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Wang T, Gao Y, Wu F, Luo L, Ma J, Hu Y. Coumarin-furo[2,3- d]pyrimidone hybrid molecules targeting human liver cancer cells: synthesis, anticancer effect, EGFR inhibition and molecular docking studies. RSC Med Chem 2024; 15:1565-1577. [PMID: 38784474 PMCID: PMC11110736 DOI: 10.1039/d3md00668a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/16/2024] [Indexed: 05/25/2024] Open
Abstract
The design, synthesis and investigation of antitumor activities of some coumarin-furo[2,3-d]pyrimidone hybrid molecules are reported. In vitro, HepG2 cells were used to investigate the cytotoxicity of 6a-n and 10a-n. The results demonstrated that coupling a furopyrimidone scaffold with coumarin through a hydrazide linker can effectively improve their synergistic anticancer activity. The coumarin-furo[2,3-d]pyrimidone combination 10a exhibited significant inhibitory activity against HepG2 cells with IC50 = 7.72 ± 1.56 μM, which is better than those of gefitinib and sorafenib. It is worth mentioning that the coumarin-furo[2,3-d]pyrimidone combination 10a showed excellent inhibition of the EGFR enzymatic activity with IC50 = 1.53 μM and 90% inhibition at 10 μM concentration. In silico investigation predicts the possibility of direct binding between the new coumarin-furo[2,3-d]pyrimidone hybrid molecules and the EGFR. The results suggest that coumarin-furo[2,3-d]pyrimidone hybrid molecules are potential antitumor agents targeting human liver cancer cells.
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Affiliation(s)
- Tianshuai Wang
- School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
- Hubei Key Lab of Wudang Local Chinese Medicine Research, School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
| | - Yumeng Gao
- School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
| | - Fengxu Wu
- School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
- Hubei Key Lab of Wudang Local Chinese Medicine Research, School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
| | - Lun Luo
- School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
- Hubei Key Lab of Wudang Local Chinese Medicine Research, School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
| | - Junkai Ma
- School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
- Hubei Key Lab of Wudang Local Chinese Medicine Research, School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
| | - Yanggen Hu
- School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
- Hubei Key Lab of Wudang Local Chinese Medicine Research, School of Pharmacy, Hubei University of Medicine Shiyan 442000 Hubei China
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2
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Zhou Y, Zhang Q, Zhao Z, Hu X, You Q, Jiang Z. Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives. Eur J Med Chem 2024; 269:116270. [PMID: 38490062 DOI: 10.1016/j.ejmech.2024.116270] [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: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
Kelch-like proteins (KLHLs) are a large family of BTB-containing proteins. KLHLs function as the substrate adaptor of Cullin 3-RING ligases (CRL3) to recognize substrates. KLHLs play pivotal roles in regulating various physiological and pathological processes by modulating the ubiquitination of their respective substrates. Mounting evidence indicates that mutations or abnormal expression of KLHLs are associated with various human diseases. Targeting KLHLs is a viable strategy for deciphering the KLHLs-related pathways and devising therapies for associated diseases. Here, we comprehensively review the known KLHLs inhibitors to date and the brilliant ideas underlying their development.
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Affiliation(s)
- Yangguo Zhou
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiong Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ziquan Zhao
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiuqi Hu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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3
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Yuan H, Cai R, Chen B, Wang Q, Wang M, An J, An W, Tao Y, Yu J, Jiang B, Zhang Y, Xu M. Acetylated KHSRP impairs DNA-damage-response-related mRNA decay and facilitates prostate cancer tumorigenesis. Mol Oncol 2024. [PMID: 38501452 DOI: 10.1002/1878-0261.13634] [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: 10/22/2023] [Revised: 01/28/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Androgen-regulated DNA damage response (DDR) is one of the essential mechanisms in prostate cancer (PCa), a hormone-sensitive disease. The heterogeneous nuclear ribonucleoprotein K (hnRNPK)-homology splicing regulatory protein known as far upstream element-binding protein 2 (KHSRP) is an RNA-binding protein that can attach to AU-rich elements in the 3' untranslated region (3'-UTR) of messenger RNAs (mRNAs) to mediate mRNA decay and emerges as a critical regulator in the DDR to preserve genome integrity. Nevertheless, how KHSRP responds to androgen-regulated DDR in PCa development remains unclear. This study found that androgen can significantly induce acetylation of KHSRP, which intrinsically drives tumor growth in xenografted mice. Moreover, enhanced KHSRP acetylation upon androgen stimuli impedes KHSRP-regulated DDR gene expression, as seen by analyzing RNA sequencing (RNA-seq) and Gene Set Enrichment Analysis (GSEA) datasets. Additionally, NAD-dependent protein deacetylase sirtuin-7 (SIRT7) is a promising deacetylase of KHSRP, and androgen stimuli impairs its interaction with KHSRP to sustain the increased KHSRP acetylation level in PCa. We first report the acetylation of KHSRP induced by androgen, which interrupts the KHSRP-regulated mRNA decay of the DDR-related genes to promote the tumorigenesis of PCa. This study provides insight into KHSRP biology and potential therapeutic strategies for PCa treatment, particularly that of castration-resistant PCa.
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Affiliation(s)
- Haihua Yuan
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Renjie Cai
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Biying Chen
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Wang
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Mengting Wang
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Junyi An
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Weishu An
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Ye Tao
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, China
| | - Bin Jiang
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Yanjie Zhang
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Ming Xu
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
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4
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Huang PN, Hsia SH, Huang KYA, Chen CJ, Wang ET, Shih SR, Lin TY. Reflecting on the 1998 enterovirus outbreak: A 25-year retrospective and learned lessons. Biomed J 2024:100715. [PMID: 38492637 DOI: 10.1016/j.bj.2024.100715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/13/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Enterovirus A71 (EV-A71) infections pose a significant public health concern in the Asia-Pacific region. EV-A71 is primarily responsible for causing hand, foot, and mouth disease (HFMD) in children. However, this virus can also lead to severe and potentially fatal neurological consequences in affected individuals. This review aims to provide a comprehensive understanding of the molecular virology, epidemiology, and recombination events associated with EV-A71. The literature extensively covers the clinical manifestations and neurological symptoms that accompany EV-A71 infections. One of the complications explored in this review is brainstem encephalitis, which can arise as a result of EV-A71 infections. Brainstem encephalitis refers to inflammation of the brainstem, a critical region responsible for various bodily functions. The review examines the underlying mechanisms, diagnostic criteria, treatment options, and prognosis for central nervous system infections involving EV-A71. Neurological complications associated with EV-A71 infections are diverse and can have severe consequences. These complications may include aseptic meningitis, acute flaccid paralysis, and acute transverse myelitis. The review delves into the pathophysiology of these complications, shedding light on the molecular mechanisms through which EV-A71 affects the central nervous system. Accurate diagnosis of EV-A71 infections is crucial for appropriate management and treatment. Treatment options for EV-A71 infections primarily focus on supportive care, as there are currently no specific antiviral drugs available for this virus. The review highlights the importance of managing symptoms, such as fever, dehydration, and pain relief, to alleviate the burden on affected individuals. Prognosis for individuals with central nervous system (CNS) infections involving EV-A71 can vary depending on the severity of the complications. The review provides insights into the long-term outcomes and potential neurological sequelae associated with EV-A71 infections. In conclusion, EV-A71 infections have emerged as a major public health concern in the Asia-Pacific region. This review aims to enhance our understanding of the molecular virology, epidemiology, and neurological complications associated with EV-A71. By examining the underlying mechanisms, diagnostic criteria, treatment options, and prognosis, this review contributes to the development of effective strategies for the prevention, diagnosis, and management of EV-A71 infections. The paper presents a comprehensive analysis of worldwide data pertaining to outbreaks of EV-A71 and HFMD. The subsequent discourse delves into the advancement and strategic formulation pertaining to the creation of vaccines targeting EV-A71. In summary, this study provides a comprehensive examination of the potential obstacles and considerations involved in the management and treatment of EV-A71 infections. Additionally, it proposes suggestions for future research and development endeavors with the objective of formulating efficacious treatment approaches for this viral infection.
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Affiliation(s)
- Peng-Nien Huang
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shao-Hsuan Hsia
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Department of Pediatric Respiratory Therapy, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Ying Arthur Huang
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Jung Chen
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - En-Tzu Wang
- Division of Acute Infectious Diseases, Centers for Disease Control, Ministry of Health and Welfare, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Tzou-Yien Lin
- Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Pediatrics, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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5
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Zhao X, Hu Y, Zhao J, Liu Y, Ma X, Chen H, Xing Y. Role of protein Post-translational modifications in enterovirus infection. Front Microbiol 2024; 15:1341599. [PMID: 38596371 PMCID: PMC11002909 DOI: 10.3389/fmicb.2024.1341599] [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: 11/20/2023] [Accepted: 01/18/2024] [Indexed: 04/11/2024] Open
Abstract
Enteroviruses (EVs) are the main cause of a number of neurological diseases. Growing evidence has revealed that successful infection with enteroviruses is highly dependent on the host machinery, therefore, host proteins play a pivotal role in viral infections. Both host and viral proteins can undergo post-translational modification (PTM) which can regulate protein activity, stability, solubility and interactions with other proteins; thereby influencing various biological processes, including cell metabolism, metabolic, signaling pathways, cell death, and cancer development. During viral infection, both host and viral proteins regulate the viral life cycle through various PTMs and different mechanisms, including the regulation of host cell entry, viral protein synthesis, genome replication, and the antiviral immune response. Therefore, protein PTMs play important roles in EV infections. Here, we review the role of various host- and virus-associated PTMs during enterovirus infection.
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Affiliation(s)
- Xiaohui Zhao
- Department of Pathogen Biology, School of Medicine, Qinghai University, Qinghai, China
| | - Yibo Hu
- Department of Orthopaedic Trauma, The Affiliated Hospital of Qinghai University, Qinghai, China
| | - Jun Zhao
- Department of Pathogen Biology, School of Medicine, Qinghai University, Qinghai, China
| | - Yan Liu
- Department of Immunology, School of Medicine, Qinghai, China
| | - Xueman Ma
- Department of Traditional Chinese Medicine, School of Medicine, Qinghai University, Qinghai, China
| | - Hongru Chen
- Department of Public Health, School of Medicine, Qinghai University, Qinghai, China
| | - Yonghua Xing
- Department of Genetics, School of Medicine, Qinghai University, Qinghai, China
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Júnior MA, Silva LC, Rocha OB, Oliveira AA, Portis IG, Alonso A, Alonso L, Silva KS, Gomes MN, Andrade CH, Soares CM, Pereira M. Proteomic identification of metabolic changes in Paracoccidioides brasiliensis induced by a nitroheteroarylchalcone. Future Microbiol 2023; 18:1077-1093. [PMID: 37424510 DOI: 10.2217/fmb-2022-0150] [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: 07/11/2023] Open
Abstract
Aim: To access the metabolic changes caused by a chalcone derivative (LabMol-75) through a proteomic approach. Methods: Proteomic analysis was performed after 9 h of Paracoccidioides brasiliensis yeast (Pb18) cell incubation with the LabMol-75 at MIC. The proteomic findings were validated through in vitro and in silico assays. Results: Exposure to the compound led to the downregulation of proteins associated with glycolysis and gluconeogenesis, β-oxidation, the citrate cycle and the electron transport chain. Conclusion: LabMol-75 caused an energetic imbalance in the fungus metabolism and deep oxidative stress. Additionally, the in silico molecular docking approach pointed to this molecule as a putative competitive inhibitor of DHPS.
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Affiliation(s)
- Marcos Abc Júnior
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lívia C Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Olivia B Rocha
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Amanda A Oliveira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Igor G Portis
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Antonio Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lais Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Kleber Sf Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Marcelo N Gomes
- InsiChem, Goiás State University, Anápolis, Goiás, Brazil
- Faculdade Metropolitana de Anápolis, Anápolis, Goiás, Brazil
| | - Carolina H Andrade
- Laboratory for Molecular Modeling & Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Célia Ma Soares
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Maristela Pereira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
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Liu Z, Wang X, Liu L, Guan M, Jiang H, An D, Li H. Long non-coding RNA SLC7A11 antisense RNA1 promotes oral squamous cell carcinoma progression by regulating ubiquitination of K-homology type splicing regulatory protein. Arch Oral Biol 2023; 154:105762. [PMID: 37480618 DOI: 10.1016/j.archoralbio.2023.105762] [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: 04/12/2023] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/24/2023]
Abstract
OBJECTIVES This article aims to elucidate the role of Long non-coding RNA SLC7A11 antisense RNA1 (SLC7A11-AS1) in oral squamous cell carcinoma, which are expected to be useful for the oral squamous cell carcinoma diagnosis and treatment. DESIGN SLC7A11-AS1 expression was detected by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) in oral squamous cell carcinoma cell lines. Cellular localization of SLC7A11-AS1C was detected by fluorescence in situ hybridization (FISH) assays and subcellular fractionation assay. Biological functions of SLC7A11-AS1 were explored by 3-(4,5-dimethyl-2-thiazolyl)- 2,5-diphenyl-2-H-tetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), wounding healing, and transwell invasion assays in vitro, as well as mice xenograft experiments and metastasis assays in vivo. RNA pull-down, RNA immunoprecipitation, co-immunoprecipitation, ubiquitination assays, and rescue experiments were performed to determine the molecular mechanism of SLC7A11-AS1 in oral squamous cell carcinoma. RESULTS SLC7A11-AS1 is overexpressed in oral cancer tissues and cell lines. Functionally, knockdown of SLC7A11-AS1 reduced the proliferation, migration, and invasion of oral squamous cell carcinoma cells in vitro and inhibited tumor growth as well as metastasis in vivo. Mechanistically, SLC7A11-AS1 impeded the interaction between K-homology type splicing regulatory protein (KHSRP) and kelch-like 12 (KLHL12), maintaining the stability of KHSRP by restraining KHSRP degradation through the ubiquitination-proteasome pathway. Furthermore, KHSRP overexpression recovered the malignant behaviors inhibited by SLC7A11-AS1 knockdown in oral cancer cells. CONCLUSION SLC7A11-AS1 promoted oral squamous cell carcinoma development by interacting with KHSRP and maintaining KHSRP stability by preventing its degradation via the ubiquitination-proteasome pathway. Thus, SLC7A11-AS1 is a potential therapeutic target for oral cancer.
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Affiliation(s)
- Zhen Liu
- Department of Stomatology, the Eighth Medical Center of Chinese PLA General Hospital, No.17 heishanhu Road, Haidian District, Beijing 100091, China
| | - Xiaoyu Wang
- Department of Stomatology, PLA Strategic Support Force Medical Center, No.9 Anxiang Beili, Deshengmenwai, Chaoyang District, Beijing 100101, China
| | - Lin Liu
- Department of Stomatology, the First Medical Center of Chinese PLA General Hospital, No.28 Fuxing Road, Haidian District, Beijing 100853, China
| | - Miaosheng Guan
- Department of Stomatology, PLA Rocket Force Characteristic Medical Center, No.16 Xinjiekou outside Street, Haidian District, Beijing 100088, China
| | - Hao Jiang
- Department of Stomatology, the Eighth Medical Center of Chinese PLA General Hospital, No.17 heishanhu Road, Haidian District, Beijing 100091, China
| | - Dan An
- Department of Stomatology, the Eighth Medical Center of Chinese PLA General Hospital, No.17 heishanhu Road, Haidian District, Beijing 100091, China
| | - Hongbo Li
- Department of Stomatology, the First Medical Center of Chinese PLA General Hospital, No.28 Fuxing Road, Haidian District, Beijing 100853, China.
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Imon RR, Kabir Talukder ME, Akhter S, Islam MS, Ahammad F, Anis-Ul-Haque KM, Moniruzzaman M, Afroze M, Khan M, Hena Mostofa Jamal MA, Wani TA, Uddin MJ, Rahman MM. Natural defense against multi-drug resistant Pseudomonas aeruginosa: Cassia occidentalis L. in vitro and in silico antibacterial activity. RSC Adv 2023; 13:28773-28784. [PMID: 37790109 PMCID: PMC10543200 DOI: 10.1039/d3ra03923d] [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: 06/12/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023] Open
Abstract
Cassia occidentalis L. is widely used in indigenous and traditional medicine, but its impact on multi-drug resistant (MDR) bacterial infections mostly remains unknown. Therefore, this study aimed to evaluate the in vitro antibacterial efficiency of methanol and ethyl acetate extracts of C. occidentalis L. leaves (MECOL and EAECOL) against multi-drug resistant Pseudomonas aeruginosa and to identify potential antibacterial agents through computational studies targeting the LasR protein. Initially, 82 compounds were identified using GC-MS analysis, and the functional groups were determined through FT-IR analysis. Both extracts of the plant exhibited dose-dependent antibacterial activity, with MICs of 104.16 ± 36.08 μg mL-1 for MECOL and 83.33 ± 36.08 μg mL-1 for EAECOL, and an MBC of 125 μg mL-1. Among the 82 compounds, 12 potential compounds were identified based on binding scores using molecular docking with the LasR protein and MM-GBSA analysis. Furthermore, screening for ADME properties, including physicochemical features, water solubility, lipophilicity, RO5 compliance, and toxicity, identified the top three compounds: methyl dihydrojasmonate, methyl benzoate, and 4a-methyl-4,4a,5,6,7,8-hexahydro-2(3H)-naphthalenone, which also demonstrated binding affinity with the active site residues of the LpxC protein of the bacteria. Additionally, molecular dynamics (MD) simulations confirmed the binding reliability of these three phytochemicals to LasR's active pocket, comparable to the protein native inhibitory ligands (C12-HSL). The study offers scientific support for the traditional use of C. occidentalis in treating bacterial infections, highlighting the potential of the three compounds as leads for developing LasR inhibitors to combat multi-drug resistant P. aeruginosa.
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Affiliation(s)
- Raihan Rahman Imon
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Enamul Kabir Talukder
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Shahina Akhter
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong Foy's Lake Chittagong 4202 Bangladesh
| | - Md Saidul Islam
- Korea Institute of Radiological & Medical Sciences 75, Nowon-ro, Nowon-gu Seoul South Korea
| | - Foysal Ahammad
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre) Jashore 7408 Bangladesh
- Division of Biological and Biomedical Sciences (BBS), College of Health & Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU) Doha Qatar
| | - K M Anis-Ul-Haque
- Department of Chemistry, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Moniruzzaman
- Bangladesh Reference Institute for Chemical Measurements (BRICM), Bangladesh Council of Scientific and Industrial Research Dr Qudrat-i-Khuda Road, Dhanmondi Dhaka 1205 Bangladesh
| | - Mirola Afroze
- Bangladesh Reference Institute for Chemical Measurements (BRICM), Bangladesh Council of Scientific and Industrial Research Dr Qudrat-i-Khuda Road, Dhanmondi Dhaka 1205 Bangladesh
| | - Mala Khan
- Bangladesh Reference Institute for Chemical Measurements (BRICM), Bangladesh Council of Scientific and Industrial Research Dr Qudrat-i-Khuda Road, Dhanmondi Dhaka 1205 Bangladesh
| | | | - Tanveer A Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University PO Box 2457 Riyadh 11451 Saudi Arabia
| | - Mohammad Jashim Uddin
- Department of Pharmacy, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Md Mashiar Rahman
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
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9
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Schmidt J, Chiffelle J, Perez MAS, Magnin M, Bobisse S, Arnaud M, Genolet R, Cesbron J, Barras D, Navarro Rodrigo B, Benedetti F, Michel A, Queiroz L, Baumgaertner P, Guillaume P, Hebeisen M, Michielin O, Nguyen-Ngoc T, Huber F, Irving M, Tissot-Renaud S, Stevenson BJ, Rusakiewicz S, Dangaj Laniti D, Bassani-Sternberg M, Rufer N, Gfeller D, Kandalaft LE, Speiser DE, Zoete V, Coukos G, Harari A. Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors. Nat Commun 2023; 14:3188. [PMID: 37280206 DOI: 10.1038/s41467-023-38946-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
The success of cancer immunotherapy depends in part on the strength of antigen recognition by T cells. Here, we characterize the T cell receptor (TCR) functional (antigen sensitivity) and structural (monomeric pMHC-TCR off-rates) avidities of 371 CD8 T cell clones specific for neoantigens, tumor-associated antigens (TAAs) or viral antigens isolated from tumors or blood of patients and healthy donors. T cells from tumors exhibit stronger functional and structural avidity than their blood counterparts. Relative to TAA, neoantigen-specific T cells are of higher structural avidity and, consistently, are preferentially detected in tumors. Effective tumor infiltration in mice models is associated with high structural avidity and CXCR3 expression. Based on TCR biophysicochemical properties, we derive and apply an in silico model predicting TCR structural avidity and validate the enrichment in high avidity T cells in patients' tumors. These observations indicate a direct relationship between neoantigen recognition, T cell functionality and tumor infiltration. These results delineate a rational approach to identify potent T cells for personalized cancer immunotherapy.
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Affiliation(s)
- Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marta A S Perez
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Morgane Magnin
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Cesbron
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Blanca Navarro Rodrigo
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Lise Queiroz
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Petra Baumgaertner
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Michael Hebeisen
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Olivier Michielin
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Tu Nguyen-Ngoc
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Florian Huber
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Stéphanie Tissot-Renaud
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Brian J Stevenson
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sylvie Rusakiewicz
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Nathalie Rufer
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - David Gfeller
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Daniel E Speiser
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Agora Cancer Research Center, Lausanne, Switzerland.
- Center for Cell Therapy, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland.
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10
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Baby K, Maity S, Mehta CH, Nayak UY, Shenoy GG, Pai KSR, Harikumar KB, Nayak Y. Computational drug repurposing of Akt-1 allosteric inhibitors for non-small cell lung cancer. Sci Rep 2023; 13:7947. [PMID: 37193898 DOI: 10.1038/s41598-023-35122-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/12/2023] [Indexed: 05/18/2023] Open
Abstract
Non-small cell lung carcinomas (NSCLC) are the predominant form of lung malignancy and the reason for the highest number of cancer-related deaths. Widespread deregulation of Akt, a serine/threonine kinase, has been reported in NSCLC. Allosteric Akt inhibitors bind in the space separating the Pleckstrin homology (PH) and catalytic domains, typically with tryptophan residue (Trp-80). This could decrease the regulatory site phosphorylation by stabilizing the PH-in conformation. Hence, in this study, a computational investigation was undertaken to identify allosteric Akt-1 inhibitors from FDA-approved drugs. The molecules were docked at standard precision (SP) and extra-precision (XP), followed by Prime molecular mechanics-generalized Born surface area (MM-GBSA), and molecular dynamics (MD) simulations on selected hits. Post XP-docking, fourteen best hits were identified from a library of 2115 optimized FDA-approved compounds, demonstrating several beneficial interactions such as pi-pi stacking, pi-cation, direct, and water-bridged hydrogen bonds with the crucial residues (Trp-80 and Tyr-272) and several amino acid residues in the allosteric ligand-binding pocket of Akt-1. Subsequent MD simulations to verify the stability of chosen drugs to the Akt-1 allosteric site showed valganciclovir, dasatinib, indacaterol, and novobiocin to have high stability. Further, predictions for possible biological interactions were performed using computational tools such as ProTox-II, CLC-Pred, and PASSOnline. The shortlisted drugs open a new class of allosteric Akt-1 inhibitors for the therapy of NSCLC.
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Affiliation(s)
- Krishnaprasad Baby
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Swastika Maity
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Chetan Hasmukh Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Usha Y Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Gautham G Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576 104, India
| | - Karkala Sreedhara Ranganath Pai
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kuzhuvelil B Harikumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, 695014, India
| | - Yogendra Nayak
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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11
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Peng F, Zhou L, Lu W, Gan R, Lu M, Li Z, Zhang X, Wang Y, Gui J. Genomic and Transcriptional Profiles of Kelch-like ( klhl) Gene Family in Polyploid Carassius Complex. Int J Mol Sci 2023; 24:8367. [PMID: 37176071 PMCID: PMC10179623 DOI: 10.3390/ijms24098367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select Kelch-like (klhl) genes to study the evolution of the duplicated genes in the polyploid Carassius complex, including amphidiploid C. auratus and amphitriploid C. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most of Carassius klhl genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during Carassius evolution. The lineage-specific expansion and biased retention/loss of klhl genes are also found in Carassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of klhls in response to Carassius herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three C. gibelio gynogenetic clones. Finally, we find that most C. gibelio klhl genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for Cgklhl genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.
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Affiliation(s)
- Fang Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijia Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruihai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaojuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Mehri A, Mardanshahi M, Sirous H, Khanahmad H, Rostami M. Pyrimido[4,5-b]indole derivatives bearing 1,2,4-oxadiazole moiety as MDM2 inhibitor candidates in cancer treatment. Future Med Chem 2023; 15:517-532. [PMID: 37097083 DOI: 10.4155/fmc-2023-0012] [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] [Indexed: 04/26/2023] Open
Abstract
Aim: In this study, novel hybrid structures of pyrimido-indole-oxadiazole were developed as MDM2 inhibitors for restoring the regular function of the p53. Materials & methods: A multistep chemical pathway was used to synthesize the derivatives. Nutlin-3a was used as a standard lead in molecular docking and molecular dynamics simulations. Finally, cytotoxicity was evaluated against MCF-7 cancer cells versus Doxorubicin. Results: The most promising candidate was 12c, which had an NO2 group in the para position of the oxadiazole ring (IC50: 1.1 μM). A satisfactory result was obtained with the combined application of 12c and Doxorubicin (IC50 decreased to 0.63 μM), which could be potentially attributed to MDM2 inhibition. Conclusion: These hybrid structures can be further investigated as potential MDM2 inhibitors.
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Affiliation(s)
- Ali Mehri
- Department of Medicinal Chemistry, School of Pharmacy & Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
| | - Mahboubeh Mardanshahi
- Department of Medicinal Chemistry, School of Pharmacy & Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
| | - Hossein Khanahmad
- Department of Genetics & Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
| | - Mahboubeh Rostami
- Isfahan Pharmaceutical Sciences Research Center & Department of Medicinal Chemistry, School of Pharmacy & Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
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13
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Al-Mamun A, Ahammad I, Ahmed SS, Akter F, Hossain SI, Chowdhury ZM, Bhattacharjee A, Das KC, Keya CA, Salimullah M. Pharmacoinformatics and molecular dynamics simulation approach to identify anti-diarrheal potentials of Centella asiatica (L.) Urb. against Vibrio cholerae. J Biomol Struct Dyn 2023; 41:14730-14743. [PMID: 36927394 DOI: 10.1080/07391102.2023.2191736] [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: 12/13/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
Vibrio cholerae, the etiological agent of cholera, causes dehydration and severe diarrhea with the production of cholera toxin. Due to the acquired antibiotic resistance, V. cholerae has drawn attention to the establishment of novel medications to counteract the virulence and viability of the pathogen. Centella asiatica is a medicinal herb native to Bangladesh that has a wide range of medicinal and ethnobotanical applications including anti-bacterial properties. In the present investigation, a total of 25 bioactive phytochemicals of C. asiatica have been screened virtually through molecular docking, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses, and molecular dynamics simulation. Our results revealed four lead compounds as Viridiflorol (-8.7 Kcal/mol), Luteolin (-8.1 Kcal/mol), Quercetin (-8.0 Kcal/mol) and, Geranyl acetate (-7.1 Kcal/mol) against V. cholerae Toxin co-regulated pilus virulence regulatory protein (ToxT). All the lead compounds have been found to possess favorable pharmacokinetic, pharmacodynamics, and molecular dynamics properties. Toxicity analysis revealed satisfactory results with no major side effects. Molecular dynamics simulation was performed for 100 ns that revealed noteworthy conformational stability and structural compactness for all the lead compounds, especially for Quercetin. Target class prediction unveiled enzymes in most of the cases and some experimental and investigational drugs were found as structurally similar analogs of the lead compounds. These findings could aid in the development of novel therapeutics targeting Cholera disease and we strongly recommend in vitro trials of our experimental findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullah Al-Mamun
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Sheikh Sunzid Ahmed
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Farzana Akter
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Shah Imran Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | | | | | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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14
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Zhao Q, Mao Q, Zhao Z, Yuan W, He Q, Sun Q, Yao Y, Fan X. RNA independent fragment partition method based on deep learning for RNA secondary structure prediction. Sci Rep 2023; 13:2861. [PMID: 36801945 PMCID: PMC9938198 DOI: 10.1038/s41598-023-30124-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/16/2023] [Indexed: 02/19/2023] Open
Abstract
The non-coding RNA secondary structure largely determines its function. Hence, accuracy in structure acquisition is of great importance. Currently, this acquisition primarily relies on various computational methods. The prediction of the structures of long RNA sequences with high precision and reasonable computational cost remains challenging. Here, we propose a deep learning model, RNA-par, which could partition an RNA sequence into several independent fragments (i-fragments) based on its exterior loops. Each i-fragment secondary structure predicted individually could be further assembled to acquire the complete RNA secondary structure. In the examination of our independent test set, the average length of the predicted i-fragments was 453 nt, which was considerably shorter than that of complete RNA sequences (848 nt). The accuracy of the assembled structures was higher than that of the structures predicted directly using the state-of-the-art RNA secondary structure prediction methods. This proposed model could serve as a preprocessing step for RNA secondary structure prediction for enhancing the predictive performance (especially for long RNA sequences) and reducing the computational cost. In the future, predicting the secondary structure of long-sequence RNA with high accuracy can be enabled by developing a framework combining RNA-par with various existing RNA secondary structure prediction algorithms. Our models, test codes and test data are provided at https://github.com/mianfei71/RNAPar .
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Affiliation(s)
- Qi Zhao
- grid.412252.20000 0004 0368 6968College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, 110169 Liaoning China
| | - Qian Mao
- grid.411356.40000 0000 9339 3042College of Light Industry, Liaoning University, Shenyang, 110036 Liaoning China
| | - Zheng Zhao
- grid.440686.80000 0001 0543 8253College of Artificial Intelligence, Dalian Maritime University, Dalian, 116026 Liaoning China
| | - Wenxuan Yuan
- grid.412252.20000 0004 0368 6968College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, 110169 Liaoning China
| | - Qiang He
- grid.412252.20000 0004 0368 6968College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, 110169 Liaoning China
| | - Qixuan Sun
- grid.412252.20000 0004 0368 6968College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, 110169 Liaoning China
| | - Yudong Yao
- grid.217309.e0000 0001 2180 0654Department of Electrical and Computer Engineering, Stevens Institute of Technology, Hoboken, NJ 07030 USA
| | - Xiaoya Fan
- School of Software, Dalian University of Technology, Key Laboratory for Ubiquitous Network and Service Software of Liaoning Province, Dalian, 116620, Liaoning, China.
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15
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Whitehouse RL, Alwan WS, Ilyichova OV, Taylor AJ, Chandrashekaran IR, Mohanty B, Doak BC, Scanlon MJ. Fragment screening libraries for the identification of protein hot spots and their minimal binding pharmacophores. RSC Med Chem 2023; 14:135-143. [PMID: 36760747 PMCID: PMC9890547 DOI: 10.1039/d2md00253a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Fragment-based drug design relies heavily on structural information for the elaboration and optimisation of hits. The ability to identify neighbouring binding hot spots, energetically favourable interactions and conserved binding motifs in protein structures through X-ray crystallography can inform the evolution of fragments into lead-like compounds through structure-based design. The composition of fragment libraries can be designed and curated to fit this purpose and herein, we describe and compare screening libraries containing compounds comprising between 2 and 18 heavy atoms. We evaluate the properties of the compounds in these libraries and assess their ability to probe protein surfaces for binding hot spots.
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Affiliation(s)
- Rebecca L Whitehouse
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Wesam S Alwan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Olga V Ilyichova
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Australian Synchrotron, ANSTO Clayton VIC 3168 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Ashley J Taylor
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Indu R Chandrashekaran
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Bradley C Doak
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
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16
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Fang Y, Lin S, Dou Q, Gui J, Li W, Tan H, Wang Y, Zeng J, Khan A, Wei DQ. Network pharmacology- and molecular simulation-based exploration of therapeutic targets and mechanisms of heparin for the treatment of sepsis/COVID-19. J Biomol Struct Dyn 2023; 41:12586-12598. [PMID: 36661370 DOI: 10.1080/07391102.2023.2167114] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023]
Abstract
Critically infected patients with COVID-19 (coronavirus disease 2019) are prone to develop sepsis-related coagulopathy as a result of a robust immune response. The mechanism underlying the relationship between sepsis and COVID-19 is largely unknown. LMWH (low molecular weight heparin) exhibits both anti-inflammatory and anti-coagulating properties that result in a better prognosis of severely ill patients with COVID-19 co-associated with sepsis-induced coagulopathy or with a higher D-dimer value. Heparin-associated molecular targets and their mechanism of action in sepsis/COVID-19 are not well understood. In this work, we characterize the pharmacological targets, biological functions and therapeutic actions of heparin in sepsis/COVID-19 from the perspective of network pharmacology. A total of 38 potential targets for heparin action against sepsis/COVID-19 and 8 core pharmacological targets were identified, including IL6, KNG1, CXCL8, ALB, VEGFA, F2, IL10 and TNF. Moreover, enrichment analysis showed that heparin could help in treating sepsis/COVID-19 through immunomodulation, inhibition of the inflammatory response, regulation of angiogenesis and antiviral activity. The pharmacological effects of heparin against these targets were further confirmed by molecular docking and simulation analysis, suggesting that heparin exerts effective binding capacity by targeting the essential residues in sepsis/COVID-19. Prospective clinical practice evaluations may consider the use of these key prognostic indicators for the treatment of sepsis/COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yitian Fang
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
| | - Shenggeng Lin
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingli Dou
- Department of Emergency Medicine, Affiliated Baoan Hospital of Shenzhen, Southern Medical University, Shenzhen, Guangdong, China
| | - Jianjun Gui
- Department of Emergency Medicine, Affiliated Baoan Hospital of Shenzhen, Southern Medical University, Shenzhen, Guangdong, China
| | - Weimin Li
- National Tuberculosis Clinical Lab of China, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongsheng Tan
- Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanjing Wang
- Engineering Research Center of Cell and Therapeutics Antibody, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
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17
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He XH, You CZ, Jiang HL, Jiang Y, Xu HE, Cheng X. AlphaFold2 versus experimental structures: evaluation on G protein-coupled receptors. Acta Pharmacol Sin 2023; 44:1-7. [PMID: 35778488 PMCID: PMC9813356 DOI: 10.1038/s41401-022-00938-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/06/2022] [Indexed: 01/18/2023] Open
Abstract
As important drug targets, G protein-coupled receptors (GPCRs) play pivotal roles in a wide range of physiological processes. Extensive efforts of structural biology have been made on the study of GPCRs. However, a large portion of GPCR structures remain unsolved due to structural instability. Recently, AlphaFold2 has been developed to predict structure models of many functionally important proteins including all members of the GPCR family. Herein we evaluated the accuracy of GPCR structure models predicted by AlphaFold2. We revealed that AlphaFold2 could capture the overall backbone features of the receptors. However, the predicted models and experimental structures were different in many aspects including the assembly of the extracellular and transmembrane domains, the shape of the ligand-binding pockets, and the conformation of the transducer-binding interfaces. These differences impeded the use of predicted structure models in the functional study and structure-based drug design of GPCRs, which required reliable high-resolution structural information.
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Affiliation(s)
- Xin-Heng He
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chong-Zhao You
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua-Liang Jiang
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
- Lingang Laboratory, Shanghai, 200031, China
| | - Yi Jiang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Lingang Laboratory, Shanghai, 200031, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xi Cheng
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China.
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18
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Rani J, Bhargav A, Khan FI, Ramachandran S, Lai D, Bajpai U. In silico prediction of natural compounds as potential multi-target inhibitors of structural proteins of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:12118-12134. [PMID: 34486935 PMCID: PMC8425474 DOI: 10.1080/07391102.2021.1968497] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a colossal loss to human health and lives and has deeply impacted socio-economic growth. Remarkable efforts have been made by the scientific community in containing the virus by successful development of vaccines and diagnostic kits. Initiatives towards drug repurposing and discovery have also been undertaken. In this study, we compiled the known natural anti-viral compounds using text mining of the literature and examined them against four major structural proteins of SARS-CoV-2, namely, spike (S) protein, nucleocapsid (N) protein, membrane (M) protein and envelope (E) protein. Following computational approaches, we identified fangchinoline and versicolactone C as the compounds to exhibit strong binding to the target proteins and causing structural deformation of three structural proteins (N, S and M). We recommend the inhibitory effects of these compounds from our study should be experimentally validated against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jyoti Rani
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India,G N Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research – Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Anasuya Bhargav
- G N Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research – Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Srinivasan Ramachandran
- G N Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research – Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,Srinivasan Ramchandran ;
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China,Dakun Lai
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India,CONTACT Urmi Bajpai ;
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19
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Verkhivker GM, Agajanian S, Oztas D, Gupta G. Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. J Biomol Struct Dyn 2022; 40:9724-9741. [PMID: 34060425 DOI: 10.1080/07391102.2021.1933594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this study, we used an integrative computational approach to examine molecular mechanisms underlying functional effects of the D614G mutation by exploring atomistic modeling of the SARS-CoV-2 spike proteins as allosteric regulatory machines. We combined coarse-grained simulations, protein stability and dynamic fluctuation communication analysis with network-based community analysis to examine structures of the native and mutant SARS-CoV-2 spike proteins in different functional states. Through distance fluctuations communication analysis, we probed stability and allosteric communication propensities of protein residues in the native and mutant SARS-CoV-2 spike proteins, providing evidence that the D614G mutation can enhance long-range signaling of the allosteric spike engine. By combining functional dynamics analysis and ensemble-based alanine scanning of the SARS-CoV-2 spike proteins we found that the D614G mutation can improve stability of the spike protein in both closed and open forms, but shifting thermodynamic preferences towards the open mutant form. Our results revealed that the D614G mutation can promote the increased number of stable communities and allosteric hub centers in the open form by reorganizing and enhancing the stability of the S1-S2 inter-domain interactions and restricting mobility of the S1 regions. This study provides atomistic-based view of allosteric communications in the SARS-CoV-2 spike proteins, suggesting that the D614G mutation can exert its primary effect through allosterically induced changes on stability and communications in the residue interaction networks.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gennady M Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA, USA.,Depatment of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA
| | - Steve Agajanian
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Deniz Oztas
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
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20
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Ye G, Wang J, Yang W, Li J, Ye M, Jin X. The roles of KLHL family members in human cancers. Am J Cancer Res 2022; 12:5105-5139. [PMID: 36504893 PMCID: PMC9729911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
The Kelch-like (KLHL) family members consist of three domains: bric-a-brac, tramtrack, broad complex/poxvirus and zinc finger domain, BACK domain and Kelch domain, which combine and interact with Cullin3 to form an E3 ubiquitin ligase. Research has indicated that KLHL family members ubiquitinate target substrates to regulate physiological and pathological processes, including tumorigenesis and progression. KLHL19, a member of the KLHL family, is associated with tumorigenesis and drug resistance. However, the regulation and cross talks of other KLHL family members, which also play roles in cancer, are still unclear. Our review mainly explores studies concerning the roles of other KLHL family members in tumor-related regulation to provide novel insights into KLHL family members.
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Affiliation(s)
- Ganghui Ye
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Jie Wang
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Weili Yang
- Yinzhou People’s Hospital of Medical School, Ningbo UniversityNingbo 315040, Zhejiang, P. R. China
| | - Jinyun Li
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
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21
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Mucha B, Qie S, Bajpai S, Tarallo V, Diehl JN, Tedeschi F, Zhou G, Gao Z, Flashner S, Klein-Szanto AJ, Hibshoosh H, Masataka S, Chajewski OS, Majsterek I, Pytel D, Hatzoglou M, Der CJ, Nakagawa H, Bass AJ, Wong KK, Fuchs SY, Rustgi AK, Jankowsky E, Diehl JA. Tumor suppressor mediated ubiquitylation of hnRNPK is a barrier to oncogenic translation. Nat Commun 2022; 13:6614. [PMID: 36329064 PMCID: PMC9633729 DOI: 10.1038/s41467-022-34402-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Heterogeneous Nuclear Ribonucleoprotein K (hnRNPK) is a multifunctional RNA binding protein (RBP) localized in the nucleus and the cytoplasm. Abnormal cytoplasmic enrichment observed in solid tumors often correlates with poor clinical outcome. The mechanism of cytoplasmic redistribution and ensuing functional role of cytoplasmic hnRNPK remain unclear. Here we demonstrate that the SCFFbxo4 E3 ubiquitin ligase restricts the pro-oncogenic activity of hnRNPK via K63 linked polyubiquitylation, thus limiting its ability to bind target mRNA. We identify SCFFbxo4-hnRNPK responsive mRNAs whose products regulate cellular processes including proliferation, migration, and invasion. Loss of SCFFbxo4 leads to enhanced cell invasion, migration, and tumor metastasis. C-Myc was identified as one target of SCFFbxo4-hnRNPK. Fbxo4 loss triggers hnRNPK-dependent increase in c-Myc translation, thereby contributing to tumorigenesis. Increased c-Myc positions SCFFbxo4-hnRNPK dysregulated cancers for potential therapeutic interventions that target c-Myc-dependence. This work demonstrates an essential role for limiting cytoplasmic hnRNPK function in order to maintain translational and cellular homeostasis.
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Affiliation(s)
- Bartosz Mucha
- Department of Biochemistry, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Shuo Qie
- Department of Biochemistry, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Sagar Bajpai
- Department of Biochemistry, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Vincenzo Tarallo
- Department of Biochemistry, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frank Tedeschi
- Department of Biochemistry, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
- Center for RNA Science and Therapeutics, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Gao Zhou
- Center for RNA Science and Therapeutics, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Samuel Flashner
- Division of Hematology-Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Hanina Hibshoosh
- Division of Hematology-Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Shimonosono Masataka
- Division of Hematology-Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Olga S Chajewski
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 60 Narutowicza St. 90-136, Lodz, Poland
| | - Dariusz Pytel
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 60 Narutowicza St. 90-136, Lodz, Poland
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Channing J Der
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Adam J Bass
- Division of Hematology-Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Kwok-Kin Wong
- Division of Hematology and Medical Oncology, Perlmutter Cancer Center, New York University, New York, NY, 10016, USA
| | - Serge Y Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anil K Rustgi
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
- Center for RNA Science and Therapeutics, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - J Alan Diehl
- Department of Biochemistry, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Center for RNA Science and Therapeutics, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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22
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Verkhivker GM, Agajanian S, Kassab R, Krishnan K. Frustration-driven allosteric regulation and signal transmission in the SARS-CoV-2 spike omicron trimer structures: a crosstalk of the omicron mutation sites allosterically regulates tradeoffs of protein stability and conformational adaptability. Phys Chem Chem Phys 2022; 24:17723-17743. [PMID: 35839100 DOI: 10.1039/d2cp01893d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dissecting the regulatory principles underlying function and activity of the SARS-CoV-2 spike protein at the atomic level is of paramount importance for understanding the mechanisms of virus transmissibility and immune escape. In this work, we introduce a hierarchical computational approach for atomistic modeling of allosteric mechanisms in the SARS-CoV-2 Omicron spike proteins and present evidence of a frustration-based allostery as an important energetic driver of the conformational changes and spike activation. By examining conformational landscapes and the residue interaction networks in the SARS-CoV-2 Omicron spike protein structures, we have shown that the Omicron mutational sites are dynamically coupled and form a central engine of the allosterically regulated spike machinery that regulates the balance and tradeoffs between conformational plasticity, protein stability, and functional adaptability. We have found that the Omicron mutational sites at the inter-protomer regions form regulatory hotspot clusters that control functional transitions between the closed and open states. Through perturbation-based modeling of allosteric interaction networks and diffusion analysis of communications in the closed and open spike states, we have quantified the allosterically regulated activation mechanism and uncover specific regulatory roles of the Omicron mutations. Atomistic reconstruction of allosteric communication pathways and kinetic modeling using Markov transient analysis reveal that the Omicron mutations form the inter-protomer electrostatic bridges that operate as a network of coupled regulatory switches that could control global conformational changes and signal transmission in the spike protein. The results of this study have revealed distinct and yet complementary roles of the Omicron mutation sites as a network of hotspots that enable allosteric modulation of structural stability and conformational changes which are central for spike activation and virus transmissibility.
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Affiliation(s)
- Gennady M Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA.,Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Steve Agajanian
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Ryan Kassab
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Keerthi Krishnan
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
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23
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Zhai F, Li J, Ye M, Jin X. The functions and effects of CUL3-E3 ligases mediated non-degradative ubiquitination. Gene X 2022; 832:146562. [PMID: 35580799 DOI: 10.1016/j.gene.2022.146562] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 02/09/2023] Open
Abstract
Ubiquitination of substrates usually have two fates: one is degraded by 26S proteasome, and the other is non-degradative ubiquitination modification which is associated with cell cycle regulation, chromosome inactivation, protein transportation, tumorigenesis, achondroplasia, and neurological diseases. Cullin3 (CUL3), a scaffold protein, binding with the Bric-a-Brac-Tramtrack-Broad-complex (BTB) domain of substrates recognition adaptor and RING-finger protein 1 (RBX1) form ubiquitin ligases (E3). Based on the current researches, this review has summarized the functions and effects of CUL3-E3 ligases mediated non-degradative ubiquitination.
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Affiliation(s)
- Fengguang Zhai
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jingyun Li
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathphysiology, Medical School of Ningbo University, Ningbo 315211, China.
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24
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Méheust R, Castelle CJ, Jaffe AL, Banfield JF. Conserved and lineage-specific hypothetical proteins may have played a central role in the rise and diversification of major archaeal groups. BMC Biol 2022; 20:154. [PMID: 35790962 PMCID: PMC9258230 DOI: 10.1186/s12915-022-01348-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Archaea play fundamental roles in the environment, for example by methane production and consumption, ammonia oxidation, protein degradation, carbon compound turnover, and sulfur compound transformations. Recent genomic analyses have profoundly reshaped our understanding of the distribution and functionalities of Archaea and their roles in eukaryotic evolution. RESULTS Here, 1179 representative genomes were selected from 3197 archaeal genomes. The representative genomes clustered based on the content of 10,866 newly defined archaeal protein families (that will serve as a community resource) recapitulates archaeal phylogeny. We identified the co-occurring proteins that distinguish the major lineages. Those with metabolic roles were consistent with experimental data. However, two families specific to Asgard were determined to be new eukaryotic signature proteins. Overall, the blocks of lineage-specific families are dominated by proteins that lack functional predictions. CONCLUSIONS Given that these hypothetical proteins are near ubiquitous within major archaeal groups, we propose that they were important in the origin of most of the major archaeal lineages. Interestingly, although there were clearly phylum-specific co-occurring proteins, no such blocks of protein families were shared across superphyla, suggesting a burst-like origin of new lineages early in archaeal evolution.
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Affiliation(s)
- Raphaël Méheust
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, CA, USA. .,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, Evry, France.
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA. .,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
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25
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Xue B, Chaddha M, Elasbali AM, Zhu Z, Jairajpuri DS, Alhumaydhi FA, Mohammad T, Abdulmonem WA, Sharaf SE, Hassan MI. Death-Associated Protein Kinase 3 Inhibitors Identified by Virtual Screening for Drug Discovery in Cancer and Hypertension. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:404-413. [PMID: 35759452 DOI: 10.1089/omi.2022.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Death-associated protein kinase 3 (DAPK3) is a serine/threonine protein kinase that regulates apoptosis, autophagy, transcription, and actin cytoskeleton reorganization. DAPK3 induces morphological alterations in apoptosis when overexpressed, and it is considered a potential drug target in antihypertensive and anticancer drug development. In this article, we report new findings from a structure-guided virtual screening for discovery of phytochemicals that could modulate the elevated expression of DAPK3, and with an eye to anticancer drug discovery. We used the Indian Medicinal Plants, Phytochemistry and Therapeutics (IMPPAT), a curated database, as part of the methodology. The potential initial hits were identified based on their physicochemical properties and binding affinity toward DAPK3. Subsequently, various filters for drug likeness followed by interaction analysis and molecular dynamics (MD) simulations for 100 nsec were performed to explore the conformational sampling and stability of DAPK3 with the candidate molecules. Notably, the data from all-atom MD simulations and principal component analysis suggested that DAPK3 forms stable complexes with ketanserin and rotenone. In conclusion, this study supports the idea that ketanserin and rotenone bind to DAPK3, and show stability, which can be further explored as promising scaffolds in drug development and therapeutics innovation in clinical contexts such as hypertension and various types of cancer.
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Affiliation(s)
- Bin Xue
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Muskan Chaddha
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Sakakah, Saudi Arabia
| | - Zhixin Zhu
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraidah, Saudia Arabia
| | - Sharaf E Sharaf
- Pharmaceutical Chemistry Department, College of Pharmacy Umm Al-Qura University, Makkah, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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26
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Li B, Roden DM, Capra JA. The 3D mutational constraint on amino acid sites in the human proteome. Nat Commun 2022; 13:3273. [PMID: 35672414 PMCID: PMC9174330 DOI: 10.1038/s41467-022-30936-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/19/2022] [Indexed: 12/16/2022] Open
Abstract
Quantification of the tolerance of protein sites to genetic variation has become a cornerstone of variant interpretation. We hypothesize that the constraint on missense variation at individual amino acid sites is largely shaped by direct interactions with 3D neighboring sites. To quantify this constraint, we introduce a framework called COntact Set MISsense tolerance (or COSMIS) and comprehensively map the landscape of 3D mutational constraint on 6.1 million amino acid sites covering 16,533 human proteins. We show that 3D mutational constraint is pervasive and that the level of constraint is strongly associated with disease relevance both at the site and the protein level. We demonstrate that COSMIS performs significantly better at variant interpretation tasks than other population-based constraint metrics while also providing structural insight into the functional roles of constrained sites. We anticipate that COSMIS will facilitate the interpretation of protein-coding variation in evolution and prioritization of sites for mechanistic investigation.
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Affiliation(s)
- Bian Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37203, USA.
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Departments of Pharmacology and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37203, USA.
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94143, USA.
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27
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Palzer KA, Bolduan V, Käfer R, Kleinert H, Bros M, Pautz A. The Role of KH-Type Splicing Regulatory Protein (KSRP) for Immune Functions and Tumorigenesis. Cells 2022; 11:cells11091482. [PMID: 35563788 PMCID: PMC9104899 DOI: 10.3390/cells11091482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 12/11/2022] Open
Abstract
Post-transcriptional control of gene expression is one important mechanism that enables stringent and rapid modulation of cytokine, chemokines or growth factors expression, all relevant for immune or tumor cell function and communication. The RNA-binding protein KH-type splicing regulatory protein (KSRP) controls the mRNA stability of according genes by initiation of mRNA decay and inhibition of translation, and by enhancing the maturation of microRNAs. Therefore, KSRP plays a pivotal role in immune cell function and tumor progression. In this review, we summarize the current knowledge about KSRP with regard to the regulation of immunologically relevant targets, and the functional role of KSRP on immune responses and tumorigenesis. KSRP is involved in the control of myeloid hematopoiesis. Further, KSRP-mediated mRNA decay of pro-inflammatory factors is necessary to keep immune homeostasis. In case of infection, functional impairment of KSRP is important for the induction of robust immune responses. In this regard, KSRP seems to primarily dampen T helper cell 2 immune responses. In cancer, KSRP has often been associated with tumor growth and metastasis. In summary, aside of initiation of mRNA decay, the KSRP-mediated regulation of microRNA maturation seems to be especially important for its diverse biological functions, which warrants further in-depth examination.
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Affiliation(s)
- Kim-Alicia Palzer
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (K.-A.P.); (R.K.); (H.K.)
| | - Vanessa Bolduan
- Department of Dermatology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (V.B.); (M.B.)
| | - Rudolf Käfer
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (K.-A.P.); (R.K.); (H.K.)
| | - Hartmut Kleinert
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (K.-A.P.); (R.K.); (H.K.)
| | - Matthias Bros
- Department of Dermatology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (V.B.); (M.B.)
| | - Andrea Pautz
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany; (K.-A.P.); (R.K.); (H.K.)
- Correspondence: ; Tel.: +49-6131-179276; Fax: +49-6131-179042
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Verkhivker GM, Agajanian S, Kassab R, Krishnan K. Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. J Chem Inf Model 2022; 62:1956-1978. [PMID: 35377633 DOI: 10.1021/acs.jcim.2c00124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The structural and functional studies of the SARS-CoV-2 spike protein variants revealed an important role of the D614G mutation that is shared across many variants of concern (VOCs), suggesting the effect of this mutation on the enhanced virus infectivity and transmissibility. The recent structural and biophysical studies provided important evidence about multiple conformational substates of the D614G spike protein. The development of a plausible mechanistic model that can explain the experimental observations from a more unified thermodynamic perspective is an important objective of the current work. In this study, we employed efficient and accurate coarse-grained simulations of multiple structural substates of the D614G spike trimers together with the ensemble-based mutational frustration analysis to characterize the dynamics signatures of the conformational landscapes. By combining the local frustration profiling of the conformational states with residue-based mutational scanning of protein stability and network analysis of allosteric interactions and communications, we determine the patterns of mutational sensitivity in the functional regions and sites of variants. We found that the D614G mutation may induce a considerable conformational adaptability of the open states in the SARS-CoV-2 spike protein without compromising the folding stability and integrity of the spike protein. The results suggest that the D614G mutant may employ a hinge-shift mechanism in which the dynamic couplings between the site of mutation and the interprotomer hinge modulate the interdomain interactions, global mobility change, and the increased stability of the open form. This study proposes that mutation-induced modulation of the conformational flexibility and energetic frustration at the interprotomer interfaces may serve as an efficient mechanism for allosteric regulation of the SARS-CoV-2 spike proteins.
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Affiliation(s)
- Gennady M Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Steve Agajanian
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Ryan Kassab
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Keerthi Krishnan
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
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Lv F, Li X, Wang Y. An extraction from Trametes robiniophila Murr. ( Huaier) inhibits non-small cell lung cancer proliferation via targeting to epidermal growth factor receptor. Bioengineered 2022; 13:10931-10943. [PMID: 35470770 PMCID: PMC9162005 DOI: 10.1080/21655979.2022.2066757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 12/04/2022] Open
Abstract
An extraction from Trametes robiniophila Murr. (Huaier) is a kind of natural fungus growing from the sophora japonica tree. Huaier is widely applied to cure the hepatocellular cancer (HCC). However, the medicinal fungus' curative result on non-small-cell lung cancer (NSCLC) is not well elaborated. In this study, we applied in vitro experiments to study Huaier's curative result on NSCLC. The potential Huaier targets were predicted using bioinformatics and validated by western blotting. We further elucidated the mechanism of Huaier targeting by molecular docking, kinase activity assay, CEllular Thermal Shift Assays (CETSAs). At last, in vivo curative result was verified further. Huaier weakened proliferation and promoted apoptosis of the NSCLC cell lines. According to bioinformatics, Epidermal Growth Factor Receptor (EGFR) may be the target of Huaier. Western blotting showed that Huaier can attenuate the activation of EGFR and we found that Huaier can dock to EGFR. Huaier significantly inhibited the tumor growth by weakening the expression of p-EGFR in vivo. This study offers a new idea for further understanding of Huaier and shows its potential as a therapeutic agent.
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Affiliation(s)
- Fei Lv
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaoqi Li
- Third Department of Oncology, The People’s Hospital of Liaoning Province
| | - Ying Wang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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30
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Dabaeva VV, Baghdasaryan MR, Paronikyan RG, Nazaryan IM, Hakobyan HG, Hunanyan LS, Paronikyan EG, Dashyan SS. Synthesis, Neurotropic Activity, and Molecular Docking of New Condensed Thieno[2,3-b]pyridine Derivatives. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022010034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Brink A, Jacobs FJF, Helliwell JR. Trends in coordination of rhenium organometallic complexes in the Protein Data Bank. IUCRJ 2022; 9:180-193. [PMID: 35371500 PMCID: PMC8895017 DOI: 10.1107/s2052252522000665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Radiopharmaceutical development has similar overall characteristics to any biomedical drug development requiring a compound's stability, aqueous solubility and selectivity to a specific disease site. However, organometallic complexes containing 188/186Re or 99mTc involve a d-block transition-metal radioactive isotope and therefore bring additional factors such as metal oxidation states, isotope purity and half life into play. This topical review is focused on the development of radiopharmaceuticals containing the radioisotopes of rhenium and technetium and, therefore, on the occurrence of these organometallic complexes in protein structures in the Worldwide Protein Data Bank (wwPDB). The purpose of incorporating the group 7 transition metals of rhenium/technetium in the protein and the reasons for study by protein crystallography are described, as certain PDB studies were not aimed at drug development. Technetium is used as a medical diagnostic agent and involves the 99mTc isotope which decays to release gamma radiation, thereby employed for its use in gamma imaging. Due to the periodic relationship among group 7 transition metals, the coordination chemistry of rhenium is similar (but not identical) to that of technetium. The types of reactions the potential model radiopharmaceutical would prefer to partake in, and by extension knowing which proteins and biomolecules the compound would react with in vivo, are needed. Crystallography studies, both small molecule and macromolecular, are a key aspect in understanding chemical coordination. Analyses of bonding modes, coordination to particular residues and crystallization conditions are presented. In our Forward look as a concluding summary of this topical review, the question we ask is: what is the best way for this field to progress?
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Affiliation(s)
- Alice Brink
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
| | - Francois J. F. Jacobs
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
| | - John R. Helliwell
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
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32
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Wang Y, Dan K, Xue X, Chen B, Chen C. Curcumin assists anti-EV71 activity of IFN-α by inhibiting IFNAR1 reduction in SH-SY5Y cells. Gut Pathog 2022; 14:8. [PMID: 35151347 PMCID: PMC8840321 DOI: 10.1186/s13099-022-00481-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/01/2022] [Indexed: 12/30/2022] Open
Abstract
Background and aim Enterovirus 71(EV71) can cause severe hand, foot, and mouth disease (HFMD) with brain tissue involvement. Few effective anti-EV71 drugs are presently available in clinical practice. Interferon-α (IFN-α) was ineffective while Curcumin was effective in restricting EV71 replication in non-neuronal cells. Ubiquitin–proteasome-mediated degradation of interferon-alpha receptor 1 (IFNAR1) protein contributes to IFN-α resistance. Current study aimed to determine synergistic inhibition of EV71 by Curcumin and IFN-α in human neuroblastoma SH-SY5Y cells. Methods SH-SY5Y cells were infected with mock-/Curcumin-pre-incubated EV71 or transfected with plasmid containing interferon-stimulated response element (ISRE) or mRNA containing viral internal ribosomal entry site (IRES) following by post-treatment with Curcumin with or without IFN-α. Supernatant IFN-α/β was detected by ELISA. ISRE, IRSE, proteasome and deubiquitinating activity were measured by luciferase assay. EV71 RNA and viral protein or IFNAR1 were determined by qPCR and western blot, respectively. Results EV71 flailed to completely block IFN-α/β production but inhibited IFN-α signal. Curcumin only slightly inhibited EV71 proliferation without modulating virus attachment and internalization. However, Curcumin addition restored IFN-α-mediated ISRE activity thus significantly inhibiting EV71 replication. Furthermore, EV71 also reduced IFNAR1 protein with proteasome-dependence in SH-SY5Y cells, which can be reversed by Curcumin addition with the evidence that it lowered proteasome activity. Conclusion These data demonstrate that Curcumin assists anti-EV71 activity of IFN-α by inhibiting IFNAR1 reduction via ubiquitin–proteasome disruption in SH-SY5Y cells.
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33
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Dong Y, Zhang S, Zhao L. Unraveling the Structural Development of
Peptide‐Coordinated Iron‐Sulfur
Clusters: Prebiotic Evolution and Biosynthetic Strategies. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yijun Dong
- School of Life Sciences, Tsinghua University Beijing 100084 China
| | - Siqi Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
| | - Liang Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
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34
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RNA-Binding Proteins as Regulators of Internal Initiation of Viral mRNA Translation. Viruses 2022; 14:v14020188. [PMID: 35215780 PMCID: PMC8879377 DOI: 10.3390/v14020188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Viruses are obligate intracellular parasites that depend on the host’s protein synthesis machinery for translating their mRNAs. The viral mRNA (vRNA) competes with the host mRNA to recruit the translational machinery, including ribosomes, tRNAs, and the limited eukaryotic translation initiation factor (eIFs) pool. Many viruses utilize non-canonical strategies such as targeting host eIFs and RNA elements known as internal ribosome entry sites (IRESs) to reprogram cellular gene expression, ensuring preferential translation of vRNAs. In this review, we discuss vRNA IRES-mediated translation initiation, highlighting the role of RNA-binding proteins (RBPs), other than the canonical translation initiation factors, in regulating their activity.
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35
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Arnaud M, Chiffelle J, Genolet R, Navarro Rodrigo B, Perez MAS, Huber F, Magnin M, Nguyen-Ngoc T, Guillaume P, Baumgaertner P, Chong C, Stevenson BJ, Gfeller D, Irving M, Speiser DE, Schmidt J, Zoete V, Kandalaft LE, Bassani-Sternberg M, Bobisse S, Coukos G, Harari A. Sensitive identification of neoantigens and cognate TCRs in human solid tumors. Nat Biotechnol 2022; 40:656-660. [PMID: 34782741 PMCID: PMC9110298 DOI: 10.1038/s41587-021-01072-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022]
Abstract
The identification of patient-specific tumor antigens is complicated by the low frequency of T cells specific for each tumor antigen. Here we describe NeoScreen, a method that enables the sensitive identification of rare tumor (neo)antigens and of cognate T cell receptors (TCRs) expressed by tumor-infiltrating lymphocytes. T cells transduced with tumor antigen-specific TCRs identified by NeoScreen mediate regression of established tumors in patient-derived xenograft mice.
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Affiliation(s)
- Marion Arnaud
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Johanna Chiffelle
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Raphael Genolet
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Blanca Navarro Rodrigo
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Marta A. S. Perez
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Florian Huber
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Morgane Magnin
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Tu Nguyen-Ngoc
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Philippe Guillaume
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Petra Baumgaertner
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Chloe Chong
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Brian J. Stevenson
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Gfeller
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Melita Irving
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Daniel E. Speiser
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Julien Schmidt
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Vincent Zoete
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lana E. Kandalaft
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sara Bobisse
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland. .,Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland. .,Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland.
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland. .,Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland. .,Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland.
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Sabatino V, Orefice I, Marotta P, Ambrosino L, Chiusano ML, d'Ippolito G, Romano G, Fontana A, Ferrante MI. Silencing of a Pseudo-nitzschia arenysensis lipoxygenase transcript leads to reduced oxylipin production and impaired growth. THE NEW PHYTOLOGIST 2022; 233:809-822. [PMID: 34533849 DOI: 10.1111/nph.17739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Because of their importance as chemical mediators, the presence of a rich and varied family of lipoxygenase (LOX) products, collectively named oxylipins, has been investigated thoroughly in diatoms, and the involvement of these products in important processes such as bloom regulation has been postulated. Nevertheless, little information is available on the enzymes and pathways operating in these protists. Exploiting transcriptome data, we identified and characterized a LOX gene, PaLOX, in Pseudo-nitzschia arenysensis, a marine diatom known to produce different species of oxylipins by stereo- and regio-selective oxidation of eicosapentaenoic acid (EPA) at C12 and C15. PaLOX RNA interference correlated with a decrease of the lipid-peroxidizing activity and oxylipin synthesis, as well as with a reduction of growth of P. arenysensis. In addition, sequence analysis and structure models of the C-terminal part of the predicted protein closely fitted with the data for established LOXs from other organisms. The presence in the genome of a single LOX gene, whose downregulation impairs both 12- and 15-oxylipins synthesis, together with the in silico 3D protein modelling suggest that PaLOX encodes for a 12/15S-LOX with a dual specificity, and provides additional support to the correlation between cell growth and oxylipin biosynthesis in diatoms.
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Affiliation(s)
- Valeria Sabatino
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Ida Orefice
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Pina Marotta
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Luca Ambrosino
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Maria Luisa Chiusano
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
- Department of Agriculture, Università degli Studi di Napoli Federico II, Portici, 80055, Italy
| | - Giuliana d'Ippolito
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli - Naples, I-80078, Italy
| | - Giovanna Romano
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Angelo Fontana
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Pozzuoli - Naples, I-80078, Italy
- Laboratory of Bio-Organic Chemistry and Chemical Biology, Dipartimento di Biologia, Università di Napoli "Federico II", Via Cupa Nuova Cinthia 21, Napoli, 80126, Italy
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37
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Zardecki C, Dutta S, Goodsell DS, Lowe R, Voigt M, Burley SK. PDB-101: Educational resources supporting molecular explorations through biology and medicine. Protein Sci 2022; 31:129-140. [PMID: 34601771 PMCID: PMC8740840 DOI: 10.1002/pro.4200] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 01/03/2023]
Abstract
The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic-level three-dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB-101 was launched to support teachers, students, and the general public in PDB archive exploration (pdb101.rcsb.org). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB-101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB-101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year-on-year. In addition, PDB-101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB-101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.
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Affiliation(s)
- Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Shuchismita Dutta
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Rutgers Cancer Institute of New JerseyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - David S. Goodsell
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Rutgers Cancer Institute of New JerseyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA,Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Institute for Quantitative BiomedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA,Rutgers Cancer Institute of New JerseyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA,Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of California San DiegoLa JollaCaliforniaUSA,Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
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38
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Contessoto VG, de Oliveira VM, Leite VBP. Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments. Methods Mol Biol 2022; 2376:303-315. [PMID: 34845616 DOI: 10.1007/978-1-0716-1716-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Computational coarse-grained models play a fundamental role as a research tool in protein folding, and they are important in bridging theory and experiments. Folding mechanisms are generally discussed using the energy landscape framework, which is well mapped within a class of simplified structure-based models. In this chapter, simplified computer models are discussed with special focus on structure-based ones.
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Affiliation(s)
| | - Vinícius M de Oliveira
- Brazilian Biosciences National Laboratory, LNBio/CNPEM, Campinas, SP, Brazil
- São Paulo State University, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
| | - Vitor B P Leite
- São Paulo State University, IBILCE/UNESP, São José do Rio Preto, SP, Brazil.
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39
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Lu H, Li F, Yuan L, Domenzain I, Yu R, Wang H, Li G, Chen Y, Ji B, Kerkhoven EJ, Nielsen J. Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. Mol Syst Biol 2021; 17:e10427. [PMID: 34676984 PMCID: PMC8532513 DOI: 10.15252/msb.202110427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations.
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Affiliation(s)
- Hongzhong Lu
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Feiran Li
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Le Yuan
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Iván Domenzain
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Rosemary Yu
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Hao Wang
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- National Bioinformatics Infrastructure SwedenScience for Life LaboratoryChalmers University of TechnologyGothenburgSweden
| | - Gang Li
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Yu Chen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Boyang Ji
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Eduard J Kerkhoven
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
- BioInnovation InstituteCopenhagen NDenmark
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40
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Peng Y, Li S, Onufriev A, Landsman D, Panchenko AR. Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails. Nat Commun 2021; 12:5280. [PMID: 34489435 PMCID: PMC8421395 DOI: 10.1038/s41467-021-25568-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 08/17/2021] [Indexed: 12/19/2022] Open
Abstract
Little is known about the roles of histone tails in modulating nucleosomal DNA accessibility and its recognition by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full nucleosome, totaling 65 microseconds of molecular dynamics simulations. We observe rapid conformational transitions between tail bound and unbound states, and characterize kinetic and thermodynamic properties of histone tail-DNA interactions. Different histone types exhibit distinct binding modes to specific DNA regions. Using a comprehensive set of experimental nucleosome complexes, we find that the majority of them target mutually exclusive regions with histone tails on nucleosomal/linker DNA around the super-helical locations ± 1, ± 2, and ± 7, and histone tails H3 and H4 contribute most to this process. These findings are explained within competitive binding and tail displacement models. Finally, we demonstrate the crosstalk between different histone tail post-translational modifications and mutations; those which change charge, suppress tail-DNA interactions and enhance histone tail dynamics and DNA accessibility. The intrinsic disorder of histone tails poses challenges in their characterization. Here the authors apply extensive molecular dynamics simulations of the full nucleosome to show reversible binding to DNA with specific binding modes of different types of histone tails, where charge-altering modifications suppress tail-DNA interactions and may boost interactions between nucleosomes and nucleosome-binding proteins.
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Affiliation(s)
- Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Alexey Onufriev
- Physics Department, Virginia Tech, VA, USA.,Computer Science Department, Virginia Tech, VA, USA.,Center for Soft Matter and Biological Physics, Virginia Tech, VA, USA
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada.
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41
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Lizbeth RSG, Jazmín GM, José CB, Marlet MA. Immunoinformatics study to search epitopes of spike glycoprotein from SARS-CoV-2 as potential vaccine. J Biomol Struct Dyn 2021; 39:4878-4892. [PMID: 32583729 PMCID: PMC7332869 DOI: 10.1080/07391102.2020.1780944] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/07/2020] [Indexed: 11/01/2022]
Abstract
The Coronavirus disease named COVID-19 is caused by the virus reported in 2019 first identified in China. The cases of this disease have increased and as of June 1st, 2020 there are more than 216 countries affected. Pharmacological treatments have been proposed based on the resemblance of the HIV virus. With regard to prevention there is no vaccine, thus, we proposed to explore the spike protein due to its presence on the viral surface, and it also contains the putative viral entry receptor as well as the fusion peptide (important in the genome release). In this work we have employed In Silico techniques such as immunoinformatics tools which permit the identification of potential immunogenic regions on the viral surface (spike glycoprotein). From these analyses, we identified four epitopes E332-370, E627-651, E440-464 and E694-715 that accomplish essential features such as promiscuity, conservation grade, exposure and universality, and they also form stable complexes with MHCII molecule. We suggest that these epitopes could generate a specific immune response, and thus, they could be used for future applications such as the design of new epitope vaccines against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ramírez-Salinas Gema Lizbeth
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - García-Machorro Jazmín
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - Correa-Basurto José
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - Martínez-Archundia Marlet
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
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42
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Ma F, Zhang S, Song L, Wang B, Wei L, Zhang F. Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. Cell Biosci 2021; 11:121. [PMID: 34217372 PMCID: PMC8254218 DOI: 10.1186/s13578-021-00635-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/22/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cellular communication is an essential feature of multicellular organisms. Binding of ligands to their homologous receptors, which activate specific cell signaling pathways, is a basic type of cellular communication and intimately linked to many degeneration processes leading to diseases. MAIN BODY This study reviewed the history of ligand-receptor and presents the databases which store ligand-receptor pairs. The recently applications and research tools of ligand-receptor interactions for cell communication at single cell level by using single cell RNA sequencing have been sorted out. CONCLUSION The summary of the advantages and disadvantages of analysis tools will greatly help researchers analyze cell communication at the single cell level. Learning cell communication based on ligand-receptor interactions by single cell RNA sequencing gives way to developing new target drugs and personalizing treatment.
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Affiliation(s)
- Fen Ma
- Department of Microbiology, Harbin Medical University, Harbin, 150081 China
- Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081 China
| | - Siwei Zhang
- Department of Microbiology, Harbin Medical University, Harbin, 150081 China
- Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081 China
| | - Lianhao Song
- Department of Microbiology, Harbin Medical University, Harbin, 150081 China
- Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081 China
| | - Bozhi Wang
- Department of Microbiology, Harbin Medical University, Harbin, 150081 China
- Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081 China
| | - Lanlan Wei
- Department of Microbiology, Harbin Medical University, Harbin, 150081 China
- Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081 China
- Shenzhen Third People‘s Hospital, Second Hospital, Affiliated to Southern University of Science and Technology, Shenzhen, 518112 China
| | - Fengmin Zhang
- Department of Microbiology, Harbin Medical University, Harbin, 150081 China
- Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081 China
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43
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Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations. Biochemistry 2021; 60:1459-1484. [PMID: 33900725 PMCID: PMC8098775 DOI: 10.1021/acs.biochem.1c00139] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/12/2021] [Indexed: 12/11/2022]
Abstract
In this study, we used an integrative computational approach to examine molecular mechanisms and determine functional signatures underlying the role of functional residues in the SARS-CoV-2 spike protein that are targeted by novel mutational variants and antibody-escaping mutations. Atomistic simulations and functional dynamics analysis are combined with alanine scanning and mutational sensitivity profiling of the SARS-CoV-2 spike protein complexes with the ACE2 host receptor and the REGN-COV2 antibody cocktail(REG10987+REG10933). Using alanine scanning and mutational sensitivity analysis, we have shown that K417, E484, and N501 residues correspond to key interacting centers with a significant degree of structural and energetic plasticity that allow mutants in these positions to afford the improved binding affinity with ACE2. Through perturbation-based network modeling and community analysis of the SARS-CoV-2 spike protein complexes with ACE2, we demonstrate that E406, N439, K417, and N501 residues serve as effector centers of allosteric interactions and anchor major intermolecular communities that mediate long-range communication in the complexes. The results provide support to a model according to which mutational variants and antibody-escaping mutations constrained by the requirements for host receptor binding and preservation of stability may preferentially select structurally plastic and energetically adaptable allosteric centers to differentially modulate collective motions and allosteric interactions in the complexes with the ACE2 enzyme and REGN-COV2 antibody combination. This study suggests that the SARS-CoV-2 spike protein may function as a versatile and functionally adaptable allosteric machine that exploits the plasticity of allosteric regulatory centers to fine-tune response to antibody binding without compromising the activity of the spike protein.
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Affiliation(s)
- Gennady M. Verkhivker
- Keck Center for Science and Engineering, Schmid
College of Science and Technology, Chapman University, One
University Drive, Orange, California 92866, United States
- Depatment of Biomedical and Pharmaceutical Sciences,
Chapman University School of Pharmacy, Irvine, California
92618, United States
| | - Steve Agajanian
- Keck Center for Science and Engineering, Schmid
College of Science and Technology, Chapman University, One
University Drive, Orange, California 92866, United States
| | - Deniz Yazar Oztas
- Keck Center for Science and Engineering, Schmid
College of Science and Technology, Chapman University, One
University Drive, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid
College of Science and Technology, Chapman University, One
University Drive, Orange, California 92866, United States
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Axon-enriched lincRNA ALAE is required for axon elongation via regulation of local mRNA translation. Cell Rep 2021; 35:109053. [PMID: 33951423 DOI: 10.1016/j.celrep.2021.109053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/05/2020] [Accepted: 04/07/2021] [Indexed: 11/23/2022] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) are critical regulators involved in diverse biological processes. However, the roles and related mechanisms of lincRNAs in axon development are largely unknown. Here we report an axon-enriched lincRNA regulating axon elongation, referred to as ALAE. Profiling of highly expressed lincRNAs detected abundant and enriched ALAE in the axons of dorsal root ganglion (DRG) neurons, where it locally promoted axon elongation. Mechanically, ALAE directly interacted with the KH3-4 domains of KH-type splicing regulatory protein (KHSRP) and impeded its association with growth-associated protein 43 (Gap43) mRNA. Knockdown of ALAE reduced the protein but not the mRNA level of GAP43 in the axons of DRG neurons. Furthermore, local disruption of the interaction between ALAE and KHSRP in the axon significantly inhibited Gap43 mRNA translation, impairing axon elongation. This study implies crucial roles of axon-enriched lincRNAs in spatiotemporal regulation of local translation during axon development.
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Velázquez-Cruz A, Baños-Jaime B, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-translational Control of RNA-Binding Proteins and Disease-Related Dysregulation. Front Mol Biosci 2021; 8:658852. [PMID: 33987205 PMCID: PMC8111222 DOI: 10.3389/fmolb.2021.658852] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Cell signaling mechanisms modulate gene expression in response to internal and external stimuli. Cellular adaptation requires a precise and coordinated regulation of the transcription and translation processes. The post-transcriptional control of mRNA metabolism is mediated by the so-called RNA-binding proteins (RBPs), which assemble with specific transcripts forming messenger ribonucleoprotein particles of highly dynamic composition. RBPs constitute a class of trans-acting regulatory proteins with affinity for certain consensus elements present in mRNA molecules. However, these regulators are subjected to post-translational modifications (PTMs) that constantly adjust their activity to maintain cell homeostasis. PTMs can dramatically change the subcellular localization, the binding affinity for RNA and protein partners, and the turnover rate of RBPs. Moreover, the ability of many RBPs to undergo phase transition and/or their recruitment to previously formed membrane-less organelles, such as stress granules, is also regulated by specific PTMs. Interestingly, the dysregulation of PTMs in RBPs has been associated with the pathophysiology of many different diseases. Abnormal PTM patterns can lead to the distortion of the physiological role of RBPs due to mislocalization, loss or gain of function, and/or accelerated or disrupted degradation. This Mini Review offers a broad overview of the post-translational regulation of selected RBPs and the involvement of their dysregulation in neurodegenerative disorders, cancer and other pathologies.
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Affiliation(s)
- Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Blanca Baños-Jaime
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
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46
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Bian G, Yang J, Elango J, Wu W, Bao B, Bao C. Natural Triterpenoids Isolated from Akebia trifoliata Stem Explants Exert a Hypoglycemic Effect via α-Glucosidase Inhibition and Glucose Uptake Stimulation in Insulin-Resistant HepG2 Cells. Chem Biodivers 2021; 18:e2001030. [PMID: 33779055 DOI: 10.1002/cbdv.202001030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/25/2021] [Indexed: 12/26/2022]
Abstract
The inhibition of α-glucosidase activity is a prospective approach to attenuate postprandial hyperglycemia in the treatment of type 2 diabetes mellitus (T2DM). Herein, the inhibition of α-glucosidase by three compounds T1 -T3 of Akebia trifoliata stem, namely hederagenin (T1 ), 3-epiakebonoic acid (T2 ), and arjunolic acid (T3 ) were investigated using enzyme kinetics and molecular docking analysis. The three triterpenoids exhibited excellent inhibitory activities against α-glucosidase. T1 -T3 showed the strongest inhibition with IC50 values of 42.1±5.4, 19.6±3.2, and 11.2±2.3 μM, respectively, compared to the acarbose positive control (IC50 =106.3±8.2). Enzyme inhibition kinetics showed that triterpenoids T1 -T3 demonstrated competitive, mixed, and noncompetitive-type inhibition against α-glucosidase, respectively. The inhibition constant (Ki ) values were 21.21, 7.70, and 3.18 μM, respectively. Docking analysis determined that the interaction of ligands T1 -T3 and α-glucosidase was mainly forced by hydrogen bonds and hydrophobic interactions, which could result in improved binding to the active site of the target enzyme. The insulin resistant (IR)-HepG2 cell model used in this study (HepG2 cells exposed to 10-7 M insulin for 24 h) and glucose uptake assays showed that compounds T1 -T3 had no cytotoxicity with concentrations ranging from 6.25 to 25 μM and displayed significant stimulation of glucose uptake in IR-HepG2 cells. Thus, triterpenoids T1 -T3 showed dual therapeutic effects of α-glucosidase inhibition and glucose uptake stimulation and could be used as potential medicinal resources to investigate new antidiabetic agents for the prevention or treatment of diabetes.
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Affiliation(s)
- Guoyong Bian
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Jinbo Yang
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Jeevithan Elango
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Wenhui Wu
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, P. R. China.,National R&D Branch Center for Freshwater Aquatic Products Processing Technology, Shanghai, 201306, P. R. China
| | - Bin Bao
- National R&D Branch Center for Freshwater Aquatic Products Processing Technology, Shanghai, 201306, P. R. China
| | - Chunling Bao
- Shanghai Sixth People's Hospital East Campus, Shanghai, 201306, P. R. China
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47
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Sepay N, Saha PC, Shahzadi Z, Chakraborty A, Halder UC. A crystallography-based investigation of weak interactions for drug design against COVID-19. Phys Chem Chem Phys 2021; 23:7261-7270. [PMID: 33876086 DOI: 10.1039/d0cp05714b] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Interactions between proteins and small molecules play important roles in the inhibition of protein function. However, a lack of proper knowledge about non-covalent interactions can act as a barrier towards gaining a complete understanding of the factors that control these associations. To find effective molecules for COVID-19 inhibition, we have quantitatively investigated 143 X-ray crystal structures of the SARS-CoV-2 Mpro protein of coronavirus with covalently or non-covalently bound small molecules (SMs). Our present study is able to explain ordinary and perceptive aspects relating to protein inhibition. The active site of the protein consists of 21 amino acid residues, but only nine are actively involved in the ligand binding process. The H41, M49, and C145 residues have highest priority with respect to interactions with small molecules through hydrogen bond, CH-π, and van der Waals interactions. At the active site, this ranking of amino acids is clear, based on different spatial orientations of ligands, and consistent with the electronic properties. SMs with aromatic moieties that bind to the active site of the protein play a distinct role in the determination of the following order of interaction frequency with the amino acids: CH-π > H-bonding > polar interactions. This present study revealed that the G143 and C145 residues play crucial roles in the recognition of the carbonyl functionality of SMs through hydrogen bonding. With this knowledge in mind, an effective inhibitor small-molecule for SARS-CoV-2 Mpro was designed: docking studies showed that the designed molecule has strong binding affinity towards the protein. The non-covalent interactions in the protein-ligand complex are in good agreement with the results obtained from X-ray crystallography. Moreover, the present study focused on weak forces and their influence on protein inhibition, henceforth shedding much light on the essential requirements for moieties that should be present in a good inhibitor and their orientations at the ligand binding site.
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Affiliation(s)
- Nayim Sepay
- Department of Chemistry, Lady Brabourne College, Kolkata - 700017, India.
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48
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Almeida VM, Dias ÊR, Souza BC, Cruz JN, Santos CBR, Leite FHA, Queiroz RF, Branco A. Methoxylated flavonols from Vellozia dasypus Seub ethyl acetate active myeloperoxidase extract: in vitro and in silico assays. J Biomol Struct Dyn 2021; 40:7574-7583. [PMID: 33739225 DOI: 10.1080/07391102.2021.1900916] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study aimed to evaluate the effect of a methoxylated fraction from Vellozia dasypus Seub on myeloperoxidase (MPO)-chlorinating activity and subsequent in silico assays for binding profile prediction. Therefore, the ethyl acetate extract of aerial parts from Vellozia dasypus Seub was fractionated on open-column chromatography containing SiO2 and eluted with solvent in crescent polarity to yield a fraction with a mixture of flavonols quercetin 3-O-methyl ether (1) and 6-C-methyl quercetin 3-O-methyl ether (2). Their chemical structures were proposed by HPLC coupled to photodiode array (HPLC-DAD) and mass spectrometer using electrospray ionization multistage analysis (HPLC-MS/MS). The fraction enriched with compounds 1 and 2 inhibited more efficiently the in vitro MPO-chlorinating activity (IC50 = 40 µg/mL) than the ethyl acetate extract (IC50 = 64.0 µg/mL). Molecular docking studies revealed that these compounds interact with MPO active pocket similarly to trifluoromethyl-substituted aromatic hydroxamate, a well-known MPO inhibitor, co-crystallized at the MPO binding site (PDB ID: 4C1M). Molecular dynamics trajectories confirmed that these two molecules interact with the MPO binding site with a similar energetic pattern when compared to the crystallographic ligand. Taken together, these data expand the sources of phenolic natural compounds that may be further investigated against inflammation-related diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Verônica M Almeida
- Department of Health, State University of Feira de Santana, Feira de Santana, Brazil.,Graduate Program in Biotechnology, State University of Feira de Santana, Feira de Santana, Brazil
| | - Êuder R Dias
- Department of Health, State University of Feira de Santana, Feira de Santana, Brazil.,Graduate Program in Biotechnology, State University of Feira de Santana, Feira de Santana, Brazil
| | - Bruno C Souza
- Graduate Program in Biotechnology, State University of Feira de Santana, Feira de Santana, Brazil
| | - Jorddy N Cruz
- Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
| | - Cleydson B R Santos
- Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
| | - Franco H A Leite
- Department of Health, State University of Feira de Santana, Feira de Santana, Brazil.,Graduate Program in Biotechnology, State University of Feira de Santana, Feira de Santana, Brazil
| | - Raphael F Queiroz
- Department of Natural Sciences, State University of Southwestern Bahia, Vitória da Conquista, Brazil
| | - Alexsandro Branco
- Department of Health, State University of Feira de Santana, Feira de Santana, Brazil.,Graduate Program in Biotechnology, State University of Feira de Santana, Feira de Santana, Brazil
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49
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Rangel-Garcia CI, Salvador C, Chavez-Garcia K, Diaz-Bello B, Lopez-Gonzalez Z, Vazquez-Cruz L, Angel Vazquez-Martinez J, Ortiz-Navarrete V, Riveros-Rosas H, Escobar LI. Identification of a unique endoplasmic retention motif in the Xenopus GIRK5 channel and its contribution to oocyte maturation. FEBS Open Bio 2021; 11:1093-1108. [PMID: 33565726 PMCID: PMC8016131 DOI: 10.1002/2211-5463.13113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/17/2020] [Accepted: 02/08/2021] [Indexed: 11/17/2022] Open
Abstract
G protein‐activated inward‐rectifying potassium (K+) channels (Kir3/GIRK) participate in cell excitability. The GIRK5 channel is present in Xenopus laevis oocytes. In an attempt to investigate the physiological role of GIRK5, we identified a noncanonical di‐arginine endoplasmic reticulum (ER) retention motif (KRXY). This retention motif is located at the N‐terminal region of GIRK5, coded by two small exons found only in X. laevis and X. tropicalis. These novel exons are expressed through use of an alternative transcription start site. Mutations in the sequence KRXY produced functional channels and induced progesterone‐independent oocyte meiotic progression. The chimeric proteins enhanced green fluorescent protein (EGFP)‐GIRK5‐WT and the EGFP‐GIRK5K13AR14A double mutant, were localized to the ER and the plasma membrane of the vegetal pole of the oocyte, respectively. Silencing of GIRK5 or blocking of this channel by external barium prevented progesterone‐induced meiotic progression. The endogenous level of GIRK5 protein decreased through oocyte stages in prophase I augmenting by progesterone. In conclusion, we have identified a unique mechanism by which the expression pattern of a K+ channel evolved to control Xenopus oocyte maturation.
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Affiliation(s)
- Claudia I Rangel-Garcia
- Departamento de Fisiologia, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Carolina Salvador
- Departamento de Fisiologia, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Karla Chavez-Garcia
- Departamento de Fisiologia, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Beatriz Diaz-Bello
- Departamento de Fisiologia, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Zinaeli Lopez-Gonzalez
- Departamento de Fisiologia, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Lourdes Vazquez-Cruz
- Departamento de Fisiologia, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Julio Angel Vazquez-Martinez
- Departamento de Biomedicina Molecular, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Mexico City, Mexico
| | - Vianney Ortiz-Navarrete
- Departamento de Biomedicina Molecular, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Mexico City, Mexico
| | - Hector Riveros-Rosas
- Departamento de Bioquimica, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Laura I Escobar
- Departamento de Fisiologia, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
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50
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Grau FC, Burkovski A, Muller YA. Crystal structures of adenylylated and unadenylylated P II protein GlnK from Corynebacterium glutamicum. Acta Crystallogr D Struct Biol 2021; 77:325-335. [PMID: 33645536 PMCID: PMC7919409 DOI: 10.1107/s2059798321000735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/21/2021] [Indexed: 11/10/2022] Open
Abstract
PII proteins are ubiquitous signaling proteins that are involved in the regulation of the nitrogen/carbon balance in bacteria, archaea, and some plants and algae. Signal transduction via PII proteins is modulated by effector molecules and post-translational modifications in the PII T-loop. Whereas the binding of ADP, ATP and the concomitant binding of ATP and 2-oxoglutarate (2OG) engender two distinct conformations of the T-loop that either favor or disfavor the interaction with partner proteins, the structural consequences of post-translational modifications such as phosphorylation, uridylylation and adenylylation are far less well understood. In the present study, crystal structures of the PII protein GlnK from Corynebacterium glutamicum have been determined, namely of adenylylated GlnK (adGlnK) and unmodified unadenylylated GlnK (unGlnK). AdGlnK has been proposed to act as an inducer of the transcription repressor AmtR, and the adenylylation of Tyr51 in GlnK has been proposed to be a prerequisite for this function. The structures of unGlnK and adGlnK allow the first atomic insights into the structural implications of the covalent attachment of an AMP moiety to the T-loop. The overall GlnK fold remains unaltered upon adenylylation, and T-loop adenylylation does not appear to interfere with the formation of the two major functionally important T-loop conformations, namely the extended T-loop in the canonical ADP-bound state and the compacted T-loop that is adopted upon the simultaneous binding of Mg-ATP and 2OG. Thus, the PII-typical conformational switching mechanism appears to be preserved in GlnK from C. glutamicum, while at the same time the functional repertoire becomes expanded through the accommodation of a peculiar post-translational modification.
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Affiliation(s)
- Florian C. Grau
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 91, 91052 Erlangen, Germany
| | - Andreas Burkovski
- Division of Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Yves A. Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 91, 91052 Erlangen, Germany
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