd1 complex as well as its in vivo implications.
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Affiliation(s)
- Tal Oppenheim
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Meytal Radzinski
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Merav Braitbard
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Esther S Brielle
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ohad Yogev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eliya Goldberger
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yarden Yesharim
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, the Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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93
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Ahmed J, Walker AA, Perdomo HD, Guo S, Nixon SA, Vetter I, Okoh HI, Shehu DM, Shuaibu MN, Ndams IS, King GF, Herzig V. Two Novel Mosquitocidal Peptides Isolated from the Venom of the Bahia Scarlet Tarantula ( Lasiodora klugi). Toxins (Basel) 2023; 15:418. [PMID: 37505687 PMCID: PMC10467143 DOI: 10.3390/toxins15070418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
Effective control of diseases transmitted by Aedes aegypti is primarily achieved through vector control by chemical insecticides. However, the emergence of insecticide resistance in A. aegypti undermines current control efforts. Arachnid venoms are rich in toxins with activity against dipteran insects and we therefore employed a panel of 41 spider and 9 scorpion venoms to screen for mosquitocidal toxins. Using an assay-guided fractionation approach, we isolated two peptides from the venom of the tarantula Lasiodora klugi with activity against adult A. aegypti. The isolated peptides were named U-TRTX-Lk1a and U-TRTX-Lk2a and comprised 41 and 49 residues with monoisotopic masses of 4687.02 Da and 5718.88 Da, respectively. U-TRTX-Lk1a exhibited an LD50 of 38.3 pmol/g when injected into A. aegypti and its modeled structure conformed to the inhibitor cystine knot motif. U-TRTX-Lk2a has an LD50 of 45.4 pmol/g against adult A. aegypti and its predicted structure conforms to the disulfide-directed β-hairpin motif. These spider-venom peptides represent potential leads for the development of novel control agents for A. aegypti.
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Affiliation(s)
- Jamila Ahmed
- Department of Zoology, Ahmadu Bello University Zaria, Kaduna 810107, Nigeria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew A. Walker
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Queensland, Brisbane, QLD 4072, Australia
| | - Hugo D. Perdomo
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Shaodong Guo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Queensland, Brisbane, QLD 4072, Australia
| | - Samantha A. Nixon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Queensland, Brisbane, QLD 4072, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Pharmacy, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Hilary I. Okoh
- Department of Animal and Environmental Biology, Federal University Oye-Ekiti, Oye 371104, Nigeria
| | - Dalhatu M. Shehu
- Department of Zoology, Ahmadu Bello University Zaria, Kaduna 810107, Nigeria
| | - Mohammed N. Shuaibu
- Department of Biochemistry, Ahmadu Bello University Zaria, Kaduna 810107, Nigeria
- Centre for Biotechnology Research and Training, Ahmadu Bello University Zaria, Kaduna 810107, Nigeria
| | - Iliya S. Ndams
- Department of Zoology, Ahmadu Bello University Zaria, Kaduna 810107, Nigeria
| | - Glenn F. King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Queensland, Brisbane, QLD 4072, Australia
| | - Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
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Yoshizue T, Brindha S, Wongnak R, Takemae H, Oba M, Mizutani T, Kuroda Y. Antisera Produced Using an E. coli-Expressed SARS-CoV-2 RBD and Complemented with a Minimal Dose of Mammalian-Cell-Expressed S1 Subunit of the Spike Protein Exhibits Improved Neutralization. Int J Mol Sci 2023; 24:10583. [PMID: 37445760 DOI: 10.3390/ijms241310583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
E. coli-expressed proteins could provide a rapid, cost-effective, and safe antigen for subunit vaccines, provided we can produce them in a properly folded form inducing neutralizing antibodies. Here, we use an E. coli-expressed SARS-CoV-2 receptor-binding domain (RBD) of the spike protein as a model to examine whether it yields neutralizing antisera with effects comparable to those generated by the S1 subunit of the spike protein (S1 or S1 subunit, thereafter) expressed in mammalian cells. We immunized 5-week-old Jcl-ICR female mice by injecting RBD (30 µg) and S1 subunit (5 µg) according to four schemes: two injections 8 weeks apart with RBD (RBD/RBD), two injections with S1 (S1/S1), one injection with RBD, and the second one with S1 (RBD/S1), and vice versa (S1/RBD). Ten weeks after the first injection (two weeks after the second injection), all combinations induced a strong immune response with IgG titer > 105 (S1/RBD < S1/S1 < RBD/S1 < RBD/RBD). In addition, the neutralization effect of the antisera ranked as S1/RBD~RBD/S1 (80%) > S1/S1 (56%) > RBD/RBD (42%). These results indicate that two injections with E. coli-expressed RBD, or mammalian-cell-produced spike S1 subunit alone, can provide some protection against SARS-CoV-2, but a mixed injection scheme yields significantly higher protection.
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Affiliation(s)
- Takahiro Yoshizue
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Japan
| | - Subbaian Brindha
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu-shi 183-8538, Japan
| | - Rawiwan Wongnak
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Japan
| | - Hitoshi Takemae
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu-shi 183-8538, Japan
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Mami Oba
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu-shi 183-8538, Japan
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Tetsuya Mizutani
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu-shi 183-8538, Japan
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu-shi 183-8538, Japan
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95
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Lone MA, Zeng S, Bourquin F, Wang M, Huang S, Lin Z, Tang B, Zhang R, Hornemann T. SPTLC1 p.Leu38Arg, a novel mutation associated with childhood ALS. Biochim Biophys Acta Mol Cell Biol Lipids 2023:159359. [PMID: 37348646 DOI: 10.1016/j.bbalip.2023.159359] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/27/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neuromuscular disease. Recently, several gain-of-function mutations in SPTLC1 were associated with juvenile ALS. SPTLC1 encodes for a subunit of the serine-palmitoyltransferase (SPT) - the rate-limiting enzyme in the de novo synthesis of sphingolipids (SL). SPT synthesized long chain bases from serine and palmitoyl-CoA. SPT activity, and thus overall levels of de novo produced SL, are regulated by feedback inhibition mediated by ORMDL1-3 proteins. Here we report a novel SPTLC1p.L38R mutation in a young Chinese girl with a signature of juvenile ALS. The patient presented with muscular weakness and atrophy, tongue tremor and fasciculation, breathing problems and positive pyramidal signs. All SPTLC1-ALS mutations including the SPTLC1 p.L38R are located within the membrane-spanning domain of the protein and impede enzyme regulation by ORMDL3. Pertinent to the altered SPTLC1-ORMDL3 interaction, lipid analysis showed overall increased SL levels in the patient plasma. An increased SL de novo synthesis of the mutant was confirmed in a L38R mutant expression HEK293 cell model. Primarily dihydro-sphingolipids (dhSL) were found increased in patient plasma as well as mutant expressing cells. Increased dhSL formation has been previously associated with neurotoxicity and might be involved in the pathomechanism of the SPTLC1-ALS mutations.
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Affiliation(s)
- Museer A Lone
- Institute for Clinical Chemistry, University Hospital and University of Zürich, Zürich, Switzerland
| | - Sen Zeng
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Florence Bourquin
- Institute for Biochemistry, University of Zürich; Zürich, Switzerland
| | - Mengli Wang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Shunxiang Huang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhiqiang Lin
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
| | - Ruxu Zhang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China.
| | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital and University of Zürich, Zürich, Switzerland.
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96
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Lee YR, Kim YC, Won SY, Jeong MJ, Park KJ, Park HC, Roh IS, Kang HE, Sohn HJ, Jeong BH. Identification of a novel risk factor for chronic wasting disease (CWD) in elk: S100G single nucleotide polymorphism (SNP) of the prion protein gene (PRNP). Vet Res 2023; 54:48. [PMID: 37328789 DOI: 10.1186/s13567-023-01177-7] [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: 10/18/2022] [Accepted: 04/06/2023] [Indexed: 06/18/2023] Open
Abstract
Prion diseases are fatal and malignant infectious encephalopathies induced by the pathogenic form of prion protein (PrPSc) originating from benign prion protein (PrPC). A previous study reported that the M132L single nucleotide polymorphism (SNP) of the prion protein gene (PRNP) is associated with susceptibility to chronic wasting disease (CWD) in elk. However, a recent meta-analysis integrated previous studies that did not find an association between the M132L SNP and susceptibility to CWD. Thus, there is controversy about the effect of M132L SNP on susceptibility to CWD. In the present study, we investigated novel risk factors for CWD in elk. We investigated genetic polymorphisms of the PRNP gene by amplicon sequencing and compared genotype, allele, and haplotype frequencies between CWD-positive and CWD-negative elk. In addition, we performed a linkage disequilibrium (LD) analysis by the Haploview version 4.2 program. Furthermore, we evaluated the 3D structure and electrostatic potential of elk prion protein (PrP) according to the S100G SNP using AlphaFold and the Swiss-PdbViewer 4.1 program. Finally, we analyzed the free energy change of elk PrP according to the S100G SNP using I-mutant 3.0 and CUPSAT. We identified 23 novel SNP of the elk PRNP gene in 248 elk. We found a strong association between PRNP SNP and susceptibility to CWD in elk. Among those SNP, S100G is the only non-synonymous SNP. We identified that S100G is predicted to change the electrostatic potential and free energy of elk PrP. To the best of our knowledge, this was the first report of a novel risk factor, the S100G SNP, for CWD.
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Affiliation(s)
- Yu-Ran Lee
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Yong-Chan Kim
- Department of Biological Sciences, Andong National University, Andong, 36729, Republic of Korea
| | - Sae-Young Won
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Min-Ju Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Kyung-Je Park
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Hoo-Chang Park
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - In-Soon Roh
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Hae-Eun Kang
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Hyun-Joo Sohn
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
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97
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Bourganou MV, Kontopodis E, Tsangaris GT, Pierros V, Vasileiou NGC, Mavrogianni VS, Fthenakis GC, Katsafadou AI. Unique Peptides of Cathelicidin-1 in the Early Detection of Mastitis-In Silico Analysis. Int J Mol Sci 2023; 24:10160. [PMID: 37373309 DOI: 10.3390/ijms241210160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/31/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Based on the results of previously performed clinical studies, cathelicidin-1 has been proposed as a potential biomarker for the early diagnosis of mastitis in ewes. It has been hypothesized that the detection of unique peptides (defined as a peptide, irrespective of its length, that exists in only one protein of a proteome of interest) and core unique peptides (CUPs) (representing the shortest peptide that is unique) of cathelicidin-1 may potentially improve its identification and consequently the diagnosis of sheep mastitis. Peptides of sizes larger than those of the size of CUPs, which include consecutive or over-lapping CUPs, have been defined as 'composite core unique peptides' (CCUPs). The primary objective of the present study was the investigation of the sequence of cathelicidin-1 detected in ewes' milk in order to identify its unique peptides and core unique peptides, which would reveal potential targets for accurate detection of the protein. An additional objective was the detection of unique sequences among the tryptic digest peptides of cathelicidin-1, which would improve accuracy of identification of the protein when performing targeted MS-based proteomics. The potential uniqueness of each peptide of cathelicidin-1 was investigated using a bioinformatics tool built on a big data algorithm. A set of CUPs was created and CCUPs were also searched. Further, the unique sequences in the tryptic digest peptides of cathelicidin-1 were also detected. Finally, the 3D structure of the protein was analyzed from predicted models of proteins. In total, 59 CUPs and four CCUPs were detected in cathelicidin-1 of sheep origin. Among tryptic digest peptides, there were six peptides that were unique in that protein. After 3D structure analysis of the protein, 35 CUPs were found on the core of cathelicidin-1 of sheep origin and among them, 29 were located on amino acids in regions of the protein with 'very high' or 'confident' estimates of confidence of the structure. Ultimately, the following six CUPs: QLNEQ, NEQS, EQSSE, QSSEP, EDPD, DPDS, are proposed as potential antigenic targets for cathelicidin-1 of sheep. Moreover, another six unique peptides were detected in tryptic digests and offer novel mass tags to facilitate the detection of cathelicidin-1 during MS-based diagnostics.
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Affiliation(s)
- Maria V Bourganou
- Faculty of Public and One Health, University of Thessaly, 43100 Karditsa, Greece
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Evangelos Kontopodis
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - George Th Tsangaris
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vasileios Pierros
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
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98
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Jalal D, Samir O, Elzayat MG, El-Shqanqery HE, Diab AA, ElKaialy L, Mohammed AM, Hamdy D, Matar IK, Amer K, Elnakib M, Hassan W, Mansour T, Soliman S, Hassan R, Al-Toukhy GM, Hammad M, Abdo I, Sayed AA. Genomic characterization of SARS-CoV-2 in Egypt: insights into spike protein thermodynamic stability. Front Microbiol 2023; 14:1190133. [PMID: 37333655 PMCID: PMC10273679 DOI: 10.3389/fmicb.2023.1190133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
The overall pattern of the SARS-CoV-2 pandemic so far has been a series of waves; surges in new cases followed by declines. The appearance of novel mutations and variants underlie the rises in infections, making surveillance of SARS-CoV-2 mutations and prediction of variant evolution of utmost importance. In this study, we sequenced 320 SARS-CoV-2 viral genomes isolated from patients from the outpatient COVID-19 clinic in the Children's Cancer Hospital Egypt 57357 (CCHE 57357) and the Egypt Center for Research and Regenerative Medicine (ECRRM). The samples were collected between March and December 2021, covering the third and fourth waves of the pandemic. The third wave was found to be dominated by Nextclade 20D in our samples, with a small number of alpha variants. The delta variant was found to dominate the fourth wave samples, with the appearance of omicron variants late in 2021. Phylogenetic analysis reveals that the omicron variants are closest genetically to early pandemic variants. Mutation analysis shows SNPs, stop codon mutation gain, and deletion/insertion mutations, with distinct patterns of mutations governed by Nextclade or WHO variant. Finally, we observed a large number of highly correlated mutations, and some negatively correlated mutations, and identified a general inclination toward mutations that lead to enhanced thermodynamic stability of the spike protein. Overall, this study contributes genetic and phylogenetic data, as well as provides insights into SARS-CoV-2 viral evolution that may eventually help in the prediction of evolving mutations for better vaccine development and drug targets.
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Affiliation(s)
- Deena Jalal
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Omar Samir
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Mariam G. Elzayat
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Hend E. El-Shqanqery
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Aya A. Diab
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Lamiaa ElKaialy
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Aya M. Mohammed
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Donia Hamdy
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Islam K. Matar
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
- Department of Chemistry, Saint Mary’s University, Halifax, NS, Canada
| | - Khaled Amer
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Mostafa Elnakib
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Wael Hassan
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Tarek Mansour
- Department of Virology and Immunology, National Cancer Institute, Cairo University, Cairo, Egypt
- Department of Clinical Pathology, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Sonia Soliman
- Department of Clinical Pathology, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Reem Hassan
- Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt
- Molecular Microbiology Unit, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Ghada M. Al-Toukhy
- Department of Virology and Immunology, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Mahmoud Hammad
- Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
- Department of Pediatric Oncology, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Ibrahim Abdo
- Department of Clinical Pharmacy, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Ahmed A. Sayed
- Department of Basic Research, Genomics and Epigenomics Program, Children’s Cancer Hospital Egypt 57357, Cairo, Egypt
- Faculty of Science, Department of Biochemistry, Ain Shams University, Cairo, Egypt
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99
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Moustafa RI, Faraag AHI, El-Shenawy R, Agwa MM, Elsayed H. Harnessing immunoinformatics for developing a multiple-epitope peptide-based vaccination approach against SARS-CoV-2 spike protein. Saudi J Biol Sci 2023; 30:103661. [PMID: 37163156 PMCID: PMC10141799 DOI: 10.1016/j.sjbs.2023.103661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 05/11/2023] Open
Abstract
COVID-19 has spread to over 200 countries with variable severity and mortality rates. Computational analysis is a valuable tool for developing B-cell and T-cell epitope-based vaccines. In this study, by harnessing immunoinformatics tools, we designed a multiple-epitope vaccine to protect against COVID-19. The candidate epitopes were designed from highly conserved regions of the SARS-CoV-2 spike (S) glycoprotein. The consensus amino acids sequence of ten SARS-CoV-2 variants including Gamma, Beta, Epsilon, Delta, Alpha, Kappa, Iota, Lambda, Mu, and Omicron was involved. Applying the multiple sequence alignment plugin and the antigenic prediction tools of Geneious prime 2021, ten predicted variants were identified and consensus S-protein sequences were used to predict the antigenic part. According to ElliPro analysis of S-protein B-cell prediction, we explored 22 continuous linear epitopes with high scores ranging from 0.879 to 0.522. First, we reported five promising epitopes: BE1 1115-1192, BE2 481-563, BE3 287-313, BE4 62-75, and BE5 112-131 with antigenicity scores of 0.879, 0.86, 0.813, 0.779, and 0.765, respectively, while only nine discontinuous epitopes scored between 0.971 and 0.511. Next, we identified 194 Major Histocompatibility Complex (MHC) - I and 156 MHC - II epitopes with antigenic characteristics. These spike-specific peptide-epitopes with characteristically high immunogenic and antigenic scores have the potential as a SARS-CoV-2 multiple-epitope peptide-based vaccination strategy. Nevertheless, further experimental investigations are needed to test for the vaccine efficacy and efficiency.
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Affiliation(s)
- Rehab I Moustafa
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, Egypt
| | - Ahmed H I Faraag
- Botany and Microbiology Department, Faculty of Science, Helwan University, Egypt
- School of Biotechnology, Badr University in Cairo, Egypt
| | | | - Mona M Agwa
- Department of Chemistry of Natural and Microbial Products, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Egypt
| | - Hassan Elsayed
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, Egypt
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100
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Wang Y, Li S, Yan Z, Guo Y, Zhang L. Computational insights into novel inhibitor indole-heterocycle specific against glycogen phosphorylase isoenzymes interaction mechanism. Future Med Chem 2023; 15:913-922. [PMID: 37395076 DOI: 10.4155/fmc-2023-0084] [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] [Indexed: 07/04/2023] Open
Abstract
Background: Glycogen phosphorylase (GP) is a potential drug target. As the three subtypes of GP are highly conserved, it is difficult to research their specificity. However, compound 1 inhibits the GP subtypes differently and was studied to aid in designing specific inhibitors. Results: Molecular docking showed that the ligands in GP subtype complexes had some differences in spatial conformation and binding modes, stabilized by polar and nonpolar interactions. The results were confirmed through kinetic experiments, with affinities of -85.230 (brain GP), -73.809 (liver GP) and -66.061 kJ/mol (muscle GP). Conclusion: The study provides insight into the possible reasons for differences in compound 1's inhibitory activity against the GP subtypes and offers guidance in designing target molecules for regulating selectivity among the subtypes.
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Affiliation(s)
- Youde Wang
- Key Laboratory of Traditional Chinese Medicine Research & Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde, 067000, China
| | - Shuai Li
- Key Laboratory of Traditional Chinese Medicine Research & Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde, 067000, China
| | - Zhiwei Yan
- Key Laboratory of Traditional Chinese Medicine Research & Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde, 067000, China
| | - Yachun Guo
- Department of Pathogen Biology, Chengde Medical University, Chengde, Hebei, 067000, China
| | - Liying Zhang
- Key Laboratory of Traditional Chinese Medicine Research & Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde, 067000, China
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