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Chen Y, Fan Z, Luo Z, Kang X, Wan R, Li F, Lin W, Han Z, Qi B, Lin J, Sun Y, Huang J, Xu Y, Chen S. Impacts of Nutlin-3a and exercise on murine double minute 2-enriched glioma treatment. Neural Regen Res 2025; 20:1135-1152. [PMID: 38989952 DOI: 10.4103/nrr.nrr-d-23-00875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/21/2023] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00029/figure1/v/2024-07-06T104127Z/r/image-tiff Recent research has demonstrated the impact of physical activity on the prognosis of glioma patients, with evidence suggesting exercise may reduce mortality risks and aid neural regeneration. The role of the small ubiquitin-like modifier (SUMO) protein, especially post-exercise, in cancer progression, is gaining attention, as are the potential anti-cancer effects of SUMOylation. We used machine learning to create the exercise and SUMO-related gene signature (ESLRS). This signature shows how physical activity might help improve the outlook for low-grade glioma and other cancers. We demonstrated the prognostic and immunotherapeutic significance of ESLRS markers, specifically highlighting how murine double minute 2 (MDM2), a component of the ESLRS, can be targeted by nutlin-3. This underscores the intricate relationship between natural compounds such as nutlin-3 and immune regulation. Using comprehensive CRISPR screening, we validated the effects of specific ESLRS genes on low-grade glioma progression. We also revealed insights into the effectiveness of Nutlin-3a as a potent MDM2 inhibitor through molecular docking and dynamic simulation. Nutlin-3a inhibited glioma cell proliferation and activated the p53 pathway. Its efficacy decreased with MDM2 overexpression, and this was reversed by Nutlin-3a or exercise. Experiments using a low-grade glioma mouse model highlighted the effect of physical activity on oxidative stress and molecular pathway regulation. Notably, both physical exercise and Nutlin-3a administration improved physical function in mice bearing tumors derived from MDM2-overexpressing cells. These results suggest the potential for Nutlin-3a, an MDM2 inhibitor, with physical exercise as a therapeutic approach for glioma management. Our research also supports the use of natural products for therapy and sheds light on the interaction of exercise, natural products, and immune regulation in cancer treatment.
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Affiliation(s)
- Yisheng Chen
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhongcheng Fan
- Department of Orthopedic Surgery, Hainan Province Clinical Medical Center, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, Hainan Province, China
| | - Zhiwen Luo
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xueran Kang
- Department of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renwen Wan
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Fangqi Li
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Weiwei Lin
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhihua Han
- Department of Orthopedics, Shanghai General Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, China
| | - Beijie Qi
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinrong Lin
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaying Sun
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiebin Huang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Shiyi Chen
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
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2
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Qiao X, Wu X, Chen S, Niu MM, Hua H, Zhang Y. Discovery of novel and potent dual-targeting AXL/HDAC2 inhibitors for colorectal cancer treatment via structure-based pharmacophore modelling, virtual screening, and molecular docking, molecular dynamics simulation studies, and biological evaluation. J Enzyme Inhib Med Chem 2024; 39:2295241. [PMID: 38134358 PMCID: PMC10763849 DOI: 10.1080/14756366.2023.2295241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. Nowadays, owing to the complex mechanism of tumorigenesis, simultaneous inhibition of multiple targets is an important anticancer strategy. Recent studies have demonstrated receptor tyrosine kinase AXL (AXL) and histone deacetylase 2 (HDAC2) are closely associated with colorectal cancer. Herein, we identified five hit compounds concurrently targeting AXL and HDAC2 using virtual screening. Inhibitory experiments revealed these hit compounds potently inhibited AXL and HDAC2 in the nanomolar range. Among them, Hit-3 showed the strongest inhibitory effects which were better than that of the positive control groups. Additionally, MD assays showed that Hit-3 could bind stably to the AXL and HDAC2 active pockets. Further MTT assays demonstrated that Hit-3 showed potent anti-proliferative activity. Most importantly, Hit-3 exhibited significant in vivo antitumor efficacy in xenograft models. Collectively, this study is the first discovery of dual-targeting AXL/HDAC2 inhibitors for colorectal cancer treatment.
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Affiliation(s)
- Xiao Qiao
- Department of Gastroenterology, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, China
| | - Xiangyu Wu
- Department of Gastroenterology, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, China
| | - Shutong Chen
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Huilian Hua
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yan Zhang
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
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3
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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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4
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Xiong L, Liu Y, Wang Y, Zhao H, Song X, Fan W, Zhang L, Zhang Y. The protective effect of Lonicera japonica Thunb. against lipopolysaccharide-induced acute lung injury in mice: Modulation of inflammation, oxidative stress, and ferroptosis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 331:118333. [PMID: 38750986 DOI: 10.1016/j.jep.2024.118333] [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: 04/01/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/21/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Various components of Lonicera japonica Thunb. (LJT) exhibit pharmacological activities, including anti-inflammatory and antioxidant effects. Nevertheless, the relationship between LJT and ferroptosis remains largely unexplored. AIM OF THE STUDY The purpose of this research was to look into the role of LJT in regulating LPS-induced ferroptosis in ALI and to compare the effects of different parts of LJT. MATERIALS AND METHODS We established a mice ALI model by treating with LPS. Administered mice with different doses of Lonicerae Japonicae Flos (LJF), Lonicera Japonica Leaves (LJL) and Lonicerae Caulis (LRC) extracts, respectively. The levels of IL-6, IL-1β, TNF-α, IL-4, IL-10, and PGE2 in bronchoalveolar lavage fluid (BALF) were measured using enzyme-linked immunosorbent assay. Furthermore, the concentrations of superoxide dismutase (SOD), malondialdehyde (MDA), glutathione (GSH), reactive oxygen species (ROS), and total ferrous ions (Fe2+) in lung tissues were evaluated. Hematoxylin and eosin staining was conducted to examine the morphological structure of lung tissues. Transmission electron microscopy was used to investigate the ultrastructural morphology of mitochondria. Furthermore, the effects of LJT were evaluated via immunohistochemical staining, western blotting, and quantitative real-time polymerase chain reaction analyses. Finally, employing molecular docking and molecular dynamics research techniques, we aimed to identify crucial components in LJT that might inhibit ferroptosis by targeting nuclear factor erythroid 2-related factor 2 (Nrf2) and glutathione peroxidase 4 (GPX4). RESULTS We observed that pretreatment with LJT significantly mitigated LPS-induced lung injury and suppressed ferroptosis. This was supported by reduced accumulation of pro-inflammatory cytokines, ROS, MDA, and Fe2+, along with increased levels of anti-inflammatory cytokines, SOD, GSH, Nrf2, and GPX4 in the lung tissues of ALI mice. Luteolin-7-O-rutinoside, apigenin-7-O-rutinoside, and amentoflavone in LJT exhibit excellent docking effects with key targets of ferroptosis, Nrf2 and GPX4. CONCLUSIONS Pretreatment with LJT may alleviate LPS-induced ALI, possibly by suppressing ferroptosis. Our initial results indicate that LJT activates the Nrf2/GPX4 axis, providing protection against ferroptosis in ALI. This finding offers a promising therapeutic candidate for ALI treatment.
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Affiliation(s)
- Lewen Xiong
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Yan Liu
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Yang Wang
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Hongwei Zhao
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Xiaochen Song
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Wenjing Fan
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Longfei Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Yongqing Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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5
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Chiu PL, Orjuela JD, de Groot BL, Aponte Santamaría C, Walz T. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 2024; 12:RP90851. [PMID: 39222068 PMCID: PMC11368405 DOI: 10.7554/elife.90851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.
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Affiliation(s)
- Po-Lin Chiu
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Juan D Orjuela
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Biomedical Engineering Department, Universidad de los AndesBogotáColombia
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Camilo Aponte Santamaría
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
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6
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Xiong L, Xuan J, Zhao H, Zhang Z, Wang H, Yan P, Zhang Y, Liu Y, Zhang L. Revealing the material basis and mechanism for the inhibition of intestinal peristalsis by Zingiber officinale Roscoe through integrated metabolomics, serum pharmacochemistry, and network pharmacology. Biomed Chromatogr 2024; 38:e5932. [PMID: 38922712 DOI: 10.1002/bmc.5932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Abnormal relaxation and contraction of intestinal smooth muscle can cause various intestinal diseases. Diarrhea is a common and important public health problem worldwide in epidemiology. Zingiber officinale Roscoe (fresh ginger) has been found to treat diarrhea, but the material basis and mechanism of action that inhibits intestinal peristalsis remain unclear. Metabolomics and serum pharmacology were used to identify differential metabolites, metabolic pathways, and pharmacodynamic substances, and were then combined with network pharmacology to explore the potential targets of ginger that inhibit intestinal peristalsis during diarrhea treatment, and the targets identified were verified using molecular docking and molecular dynamic simulation. We found that 25 active components of ginger (the six most relevant components), 35 potential key targets (three core targets), 40 differential metabolites (four key metabolites), and four major metabolic pathways were involved in the process by which ginger inhibits intestinal peristalsis during diarrhea treatment. This study reveals the complex mechanism of action and pharmacodynamic material basis of ginger in the inhibition of intestinal peristalsis, and this information helps in the development of new Chinese medicine to treat diarrhea and lays the foundation for the clinical application of ginger.
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Affiliation(s)
- Lewen Xiong
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jing Xuan
- Shandong Agriculture and Engineering University, Jinan, China
| | - Hongwei Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhaoyu Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Haonan Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Peizheng Yan
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yongqing Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yan Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Longfei Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
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7
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Vidal-Calvo EE, Martin-Salazar A, Choudhary S, Dagil R, Raghavan SSR, Duvnjak L, Nordmaj MA, Clausen TM, Skafte A, Oberkofler J, Wang K, Agerbæk MØ, Løppke C, Jørgensen AM, Ropac D, Mujollari J, Willis S, Garcias López A, Miller RL, Karlsson RTG, Goerdeler F, Chen YH, Colaço AR, Wang Y, Lavstsen T, Martowicz A, Nelepcu I, Marzban M, Oo HZ, Ørum-Madsen MS, Wang Y, Nielsen MA, Clausen H, Wierer M, Wolf D, Gögenur I, Theander TG, Al-Nakouzi N, Gustavsson T, Daugaard M, Salanti A. Tumor-agnostic cancer therapy using antibodies targeting oncofetal chondroitin sulfate. Nat Commun 2024; 15:7553. [PMID: 39215044 PMCID: PMC11364678 DOI: 10.1038/s41467-024-51781-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Molecular similarities between embryonic and malignant cells can be exploited to target tumors through specific signatures absent in healthy adult tissues. One such embryonic signature tumors express is oncofetal chondroitin sulfate (ofCS), which supports disease progression and dissemination in cancer. Here, we report the identification and characterization of phage display-derived antibody fragments recognizing two distinct ofCS epitopes. These antibody fragments show binding affinity to ofCS in the low nanomolar range across a broad selection of solid tumor types in vitro and in vivo with minimal binding to normal, inflamed, or benign tumor tissues. Anti-ofCS antibody drug conjugates and bispecific immune cell engagers based on these targeting moieties disrupt tumor progression in animal models of human and murine cancers. Thus, anti-ofCS antibody fragments hold promise for the development of broadly effective therapeutic and diagnostic applications targeting human malignancies.
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Affiliation(s)
- Elena Ethel Vidal-Calvo
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark.
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark.
| | - Anne Martin-Salazar
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Swati Choudhary
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark
| | - Robert Dagil
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark
| | - Sai Sundar Rajan Raghavan
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lara Duvnjak
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark
| | - Mie Anemone Nordmaj
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Ann Skafte
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark
| | - Jan Oberkofler
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Kaituo Wang
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Ø Agerbæk
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VARCT Diagnostics, Copenhagen, Denmark
| | - Caroline Løppke
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Amalie Mundt Jørgensen
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VARCT Diagnostics, Copenhagen, Denmark
| | - Daria Ropac
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Joana Mujollari
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Shona Willis
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Agnès Garcias López
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rebecca Louise Miller
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Richard Torbjörn Gustav Karlsson
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Felix Goerdeler
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Ana R Colaço
- Proteomics Research Infrastructure, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Thomas Lavstsen
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Agnieszka Martowicz
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Irina Nelepcu
- Vancouver Prostate Centre, Vancouver Coastal Health Research Institutes, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mona Marzban
- Vancouver Prostate Centre, Vancouver Coastal Health Research Institutes, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Htoo Zarni Oo
- Vancouver Prostate Centre, Vancouver Coastal Health Research Institutes, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Maj Sofie Ørum-Madsen
- Vancouver Prostate Centre, Vancouver Coastal Health Research Institutes, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver Coastal Health Research Institutes, Vancouver, BC, Canada
| | - Morten A Nielsen
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Wierer
- Proteomics Research Infrastructure, University of Copenhagen, Copenhagen, Denmark
| | - Dominik Wolf
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck, Innsbruck, Austria
| | - Ismail Gögenur
- Center for Surgical Science, Department of Surgery, Zealand University Hospital Køge, Køge, Denmark
| | - Thor G Theander
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark
| | - Nader Al-Nakouzi
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark
- Vancouver Prostate Centre, Vancouver Coastal Health Research Institutes, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tobias Gustavsson
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark
| | - Mads Daugaard
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark.
- Vancouver Prostate Centre, Vancouver Coastal Health Research Institutes, Vancouver, BC, Canada.
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Ali Salanti
- Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark.
- VAR2 Pharmaceuticals ApS, Copenhagen, Denmark.
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8
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Kalbfleisch TS, Ahammad T, Lorigan GA, Jaeger VW. Thermodynamic Details of Pinholin S 2168 Activation Revealed Using Alchemical Free Energy Simulations. J Phys Chem B 2024. [PMID: 39197172 DOI: 10.1021/acs.jpcb.4c03302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Pinholin S2168 is a viral integral membrane protein whose function is to form nanoscopic "pinholes" in bacterial cell membranes to induce cell lysis as part of the viral replication cycle. Pinholin can transition from an inactive to an active conformation by exposing a transmembrane domain (TMD1) to the extracellular fluid. Upon activation, several copies of the protein assemble via interactions among a second transmembrane domain (TMD2) to form a single pore, thus hastening cell lysis and viral escape. The following experiments provide conformational descriptors of pinholin in active and inactive states and elucidate the molecular driving forces that control pinholin activity. In the present study, molecular dynamics (MD) simulations have been used to refine experimentally derived conformational descriptors into an atomistically detailed model of irsS2168, an antiholin mutant. To provide additional details about the thermodynamics of pinholin activation and to overcome large intrinsic kinetic barriers to activation, alchemical free energy simulations have been conducted. Alchemical mutations reveal the change in folding free energy upon mutation. The results suggest that alchemical mutations are an effective tool to rationalize experimental observations and predict the effects of site mutations on conformational states for proteins integrated into lipid bilayers. S16F, A17Q, A17Q+G21Q, and A17Q+G21Q+G14Q mutants reveal how changes in hydrophilicity and disruption of the glycine zipper motif influence pinholin's thermodynamic equilibrium, favoring the active conformation. These findings align with experimental observations from DEER spectroscopy, demonstrating that mutations increasing the hydrophilicity of TMD1 promote activation by making TMD1 more likely to exit the membrane and enter the extracellular fluid.
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Affiliation(s)
- Theodore S Kalbfleisch
- Department of Chemical Engineering, University of Louisville, Louisville, Kentucky 40292, United States
| | - Tanbir Ahammad
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Vance W Jaeger
- Department of Chemical Engineering, University of Louisville, Louisville, Kentucky 40292, United States
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9
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Thomas N, Sanyal T, Greisen P, Deibler K. Structure-Based Computational Scanning of Chemical Modification Sites in Biologics. ACS OMEGA 2024; 9:36787-36794. [PMID: 39220547 PMCID: PMC11360052 DOI: 10.1021/acsomega.4c05857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
To address the challenges of short half-life, immunogenicity, and nonspecific distribution, chemical modifications of peptide and protein-based drugs have emerged as a versatile strategy for improving their therapeutic efficacy. One such modification involves the derivatization of peptides and proteins with fatty acids, which can protract their half-life, modify their biodistribution, and potentially enable targeted delivery to specific tissues or disease sites of interest. However, the present strategies for the synthesis of such synthetically modified biologics require numerous rounds of experimental testing and often yield unstable, inactive, or heterogeneous products. To address the inefficiencies in designing modified biologics, we developed a hybrid computational workflow that integrates RosettaMatch from the Rosetta suite of protein modeling tools with molecular dynamics (MD) simulations. This approach not only reduces the number of amino acid positions that need to be experimentally tested by targeting only the most promising candidates for modification but also expedites the design of chemically modified biologics with the desired properties, ensuring a rapid and cost-effective development cycle. Although we demonstrate the utility of our method on a peptide therapeutic, GLP-1, with different fatty acid derivatizations, this straightforward approach has the potential to streamline the design process of a diverse range of chemically modified therapeutics, enabling tailored enhancements to their pharmacokinetic properties.
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Affiliation(s)
| | | | | | - Kristine Deibler
- Digital Science and Innovation, Novo Nordisk Research Center Seattle Inc., Seattle, Washington 98101, United States
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10
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Dziadek ŁJ, Sieradzan AK, Czaplewski C, Zalewski M, Banaś F, Toczek M, Nisterenko W, Grudinin S, Liwo A, Giełdoń A. Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution. J Chem Theory Comput 2024. [PMID: 39171852 DOI: 10.1021/acs.jctc.4c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
In this paper, we evaluated the ability of four coarse-grained methods to predict protein flexible regions with potential biological importance, UNRES-flex, UNRES-DSSP-flex (based on the united residue model of polypeptide chains without and with secondary structure restraints, respectively), CABS-flex (based on the C-α, C-β, and side chain model), and nonlinear rigid block normal mode analysis (NOLB) with a set of 100 protein structures determined by NMR spectroscopy or X-ray crystallography, with all secondary structure types. End regions with high fluctuations were excluded from analysis. The Pearson and Spearman correlation coefficients were used to quantify the conformity between the calculated and experimental fluctuation profiles, the latter determined from NMR ensembles and X-ray B-factors, respectively. For X-ray structures (corresponding to proteins in a crowded environment), NOLB resulted in the best agreement between the predicted and experimental fluctuation profiles, while for NMR structures (corresponding to proteins in solution), the ranking of performance is CABS-flex > UNRES-DSSP-flex > UNRES-flex > NOLB; however, CABS-flex sometimes exaggerated the extent of small fluctuations, as opposed to UNRES-DSSP-flex.
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Affiliation(s)
- Ł J Dziadek
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - A K Sieradzan
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - C Czaplewski
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 02455, Republic of Korea
| | - M Zalewski
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - F Banaś
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - M Toczek
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - W Nisterenko
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - S Grudinin
- LJK, University Grenoble Alpes, CNRS, Grenoble INP, F-38000 Grenoble, France
| | - A Liwo
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - A Giełdoń
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
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11
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Pardo-Avila F, Kudva R, Levitt M, von Heijne G. Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.20.608737. [PMID: 39229094 PMCID: PMC11370347 DOI: 10.1101/2024.08.20.608737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Nascent polypeptide chains (NCs) are extruded from the ribosome through an exit tunnel (ET) traversing the large ribosomal subunit. The ET's irregular and chemically complex wall allows for various NC-ET interactions. Translational arrest peptides (APs) bind in the ET to induce translational arrest, a property that can be exploited to study NC-ET interactions by Force Profile Analysis (FPA). We employed FPA and molecular dynamics (MD) simulations to investigate how individual residues placed in a glycine-serine repeat segment within an AP-stalled NC interact with the ET to exert a pulling force on the AP and release stalling. Our results indicate that large and hydrophobic residues generate a pulling force on the NC when placed ≳10 residues away from the peptidyl transfer center (PTC). Moreover, an asparagine placed 12 residues from the PTC makes a specific stabilizing interaction with the tip of ribosomal protein uL22 that reduces the pulling force on the NC, while a lysine or leucine residue in the same position increases the pulling force. Finally, the MD simulations suggest how the Mannheimia succiniproducens SecM AP interacts with the ET to promote translational stalling.
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12
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Zhou W, Liu J, Chambreau SD, Vaghjiani GL. Dynamics and thermochemistry of the negatively charged clusters in a 2-hydroxyethylhydrazinium nitrate ionic liquid system. Phys Chem Chem Phys 2024; 26:21697-21711. [PMID: 39092620 DOI: 10.1039/d4cp02329c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The formation and fragmentation of negatively charged 2-hydroxyethylhydrazinium nitrate ([HOCH2CH2NH2NH2]+NO3-, HEHN) ionic liquid clusters were examined using a guided-ion beam tandem mass spectrometer furnished with collision-induced dissociation of selected ions with Xe atoms. Measurements included the compositions of cluster ions formed in the ionization source, and the dissociation products, cross sections, and 0 K threshold energies for individually selected cluster ions. To identify the structures of the main cluster ion series [(HEHN)n(HNO3)0-1NO3]- formed, molecular dynamics simulations were employed to create initial geometry guesses, followed by optimization at the ωB97XD/6-31+G(d,p) level of theory, from which global minimum structures were identified for reaction thermodynamics analyses. A comparison was made between the cluster formation and fragmentation in the negatively charged 2-hydroxyethylhydrazinium nitrate with those in the positive mode (reported by W. Zhou et al., Phys. Chem. Chem. Phys., 2023, 25, 17370). In both modes, the cluster ions were predominantly composed of m/z below 350; loss of a neutral 2-hydroxyethylhydrazinium nitrate ion pair represents the most important cluster fragmentation pathway, followed by intra-ion pair proton transfer-mediated 2-hydroxyethylhydrazine and HNO3 elimination; and all clusters started to dissociate at threshold energies less than 1.5 eV. The overwhelming similarities in the formation and fragmentation chemistry of positively vs. negatively charged 2-hydroxyethylhydrazinium nitrate clusters may be attributed to their inherent ionic nature and high electric conductivities.
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Affiliation(s)
- Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA.
- PhD Program in Chemistry, the Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA.
- PhD Program in Chemistry, the Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Steven D Chambreau
- Jacobs Technology, Inc., Air Force Research Laboratory, Edwards Air Force Base, California 93524, USA
| | - Ghanshyam L Vaghjiani
- In-Space Propulsion Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRS, Edwards Air Force Base, California 93524, USA
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13
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Crane SA, Jiménez-Ángeles F, Wang Y, Ortuno Macias LE, Marmorstein JG, Deng J, Molaei M, Petersson EJ, Radhakrishnan R, de la Fuente-Nunez C, Olvera de la Cruz M, Tu RS, Maldarelli C, Dmochowski IJ, Stebe KJ. Interfacial rheology of lanthanide binding peptide surfactants at the air-water interface. SOFT MATTER 2024. [PMID: 39129466 DOI: 10.1039/d4sm00493k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Peptide surfactants (PEPS) are studied to capture and retain rare earth elements (REEs) at air-water interfaces to enable REE separations. Peptide sequences, designed to selectively bind REEs, depend crucially on the position of ligands within their binding loop domain. These ligands form a coordination sphere that wraps and retains the cation. We study variants of lanthanide binding tags (LBTs) designed to complex strongly with Tb3+. The peptide LBT5- (with net charge -5) is known to bind Tb3+ and adsorb with more REE cations than peptide molecules, suggesting that undesired non-specific coulombic interactions occur. Rheological characterization of interfaces of LBT5- and Tb3+ solutions reveal the formation of an interfacial gel. To probe whether this gelation reflects chelation among intact adsorbed LBT5-:Tb3+ complexes or destruction of the binding loop, we study a variant, LBT3-, designed to form net neutral LBT3-:Tb3+ complexes. Solutions of LBT3- and Tb3+ form purely viscous layers in the presence of excess Tb3+, indicating that each peptide binds a single REE in an intact coordination sphere. We introduce the variant RR-LBT3- with net charge -3 and anionic ligands outside of the coordination sphere. We find that such exposed ligands promote interfacial gelation. Thus, a nuanced requirement for interfacial selectivity of PEPS is proposed: that anionic ligands outside of the coordination sphere must be avoided to prevent the non-selective recruitment of REE cations. This view is supported by simulation, including interfacial molecular dynamics simulations, and interfacial metadynamics simulations of the free energy landscape of the binding loop conformational space.
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Affiliation(s)
- Stephen A Crane
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Felipe Jiménez-Ángeles
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Luis E Ortuno Macias
- Department of Chemical Engineering, The City College of New York, New York, NY 10031, USA
- Levich Institute, The City College of New York, New York, NY 10031, USA
| | - Jason G Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiayi Deng
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Mehdi Molaei
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cesar de la Fuente-Nunez
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Insitute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Raymond S Tu
- Department of Chemical Engineering, The City College of New York, New York, NY 10031, USA
| | - Charles Maldarelli
- Department of Chemical Engineering, The City College of New York, New York, NY 10031, USA
- Levich Institute, The City College of New York, New York, NY 10031, USA
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathleen J Stebe
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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14
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Nicolás-Apolinar B, Ibarra-Tandi B, López-Lemus J, Luis-Jiménez DP. Influence of molecular parameters on the representativeness of interfacial properties of simple fluids. J Chem Phys 2024; 161:054711. [PMID: 39092958 DOI: 10.1063/5.0210919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
New parameterizations for the Lennard-Jones 12/6 potential capable of reproducing the vapor pressure and surface tension with sufficient precision, but not the liquid-vapor equilibrium densities for the case of simple fluids that include Ar, Kr, Xe, Ne, and CH4 are presented in this work. These results are compared with those derived from the family of Mie(n, 6) potentials, which adequately reproduce the coexistence curve and the vapor pressure, leaving aside the surface tension. In addition, a detailed analysis is presented on different parameterizations and methodologies, which have been developed in recent decades to estimate the interfacial properties of interest here for simple fluids, such as argon, which is a molecule that is, in principle, "simple" to study but that clearly reveals the enormous discrepancy between the results reported in the literature throughout these years. These facts undoubtedly reveal one of the fundamental problems in the context of molecular thermodynamics of fluids: reproducing different thermodynamic properties with sufficient precision from a single set of free parameters for some interaction potential. In order to show the scope of the parameterizations presented for the Lennard-Jones model, they were successfully applied to the case of binary mixtures, which included Ar-Kr, Ar-CH4, and Xe-Kr. Finally, and with the aim of showing a possible solution to the problem posed in this research, results of the same interfacial properties above mentioned for argon and methane were presented in this work by using a set of molecular interactions, called ANC2s, whose flexibility allowed to reproduce the experimental evidence with just one parameterization. The results reported in this work were generated using molecular dynamics simulations.
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Affiliation(s)
- B Nicolás-Apolinar
- Facultad de Ciencias, Universidad Autónoma del Estado de México, CP 50200 Toluca, Mexico
| | - B Ibarra-Tandi
- Facultad de Ciencias, Universidad Autónoma del Estado de México, CP 50200 Toluca, Mexico
| | - J López-Lemus
- Facultad de Ciencias, Universidad Autónoma del Estado de México, CP 50200 Toluca, Mexico
| | - D P Luis-Jiménez
- CONACYT Research Fellow-Centro de Ingeniería y Desarrollo Industrial, CP 76130 Querétaro, Mexico
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15
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Del Regno R, Della Sala P, Santonoceta GDG, Neri P, De Rosa M, Talotta C, Sgarlata C, De Simone A, Gaeta C. Under the Influence of Water: Molecular Recognition of Organic Hydrophilic Molecules in Water with a Prismarene Host Driven by Hydration Effects. Chemistry 2024; 30:e202401734. [PMID: 38850206 DOI: 10.1002/chem.202401734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
A water-soluble prism[5]arene host can form endo-cavity complexes with hydrophilic organic substances in water by displacing frustrated water molecules from its deep cavity. Water molecules structured at both rims of the prismarene host can mediate hydrogen bonding interactions with the guest. Water-mediated hydrogen bonding interactions were invoked here to elucidate the elevated binding affinities and selectivity of the prismarene host toward hydrophilic organic guests. We show that water at the interface of a host-guest complex can act as an extension of the host structure, facilitating the accommodation of neutral guests within the binding site. This study highlights the crucial role of water in facilitating supramolecular interactions between a deep-cavity prismarene host and organic hydrophilic guests in aqueous medium.
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Affiliation(s)
- Rocco Del Regno
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano, I-84084, Italy
| | - Paolo Della Sala
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano, I-84084, Italy
| | - Giuseppina D G Santonoceta
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125, Catania, Italy
| | - Placido Neri
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano, I-84084, Italy
| | - Margherita De Rosa
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano, I-84084, Italy
| | - Carmen Talotta
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano, I-84084, Italy
| | - Carmelo Sgarlata
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125, Catania, Italy
| | - Alfonso De Simone
- Dipartimento di Farmacia, Università di Napoli, Via Domenico Montesano, 49, I-80131, Napoli, Italy
| | - Carmine Gaeta
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano, I-84084, Italy
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16
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Zhou Z, Zhu F, Ma S, Tan C, Yang H, Zhang P, Xu Y, Qin R, Luo Y, Chen J, Pan P. Design of Cryptococcus neoformans multi-epitope vaccine based on immunoinformatics method. Med Mycol 2024; 62:myae080. [PMID: 39122658 DOI: 10.1093/mmy/myae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/01/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024] Open
Abstract
Cryptococcus neoformans is a widely distributed opportunistic pathogenic fungus. While C. neoformans commonly infects immunocompromised individuals, it can also affect those who are immunocompetent. Transmission of C. neoformans primarily occurs through the respiratory tract, leading to the development of meningitis. The mortality rate of Cryptococcal meningitis is high, and treatment options are limited. Cryptococcus neoformans infections pose a significant public health threat and currently lack targeted and effective response strategies. This study aimed to screen T lymphocyte (cytotoxic T lymphocyte and helper T lymphocyte) and B lymphocyte epitopes derived from four C. neoformans antigens and develop two multi-epitope vaccines by combining them with various adjuvants. Molecular docking results demonstrated that the vaccines bind stably to Toll-like receptor 4 ( and induce innate immunity. The credibility of the molecular docking results was validated through subsequent molecular dynamics simulations. Furthermore, the results of immune simulation analyses underscored the multi-epitope vaccine's capability to effectively induce robust humoral and cellular immune responses within the host organism. These two vaccines have demonstrated theoretical efficacy against C. neoformans infection as indicated by computer analysis. Nevertheless, additional experimental validation is essential to substantiate the protective efficacy of the vaccines.
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Affiliation(s)
- Ziyou Zhou
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Yizhong Xu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Rongliu Qin
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Yuying Luo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
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Foran G, Hallam RD, Megaly M, Turgambayeva A, Antfolk D, Li Y, Luca VC, Necakov A. Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.17.533124. [PMID: 39131356 PMCID: PMC11312450 DOI: 10.1101/2023.03.17.533124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The Notch receptor is a pleiotropic signaling protein that translates intercellular ligand interactions into changes in gene expression via the nuclear localization of the Notch intracellular Domain (NICD). Using a combination of immunohistochemistry, RNA in situ, Optogenetics and super-resolution live imaging of transcription in human cells, we show that the N1ICD can form condensates that positively facilitate Notch target gene expression. We determined that N1ICD undergoes Phase Separation Coupled Percolation (PSCP) into transcriptional condensates, which recruit, enrich, and encapsulate a broad set of core transcriptional proteins. We show that the capacity for condensation is due to the intrinsically disordered transcriptional activation domain of the N1ICD. In addition, the formation of such transcriptional condensates acts to promote Notch-mediated super enhancer-looping and concomitant activation of the MYC protooncogene expression. Overall, we introduce a novel mechanism of Notch1 activity in which discrete changes in nuclear N1ICD abundance are translated into the assembly of transcriptional condensates that facilitate gene expression by enriching essential transcriptional machineries at target genomic loci.
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Affiliation(s)
- Gregory Foran
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Ryan Douglas Hallam
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Marvel Megaly
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Anel Turgambayeva
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Daniel Antfolk
- Department of Immunology, Moffitt Cancer Centre, Tampa, FL, USA
| | - Yifeng Li
- Department of Computer Science, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Vincent C. Luca
- Department of Immunology, Moffitt Cancer Centre, Tampa, FL, USA
| | - Aleksandar Necakov
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
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Yu D, Li H, Liu Y, Yang X, Yang W, Fu Y, Zuo YA, Huang X. Application of the molecular dynamics simulation GROMACS in food science. Food Res Int 2024; 190:114653. [PMID: 38945587 DOI: 10.1016/j.foodres.2024.114653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.
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Affiliation(s)
- Dongping Yu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Haiping Li
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China.
| | - Yuzi Liu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xingqun Yang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Wei Yang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yiran Fu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yi-Ao Zuo
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xianya Huang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
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Li Z, Hu Y, Yu C, Fei K, Shen L, Liu Y, Nakanishi H. Semi-rational engineering of D-allulose 3-epimerase for simultaneously improving the catalytic activity and thermostability based on D-allulose biosensor. Biotechnol J 2024; 19:e2400280. [PMID: 39167550 DOI: 10.1002/biot.202400280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/23/2024]
Abstract
BACKGROUND D-Allulose is one of the most well-known rare sugars widely used in food, cosmetics, and pharmaceutical industries. The most popular method for D-allulose production is the conversion from D-fructose catalyzed by D-allulose 3-epimerase (DAEase). To address the general problem of low catalytic efficiency and poor thermostability of wild-type DAEase, D-allulose biosensor was adopted in this study to develop a convenient and efficient method for high-throughput screening of DAEase variants. RESULTS The catalytic activity and thermostability of DAEase from Caballeronia insecticola were simultaneously improved by semi-rational molecular modification. Compared with the wild-type enzyme, DAEaseS37N/F157Y variant exhibited 14.7% improvement in the catalytic activity and the half-time value (t1/2) at 65°C increased from 1.60 to 27.56 h by 17.23-fold. To our delight, the conversion rate of D-allulose was 33.6% from 500-g L-1 D-fructose in 1 h by Bacillus subtilis WB800 whole cells expressing this DAEase variant. Furthermore, the practicability of cell immobilization was evaluated and more than 80% relative activity of the immobilized cells was maintained from the second to seventh cycle. CONCLUSION All these results indicated that the DAEaseS37N/F157Y variant would be a potential candidate for the industrial production of D-allulose.
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Affiliation(s)
- Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Yangfan Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Cheng Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Kangqing Fei
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Liqun Shen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Yishi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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20
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Mykuliak VV, Rahikainen R, Ball NJ, Bussi G, Goult BT, Hytönen VP. Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force. PLoS Comput Biol 2024; 20:e1012341. [PMID: 39110765 PMCID: PMC11333002 DOI: 10.1371/journal.pcbi.1012341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/19/2024] [Accepted: 07/21/2024] [Indexed: 08/21/2024] Open
Abstract
Vinculin binds to specific sites of mechanically unfolded talin rod domains to reinforce the coupling of the cell's exterior to its force generation machinery. Force-dependent vinculin-talin complexation and dissociation was previously observed as contraction or extension of the unfolded talin domains respectively using magnetic tweezers. However, the structural mechanism underlying vinculin recognition of unfolded vinculin binding sites (VBSs) in talin remains unknown. Using molecular dynamics simulations, we demonstrate that a VBS dynamically refolds under force, and that vinculin can recognize and bind to partially unfolded VBS states. Vinculin binding enables refolding of the mechanically strained VBS and stabilizes its folded α-helical conformation, providing resistance against mechanical stress. Together, these results provide an understanding of a recognition mechanism of proteins unfolded by force and insight into the initial moments of how vinculin binds unfolded talin rod domains during the assembly of this mechanosensing meshwork.
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Affiliation(s)
- Vasyl V. Mykuliak
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Rolle Rahikainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Neil J. Ball
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, Trieste, Italy
| | - Benjamin T. Goult
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Vesa P. Hytönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
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21
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Chen Y, Yan Y, Chen J, Zheng B, Jiang Y, Kang Z, Wu J. A Novel AHAS-Inhibiting Herbicide Candidate for Controlling Leptochloa chinensis: A Devastating Weedy Grass in Rice Fields. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16140-16151. [PMID: 39007211 DOI: 10.1021/acs.jafc.4c03891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Given the prevalence of the malignant weed Chinese Sprangletop (Leptochloa chinensis (L.) Nees) in rice fields, the development of novel herbicides against this weed has aroused wide interest. Here, we report a novel diphenyl ether-pyrimidine hybrid, DEP-5, serving as a systematic pre/postemergence herbicide candidate for broad-spectrum weed control in rice fields, specifically for L. chinensis. Notably, DEP-5 exhibits over 80% herbicidal activity against the resistant biotypes even at 37.5 g a.i./ha under greenhouse conditions and has complete control of L. chinensis at 150 g a.i./ha in the rice fields. We uncover that DEP-5 acts as a noncompetitive inhibitor of acetohydroxyacid synthase (AHAS) with an inhibition constant (Ki) of 39.4 μM. We propose that DEP-5 binds to AHAS in two hydrophobic-driven binding modes that differ from commercial AHAS inhibitors. Overall, these findings demonstrate that DEP-5 has great potential to be developed into a herbicide for L. chinensis control and inspire fresh concepts for novel AHAS-inhibiting herbicide design.
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Affiliation(s)
- Yinglu Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yitao Yan
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Jie Chen
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
| | - Ben Zheng
- Hangzhou Jingyinkang Biological Technology Co., Ltd., Hangzhou 311110, China
| | - Youwei Jiang
- Hangzhou Jingyinkang Biological Technology Co., Ltd., Hangzhou 311110, China
| | | | - Jun Wu
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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22
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Chen Y, Huang L, Luo Z, Han D, Luo W, Wan R, Li Y, Ge Y, Lin WW, Xie Y, Sun M, Wang Q, Li Z, Chen S, Yang Y, Huang B, Xu Y. Pantothenate-encapsulated liposomes combined with exercise for effective inhibition of CRM1-mediated PKM2 translocation in Alzheimer's therapy. J Control Release 2024; 373:336-357. [PMID: 38996921 DOI: 10.1016/j.jconrel.2024.07.010] [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: 03/22/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/14/2024]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative condition characterized by metabolic imbalances and neuroinflammation, posing a formidable challenge in medicine due to the lack of effective treatments. Despite considerable research efforts, a cure for AD remains elusive, with current therapies primarily focused on symptom management rather than addressing the disease's underlying causes. This study initially discerned, through Mendelian randomization analysis that elevating pantothenate levels significantly contributes to the prophylaxis of Alzheimer's disease. We explore the therapeutic potential of pantothenate encapsulated in liposomes (Pan@TRF@Liposome NPs), targeting the modulation of CRM1-mediated PKM2 nuclear translocation, a critical mechanism in AD pathology. Additionally, we investigate the synergistic effects of exercise, proposing a combined approach to AD treatment. Exercise-induced metabolic alterations share significant similarities with those associated with dementia, suggesting a potential complementary effect. The Pan@TRF@Liposome NPs exhibit notable biocompatibility, showing no liver or kidney toxicity in vivo, while demonstrating stability and effectiveness in modulating CRM1-mediated PKM2 nuclear translocation, thereby reducing neuroinflammation and neuronal apoptosis. The combined treatment of exercise and Pan@TRF@Liposome NP administration in an AD animal model leads to improved neurofunctional outcomes and cognitive performance. These findings highlight the nanoparticles' role as effective modulators of CRM1-mediated PKM2 nuclear translocation, with significant implications for mitigating neuroinflammation and neuronal apoptosis. Together with exercise, this dual-modality approach could offer new avenues for enhancing cognitive performance and neurofunctional outcomes in AD, marking a promising step forward in developing treatment strategies for this challenging disorder.
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Affiliation(s)
- Yisheng Chen
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China; Department of Medical Sciences, Ningde Normal University College of Medical Sciences, No. 1 Xueyuan Road, Jiaocheng District, Ningde City, Fujian, China
| | - Lei Huang
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, 01605, MA, USA.
| | - Zhiwen Luo
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Dan Han
- Department of Emergency Medicine and Intensive Care, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Luo
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Renwen Wan
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yan Li
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan 750004, China
| | - Yunshen Ge
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei-Wei Lin
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310009, Zhejiang, China
| | - Yuchun Xie
- Jiangsu Province Geriatric Hospital, China
| | - Mingming Sun
- Laboratory Animal Center, Guangxi Medical University, Nanning, Guangxi, China
| | - Qian Wang
- Department of Central Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, Shandong, China
| | - Zhiwei Li
- Clinical Laboratory Center, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, PR China
| | - Shiyi Chen
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China.
| | - Yi Yang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan 750004, China.
| | - Bin Huang
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China.
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China.
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23
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Liu F, Li T, Gong H, Tian F, Bai Y, Wang H, Yang C, Li Y, Guo F, Liu S, Chen Q. Structural insights into the molecular effects of the anthelmintics monepantel and betaine on the Caenorhabditis elegans acetylcholine receptor ACR-23. EMBO J 2024:10.1038/s44318-024-00165-7. [PMID: 39009676 DOI: 10.1038/s44318-024-00165-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024] Open
Abstract
Anthelmintics are drugs used for controlling pathogenic helminths in animals and plants. The natural compound betaine and the recently developed synthetic compound monepantel are both anthelmintics that target the acetylcholine receptor ACR-23 and its homologs in nematodes. Here, we present cryo-electron microscopy structures of ACR-23 in apo, betaine-bound, and betaine- and monepantel-bound states. We show that ACR-23 forms a homo-pentameric channel, similar to some other pentameric ligand-gated ion channels (pLGICs). While betaine molecules are bound to the classical neurotransmitter sites in the inter-subunit interfaces in the extracellular domain, monepantel molecules are bound to allosteric sites formed in the inter-subunit interfaces in the transmembrane domain of the receptor. Although the pore remains closed in betaine-bound state, monepantel binding results in an open channel by wedging into the cleft between the transmembrane domains of two neighboring subunits, which causes dilation of the ion conduction pore. By combining structural analyses with site-directed mutagenesis, electrophysiology and in vivo locomotion assays, we provide insights into the mechanism of action of the anthelmintics monepantel and betaine.
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Affiliation(s)
- Fenglian Liu
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Tianyu Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 201204, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Huihui Gong
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Fei Tian
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yan Bai
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Haowei Wang
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Chonglin Yang
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yang Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Fei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Sheng Liu
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, 518026, China.
- Department of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, 518038, China.
| | - Qingfeng Chen
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
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24
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Antalík A, Levy A, Kvedaravičiūtė S, Johnson SK, Carrasco-Busturia D, Raghavan B, Mouvet F, Acocella A, Das S, Gavini V, Mandelli D, Ippoliti E, Meloni S, Carloni P, Rothlisberger U, Olsen JMH. MiMiC: A high-performance framework for multiscale molecular dynamics simulations. J Chem Phys 2024; 161:022501. [PMID: 38990116 DOI: 10.1063/5.0211053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/15/2024] [Indexed: 07/12/2024] Open
Abstract
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data (MPMD) paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.
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Affiliation(s)
- Andrej Antalík
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Andrea Levy
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Sonata Kvedaravičiūtė
- DTU Chemistry, Technical University of Denmark (DTU), DK-2800 Kongens Lyngby, Denmark
| | - Sophia K Johnson
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Bharath Raghavan
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
- Department of Physics, RWTH Aachen University, Aachen 52074, Germany
| | - François Mouvet
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Sambit Das
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vikram Gavini
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Davide Mandelli
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
| | - Simone Meloni
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie (DOCPAS), Università degli Studi di Ferrara (Unife), I-44121 Ferrara, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
- Department of Physics, RWTH Aachen University, Aachen 52074, Germany
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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25
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Sahalianov I, Abrahamsson T, Priyadarshini D, Mousa AH, Arja K, Gerasimov JY, Linares M, Simon DT, Olsson R, Baryshnikov G, Berggren M, Musumeci C. Tuning the Emission of Bis-ethylenedioxythiophene-thiophenes upon Aggregation. J Phys Chem B 2024; 128:6581-6588. [PMID: 38942741 PMCID: PMC11247477 DOI: 10.1021/acs.jpcb.4c02891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The ability of small lipophilic molecules to penetrate the blood-brain barrier through transmembrane diffusion has enabled researchers to explore new diagnostics and therapies for brain disorders. Until now, therapies targeting the brain have mainly relied on biochemical mechanisms, while electrical treatments such as deep brain stimulation often require invasive procedures. An alternative to implanting deep brain stimulation probes could involve administering small molecule precursors intravenously, capable of crossing the blood-brain barrier, and initiating the formation of conductive polymer networks in the brain through in vivo polymerization. This study examines the aggregation behavior of five water-soluble conducting polymer precursors sharing the same conjugate core but differing in side chains, using spectroscopy and various computational chemistry tools. Our findings highlight the significant impact of side chain composition on both aggregation and spectroscopic response.
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Affiliation(s)
- Ihor Sahalianov
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
- Wallenberg Initiative Materials Science for Sustainability, ITN, Linköping University, Norrköping 60174, Sweden
| | - Tobias Abrahamsson
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
| | - Diana Priyadarshini
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
| | - Abdelrazek H Mousa
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Katriann Arja
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
| | - Jennifer Y Gerasimov
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
| | - Mathieu Linares
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
- Group of Scientific Visualization, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
| | - Daniel T Simon
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
| | - Roger Olsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
- Chemical Biology & Therapeutics, Department of Experimental Medical Science, Lund University, Lund SE-221 84, Sweden
| | - Glib Baryshnikov
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
- Wallenberg Initiative Materials Science for Sustainability, ITN, Linköping University, Norrköping 60174, Sweden
| | - Magnus Berggren
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
| | - Chiara Musumeci
- Laboratory of Organic Electronics, Department of Science and Technology, Linkoping University, Norrkoping SE-60174, Sweden
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Lundborg M, Wennberg C, Lindahl E, Norlén L. Simulating the Skin Permeation Process of Ionizable Molecules. J Chem Inf Model 2024; 64:5295-5302. [PMID: 38917349 PMCID: PMC11234375 DOI: 10.1021/acs.jcim.4c00722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
It is commonly assumed that ionizable molecules, such as drugs, permeate through the skin barrier in their neutral form. By using molecular dynamics simulations of the charged and neutral states separately, we can study the dynamic protonation behavior during the permeation process. We have studied three weak acids and three weak bases and conclude that the acids are ionized to a larger extent than the bases, when passing through the headgroup region of the lipid barrier structure, at pH values close to their pKa. It can also be observed that even if these dynamic protonation simulations are informative, in the cases studied herein they are not necessary for the calculation of permeability coefficients. It is sufficient to base the calculations only on the neutral form, as is commonly done.
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Affiliation(s)
- Magnus Lundborg
- SciLifeLab, ERCO Pharma AB, 171 65 Solna, Sweden
- Department of Applied Physics, SciLifeLab, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Christian Wennberg
- SciLifeLab, ERCO Pharma AB, 171 65 Solna, Sweden
- UC AB, 111 64 Stockholm, Sweden
| | - Erik Lindahl
- Department of Biophysics and Biochemistry, SciLifeLab, Stockholm University, 106 91 Stockholm, Sweden
- Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Lars Norlén
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, 171 77 Solna, Sweden
- Dermatology Clinic, Karolinska University Hospital, 171 77 Solna, Sweden
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27
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Rizuan A, Shenoy J, Mohanty P, dos Passos PMS, Mercado Ortiz JF, Bai L, Viswanathan R, Wang SH, Johnson V, Mamede LD, Ayala YM, Ghirlando R, Mittal J, Fawzi NL. Structural details of helix-mediated TDP-43 C-terminal domain multimerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602258. [PMID: 39005345 PMCID: PMC11245101 DOI: 10.1101/2024.07.05.602258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The primarily disordered C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43), a key nuclear protein in RNA metabolism, forms neuronal inclusions in several neurodegenerative diseases. A conserved region (CR, spanning residues 319-341) in CTD forms transient helix-helix contacts important for its higher-order oligomerization and function that are disrupted by ALS-associated mutations. However, the structural details of CR assembly and the explanation for several ALS-associated variants' impact on phase separation and function remain unclear due to challenges in analyzing the dynamic association of TDP-43 CTD using traditional structural biology approaches. By employing an integrative approach, combining biophysical experiments, biochemical assays, AlphaFold2-Multimer (AF2-Multimer), and atomistic simulations, we generated structural models of helical oligomerization of TDP-43 CR. Using NMR, we first established that the native state of TDP-43 CR under physiological conditions is α-helical. Next, alanine scanning mutagenesis revealed that while hydrophobic residues in the CR are important for CR assembly, phase separation and TDP-43 nuclear retention function, polar residues down regulate these processes. Finally, pairing AF2-Multimer modeling with AAMD simulations indicated that dynamic, oligomeric assemblies of TDP-43 that are stabilized by a methionine-rich core with specific contributions from a tryptophan/leucine pair. In conclusion, our results advance the structural understanding of the mechanisms driving TDP-43 function and provide a window into the initial stages of its conversion into pathogenic aggregates.
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Affiliation(s)
- Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Jayakrishna Shenoy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Patricia M. S. dos Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - José F. Mercado Ortiz
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Leanna Bai
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Renjith Viswanathan
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Victoria Johnson
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Lohany D. Mamede
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Yuna M. Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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28
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Balkrishna A, Sharma Y, Dabas S, Arya V, Dabas A. Molecular Mechanism of Cynodon dactylon Phytosterols Targeting MAPK3 and PARP1 to Combat Epithelial Ovarian Cancer: A Multifaceted Computational Approach. Cell Biochem Biophys 2024:10.1007/s12013-024-01375-w. [PMID: 38961033 DOI: 10.1007/s12013-024-01375-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/05/2024]
Abstract
Epithelial Ovarian Cancer (EOC) presents a global health concern, necessitating the development of innovative therapeutic strategies to combat its impact. This study was employed to investigate the unexplored therapeutic efficacy of Cynodon dactylon phytochemicals against EOC using a multifaceted computational approach. A total of 19 out of 89 rigorously curated phytochemicals were assessed as potential drug targets via ADMET profiling, while protein-protein interaction analysis scrutinized the top 20 hub genes among 264 disease targets, revealing their involvement in cancer-related pathways and underscoring their significance in EOC pathogenesis. In molecular docking, Stigmasterol acetate showed the highest binding affinity (-10.9 kcal/mol) with Poly [ADP-ribose] polymerase-1 (PDB: 1UK1), while Arundoin and Beta-Sitosterol exhibited strong affinities (-10.4 kcal/mol and -10.1 kcal/mol, respectively); additionally, Beta-Sitosterol interacting with Mitogen-activated protein kinase 3 (PDB: 4QTB) showed a binding affinity of -10.1 kcal/mol, forming 2 hydrogen bonds and a total of 10 bonds with 10 residues. Molecular dynamics simulations exhibited the significant structural stability of the Beta-Sitosterol-4QTB complex with superior binding free energy (-36.61 kcal/mol) among the three complexes. This study identified C. dactylon phytosterols, particularly Beta-Sitosterol, as effective in targeting MAPK3 and PARP1 to combat EOC, laying the groundwork for further experimental validation and drug development efforts.
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Affiliation(s)
- Acharya Balkrishna
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India
- University of Patanjali, Patanjali Yogpeeth, Haridwar, 249405, Uttarakhand, India
| | - Yoganshi Sharma
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India
| | - Shakshi Dabas
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India
| | - Vedpriya Arya
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India
- University of Patanjali, Patanjali Yogpeeth, Haridwar, 249405, Uttarakhand, India
| | - Anurag Dabas
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India.
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29
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Im JK, Seo DH, Yu JS, Yoo SH. Efficient and novel biosynthesis of myricetin α-triglucoside with improved solubility using amylosucrase from Deinococcus deserti. Int J Biol Macromol 2024; 273:133205. [PMID: 38885871 DOI: 10.1016/j.ijbiomac.2024.133205] [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: 03/14/2024] [Revised: 06/02/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Although myricetin (3,3',4',5,5',7-hexahydroxyflavone, MYR) has a high antioxidant capacity and health functions, its use as a functional food material is limited owing to its low stability and water solubility. Amylosucrase (ASase) is capable of biosynthesizing flavonol α-glycoside using flavonols as acceptor molecules and sucrose as a donor molecule. Here, ASase from Deinococcus deserti (DdAS) efficiently biosynthesizes a novel MYR α-triglucoside (MYRαG3) using MYR as the acceptor molecule. Comparative homology analysis and computational simulation revealed that DdAS has a different active pocket for the transglycosylation reaction. DdAS produced MYRαG3 with a conversion efficiency of 67.4 % using 10 mM MYR and 50 mM sucrose as acceptor and donor molecules, respectively. The structure of MYRαG3 was identified as MYR 4'-O-4″,6″-tri-O-α-D-glucopyranoside using NMR and LC-MS. In silico analysis confirmed that DdAS has a distinct active pocket compared to other ASases. In addition, molecular docking simulations predicted the synthetic sequence of MYRαG3. Furthermore, MYRαG3 showed a similar DPPH radical scavenging activity of 49 %, comparable to MYR, but with significantly higher water solubility, which increased from 0.03 μg/mL to 511.5 mg/mL. In conclusion, this study demonstrated the efficient biosynthesis of a novel MYRαG3 using DdAS and highlighted the potential of MYRαG3 as a functional material.
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Affiliation(s)
- Joong-Ki Im
- Department of Food Science & Biotechnology, Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Dong-Ho Seo
- Department of Food Science & Biotechnology, Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Jae Sik Yu
- Department of Integrative Sciences and Industry, Sejong University, Seoul 05006, Republic of Korea
| | - Sang-Ho Yoo
- Department of Food Science & Biotechnology, Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea.
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30
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Jung J, Yagi K, Tan C, Oshima H, Mori T, Yu I, Matsunaga Y, Kobayashi C, Ito S, Ugarte La Torre D, Sugita Y. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. J Phys Chem B 2024; 128:6028-6048. [PMID: 38876465 PMCID: PMC11215777 DOI: 10.1021/acs.jpcb.4c02096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/16/2024]
Abstract
GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational dynamics of a single biomolecule, as well as molecular interactions in large biomolecular assemblies and between multiple biomolecules in cellular environments. To achieve the latter purpose, the earlier versions of GENESIS emphasized high performance in atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale MD simulations that include atomistic, coarse-grained, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. They demonstrate high performance and are integrated with enhanced conformational sampling algorithms and free-energy calculations without using external programs except for the QM programs. In this article, we review new functions, molecular models, and other essential features in GENESIS version 2.1 and discuss ongoing developments for future releases.
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Affiliation(s)
- Jaewoon Jung
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Cheng Tan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Graduate
School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Takaharu Mori
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department
of Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Isseki Yu
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department
of Bioinformatics, Maebashi Institute of
Technology, Maebashi, Gunma 371-0816, Japan
| | - Yasuhiro Matsunaga
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Graduate
School of Science and Engineering, Saitama
University, Saitama 338-8570, Japan
| | - Chigusa Kobayashi
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Shingo Ito
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Diego Ugarte La Torre
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
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31
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Xiong F, Zhang Y, Jiao J, Zhu Y, Mo T, Li Y. Towards new bioactive fluorine-containing 1,3,4-oxadiazole-amide derivatives: synthesis, antibacterial activity, molecular docking and molecular dynamics simulation study. Mol Divers 2024:10.1007/s11030-024-10893-x. [PMID: 38900333 DOI: 10.1007/s11030-024-10893-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Through the approach of molecular hybridization, this study rationally designed and synthesized new trifluoromethyl-1,3,4-oxadiazole amide derivatives, denoted as 1a-1n. The findings reveal that these novel molecules exhibit potent inhibitory effects against various bacterial strains. Thereinto, compounds 1c, 1d, 1i, 1j and 1n, demonstrate relatively superior antimicrobial performance against B. cereus FM314, with a minimum inhibitory concentration (MIC) of 0.03907 μg/mL. Molecular docking analysis suggests the potential importance of the Ser57 and Thr125 amino acid residues (PDB ID: 4EI9) in contributing to the inhibitory activity against B. cereus. The consistency of these results was further corroborated through subsequent molecular dynamics simulations and MMPBSA validations. The insights gained from this study serve to facilitate the rational design and efficient development of novel eco-friendly antimicrobial inhibitors based on the trifluoromethyl-1,3,4-oxadiazole amide scaffold.
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Affiliation(s)
- Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China.
| | - Yanjun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Jinlong Jiao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Yiren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China.
| | - Yeji Li
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
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32
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Hu A, Chen H, Pang W, Pu X, Qi Z, Chen H. Identification of potential modulators for human GPD1 by docking-based virtual screening, molecular dynamics simulations, binding free energy calculations, and DeLA-drug analysis. Sci Rep 2024; 14:14123. [PMID: 38898093 PMCID: PMC11187211 DOI: 10.1038/s41598-024-61439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 05/06/2024] [Indexed: 06/21/2024] Open
Abstract
Cytosolic Glycerol-3-phosphate dehydrogenase 1 (GPD1, EC 1.1.1.8) plays a pivotal role in regulating the Embden-Meyerhof glucose glycolysis pathway (E-M pathway), as well as in conditions such as Huntington's disease, cancer, and its potential role as a specific marker for Dormant Glioma Stem Cells. In this study, we conducted virtual screening using the ZINC database ( http://zinc.docking.org/ ) and the GPD1 structure to identify potential GPD1 modulators. The investigation involved screening active candidate ligands using ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) parameters, combined with molecular docking, pose analysis, and interaction analysis based on Lipinski and Veber criteria. Subsequently, the top 10 ligands were subjected to 200 ns all-atom molecular dynamics (M.D.) simulations, and binding free energies were calculated. The findings revealed that specific residues, namely TRP14, PRO94, LYS120, ASN151, THR264, ASP260, and GLN298, played a crucial role in ensuring system stability. Furthermore, through a comprehensive analysis involving molecular docking, molecular M.D., and DeLA-Drug, we identified 10 promising small molecules. These molecules represent potential lead compounds for developing effective therapeutics targeting GPD1-associated diseases, thereby contributing to a deeper understanding of GPD1-associated mechanisms. This study's significance lies in identifying key residues associated with GPD1 and discovering valuable small molecules, providing a foundation for further research and development.
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Affiliation(s)
- Anzheng Hu
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, Guangxi, China
| | - Hongwei Chen
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, Guangxi, China
| | - Wenwei Pang
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xiaojie Pu
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, Guangxi, China
| | - Zhongquan Qi
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Haiyan Chen
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, Guangxi, China.
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33
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Roque-Borda CA, Primo LMDG, Franzyk H, Hansen PR, Pavan FR. Recent advances in the development of antimicrobial peptides against ESKAPE pathogens. Heliyon 2024; 10:e31958. [PMID: 38868046 PMCID: PMC11167364 DOI: 10.1016/j.heliyon.2024.e31958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Multi-drug resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are a global health threat. The severity of the problem lies in its impact on mortality, therapeutic limitations, the threat to public health, and the costs associated with managing infections caused by these resistant strains. Effectively addressing this challenge requires innovative approaches to research, the development of new antimicrobials, and more responsible antibiotic use practices globally. Antimicrobial peptides (AMPs) are a part of the innate immune system of all higher organisms. They are short, cationic and amphipathic molecules with broad-spectrum activity. AMPs interact with the negatively charged bacterial membrane. In recent years, AMPs have attracted considerable interest as potential antibiotics. However, AMPs have low bioavailability and short half-lives, which may be circumvented by chemical modification. This review presents recent in vitro and in silico strategies for the modification of AMPs to improve their stability and application in preclinical experiments.
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Affiliation(s)
- Cesar Augusto Roque-Borda
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, Brazil
- Universidad Católica de Santa María, Vicerrectorado de Investigación, Arequipa, Peru
| | | | - Henrik Franzyk
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, Denmark
| | - Paul Robert Hansen
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, Denmark
| | - Fernando Rogério Pavan
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, Brazil
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34
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Yang Y, Chen J, Luo Y, Liu P, Xia M, Zhou S, Meng L, Chen Y, Bate B. Molecular Dynamics Simulation of the Interaction within the Carboxymethyl Cellulose-Modified Montmorillonite Lamellae at Aggressive CuCl 2 Concentrations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:11732-11744. [PMID: 38770950 DOI: 10.1021/acs.langmuir.4c01157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
To elucidate the degradation mechanism of the CMC-modified MMT composite at aggressive Cu2+ concentrations, large scale molecular dynamics simulation was conducted for CuCl2 concentrations ranging from 0 to 800 mM. Both CMC and MMT followed the Langmuir isotherm for Cu2+ adsorption, and the adsorption capacity of CMC (8.75 mmol/g) was much higher than that of MMT (0.83 mmol/g). Despite the CMC mass ratio being only 4.1%, it adsorbed up to 34.3% of the total adsorbed Cu2+. The Cu2+ attraction ability hierarchy of oxygen-containing functional groups in the CMC is as follows: carboxylic oxygens > alcoholic oxygens > carbinolic oxygens > bridging oxygens > glucose oxygens. Carboxyls were the most effective in chelating and complexing with Cu2+, and they could be intentionally added in artificially synthesized polymer-MMT composites for Cu2+ containment. Formation of the Cu2+ cation bridge between CMC and MMT at aggressive CuCl2 concentrations contributed to the transition of CMC density distribution from unimodality to bimodality and enhanced resistance of polymer elution. As the CuCl2 concentration increased, the stoichiometric ratio between the chelated Cu2+ and carboxylic oxygens increased from 1:2 to 1:1, suggesting the evolution of the Cu2+ chelation mechanism.
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Affiliation(s)
- Yixin Yang
- Institute of Geotechnical Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Jiakai Chen
- Institute of Geotechnical Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Luo
- Institute of Geotechnical Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Pengfei Liu
- Institute of Geotechnical Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Min Xia
- The Architectural Design & Research Institute of Zhejiang University Co., Ltd., Hangzhou 310058, China
| | - Sheng Zhou
- Institute of Geotechnical Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Longlong Meng
- Institute of Geotechnical Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Yunmin Chen
- Institute of Geotechnical Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Bate Bate
- Institute of Geotechnical Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
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35
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Pereira AMG, de Oliveira VM, da Rocha MN, Roberto CHA, Cajazeiras FFM, Guedes JM, Marinho MM, Teixeira AMR, Marinho ES, de Lima-Neto P, Dos Santos HS. Structure and Ligand Based Virtual Screening and MPO Topological Analysis of Triazolo Thiadiazepine-fused Coumarin Derivatives as Anti-Parkinson Drug Candidates. Mol Biotechnol 2024:10.1007/s12033-024-01200-y. [PMID: 38834896 DOI: 10.1007/s12033-024-01200-y] [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: 04/15/2024] [Accepted: 05/10/2024] [Indexed: 06/06/2024]
Abstract
Parkinson's disease (PD) is a debilitating condition that can cause locomotor problems in affected patients, such as tremors and body rigidity. PD therapy often includes the use of monoamine oxidase B (MAOB) inhibitors, particularly phenylhalogen compounds and coumarin-based semi-synthetic compounds. The objective of this study was to analyze the structural, pharmacokinetic, and pharmacodynamic profile of a series of Triazolo Thiadiazepine-fused Coumarin Derivatives (TDCDs) against MAOB, in comparison with the inhibitor safinamide. To achieve this goal, we utilized structure-based virtual screening techniques, including target prediction and absorption, distribution, metabolism, and excretion (ADME) prediction based on multi-parameter optimization (MPO) topological analysis, as well as ligand-based virtual screening techniques, such as docking and molecular dynamics. The findings indicate that the TDCDs exhibit structural similarity to other bioactive compounds containing coumarin and MAOB-binding azoles, which are present in the ChEMBL database. The topological analyses suggest that TDCD3 has the best ADME profile, particularly due to the alignment between low lipophilicity and high polarity. The coumarin and triazole portions make a strong contribution to this profile, resulting in a permeability with Papp estimated at 2.15 × 10-5 cm/s, indicating high cell viability. The substance is predicted to be metabolically stable. It is important to note that this is an objective evaluation based on the available data. Molecular docking simulations showed that the ligand has an affinity energy of - 8.075 kcal/mol with MAOB and interacts with biological substrate residues such as Pro102 and Phe103. The results suggest that the compound has a safe profile in relation to the MAOB model, making it a promising active ingredient for the treatment of PD.
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Affiliation(s)
- Antônio Mateus Gomes Pereira
- Doctoral Program in Biotechnology, Northeast Biotechnology Network, State University of Ceará, Fortaleza, CE, Brazil
- Center of Molecular Bioprospecting and Applied Experimentation, University Center INTA - UNINTA, Sobral, CE, Brazil
| | | | - Matheus Nunes da Rocha
- Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | | | | | - Jesyka Macêdo Guedes
- Center of Exact Sciences and Technology, State University Vale Do Acaraú, Sobral, CE, Brazil
| | - Márcia Machado Marinho
- Center of Exact Sciences and Technology, State University Vale Do Acaraú, Sobral, CE, Brazil
| | | | - Emmanuel Silva Marinho
- Postgraduate Program in Natural Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | - Pedro de Lima-Neto
- Department of Analytical Chemistry and Phisicochemistry, Federal University of Ceará, Campus Do Pici, Fortaleza, CE, Brazil
| | - Hélcio Silva Dos Santos
- Center of Exact Sciences and Technology, State University Vale Do Acaraú, Sobral, CE, Brazil.
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36
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Schmidt B, Hildebrandt A. From GPUs to AI and quantum: three waves of acceleration in bioinformatics. Drug Discov Today 2024; 29:103990. [PMID: 38663581 DOI: 10.1016/j.drudis.2024.103990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/05/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
The enormous growth in the amount of data generated by the life sciences is continuously shifting the field from model-driven science towards data-driven science. The need for efficient processing has led to the adoption of massively parallel accelerators such as graphics processing units (GPUs). Consequently, the development of bioinformatics methods nowadays often heavily depends on the effective use of these powerful technologies. Furthermore, progress in computational techniques and architectures continues to be highly dynamic, involving novel deep neural network models and artificial intelligence (AI) accelerators, and potentially quantum processing units in the future. These are expected to be disruptive for the life sciences as a whole and for drug discovery in particular. Here, we identify three waves of acceleration and their applications in a bioinformatics context: (i) GPU computing, (ii) AI and (iii) next-generation quantum computers.
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Affiliation(s)
- Bertil Schmidt
- Institut für Informatik, Johannes Gutenberg University, Mainz, Germany.
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37
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Schlimgen RR, Peterson FC, Heukers R, Smit MJ, McCorvy JD, Volkman BF. Structural basis for selectivity and antagonism in extracellular GPCR-nanobodies. Nat Commun 2024; 15:4611. [PMID: 38816420 PMCID: PMC11139983 DOI: 10.1038/s41467-024-49000-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are pivotal therapeutic targets, but their complex structure poses challenges for effective drug design. Nanobodies, or single-domain antibodies, have emerged as a promising therapeutic strategy to target GPCRs, offering advantages over traditional small molecules and antibodies. However, an incomplete understanding of the structural features enabling GPCR-nanobody interactions has limited their development. In this study, we investigate VUN701, a nanobody antagonist targeting the atypical chemokine receptor 3 (ACKR3). We determine that an extended CDR3 loop is required for ACKR3 binding. Uncommon in most nanobodies, an extended CDR3 is prevalent in GPCR-targeting nanobodies. Combining experimental and computational approaches, we map an inhibitory ACKR3-VUN701 interface and define a distinct conformational mechanism for GPCR inactivation. Our results provide insights into class A GPCR-nanobody selectivity and suggest a strategy for the development of these new therapeutic tools.
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Affiliation(s)
- Roman R Schlimgen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Raimond Heukers
- Amsterdam Institute of Molecular and Life Sciences, Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit, 1081 HZ, Amsterdam, The Netherlands
| | - Martine J Smit
- Amsterdam Institute of Molecular and Life Sciences, Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit, 1081 HZ, Amsterdam, The Netherlands
| | - John D McCorvy
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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38
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Mas Magre I, Grima Torres R, Cela Espín JM, Gutierrez Moreno JJ. The NOMAD mini-apps: A suite of kernels from ab initio electronic structure codes enabling co-design in high-performance computing. OPEN RESEARCH EUROPE 2024; 4:35. [PMID: 38974408 PMCID: PMC11224708 DOI: 10.12688/openreseurope.16920.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
This article introduces a suite of mini-applications (mini-apps) designed to optimise computational kernels in ab initio electronic structure codes. The suite is developed from flagship applications participating in the NOMAD Center of Excellence, such as the ELPA eigensolver library and the GW implementations of the exciting, Abinit, and FHI-aims codes. The mini-apps were identified by targeting functions that significantly contribute to the total execution time in the parent applications. This strategic selection allows for concentrated optimisation efforts. The suite is designed for easy deployment on various High-Performance Computing (HPC) systems, supported by an integrated CMake build system for straightforward compilation and execution. The aim is to harness the capabilities of emerging (post)exascale systems, which necessitate concurrent hardware and software development - a concept known as co-design. The mini-app suite serves as a tool for profiling and benchmarking, providing insights that can guide both software optimisation and hardware design. Ultimately, these developments will enable more accurate and efficient simulations of novel materials, leveraging the full potential of exascale computing in material science research.
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Affiliation(s)
- Isidre Mas Magre
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, Barcelona, 08034, Spain
| | - Rogeli Grima Torres
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, Barcelona, 08034, Spain
| | - José María Cela Espín
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, Barcelona, 08034, Spain
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39
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Truong DT, Ho K, Nhi HTY, Nguyen VH, Dang TT, Nguyen MT. Imidazole[1,5-a]pyridine derivatives as EGFR tyrosine kinase inhibitors unraveled by umbrella sampling and steered molecular dynamics simulations. Sci Rep 2024; 14:12218. [PMID: 38806555 PMCID: PMC11133355 DOI: 10.1038/s41598-024-62743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
Although the use of the tyrosine kinase inhibitors (TKIs) has been proved that it can save live in a cancer treatment, the currently used drugs bring in many undesirable side-effects. Therefore, the search for new drugs and an evaluation of their efficiency are intensively carried out. Recently, a series of eighteen imidazole[1,5-a]pyridine derivatives were synthetized by us, and preliminary analyses pointed out their potential to be an important platform for pharmaceutical development owing to their promising actions as anticancer agents and enzyme (kinase, HIV-protease,…) inhibitors. In the present theoretical study, we further analyzed their efficiency in using a realistic scenario of computational drug design. Our protocol has been developed to not only observe the atomistic interaction between the EGFR protein and our 18 novel compounds using both umbrella sampling and steered molecular dynamics simulations, but also determine their absolute binding free energies. Calculated properties of the 18 novel compounds were in detail compared with those of two known drugs, erlotinib and osimertinib, currently used in cancer treatment. Inspiringly the simulation results promote three imidazole[1,5-a]pyridine derivatives as promising inhibitors into a further step of clinical trials.
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Affiliation(s)
- Duc Toan Truong
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Kiet Ho
- Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City, 70000, Vietnam
| | - Huynh Thi Yen Nhi
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Van Ha Nguyen
- Faculty of Chemistry, VNU University of Science, Vietnam National University, Hanoi, 19 Le Thanh Tong, Hoan Kiem, Hanoi, 11021, Vietnam
| | - Tuan Thanh Dang
- Faculty of Chemistry, VNU University of Science, Vietnam National University, Hanoi, 19 Le Thanh Tong, Hoan Kiem, Hanoi, 11021, Vietnam
| | - Minh Tho Nguyen
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
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40
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Yan X, Kuster D, Mohanty P, Nijssen J, Pombo-García K, Rizuan A, Franzmann TM, Sergeeva A, Passos PM, George L, Wang SH, Shenoy J, Danielson HL, Honigmann A, Ayala YM, Fawzi NL, Mittal J, Alberti S, Hyman AA. Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576837. [PMID: 38328053 PMCID: PMC10849624 DOI: 10.1101/2024.01.23.576837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Cytosolic aggregation of the nuclear protein TDP-43 is associated with many neurodegenerative diseases, but the triggers for TDP-43 aggregation are still debated. Here, we demonstrate that TDP-43 aggregation requires a double event. One is up-concentration in stress granules beyond a threshold, and the other is oxidative stress. These two events collectively induce intra-condensate demixing, giving rise to a dynamic TDP-43 enriched phase within stress granules, which subsequently transitions into pathological aggregates. Mechanistically, intra-condensate demixing is triggered by local unfolding of the RRM1 domain for intermolecular disulfide bond formation and by increased hydrophobic patch interactions in the C-terminal domain. By engineering TDP-43 variants resistant to intra-condensate demixing, we successfully eliminate pathological TDP-43 aggregates in cells. We conclude that up-concentration inside condensates and simultaneous exposure to environmental stress could be a general pathway for protein aggregation, with intra-condensate demixing constituting a key intermediate step.
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Affiliation(s)
- Xiao Yan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
| | - David Kuster
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
- These authors contributed equally
| | - Jik Nijssen
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Karina Pombo-García
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
| | - Titus M. Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Aleksandra Sergeeva
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Patricia M. Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Leah George
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Jayakrishna Shenoy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Helen L. Danielson
- Center for Biomedical Engineering, Brown University; Providence, RI 02912; USA
| | - Alf Honigmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Yuna M. Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
- Department of Chemistry, Texas A&M University; College Station, TX 77843; USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University; College Station, TX 77843; USA
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- Lead contact
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41
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Kar M, Vogel LT, Chauhan G, Felekyan S, Ausserwöger H, Welsh TJ, Dar F, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Solutes unmask differences in clustering versus phase separation of FET proteins. Nat Commun 2024; 15:4408. [PMID: 38782886 PMCID: PMC11116469 DOI: 10.1038/s41467-024-48775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Phase separation and percolation contribute to phase transitions of multivalent macromolecules. Contributions of percolation are evident through the viscoelasticity of condensates and through the formation of heterogeneous distributions of nano- and mesoscale pre-percolation clusters in sub-saturated solutions. Here, we show that clusters formed in sub-saturated solutions of FET (FUS-EWSR1-TAF15) proteins are affected differently by glutamate versus chloride. These differences on the nanoscale, gleaned using a suite of methods deployed across a wide range of protein concentrations, are prevalent and can be unmasked even though the driving forces for phase separation remain unchanged in glutamate versus chloride. Strikingly, differences in anion-mediated interactions that drive clustering saturate on the micron-scale. Beyond this length scale the system separates into coexisting phases. Overall, we find that sequence-encoded interactions, mediated by solution components, make synergistic and distinct contributions to the formation of pre-percolation clusters in sub-saturated solutions, and to the driving forces for phase separation.
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Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anjana R Kamath
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Anthony A Hyman
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany.
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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42
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Zhou J, Sun P, Wang Y, Qiu R, Yang Z, Guo J, Li Z, Xiao S, Fang L. Deep profiling of potential substrate atlas of porcine epidemic diarrhea virus 3C-like protease. J Virol 2024; 98:e0025324. [PMID: 38591878 PMCID: PMC11092332 DOI: 10.1128/jvi.00253-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
Coronavirus (CoV) 3C-like protease (3CLpro) is essential for viral replication and is involved in immune escape by proteolyzing host proteins. Deep profiling the 3CLpro substrates in the host proteome extends our understanding of viral pathogenesis and facilitates antiviral drug discovery. Here, 3CLpro from porcine epidemic diarrhea virus (PEDV), an enteropathogenic CoV, was used as a model which to identify the potential 3CLpro cleavage motifs in all porcine proteins. We characterized the selectivity of PEDV 3CLpro at sites P5-P4'. We then compiled the 3CLpro substrate preferences into a position-specific scoring matrix and developed a 3CLpro profiling strategy to delineate the protein substrate landscape of CoV 3CLpro. We identified 1,398 potential targets in the porcine proteome containing at least one putative cleavage site and experimentally validated the reliability of the substrate degradome. The PEDV 3CLpro-targeted pathways are involved in mRNA processing, translation, and key effectors of autophagy and the immune system. We also demonstrated that PEDV 3CLpro suppresses the type 1 interferon (IFN-I) cascade via the proteolysis of multiple signaling adaptors in the retinoic acid-inducible gene I (RIG-I) signaling pathway. Our composite method is reproducible and accurate, with an unprecedented depth of coverage for substrate motifs. The 3CLpro substrate degradome establishes a comprehensive substrate atlas that will accelerate the investigation of CoV pathogenicity and the development of anti-CoV drugs.IMPORTANCECoronaviruses (CoVs) are major pathogens that infect humans and animals. The 3C-like protease (3CLpro) encoded by CoV not only cleaves the CoV polyproteins but also degrades host proteins and is considered an attractive target for the development of anti-CoV drugs. However, the comprehensive characterization of an atlas of CoV 3CLpro substrates is a long-standing challenge. Using porcine epidemic diarrhea virus (PEDV) 3CLpro as a model, we developed a method that accurately predicts the substrates of 3CLpro and comprehensively maps the substrate degradome of PEDV 3CLpro. Interestingly, we found that 3CLpro may simultaneously degrade multiple molecules responsible for a specific function. For instance, it cleaves at least four adaptors in the RIG-I signaling pathway to suppress type 1 interferon production. These findings highlight the complexity of the 3CLpro substrate degradome and provide new insights to facilitate the development of anti-CoV drugs.
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Affiliation(s)
- Junwei Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Peng Sun
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yuanqing Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Runhui Qiu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhixiang Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jiahui Guo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhuang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Truong DT, Ho K, Pham DQH, Chwastyk M, Nguyen-Minh T, Nguyen MT. Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics. Sci Rep 2024; 14:10475. [PMID: 38714683 PMCID: PMC11076533 DOI: 10.1038/s41598-024-59899-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/16/2024] [Indexed: 05/10/2024] Open
Abstract
To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.
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Affiliation(s)
- Duc Toan Truong
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Kiet Ho
- Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City, 70000, Vietnam
| | | | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Thai Nguyen-Minh
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000, Vietnam
| | - Minh Tho Nguyen
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
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Mohanty P, Phan TM, Mittal J. Transient interdomain interactions modulate the monomeric structural ensemble and oligomerization landscape of Huntingtin Exon 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592468. [PMID: 38766024 PMCID: PMC11100600 DOI: 10.1101/2024.05.03.592468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Polyglutamine expansion (≥ 36 residues) within the N-terminal exon-1 of Huntingtin (Httex1) leads to Huntington's disease, a neurogenerative condition marked by the presence of intranuclear Htt inclusions. Notably, the polyglutamine tract in Httex1 is flanked by an N-terminal coiled-coil domain - N17 (17 amino acids), which undergoes self-association to promote the formation of soluble Httex1 oligomers and brings the aggregation-prone polyQ tracts in close spatial proximity. However, the mechanisms underlying the subsequent conversion of soluble oligomers into insoluble β-rich aggregates with increasing polyQ length, remain unclear. Current knowledge suggests that expansion of the polyQ tract increases its helicity, and this favors its oligomerization and aggregation. In addition, studies utilizing conformation-specific antibodies and a stable coiled-coil heterotetrametric system fused to polyQ indicate that domain "cross-talk" (i.e., interdomain interactions) may be necessary to efficiently promote the emergence of toxic conformations (in monomers and oligomers) and fibrillar aggregation. Here, we performed extensive atomistic molecular dynamics (MD) simulations (aggregate time ∼ 0.7 ms) of N17-polyQ fragments to uncover the interplay between structural transformation and domain "cross-talk" on the monomeric structural ensemble and oligomerization landscape of Httex1. Our simulation ensembles of N17-polyQ monomers validated against 13 C NMR chemical shifts indicated that in addition to elevated α-helicity, polyQ expansion also favors transient, interdomain (N17-polyQ) interactions which result in the emergence of β-conformations. Further, interdomain interactions decreased the overall stability of N17-mediated dimers by counteracting the stabilizing effect of increased α-helicity and promoted a heterogenous oligomerization landscape on the sub-microsecond timescale. Overall, our study uncovers the significance of domain "cross-talk" in modulating the monomeric conformational ensemble and oligomerization landscape of Httex1 to favor the formation of amyloid aggregates.
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45
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Pathak RK, Jung DW, Shin SH, Ryu BY, Lee HS, Kim JM. Deciphering the mechanisms and interactions of the endocrine disruptor bisphenol A and its analogs with the androgen receptor. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133935. [PMID: 38442602 DOI: 10.1016/j.jhazmat.2024.133935] [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: 11/29/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Bisphenol A (BPA) and its various forms used as BPA alternatives in industries are recognized toxic compounds and antiandrogenic endocrine disruptors. These chemicals are widespread in the environment and frequently detected in biological samples. Concerns exist about their impact on hormones, disrupting natural biological processes in humans, together with their negative impacts on the environment and biotic life. This study aims to characterize the interaction between BPA analogs and the androgen receptor (AR) and the effect on the receptor's normal activity. To achieve this goal, molecular docking was conducted with BPA and its analogs and dihydrotestosterone (DHT) as a reference ligand. Four BPA analogs exhibited higher affinity (-10.2 to -8.7 kcal/mol) for AR compared to BPA (-8.6 kcal/mol), displaying distinct interaction patterns. Interestingly, DHT (-11.0 kcal/mol) shared a binding pattern with BPA. ADMET analysis of the top 10 compounds, followed by molecular dynamics simulations, revealed toxicity and dynamic behavior. Experimental studies demonstrated that only BPA disrupts DHT-induced AR dimerization, thereby affecting AR's function due to its binding nature. This similarity to DHT was observed during computational analysis. These findings emphasize the importance of targeted strategies to mitigate BPA toxicity, offering crucial insights for interventions in human health and environmental well-being.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Da-Woon Jung
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Seung-Hee Shin
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Buom-Yong Ryu
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Hee-Seok Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea; Department of Food Safety and Regulatory Science, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea.
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea.
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46
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He ZC, Zhang T, Peng W, Mei Q, Wang QZ, Ding F. Exploring the neurotoxicity of chiral dinotefuran towards nicotinic acetylcholine receptors: Enantioselective insights into species selectivity. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134020. [PMID: 38521037 DOI: 10.1016/j.jhazmat.2024.134020] [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: 12/22/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Dinotefuran is a chiral neonicotinoid that is widely distributed in environmental matrices, but its health risks to different organisms are poorly understood. This study investigated the neurotoxic responses of honeybee/cotton aphid nicotinic acetylcholine receptors (nAChRs) to chiral dinotefuran at the enantiomeric scale and demonstrated the microscopic mechanism of species selectivity in nAChR-mediated enantioselective neurotoxicity. The findings indicated that (S)-dinotefuran had a higher affinity for honeybee nAChR than (R)-dinotefuran whereas both enantiomers exhibited similar bioactivity toward cotton aphid nAChR. The results of dynamic neurotoxic processes indicated the association of conformational changes induced by chiral dinotefuran with its macroscopic neurotoxicity, and (R)-dinotefuran, which exhibit low toxicity to honeybee, was found to induce significant conformational changes in the enantioselective neurotoxic reaction, as supported by the average root-mean-square fluctuation (0.35 nm). Energy decomposition results indicated that electrostatic contribution (ΔGele) is the critical energy term that leads to substantial enantioselectivity, and both Trp-51 (-2.57 kcal mol-1) and Arg-75 (-4.86 kcal mol-1), which form a hydrogen-bond network, are crucial residues in mediating the species selectivity for enantioselective neurotoxic responses. Clearly, this study provides experimental evidence for a comprehensive assessment of the health hazards of chiral dinotefuran.
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Affiliation(s)
- Zhi-Cong He
- School of Water and Environment, Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Key Laboratory of Ecohydrology and Water Security in Arid and Semi-Arid Regions of Ministry of Water Resources, Chang'an University, Xi'an 710054, China
| | - Tao Zhang
- School of Water and Environment, Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Key Laboratory of Ecohydrology and Water Security in Arid and Semi-Arid Regions of Ministry of Water Resources, Chang'an University, Xi'an 710054, China
| | - Wei Peng
- State Key Laboratory of Loess and Quaternary Geology, Center for Excellence in Quaternary Science and Global Change, Key Laboratory of Aerosol Chemistry and Physics, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Qiong Mei
- School of Water and Environment, Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Key Laboratory of Ecohydrology and Water Security in Arid and Semi-Arid Regions of Ministry of Water Resources, Chang'an University, Xi'an 710054, China; School of Land Engineering, Chang'an University, Xi'an 710054, China
| | - Qi-Zhao Wang
- School of Water and Environment, Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Key Laboratory of Ecohydrology and Water Security in Arid and Semi-Arid Regions of Ministry of Water Resources, Chang'an University, Xi'an 710054, China
| | - Fei Ding
- School of Water and Environment, Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Key Laboratory of Ecohydrology and Water Security in Arid and Semi-Arid Regions of Ministry of Water Resources, Chang'an University, Xi'an 710054, China.
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47
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Tayyeb JZ, Mondal S, Anisur Rahman M, Kumar S, Bayıl I, Akash S, Hossain MS, Alqahtani T, Zaki MEA, Oliveira JIN. Identification of Helicobacter pylori-carcinogenic TNF-alpha-inducing protein inhibitors via daidzein derivatives through computational approaches. J Cell Mol Med 2024; 28:e18358. [PMID: 38693868 PMCID: PMC11063725 DOI: 10.1111/jcmm.18358] [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: 12/30/2023] [Revised: 03/10/2024] [Accepted: 03/18/2024] [Indexed: 05/03/2024] Open
Abstract
Gastric cancer is considered a class 1 carcinogen that is closely linked to infection with Helicobacter pylori (H. pylori), which affects over 1 million people each year. However, the major challenge to fight against H. pylori and its associated gastric cancer due to drug resistance. This research gap had led our research team to investigate a potential drug candidate targeting the Helicobacter pylori-carcinogenic TNF-alpha-inducing protein. In this study, a total of 45 daidzein derivatives were investigated and the best 10 molecules were comprehensively investigated using in silico approaches for drug development, namely pass prediction, quantum calculations, molecular docking, molecular dynamics simulations, Lipinski rule evaluation, and prediction of pharmacokinetics. The molecular docking study was performed to evaluate the binding affinity between the target protein and the ligands. In addition, the stability of ligand-protein complexes was investigated by molecular dynamics simulations. Various parameters were analysed, including root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), hydrogen bond analysis, principal component analysis (PCA) and dynamic cross-correlation matrix (DCCM). The results has confirmed that the ligand-protein complex CID: 129661094 (07) and 129664277 (08) formed stable interactions with the target protein. It was also found that CID: 129661094 (07) has greater hydrogen bond occupancy and stability, while the ligand-protein complex CID 129664277 (08) has greater conformational flexibility. Principal component analysis revealed that the ligand-protein complex CID: 129661094 (07) is more compact and stable. Hydrogen bond analysis revealed favourable interactions with the reported amino acid residues. Overall, this study suggests that daidzein derivatives in particular show promise as potential inhibitors of H. pylori.
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Affiliation(s)
- Jehad Zuhair Tayyeb
- Department of Clinical Biochemistry, College of MedicineUniversity of JeddahJeddahSaudi Arabia
| | - Shibam Mondal
- Pharmacy Discipline, School of Life SciencesKhulna UniversityKhulnaBangladesh
| | | | - Swapon Kumar
- Department of PharmacyJahangirnagar UniversitySavarBangladesh
| | - Imren Bayıl
- Department of Bioinformatics and Computational BiologyGaziantep UniversityGaziantepTurkey
| | - Shopnil Akash
- Department of PharmacyDaffodil International UniversityDhakaBangladesh
| | | | - Taha Alqahtani
- Department of Pharmacology, College of PharmacyKing Khalid UniversityAbhaSaudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, College of ScienceImam Mohammad Ibn Saud Islamic UniversityRiyadhSaudi Arabia
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience CenterFederal University of Rio Grande do NorteNatalBrazil
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48
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Feng M, Chan KC, Zhong Q, Zhou R. In silico design of high-affinity antigenic peptides for HLA-B44. Int J Biol Macromol 2024; 267:131356. [PMID: 38574928 DOI: 10.1016/j.ijbiomac.2024.131356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Cancer cell-killing by CD8+ T cells demands effective tumor antigen presentation by human leukocyte antigen class I (HLA-I) molecules. Screening and designing highly immunogenic neoantigens require quantitative computations to reliably predict HLA-peptide binding affinities. Here, with all-atom molecular dynamics (MD) simulations and free energy perturbation (FEP) methods, we design a collection of antigenic peptide candidates through in silico mutagenesis studies on immunogenic neoantigens, yielding enhanced binding affinities to HLA-B*44:02. In-depth structural dissection shows that introducing positively charged residues such as arginine to position 6 or lysine to position 7 of the candidates triggers conformational shifts in both peptides and the antigen-binding groove of the HLA, following the "induced-fit" mechanism. Enhancement in binding affinities compared to the wild-type was found in three out of five mutated candidates. The HLA pocket, capable of accommodating positively charged residues in positions from 5 to 7, is designated as the "dynamic pocket". Taken together, we showcase an effective structure-based binding affinity optimization framework for antigenic peptides of HLA-B*44:02 and underscore the importance of dynamic nature of the antigen-binding groove in concert with the anchoring motifs. This work provides structural insights for rational design of favorable HLA-peptide bindings and future developments in neoantigen-based therapeutics.
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Affiliation(s)
- Mei Feng
- Lanzhou Center for Theoretical Physics, Key Laboratory of Theoretical Physics of Gansu Province, Lanzhou University, Lanzhou, Gansu 730000, China; Institute of Quantitative Biology, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China; Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China
| | - Kevin C Chan
- Institute of Quantitative Biology, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China; Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China
| | - Qinglu Zhong
- Institute of Quantitative Biology, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China; Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China; Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China; The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China; Department of Chemistry, Columbia University, New York, NY 10027, USA.
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49
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Li J, Shao Q, Xiang Y, Li J, Chen J, Du G, Kang Z, Wang Y. High-activity recombinant human carboxypeptidase B expression in Pichia pastoris through rational protein engineering and enhancing secretion from the Golgi apparatus to the plasma membrane. Biotechnol J 2024; 19:e2400098. [PMID: 38797728 DOI: 10.1002/biot.202400098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024]
Abstract
Human carboxypeptidase B1 (hCPB1) is vital for recombinant insulin production, holding substantial value in the pharmaceutical industry. Current challenges include limited hCPB1 enzyme activity. In this study, recombinant hCPB1 efficient expression in Pichia pastoris was achieved. To enhance hCPB1 secretion, we conducted signal peptides screening and deleted the Vps10 sortilin domain, reducing vacuolar mis-sorting. Overexpression of Sec4p increased the fusion of secretory vesicles with the plasma membrane and improved hCPB1 secretion by 20%. Rational protein engineering generated twenty-two single-mutation mutants and identified the A178L mutation resulted in a 30% increase in hCPB1 specific activity. However, all combinational mutations that increased specific activities decreased protein expression levels. Therefore, computer-aided global protein design with PROSS was employed for the aim of improving specific activities and preserving good protein expression. Among the six designed mutants, hCPB1-P6 showed a remarkable 114% increase in the catalytic rate constant (kcat), a 137% decrease in the Michaelis constant (Km), and a 490% increase in catalytic efficiency. Most mutations occurred on the surface of hCPB1-P6, with eight sites mutated to proline. In a 5 L fermenter, hCPB1-P6 was produced by the secretion-enhanced P. pastoris chassis to 199.6 ± 20 mg L-1 with a specific activity of 96 ± 0.32 U mg-1, resulting in a total enzyme activity of 19137 ± 1131 U L-1, demonstrating significant potential for industrial applications.
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Affiliation(s)
- Jia Li
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qinan Shao
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yulong Xiang
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jianghua Li
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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50
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Ikizawa S, Hori T, Wijaya TN, Kono H, Bai Z, Kimizono T, Lu W, Tran DP, Kitao A. PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses. J Phys Chem B 2024; 128:3631-3642. [PMID: 38578072 PMCID: PMC11033871 DOI: 10.1021/acs.jpcb.4c01271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Parallel cascade selection molecular dynamics (PaCS-MD) is an enhanced conformational sampling method conducted as a "repetition of time leaps in parallel worlds", comprising cycles of multiple molecular dynamics (MD) simulations performed in parallel and selection of the initial structures of MDs for the next cycle. We developed PaCS-Toolkit, an optimized software utility enabling the use of different MD software and trajectory analysis tools to facilitate the execution of the PaCS-MD simulation and analyze the obtained trajectories, including the preparation for the subsequent construction of the Markov state model. PaCS-Toolkit is coded with Python, is compatible with various computing environments, and allows for easy customization by editing the configuration file and specifying the MD software and analysis tools to be used. We present the software design of PaCS-Toolkit and demonstrate applications of PaCS-MD variations: original targeted PaCS-MD to peptide folding; rmsdPaCS-MD to protein domain motion; and dissociation PaCS-MD to ligand dissociation from adenosine A2A receptor.
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Affiliation(s)
- Shinji Ikizawa
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Tatsuki Hori
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Tegar Nurwahyu Wijaya
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
- Department
of Chemistry, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug, Jakarta 12220, Indonesia
| | - Hiroshi Kono
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Zhen Bai
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Tatsuhiro Kimizono
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Wenbo Lu
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Duy Phuoc Tran
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Akio Kitao
- School
of Life Science and Technology, Tokyo Institute
of Technology, 2-12-2 Ookayama, Meguro, Tokyo 152-8550, Japan
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