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Wu HT, Wu BX, Fang ZX, Wu Z, Hou YY, Deng Y, Cui YK, Liu J. Lomitapide repurposing for treatment of malignancies: A promising direction. Heliyon 2024; 10:e32998. [PMID: 38988566 PMCID: PMC11234027 DOI: 10.1016/j.heliyon.2024.e32998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
The development of novel drugs from basic science to clinical practice requires several years, much effort, and cost. Drug repurposing can promote the utilization of clinical drugs in cancer therapy. Recent studies have shown the potential effects of lomitapide on treating malignancies, which is currently used for the treatment of familial hypercholesterolemia. We systematically review possible functions and mechanisms of lomitapide as an anti-tumor compound, regarding the aspects of apoptosis, autophagy, and metabolism of tumor cells, to support repurposing lomitapide for the clinical treatment of tumors.
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Affiliation(s)
- Hua-Tao Wu
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Bing-Xuan Wu
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Ze-Xuan Fang
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Zheng Wu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Yan-Yu Hou
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Yu Deng
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Yu-Kun Cui
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Jing Liu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
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Ni YL, Shen HT, Chen SP, Kuan YH. Protective effect of genkwanin against lipopolysaccharide-induced acute lung injury in mice with p38 mitogen-activated protein kinase and nuclear factor-κB pathway inhibition. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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3
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Fu X, Sun X, Zhang C, Lv N, Guo H, Xing C, Lv J, Wu J, Zhu X, Liu M, Su L. Genkwanin Prevents Lipopolysaccharide-Induced Inflammatory Bone Destruction and Ovariectomy-Induced Bone Loss. Front Nutr 2022; 9:921037. [PMID: 35811983 PMCID: PMC9260391 DOI: 10.3389/fnut.2022.921037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022] Open
Abstract
Objectives The first objective of this study was to probe the effects of genkwanin (GKA) on osteoclast. The second goal of this study was to study whether GKA can protect lipopolysaccharide (LPS) and ovariectomized (OVX) induced bone loss. Materials and Methods Various concentrations of GKA (1 and 10 mg/kg) were injected into mice. Different concentrations of GKA (1 and 5 μM) were used to detect the effects of GKA on osteoclast and osteoblast. Key Findings GKA attenuated the osteoclast differentiation promoted by RANKL and expression of marker genes containing c-fos, ctsk as well as bone resorption related gene Trap and to the suppression of MAPK signaling pathway. In addition, GKA induced BMMs cell apoptosis in vitro. Moreover, GKA prevented LPS-induced and ovariectomized-induced bone loss in mice. Conclusion Our research revealed that GKA had a potential to be an effective therapeutic agent for osteoclast-mediated osteoporosis.
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Affiliation(s)
- Xin Fu
- Institute of Translational Medicine, Shanghai University, Shanghai, China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, China
| | - Xiaochen Sun
- School of Medicine, Shanghai University, Shanghai, China
| | - Chenxi Zhang
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Nanning Lv
- Lianyungang Second People’s Hospital, Lianyungang, China
- Lianyungang Clinical School of Xuzhou Medical University, Lianyungang, China
| | - Huan Guo
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Chunlei Xing
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Juan Lv
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Jiwen Wu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Xiaoli Zhu,
| | - Mingming Liu
- Lianyungang Second People’s Hospital, Lianyungang, China
- Lianyungang Clinical School of Xuzhou Medical University, Lianyungang, China
- Mingming Liu,
| | - Li Su
- Institute of Translational Medicine, Shanghai University, Shanghai, China
- Li Su,
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4
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Min L, Wu Y, Cao G, Mi D, Chen C. A network pharmacology strategy to investigate the anti-osteoarthritis mechanism of main lignans components of Schisandrae Fructus. Int Immunopharmacol 2021; 98:107873. [PMID: 34182246 DOI: 10.1016/j.intimp.2021.107873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Osteoarthritis (OA) is a chronic age-related progressive joint disorder. Degradation of the cartilage extracellular matrix (ECM) is considered a hallmark of OA and may be a target for new therapeutic methods. Schisandrae Fructus (SF) has been shown to be effective in treating OA. The major active components of SF are lignans. However, the targets of SF and the pharmacological mechanisms underlying the effects of SF lignans in the treatment of OA have not been elucidated. Therefore, based on network pharmacology, this research predicted the treatment targets of six lignans in SF, constructed a protein-protein interaction network and identified 15 hub genes in the OA-target protein-protein interaction network. Through Gene Ontology function and pathway analyses, the gene functions of lignans in the treatment of OA were determined. Finally, the anti-OA effects of lignans and underlying mechanisms identified in the network pharmacology analysis were verified by molecular docking, real-time PCR and western blotting in vitro. The biological processes of the genes and proteins targeted by lignans in the treatment of OA included the immune response, inflammatory response, cell signal transduction and phospholipid metabolism. Moreover, 20 metabolic pathways were enriched. Network pharmacology, molecular docking and in vitro and in vivo experimental results revealed that SF, schisanhenol and gamma-schisandrin inhibited EGFR and MAPK14 gene expression by inhibiting SRC gene expression and activity and then decreased MMP 13 and collagen II protein and gene expression. This research provides a basis for further study of the anti-OA effects and mechanisms of SF, schisanhenol and gamma-schisandrin.
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Affiliation(s)
- Lingtian Min
- Department of Orthopaedics, Nantong Hospital of Traditional Chinese Medicine, the Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nantong 226000, China
| | - Yu Wu
- Department of Pharmacy, Nantong Hospital of Traditional Chinese Medicine, the Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nantong 226000, China
| | - Gang Cao
- Department of Pharmacy, Nantong Hospital of Traditional Chinese Medicine, the Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nantong 226000, China
| | - Daguo Mi
- Department of Orthopaedics, Nantong Hospital of Traditional Chinese Medicine, the Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nantong 226000, China.
| | - Cheng Chen
- Department of Orthopaedics, Suqian First Hospital, Affiliated to Nanjing Medical University, Suqian 223800, China.
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Asiedu SO, Kwofie SK, Broni E, Wilson MD. Computational Identification of Potential Anti-Inflammatory Natural Compounds Targeting the p38 Mitogen-Activated Protein Kinase (MAPK): Implications for COVID-19-Induced Cytokine Storm. Biomolecules 2021; 11:653. [PMID: 33946644 PMCID: PMC8146027 DOI: 10.3390/biom11050653] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Severely ill coronavirus disease 2019 (COVID-19) patients show elevated concentrations of pro-inflammatory cytokines, a situation commonly known as a cytokine storm. The p38 MAPK receptor is considered a plausible therapeutic target because of its involvement in the platelet activation processes leading to inflammation. This study aimed to identify potential natural product-derived inhibitory molecules against the p38α MAPK receptor to mitigate the eliciting of pro-inflammatory cytokines using computational techniques. The 3D X-ray structure of the receptor with PDB ID 3ZS5 was energy minimized using GROMACS and used for molecular docking via AutoDock Vina. The molecular docking was validated with an acceptable area under the curve (AUC) of 0.704, which was computed from the receiver operating characteristic (ROC) curve. A compendium of 38,271 natural products originating from Africa and China together with eleven known p38 MAPK inhibitors were screened against the receptor. Four potential lead compounds ZINC1691180, ZINC5519433, ZINC4520996 and ZINC5733756 were identified. The compounds formed strong intermolecular bonds with critical residues Val38, Ala51, Lys53, Thr106, Leu108, Met109 and Phe169. Additionally, they exhibited appreciably low binding energies which were corroborated via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The compounds were also predicted to have plausible pharmacological profiles with insignificant toxicity. The molecules were also predicted to be anti-inflammatory, kinase inhibitors, antiviral, platelet aggregation inhibitors, and immunosuppressive, with probable activity (Pa) greater than probable inactivity (Pi). ZINC5733756 is structurally similar to estradiol with a Tanimoto coefficient value of 0.73, which exhibits anti-inflammatory activity by targeting the activation of Nrf2. Similarly, ZINC1691180 has been reported to elicit anti-inflammatory activity in vitro. The compounds may serve as scaffolds for the design of potential biotherapeutic molecules against the cytokine storm associated with COVID-19.
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Affiliation(s)
- Seth O. Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
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Timonina D, Sharapova Y, Švedas V, Suplatov D. Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies. Comput Struct Biotechnol J 2021; 19:1302-1311. [PMID: 33738079 PMCID: PMC7933735 DOI: 10.1016/j.csbj.2021.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Local 3D-structural differences in homologous proteins contribute to functional diversity observed in a superfamily, but so far received little attention as bioinformatic analysis was usually carried out at the level of amino acid sequences. We have developed Zebra3D - the first-of-its-kind bioinformatic software for systematic analysis of 3D-alignments of protein families using machine learning. The new tool identifies subfamily-specific regions (SSRs) - patterns of local 3D-structure (i.e. single residues, loops, or secondary structure fragments) that are spatially equivalent within families/subfamilies, but are different among them, and thus can be associated with functional diversity and function-related conformational plasticity. Bioinformatic analysis of protein superfamilies by Zebra3D can be used to study 3D-determinants of catalytic activity and specific accommodation of ligands, help to prepare focused libraries for directed evolution or assist development of chimeric enzymes with novel properties by exchange of equivalent regions between homologs, and to characterize plasticity in binding sites. A companion Mustguseal web-server is available to automatically construct a 3D-alignment of functionally diverse proteins, thus reducing the minimal input required to operate Zebra3D to a single PDB code. The Zebra3D + Mustguseal combined approach provides the opportunity to systematically explore the value of SSRs in superfamilies and to use this information for protein design and drug discovery. The software is available open-access at https://biokinet.belozersky.msu.ru/Zebra3D.
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Affiliation(s)
- Daria Timonina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
| | - Yana Sharapova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
| | - Vytas Švedas
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
| | - Dmitry Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
- Corresponding author.
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7
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Sharapova Y, Švedas V, Suplatov D. Catalytic and lectin domains in neuraminidase A from Streptococcus pneumoniae are capable of an intermolecular assembly: Implications for biofilm formation. FEBS J 2020; 288:3217-3230. [PMID: 33108702 DOI: 10.1111/febs.15610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/25/2020] [Accepted: 10/19/2020] [Indexed: 01/14/2023]
Abstract
Neuraminidase A from Streptococcus pneumoniae (NanA) is a cell wall-bound modular enzyme containing one lectin and one catalytic domain. Unlike homologous NanB and NanC expressed by the same bacterium, the two domains within one NanA molecule do not form a stable interaction and are spatially separated by a 16-amino acid-long flexible linker. In this work, the ability of NanA to form intermolecular assemblies was characterized using the methods of molecular modeling and bioinformatic analysis based on crystallographic data and by bringing together previously published experimental data. It was concluded that two catalytic domains, as well as one catalytic and one lectin domain, originating from two cell wall-bound NanA molecules, can interact through a previously uncharacterized interdomain interface to form complexes stabilized by a network of intermolecular hydrogen bonds and salt bridges. Supercomputer modeling strongly indicated that artocarpin, an earlier experimentally discovered inhibitor of the pneumococcal biofilm formation, is able to bind to a site located in the catalytic domain of one NanA entity and prevent its interaction with the lectin or catalytic domain of another NanA entity, thus directly precluding the generation of intermolecular assemblies. The revealed structural adaptation is discussed as one plausible mechanism of noncatalytic participation of this potentially key pathogenicity enzyme in pneumococcal biofilm formation.
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Affiliation(s)
- Yana Sharapova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vytas Švedas
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry Suplatov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
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8
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Suplatov D, Sharapova Y, Švedas V. EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins. J Bioinform Comput Biol 2020; 18:2040011. [PMID: 32833550 DOI: 10.1142/s0219720020400119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Conformational plasticity of the functionally important regions and binding sites in protein/enzyme structures is one of the key factors affecting their function and interaction with substrates/ligands. Molecular dynamics (MD) can address the challenge of accounting for protein flexibility by predicting the time-dependent behavior of a molecular system. It has a potential of becoming a particularly important tool in protein engineering and drug discovery, but requires specialized training and skills, what impedes practical use by many investigators. We have developed the easyAmber - a comprehensive set of programs to automate the molecular dynamics routines implemented in the Amber package. The toolbox can address a wide set of tasks in computational biology struggling to account for protein flexibility. The automated workflow includes a complete set of steps from the initial "static" molecular model to the MD "production run": the full-atom model building, optimization/equilibration of the molecular system, classical/conventional and accelerated molecular dynamics simulations. The easyAmber implements advanced MD protocols, but is highly automated and easy-to-operate to attract a broad audience. The toolbox can be used on a personal desktop station equipped with a compatible gaming GPU-accelerator, as well as help to manage huge workloads on a powerful supercomputer. The software provides an opportunity to operate multiple simulations of different proteins at the same time, thus significantly increasing work efficiency. The easyAmber takes the molecular dynamics to the next level in terms of usability for complex processing of large volumes of data, thus supporting the recent trend away from inefficient "static" approaches in biology toward a deeper understanding of the dynamics in protein structures. The software is freely available for download at https://biokinet.belozersky.msu.ru/easyAmber, no login required.
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Affiliation(s)
- Dmitry Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physico-chemical Biology and Faculty of Bioengineering and Bioinformatics, Leninskiye Gory 1-73, Moscow 119991, Russia
| | - Yana Sharapova
- Lomonosov Moscow State University, Belozersky Institute of Physico-chemical Biology and Faculty of Bioengineering and Bioinformatics, Leninskiye Gory 1-73, Moscow 119991, Russia
| | - Vytas Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physico-chemical Biology and Faculty of Bioengineering and Bioinformatics, Leninskiye Gory 1-73, Moscow 119991, Russia
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9
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Jonniya NA, Kar P. Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations. J Biomol Struct Dyn 2019; 38:1306-1321. [DOI: 10.1080/07391102.2019.1602079] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Nisha A. Jonniya
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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Prakash O, Nath Dwivedi U. Identification of repurposed protein kinase B binders from FDA-approved drug library: a hybrid-structure activity relationship and systems modeling based approach. J Biomol Struct Dyn 2019; 38:660-672. [PMID: 30806166 DOI: 10.1080/07391102.2019.1585293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Food and Drug Administration (FDA)-approved drugs may be repurposed against those diseases, for which their therapeutic action has not been described. The present study deals with repurposing FDA-approved drugs for selective targeting of protein kinase B (PKB/Akt) for anti-cancer activity, through a two-tier (Cell and Target) model hybridization protocol implemented with support vector machine-based learning method. The hybridization was done as per rules of reaction kinetics. The hybridization process was facilitated as a standalone application for free access at https://github.com/undwivedi/Akt-Selective.git. The selectivity of the ligands for PKB/Akt binding was also evaluated on the basis of mitophagy system model for anti-apoptotic activity. Screening of the FDA-approved drug library, using the developed H- SAR model, led to identification of four compounds (Cas nos. 94749-08-3, 57808-66-9, 62-13-5, 76-43-7), bearing the selectivity for PKB/Akt. Since, the identified compounds have already crossed the barriers of absorption, distribution, metabolism, excretion, toxicity in clinical trials, therefore are safe to be considered for repurposing individually or in combination with other drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Om Prakash
- Department of Biochemistry, Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics & Institute for Development of Advanced Computing, ONGC Centre for Advanced Studies University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Upendra Nath Dwivedi
- Department of Biochemistry, Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics & Institute for Development of Advanced Computing, ONGC Centre for Advanced Studies University of Lucknow, Lucknow, Uttar Pradesh, India
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11
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Bezsudnova EY, Boyko KM, Nikolaeva AY, Zeifman YS, Rakitina TV, Suplatov DA, Popov VO. Biochemical and structural insights into PLP fold type IV transaminase from Thermobaculum terrenum. Biochimie 2018; 158:130-138. [PMID: 30599183 DOI: 10.1016/j.biochi.2018.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/27/2018] [Indexed: 10/27/2022]
Abstract
The high catalytic efficiency of enzymes under reaction conditions is one of the main goals in biocatalysis. Despite the dramatic progress in the development of more efficient biocatalysts by protein design, the search for natural enzymes with useful properties remains a promising strategy. The pyridoxal 5'-phosphate (PLP)-dependent transaminases represent a group of industrially important enzymes due to their ability to stereoselectively transfer amino groups between diverse substrates; however, the complex mechanism of substrate recognition and conversion makes the design of transaminases a challenging task. Here we report a detailed structural and kinetic study of thermostable transaminase from the bacterium Thermobaculum terrenum (TaTT) using the methods of enzyme kinetics, X-ray crystallography and molecular modeling. TaTT can convert L-branched-chain and L-aromatic amino acids as well as (R)-(+)-1-phenylethylamine at a high rate and with high enantioselectivity. The structures of TaTT in complex with the cofactor pyridoxal 5'-phosphate covalently bound to enzyme and in complex with its reduced form, pyridoxamine 5'-phosphate, were determined at resolutions of 2.19 Å and 1.5 Å, and deposited in the Protein Data Bank as entries 6GKR and 6Q8E, respectively. TaTT is a fold type IV PLP-dependent enzyme. In terms of structural similarity, the enzyme is close to known branched-chain amino acid aminotransferases, but differences in characteristic sequence motifs in the active site were observed in TaTT compared to canonical branched-chain amino acid aminotransferases, which can explain the improved binding of aromatic amino acids and (R)-(+)-1-phenylethylamine. This study has shown for the first time that high substrate specificity towards both various l-amino acids and (R)-primary amines can be implemented within one pyridoxal 5'-phosphate-dependent active site of fold type IV. These results complement our knowledge of the catalytic diversity of transaminases and indicate the need for further biochemical and bioinformatic studies to understand the sequence-structure-function relationship in these enzymes.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation.
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Alena Yu Nikolaeva
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Yulia S Zeifman
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
| | - Tatiana V Rakitina
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation; Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya Str. 16/10, 117997, Moscow, Russian Federation
| | - Dmitry A Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskiye Gory 1-73, Moscow, 119991, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
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