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Li P, Tian X, Zhang D, Ou H, Huang Q, Jin W, Liu R. Discovery of Loureirin analogues with colorectal cancer suppressive activity via regulating cell cycle and Fas death receptor. BMC Pharmacol Toxicol 2024; 25:36. [PMID: 38943212 PMCID: PMC11212204 DOI: 10.1186/s40360-024-00758-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/18/2024] [Indexed: 07/01/2024] Open
Abstract
Chalcones and dihydrochalcones (DHCs) are important bioactive natural products (BNPs) isolated from traditional Chinese medicine. In this study, 13 chalcones were designed with the inspiration of Loureirin, a DHC extracted from Resina Draconis, and synthesized by classical Claisen-Schmidt reactions. Afterwards the reduction reactions were carried out to obtain the corresponding DHCs. Cytotoxicity assay indicated chalcones and DHCs possessed selective cytotoxicity against colorectal cancer (CRC) cells. The preliminary structure-activity relationships (SAR) of these compounds suggested the α, β-unsaturated ketone of the chalcones were crucial for the anticancer activity. Interestingly, compounds 3d and 4c exhibited selective anticancer activity against CRC cell line HCT116 with IC50s of 8.4 and 17.9 μM but not normal cell. Moreover, 4c could also inhibit the migration and invasion of CRC cells. Mechanism investigations showed 4c could induce cell cycle G2/M arrest by regulating cell cycle-associated proteins and could also up-regulate Fas cell surface death receptor. The virtual docking further pointed out that compounds 3d and 4c could nicely bind to the Fas/FADD death domain complex (ID: 3EZQ). Furthermore, silencing of Fas significantly enhanced the proliferation of CRC cells and attenuated the cytotoxicity induced by 4c. These results suggested 4c exerted its anticancer activity possibly regulating cell cycle and Fas death receptor. In summary, this study investigated the anticancer activity and mechanism of Loureirin analogues in CRC, suggesting these compounds may warrant further investigation as promising anticancer drug candidates for the treatment of CRC.
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Affiliation(s)
- Peng Li
- School of Food and Drug, Shenzhen Polytechnic University, 7098 Liuxian Avenue, Shenzhen, 518055, China
| | - Xiangjuan Tian
- School of Food and Drug, Shenzhen Polytechnic University, 7098 Liuxian Avenue, Shenzhen, 518055, China
| | - Die Zhang
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, China
| | - Huiping Ou
- School of Food and Drug, Shenzhen Polytechnic University, 7098 Liuxian Avenue, Shenzhen, 518055, China
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, China
| | - Qiufeng Huang
- School of Food and Drug, Shenzhen Polytechnic University, 7098 Liuxian Avenue, Shenzhen, 518055, China
| | - Wenbin Jin
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, China.
| | - Ran Liu
- School of Food and Drug, Shenzhen Polytechnic University, 7098 Liuxian Avenue, Shenzhen, 518055, China.
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Roy U. Computational Investigation of Selected Spike Protein Mutations in SARS-CoV-2: Delta, Omicron, and Some Circulating Subvariants. Pathogens 2023; 13:10. [PMID: 38276156 PMCID: PMC10820870 DOI: 10.3390/pathogens13010010] [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: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Among the multiple SARS-CoV-2 variants recently reported, the Delta variant has generated the most perilous and widespread effects. Another variant, Omicron, has been identified specifically for its high transmissibility. Omicron contains numerous spike (S) protein mutations and numbers much larger than those of its predecessor variants. In this report, the author has discussed some essential structural aspects and time-based structure changes of a selected set of spike protein mutations within the Delta and Omicron variants. The expected impact of multiple point mutations within the spike protein's receptor-binding domain (RBD) and S1 of these variants are examined. Additionally, the RBDs of the more recently emerged subvariants BA.4, BA.5, and BA.2.12.1 are discussed. Within the latter group, BA.5 represents the most prevalent form of SARS-CoV-2 globally until recently. This computational work also briefly explores the temporal mutation profile for the currently circulating variants of interest (VOIs), variants under monitoring (VUMs), and variants being monitored (VBMs) including XBB.1.5, BQ.1, BA.2.75, CH.1.1, XBB, XBF, EG.5 (or Eris), and BA.2.86 (or Pirola). It is expected that these structural data can facilitate the tasks of identifying drug targets and neutralizing antibodies for the evolving variants/subvariants of SARS-CoV-2.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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Fatouros PR, Roy U, Sur S. Implications of SARS-CoV-2 spike protein interactions with Zn-bound form of ACE2: a computational structural study. Biometals 2023:10.1007/s10534-023-00491-z. [PMID: 36725769 PMCID: PMC9891659 DOI: 10.1007/s10534-023-00491-z] [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: 07/13/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023]
Abstract
The COVID-19 pandemic has generated a major interest in designing inhibitors to prevent SARS-CoV-2 binding on host cells to protect against infection. One promising approach to such research utilizes molecular dynamics simulation to identify potential inhibitors that can prevent the interaction between spike (S) protein on the virus and angiotensin converting enzyme 2 (ACE2) receptor on the host cells. In these studies, many groups have chosen to exclude the ACE2-bound zinc (Zn) ion, which is critical for its enzymatic activity. While the relatively distant location of Zn ion from the S protein binding site (S1 domain), combined with the difficulties in modeling this ion has motivated the decision of exclusion, Zn can potentially contribute to the structural stability of the entire protein, and thus, may have implications on S protein-ACE2 interaction. In this study, the authors model both the ACE2-S1 and ACE2-inhibitor (mAb) system to investigate if there are variations in structure and the readouts due to the presence of Zn ion. Although distant from the S1 or inhibitor binding region, inclusion/exclusion of Zn has statistically significant effects on the structural stability and binding free energy in these systems. In particular, the binding free energy of the ACE2-S1 and ACE2-inhibitor structures is - 3.26 and - 14.8 kcal/mol stronger, respectively, in the Zn-bound structure than in the Zn-free structures. This finding suggests that including Zn may be important in screening potentially inhibitors and may be particularly important in modeling monoclonal antibodies, which may be more sensitive to changes in antigen structure.
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Affiliation(s)
- Peter R. Fatouros
- Department of Chemical and Biomolecular Engineering, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
| | - Shantanu Sur
- Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
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Gu H, Chen Z, Ma J, Ma J, Fu L, Zhang R, Wang T, Wu R. Case report: Effectiveness of sirolimus in a de novo FAS mutation leading to autoimmune lymphoproliferative syndrome-FAS and elevated DNT/Treg ratio. Front Pediatr 2022; 10:868193. [PMID: 35967554 PMCID: PMC9366043 DOI: 10.3389/fped.2022.868193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/11/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The autoimmune lymphoproliferative syndrome (ALPS) is a rare disease characterized by defective function of the FAS death receptor, which results in chronic, non-malignant lymphoproliferation and autoimmunity accompanied by elevated numbers of double-negative (DN) T cells (T-cell receptor α/β + CD4-CD8-) and an increased risk of developing malignancies later in life. CASE DESCRIPTION Here, we report a patient with a de novo FAS mutation with a severe phenotype of ALPS-FAS. The FAS gene identified as a novel spontaneous germline heterozygous missense mutation (c.857G > A, p.G286E) in exon 9, causing an amino acid exchange and difference in hydrogen bond formation. Consequently, the treatment with sirolimus was initiated. Subsequently, the patient's clinical condition improved rapidly. Moreover, DNT ratio continuously decreased during sirolimus application. CONCLUSION We described a novel germline FAS mutation (c.857G > A, p.G286E) associated with a severe clinical phenotype of ALPS-FAS. Sirolimus effectively improved the patient clinical manifestations with obvious reduction of the DNT ratio.
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Affiliation(s)
- Hao Gu
- Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Zhenping Chen
- Hematology Center, Hematologic Disease Laboratory, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
| | - Jie Ma
- Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jingyao Ma
- Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lingling Fu
- Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Rui Zhang
- Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Tianyou Wang
- Hematology Center, Hematologic Disease Laboratory, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
| | - Runhui Wu
- Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Key Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
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Roy U. Comparative structural analyses of selected spike protein-RBD mutations in SARS-CoV-2 lineages. Immunol Res 2021; 70:143-151. [PMID: 34782989 PMCID: PMC8592829 DOI: 10.1007/s12026-021-09250-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/01/2021] [Indexed: 10/31/2022]
Abstract
The severity of COVID-19 has been observed throughout the world as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) globally claimed more than 2 million lives and left a devastating impact worldwide. Recently several virulent mutant strains of this virus, such as the B.1.1.7, B.1.351, and P1 lineages, have emerged with initial predominance in UK, South Africa, and Brazil. Another extremely pathogenic B.1.617 lineage and its sub-lineages, first detected in India, are now affecting some countries at notably stronger spread-rates. The present paper computationally examines the time-based structures of B.1.1.7, B.1.351, and P1 lineages with selected spike protein mutations. The mutations in the more recently found B.1.617 lineage and its sub-lineages are explored, and the implications for multiple point mutations of the spike protein's receptor-binding domain (RBD) are described. The selected S1 mutations within the highly contagious B.1.617.2 sub-lineage, also known as the delta variant, are examined as well.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5820, USA.
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Roy U. Structural and molecular analyses of functional epitopes and escape mutants in Japanese encephalitis virus envelope protein domain III. Immunol Res 2021; 68:81-89. [PMID: 32445181 PMCID: PMC7243247 DOI: 10.1007/s12026-020-09130-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Japanese encephalitis virus (JEV) is one of the vector borne causes of encephalitis found in southeastern Asia. This positive single-stranded RNA virus is a member of the Flaviviridae family, which notably includes dengue, tick-borne, West Nile, Zika as well as yellow fever, and transmits to humans by infected mosquitos. The main site of interactions for antibodies against this virus is the envelope protein domain III (ED3). The present report investigates the time-dependent structural and conformational changes of JEV ED3 functional epitopes and escape mutants by computer simulations. The results indicate the presence of significant structural differences between the functional epitopes and the escape mutants. Mutation-induced structural/conformational instabilities of this type can decrease the antibody neutralization activity. Among the different escape mutants studied here, Ser40Lys/Asp41Arg appear to be most unstable, while Ser40Glu/Asp41Leu exhibit the lowest structural variations. The highest level of escape mutation observed in Ser40Lys is linked to the relatively higher values of root mean square deviation/fluctuation found in the molecular dynamics simulation of this protein. Secondary-structure deviations and depletion of H bonding are other contributing factors to the protein’s increased instability. Overall, the proteins with residue 41 mutations are found to be structurally more ordered than those with residue 40 mutations. The detailed time-based structural assessment of the mutant epitopes described here may contribute to the development of novel vaccines and antiviral drugs necessary to defend against future outbreaks of JEV escape mutants.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5820, USA.
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Roy U. Insight into the structures of Interleukin-18 systems. Comput Biol Chem 2020; 88:107353. [PMID: 32769049 PMCID: PMC7392904 DOI: 10.1016/j.compbiolchem.2020.107353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/01/2020] [Accepted: 07/28/2020] [Indexed: 02/08/2023]
Abstract
Structure-based molecular designs play a critical role in the context of next generation drug development. Besides their fundamental scientific aspects, the findings established in this approach have significant implications in the expansions of target-based therapies and vaccines. Interleukin-18 (IL-18), also known as interferon gamma (IFN-γ) inducing factor, is a pro-inflammatory cytokine. The IL-18 binds first to the IL-18α receptor and forms a lower affinity complex. Upon binding with IL-18β a hetero-trimeric complex with higher affinity is formed that initiates the signal transduction process. The present study, including structural and molecular dynamics simulations, takes a close look at the structural stabilities of IL-18 and IL-18 receptor-bound ligand structures as functions of time. The results help to identify the conformational changes of the ligand due to receptor binding, as well as the structural orders of the apo and holo IL-18 protein complexes.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5820, United States.
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Roy U. Structure and Function of an Inflammatory Cytokine, Interleukin-2, Analyzed Using the Bioinformatic Approach. Protein J 2019; 38:525-536. [PMID: 31006082 DOI: 10.1007/s10930-019-09833-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The inflammatory cytokine, interleukin-2 (IL-2), is an important regulator of cellular functions. This relatively less studied member of the interleukin protein family is responsible for multiple immuno-modulatory and immuno-stimulatory tasks, like T cell activation, triggering of natural killer cells, inflammation, as well as proliferation and progression of autoimmune diseases and cancers. In this communication we report the temporally variant structural aspects of the IL-2 ligand and its receptor interfaces, based on the available crystal structures. The intended goal of this effort is to generate simulated results that could potentially aid the designs of novel structure based therapeutics.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5820, USA.
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Roy U. 3D Modeling of Tumor Necrosis Factor Receptor and Tumor Necrosis Factor-bound Receptor Systems. Mol Inform 2019; 38:e1800011. [PMID: 30632313 DOI: 10.1002/minf.201800011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 12/04/2018] [Indexed: 01/25/2023]
Abstract
The interactions between the tumor necrosis factor (TNF) and its receptor molecule are responsible for various signaling networks that are central to the functioning of human immune homeostasis. The present work is a computational study of certain structural aspects of this cell-signaling protein, specifically focusing on the molecular level analyses of the TNF receptor (TNF-R), guided by its crystallographic structure. We also examine the possible binding sites of the TNF onto TNF-R, and the associated interactions. The structural and conformational variations in the TNF-R and TNF bound TNF-R systems are examined in this context using molecular dynamics (MD) simulations. The time dependent variations of the dimeric TNF-R structures are compared with, and shown to be steadier than their isolated monomers. This dimeric stability is favored under acidic conditions. The results are used to further illustrate how 3D modeling and computer simulations can aid the structure-based approach to probing a ligand-receptor system.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5820, United States
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Roy U. Structural modeling of tumor necrosis factor: A protein of immunological importance. Biotechnol Appl Biochem 2017; 64:454-463. [PMID: 27354121 DOI: 10.1002/bab.1523] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/22/2016] [Indexed: 12/17/2022]
Abstract
Tumor necrosis factor (TNF) is a multifunctional pro-inflammatory cytokine responsible for various immunoregulatory activities. Upon binding with its receptor, TNF triggers multiple complex signaling pathways such as the activations of nuclear factor kappa B and caspase cascade, which are the leading determining factors for cell survival or cell death. The present work studies certain modeling aspects of the TNF, with comparative structural analyses of the wild and mutant types of this protein. Additionally, nanoscale molecular dynamics simulations are performed to assess the structure-property relationships of proteins as functions of time.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, and Center for Advanced Materials Processing, Clarkson University, Potsdam, NY, USA
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