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Dutta D, Al Hoque A, Paul B, Park JH, Chowdhury C, Quadir M, Banerjee S, Choudhury A, Laha S, Sepay N, Boro P, Kaipparettu BA, Mukherjee B. EpCAM-targeted betulinic acid analogue nanotherapy improves therapeutic efficacy and induces anti-tumorigenic immune response in colorectal cancer tumor microenvironment. J Biomed Sci 2024; 31:81. [PMID: 39164686 PMCID: PMC11334571 DOI: 10.1186/s12929-024-01069-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/09/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Betulinic acid (BA) has been well investigated for its antiproliferative and mitochondrial pathway-mediated apoptosis-inducing effects on various cancers. However, its poor solubility and off-target activity have limited its utility in clinical trials. Additionally, the immune modulatory role of betulinic acid analogue in the tumor microenvironment (TME) is largely unknown. Here, we designed a potential nanotherapy for colorectal cancer (CRC) with a lead betulinic acid analogue, named as 2c, carrying a 1,2,3-triazole-moiety attached to BA through a linker, found more effective than BA for inhibiting CRC cell lines, and was chosen here for this investigation. Epithelial cell adhesion molecule (EpCAM) is highly overexpressed on the CRC cell membrane. A single-stranded short oligonucleotide sequence, aptamer (Apt), that folds into a 3D-defined architecture can be used as a targeting ligand for its specific binding to a target protein. EpCAM targeting aptamer was designed for site-specific homing of aptamer-conjugated-2c-loaded nanoparticles (Apt-2cNP) at the CRC tumor site to enhance therapeutic potential and reduce off-target toxicity in normal cells. We investigated the in vitro and in vivo therapeutic efficacy and anti-tumorigenic immune response of aptamer conjugated nanotherapy in CRC-TME. METHODS After the characterization of nanoengineered aptamer conjugated betulinic acid nanotherapy, we evaluated therapeutic efficacy, tumor targeting efficiency, and anti-tumorigenic immune response using cell-based assays and mouse and rat models. RESULTS We found that Apt-2cNP improved drug bioavailability, enhanced its biological half-life, improved antiproliferative activity, and minimized off-target cytotoxicity. Importantly, in an in vivo TME, Apt-2cNP showed promising signs of anti-tumorigenic immune response (increased mDC/pDC ratio, enhanced M1 macrophage population, and CD8 T-cells). Furthermore, in vivo upregulation of pro-apoptotic while downregulation of anti-apoptotic genes and significant healing efficacy on cancer tissue histopathology suggest that Apt-2cNP had predominantly greater therapeutic potential than the non-aptamer-conjugated nanoparticles and free drug. Moreover, we observed greater tumor accumulation of the radiolabeled Apt-2cNP by live imaging in the CRC rat model. CONCLUSIONS Enhanced therapeutic efficacy and robust anti-tumorigenic immune response of Apt-2cNP in the CRC-TME are promising indicators of its potential as a prospective therapeutic agent for managing CRC. However, further studies are warranted.
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Affiliation(s)
- Debasmita Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, USA.
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India.
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Ashique Al Hoque
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, USA
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Brahamacharry Paul
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Mohiuddin Quadir
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND, USA
| | - Soumyabrata Banerjee
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
- Department of Psychology and Neuroscience Program, Central Michigan University, Mount Pleasant, MI, 48859, USA
- Department of Human Physiology, Vidyasagar University, Midnapore, 721102, West Bengal, India
| | | | - Soumik Laha
- CSIR- Indian Institute of Chemical Biology, Kolkata, India
| | - Nayim Sepay
- Department of Chemistry, Jadavpur University, Kolkata, India
| | - Priyanka Boro
- CSIR- Indian Institute of Chemical Biology, Kolkata, India
| | | | - Biswajit Mukherjee
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India.
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Semper C, Watanabe N, Karimullina E, Patel DT, Di Leo R, Castellanos M, Patel DH, Chaconas G, Savchenko A. Structure analysis of the telomere resolvase from the Lyme disease spirochete Borrelia garinii reveals functional divergence of its C-terminal domain. Nucleic Acids Res 2024; 52:8431-8442. [PMID: 38979576 DOI: 10.1093/nar/gkae580] [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: 01/29/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
Borrelia spirochetes are the causative agents of Lyme disease and relapsing fever, two of the most common tick-borne illnesses. A characteristic feature of these spirochetes is their highly segmented genomes which consists of a linear chromosome and a mixture of up to approximately 24 linear and circular extrachromosomal plasmids. The complexity of this genomic arrangement requires multiple strategies for efficient replication and partitioning during cell division, including the generation of hairpin ends found on linear replicons mediated by the essential enzyme ResT, a telomere resolvase. Using an integrative structural biology approach employing advanced modelling, circular dichroism, X-ray crystallography and small-angle X-ray scattering, we have generated high resolution structural data on ResT from B. garinii. Our data provides the first high-resolution structures of ResT from Borrelia spirochetes and revealed active site positioning in the catalytic domain. We also demonstrate that the C-terminal domain of ResT is required for both transesterification steps of telomere resolution, and is a requirement for DNA binding, distinguishing ResT from other telomere resolvases from phage and bacteria. These results advance our understanding of the molecular function of this essential enzyme involved in genome maintenance in Borrelia pathogens.
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Affiliation(s)
- Cameron Semper
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Nobuhiko Watanabe
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Elina Karimullina
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Deepak T Patel
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St, Toronto, Ontario M5G 1L6, Canada
| | - Mildred Castellanos
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Dhruvin H Patel
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - George Chaconas
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology, and Infectious Disease, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St, Toronto, Ontario M5G 1L6, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive, Calgary, Alberta T2N 4N1, Canada
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Latham AP, Tempkin JOB, Otsuka S, Zhang W, Ellenberg J, Sali A. Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606842. [PMID: 39149317 PMCID: PMC11326192 DOI: 10.1101/2024.08.06.606842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Dynamic processes involving biomolecules are essential for the function of the cell. Here, we introduce an integrative method for computing models of these processes based on multiple heterogeneous sources of information, including time-resolved experimental data and physical models of dynamic processes. We first compute integrative structure models at fixed time points and then optimally select and connect these snapshots into a series of trajectories that optimize the likelihood of both the snapshots and transitions between them. The method is demonstrated by application to the assembly process of the human Nuclear Pore Complex in the context of the reforming nuclear envelope during mitotic cell division, based on live-cell correlated electron tomography, bulk fluorescence correlation spectroscopy-calibrated quantitative live imaging, and a structural model of the fully-assembled Nuclear Pore Complex. Modeling of the assembly process improves the model precision over static integrative structure modeling alone. The method is applicable to a wide range of time-dependent systems in cell biology, and is available to the broader scientific community through an implementation in the open source Integrative Modeling Platform software.
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Affiliation(s)
- Andrew P Latham
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeremy O B Tempkin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wanlu Zhang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
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Lomakin IB, Devarkar SC, Grada A, Bunick CG. Mechanistic basis for the translation inhibition of Cutibacterium acnes by Clindamycin. J Invest Dermatol 2024:S0022-202X(24)01975-4. [PMID: 39122144 DOI: 10.1016/j.jid.2024.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/11/2024] [Accepted: 07/13/2024] [Indexed: 08/12/2024]
Abstract
Inflammation and the Gram-positive anaerobic bacterium Cutibacterium acnes, which is implicated in acne pathogenesis and pilosebaceous unit inflammation, are the main targets of antibiotic-based therapy against acne vulgaris (acne). The most widely used antibiotics in acne therapy are tetracyclines, macrolides, and lincosamides. Unfortunately, C. acnes bacteria over the past several decades have demonstrated increased resistance to these antibiotics, particularly to clindamycin. The precise knowledge of how antibiotics interact with their clinical target is needed to overcome this problem. Toward this goal, we determined the structure of clindamycin in complex with the ribosome of Cutibacterium acnes at 2.53 Å resolution using cryogenic electron microscopy. The galactose sugar moiety of clindamycin interacts with nucleotides of the 23S rRNA directly or through a conserved network of water-mediated interactions. Its propyl pyrrolidinyl group interacts with the 23S rRNA through van der Waals forces. Clindamycin binding to the Cutibacterium acnes ribosome interferes with both: proper orientation of the aminoacyl group of the A-site bound tRNA that is needed for peptide bond formation and with the extension of the nascent peptide. Our data are important for advancing understanding of antibiotic resistance and development of narrow- spectrum antibacterial drugs, which is an urgent need for contemporary antibiotic stewardship.
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Affiliation(s)
- Ivan B Lomakin
- Department of Dermatology, Yale University, New Haven, CT, 06520.
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06521.
| | - Ayman Grada
- Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106.
| | - Christopher G Bunick
- Department of Dermatology, Yale University, New Haven, CT, 06520; Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT, 06511.
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Verma J, Vashisth H. Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases. Proteins 2024; 92:905-922. [PMID: 38506327 PMCID: PMC11222054 DOI: 10.1002/prot.26685] [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: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Understanding kinase-inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A-1) of the insulin-like growth factor-I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine-arginine-aspartic acid (HRD) and aspartic acid-phenylalanine-glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C-helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824
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Štěrbová P, Wang CH, Carillo KJD, Lou YC, Kato T, Namba K, Tzou DLM, Chang WH. Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy. ACS Infect Dis 2024. [PMID: 39087906 DOI: 10.1021/acsinfecdis.4c00407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis virus (NNV), a simple nonenveloped virus in the genus of betanodavirus, infects fish and damages aquaculture worldwide. NNV has 60 conspicuous surface protrusions, each comprising three protrusion domains (P-domain) of its capsid protein. NNV uses protrusions to bind to common receptors of sialic acids on the host cell surface to initiate its entry via the endocytic pathway. However, structural alterations of NNV in response to acidic conditions encountered during this pathway remain unknown, while detailed interactions of protrusions with receptors are unclear. Here, we used cryo-EM to discover that Grouper NNV protrusions undergo low-pH-induced compaction and resting. NMR and molecular dynamics (MD) simulations were employed to probe the atomic details. A solution structure of the P-domain at pH 7.0 revealed a long flexible loop (amino acids 311-330) and a pocket outlined by this loop. Molecular docking analysis showed that the N-terminal moiety of sialic acid inserted into this pocket to interact with conserved residues inside. MD simulations demonstrated that part of this loop converted to a β-strand under acidic conditions, allowing for P-domain trimerization and compaction. Additionally, a low-pH-favored conformation is attained for the linker connecting the P-domain to the NNV shell, conferring resting protrusions. Our findings uncover novel pH-dependent conformational switching mechanisms underlying NNV protrusion dynamics potentially utilized for facilitating NNV entry, providing new structural insights into complex NNV-host interactions with the identification of putative druggable hotspots on the protrusion.
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Affiliation(s)
- Petra Štěrbová
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- College of Life Science, National Tsing Hua University, Hsinchu 30044, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | | | | | - Yuan-Chao Lou
- Biomedical Translation Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Der-Lii M Tzou
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Wei-Hau Chang
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
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7
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Patel PA, LaConte LEW, Liang C, Cecere T, Rajan D, Srivastava S, Mukherjee K. Genetic evidence for splicing-dependent structural and functional plasticity in CASK protein. J Med Genet 2024; 61:759-768. [PMID: 38670634 PMCID: PMC11290809 DOI: 10.1136/jmg-2023-109747] [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: 11/10/2023] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Pontocerebellar hypoplasia (PCH) may present with supratentorial phenotypes and is often accompanied by microcephaly. Damaging mutations in the X-linked gene CASK produce self-limiting microcephaly with PCH in females but are often lethal in males. CASK deficiency leads to early degeneration of cerebellar granule cells but its role in other regions of the brain remains uncertain. METHOD We generated a conditional Cask knockout mice and deleted Cask ubiquitously after birth at different times. We examined the clinical features in several subjects with damaging mutations clustered in the central part of the CASK protein. We have performed phylogenetic analysis and RT-PCR to assess the splicing pattern within the same protein region and performed in silico structural analysis to examine the effect of splicing on the CASK's structure. RESULT We demonstrate that deletion of murine Cask after adulthood does not affect survival but leads to cerebellar degeneration and ataxia over time. Intriguingly, damaging hemizygous CASK mutations in boys who display microcephaly and cerebral dysfunction but without PCH are known. These mutations are present in two vertebrate-specific CASK exons. These exons are subject to alternative splicing both in forebrain and hindbrain. Inclusion of these exons differentially affects the molecular structure and hence possibly the function/s of the CASK C-terminus. CONCLUSION Loss of CASK function disproportionately affects the cerebellum. Clinical data, however, suggest that CASK may have additional vertebrate-specific function/s that play a role in the mammalian forebrain. Thus, CASK has an ancient function shared between invertebrates and vertebrates as well as novel vertebrate-specific function/s.
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Affiliation(s)
- Paras A Patel
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
| | - Leslie E W LaConte
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
- Basic Science Education, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Chen Liang
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
| | - Thomas Cecere
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Deepa Rajan
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sarika Srivastava
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
- Department of Genetics, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, USA
| | - Konark Mukherjee
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
- Department of Genetics, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, USA
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Serson WR, Gishini MFS, Stupar RM, Stec AO, Armstrong PR, Hildebrand D. Identification and Candidate Gene Evaluation of a Large Fast Neutron-Induced Deletion Associated with a High-Oil Phenotype in Soybean Seeds. Genes (Basel) 2024; 15:892. [PMID: 39062671 PMCID: PMC11276498 DOI: 10.3390/genes15070892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/29/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Since the dawn of agriculture, crops have been genetically altered for desirable characteristics. This has included the selection of natural and induced mutants. Increasing the production of plant oils such as soybean (Glycine max) oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybeans, however, usually results in reduced seed protein. A soybean fast neutron population was screened for oil content, and three high oil mutants with minimal reductions in protein levels were found. Three backcross F2 populations derived from these mutants exhibited segregation for seed oil content. DNA was pooled from the high-oil and normal-oil plants within each population and assessed by comparative genomic hybridization. A deletion encompassing 20 gene models on chromosome 14 was found to co-segregate with the high-oil trait in two of the three populations. Eighteen genes in the deleted region have known functions that appear unrelated to oil biosynthesis and accumulation pathways, while one of the unknown genes (Glyma.14G101900) may contribute to the regulation of lipid droplet formation. This high-oil trait can facilitate the breeding of high-oil soybeans without protein reduction, resulting in higher meal protein levels.
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Affiliation(s)
- William R. Serson
- Department of Biology, Penn State University, Lehigh Valley, Center Valley, PA 18034, USA
| | | | - Robert M. Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA; (R.M.S.); (A.O.S.)
| | - Adrian O. Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA; (R.M.S.); (A.O.S.)
| | - Paul R. Armstrong
- United States Department of Agriculture-Agricultural Research Service, Manhattan, KS 66502, USA
| | - David Hildebrand
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA;
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Srividya N, Kim H, Simone R, Lange BM. Chemical diversity in angiosperms - monoterpene synthases control complex reactions that provide the precursors for ecologically and commercially important monoterpenoids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:28-55. [PMID: 38565299 DOI: 10.1111/tpj.16743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
Monoterpene synthases (MTSs) catalyze the first committed step in the biosynthesis of monoterpenoids, a class of specialized metabolites with particularly high chemical diversity in angiosperms. In addition to accomplishing a rate enhancement, these enzymes manage the formation and turnover of highly reactive carbocation intermediates formed from a prenyl diphosphate substrate. At each step along the reaction path, a cationic intermediate can be subject to cyclization, migration of a proton, hydride, or alkyl group, or quenching to terminate the sequence. However, enzymatic control of ligand folding, stabilization of specific intermediates, and defined quenching chemistry can maintain the specificity for forming a signature product. This review article will discuss our current understanding of how angiosperm MTSs control the reaction environment. Such knowledge allows inferences about the origin and regulation of chemical diversity, which is pertinent for appreciating the role of monoterpenoids in plant ecology but also for aiding commercial efforts that harness the accumulation of these specialized metabolites for the food, cosmetic, and pharmaceutical industries.
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Affiliation(s)
- Narayanan Srividya
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, 99164-7411, USA
| | - Hoshin Kim
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Raugei Simone
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Bernd Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, 99164-7411, USA
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Arif B, Yasir S, Saeed M, Fatmi MQ. Natural products can be potential inhibitors of metalloproteinase II from Bacteroides fragilis to intervene colorectal cancer. Heliyon 2024; 10:e32838. [PMID: 39005891 PMCID: PMC11239599 DOI: 10.1016/j.heliyon.2024.e32838] [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: 06/22/2023] [Revised: 05/03/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Bacteroides fragilis, a gram negative and obligate anaerobe bacterium, is a member of normal gut microbiota and facilitates many essential roles being performed in human body in normal circumstances specifically in Gastrointestinal or GI tract. Sometimes, due to genetics, epigenetics, and environmental factors, Bacteroides fragilis and their protein(s) start interacting with intestinal epithelium thus damaging the lining leading to colorectal cancers (CRC). To identify these protein(s), we incorporated a novel subtractive proteomics approach in the study. Metalloproteinase II (MPII), a Bacteroides fragilis toxin (bft), was investigated for its virulence and unique pathways to demonstrate its specificity and uniqueness in pathogenicity followed by molecular docking against a set of small drug-like natural molecules to discover potential inhibitors against the toxin. All these identified inhibitor-like molecules were analyzed for their ADMET calculations and detailed physiochemical properties to predict their druggability, GI absorption, blood brain barrier and skin permeation, and others. Resultantly, a total of ten compounds with the least binding energies were obtained and were subjected to protein-compound interaction analysis. Interaction analysis revealed the most common ligand-interacting residues in MPII are His 345, Glu 346, His 339, Gly 310, Tyr 341, Pro 340, Asp 187, Phe 309, Lys 307, Ile 185, Thr 308, and Pro 184. Therefore, top three compounds complexed with MPII having best binding energies were selected in order to analyze their trajectories. RMSD, RMSF, Rg and MMPBSA analysis revealed that all compounds showed good binding and keeping the complex stable and compact throughout the simulation time in addition to all properties and qualities of being a potential inhibitor against MPII.
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Affiliation(s)
- Bushra Arif
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - Saba Yasir
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Muhammad Saeed
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - M. Qaiser Fatmi
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
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Wang L, Wen Z, Liu SW, Zhang L, Finley C, Lee HJ, Fan HJS. Overview of AlphaFold2 and breakthroughs in overcoming its limitations. Comput Biol Med 2024; 176:108620. [PMID: 38761500 DOI: 10.1016/j.compbiomed.2024.108620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
Predicting three-dimensional (3D) protein structures has been challenging for decades. The emergence of AlphaFold2 (AF2), a deep learning-based machine learning method developed by DeepMind, became a game changer in the protein folding community. AF2 can predict a protein's three-dimensional structure with high confidence based on its amino acid sequence. Accurate prediction of protein structures can dramatically accelerate our understanding of biological mechanisms and provide a solid foundation for reliable drug design. Although AF2 breaks through the barriers in predicting protein structures, many rooms remain to be further studied. This review provides a brief historical overview of the development of protein structure prediction, covering template-based, template-free, and machine learning-based methods. In addition to reviewing the potential benefits (Pros) and considerations (Cons) of using AF2, this review summarizes the diverse applications, including protein structure predictions, dynamic changes, point mutation, integration of language model and experimental data, protein complex, and protein-peptide interaction. It underscores recent advancements in efficiency, reliability, and broad application of AF2. This comprehensive review offers valuable insights into the applications of AF2 and AF2-inspired AI methods in structural biology and its potential for clinically significant drug target discovery.
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Affiliation(s)
- Lei Wang
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, China
| | - Zehua Wen
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, China
| | - Shi-Wei Liu
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, China
| | - Lihong Zhang
- Digestive Department, Binhai New Area Hospital of TCM Tianjin, Tianjin, 300451, China
| | - Cierra Finley
- Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN, 38015, USA
| | - Ho-Jin Lee
- Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN, 38015, USA; Division of Natural & Mathematical Sciences, LeMoyne-Own College, Memphis, TN, 38126, USA.
| | - Hua-Jun Shawn Fan
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, China.
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Fronk AD, Manzanares MA, Zheng P, Geier A, Anderson K, Stanton S, Zumrut H, Gera S, Munch R, Frederick V, Dhingra P, Arun G, Akerman M. Development and validation of AI/ML derived splice-switching oligonucleotides. Mol Syst Biol 2024; 20:676-701. [PMID: 38664594 PMCID: PMC11148135 DOI: 10.1038/s44320-024-00034-9] [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: 09/15/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 06/05/2024] Open
Abstract
Splice-switching oligonucleotides (SSOs) are antisense compounds that act directly on pre-mRNA to modulate alternative splicing (AS). This study demonstrates the value that artificial intelligence/machine learning (AI/ML) provides for the identification of functional, verifiable, and therapeutic SSOs. We trained XGboost tree models using splicing factor (SF) pre-mRNA binding profiles and spliceosome assembly information to identify modulatory SSO binding sites on pre-mRNA. Using Shapley and out-of-bag analyses we also predicted the identity of specific SFs whose binding to pre-mRNA is blocked by SSOs. This step adds considerable transparency to AI/ML-driven drug discovery and informs biological insights useful in further validation steps. We applied this approach to previously established functional SSOs to retrospectively identify the SFs likely to regulate those events. We then took a prospective validation approach using a novel target in triple negative breast cancer (TNBC), NEDD4L exon 13 (NEDD4Le13). Targeting NEDD4Le13 with an AI/ML-designed SSO decreased the proliferative and migratory behavior of TNBC cells via downregulation of the TGFβ pathway. Overall, this study illustrates the ability of AI/ML to extract actionable insights from RNA-seq data.
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Affiliation(s)
| | | | - Paulina Zheng
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Adam Geier
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | | | | | - Hasan Zumrut
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Sakshi Gera
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Robin Munch
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | | | | | - Gayatri Arun
- Envisagenics, Inc., Long Island City, NY, 11101, USA
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13
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Saleki K, Aram C, Alijanizadeh P, Khanmirzaei MH, Vaziri Z, Ramzankhah M, Azadmehr A. Matrix metalloproteinase/Fas ligand (MMP/FasL) interaction dynamics in COVID-19: An in silico study and neuroimmune perspective. Heliyon 2024; 10:e30898. [PMID: 38803919 PMCID: PMC11128882 DOI: 10.1016/j.heliyon.2024.e30898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Background The initiator of cytokine storm in Coronavirus disease (COVID-19) is still unknown. We recently suggested a complex interaction of matrix metalloproteinases (MMPs), Fas ligand (FasL), and viral entry factors could be responsible for the cytokine outrage In COVID-19. We explored the molecular dynamics of FasL/MMP7-9 in COVID-19 conditions in silico and provide neuroimmune insights for future. Methods We enrolled and analyzed a clinical cohort of COVID-19 patients, and recorded their blood Na + levels and temperature at admission. A blood-like molecular dynamics simulation (MDS) box was then built. Four conditions were studied; MMP7/FasL (healthy), MMP7/FasL (COVID-19), MMP9-FasL (healthy), and MMP9/FasL (COVID-19). MDS was performed by GROningen MAchine for Chemical Simulation (GROMACS). We analyzed bonds, short-range energies, and free binding energies to draw conclusions on the interaction of MMP7/MMP9 and FasL to gain insights into COVID-19 immunopathology. Genevestigator was used study RNA-seq/microarray expression data of MMPs in the cells of immune and nervous systems. Finally, epitopes of MMP/FasL complexes were identified as drug targets by machine learning (ML) tools. Results MMP7-FasL (Healthy), MMP7-FasL (COVID-19), MMP9-FasL (Healthy), and MMP9-FasL (COVID-19) systems showed 0, 1, 4, and 2 salt bridges, indicating MMP9 had more salt bridges. Moreover, in both COVID-19 and normal conditions, the number of interacting residues and surface area was higher for MMP9 compared to MMP7 group. The COVID-19 MMP9-FasL group had more H-bonds compared to MMP7-FasL group (12 vs. 7). 15 epitopes for FasL-MMP9 and 10 epitopes for FasL-MMP7 were detected. Extended MD simulation for 100 ns confirmed stronger binding of MMP9 based on Molecular Mechanics Generalized Borne Surface analysis (MM-GBSA) and Coul and Leonard-Jones (LJ) short-range energies. Conclusions MMP9 interacts stronger than MMP7 with FasL, however, both molecules maintained strong interaction through the MDS. We suggested epitopes for MMP-FasL complexes as valuable therapeutic targets in COVID-19. These data could be utilized in future immune drug and protein design and repurposing efforts.
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Affiliation(s)
- Kiarash Saleki
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- Department of e-Learning, Virtual School of Medical Education and Management, Shahid Beheshti University of Medical Sciences(SBMU), Tehran, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
- National Elite Foundation, Mazandaran Province Branch, Mazandaran, Iran
| | - Cena Aram
- Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Parsa Alijanizadeh
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Hossein Khanmirzaei
- School of Medicine, Tehran University of Medical Sciences, Babol, Iran
- Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Zahra Vaziri
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Ramzankhah
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Abbas Azadmehr
- National Elite Foundation, Mazandaran Province Branch, Mazandaran, Iran
- Department of Immunology, Babol University of Medical Sciences, Babol, Iran
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14
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Paul P, Iftehimul M, Dey D, Mia MAR, Al-Khafaji K, Pal B, Biswas P, Mandal M, Hasan MN. Investigating the potent TOPO IIα inhibitors in breast cancer through the study of computational drug discovery research approaches. Mol Divers 2024:10.1007/s11030-024-10882-0. [PMID: 38773015 DOI: 10.1007/s11030-024-10882-0] [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: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 05/23/2024]
Abstract
Breast cancer (BC) is the second-leading cause of cancer after lung cancer. The disease has affected millions of people and resulted in many deaths. In the metastasis of breast cancer cells, Topoisomerase IIα plays a vital role. Therefore, this investigation aims to identify potential flavonoid compounds against BC by inhibiting this enzyme at an early stage. Based on previous studies, we selected and screened several plant-derived flavonoid compounds with potential anti-breast cancer activity using PyRx 0.8 and Schrodinger applications for preliminary molecular docking: the highest docking scores of Myricetin (-11.6 kcal/mol) and Quercetin (-10.0 kcal/mol). Next, we evaluated the top four compounds on the Way2Drug server to complete the cytotoxicity evaluation, which demonstrated anti-cancer and anti-breast cancer activity in various cell lines. According to pharmacokinetics studies, four compounds exhibited outstanding values and functioned similar to drug-like molecules. Moreover, Myricetin, Quercetin, and Morin displayed the highest number of hydrogen bonds, with the corresponding receptor forming residues asn120, thr147, and lys168. The protein-ligand complexes were validated using the Desmond simulator, and their data were compared to the anti-breast cancer drug Doxorubicin. In the simulation analysis, various parameters were evaluated, including RMSD, RMSF, Rg, SASA, MolSA, PSA, and hydrogen bond interaction. Finally, validated our dynamic simulation result with MM-GBSA operation, and Myricetin and Quercetin had the greatest score of -72.74344651, -66.66771823 kcal/mol, which is outstanding than the control drug. Hence, the computational research approach determined that Myricetin, Quercetin, and Morin could be industrially developed for the alternative treatment of breast cancer following additional confirmation from animal and cell line studies.
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Affiliation(s)
- Priyanka Paul
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj, 8100, Bangladesh
| | - Md Iftehimul
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj, 8100, Bangladesh
| | - Md Abdur Rashid Mia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, International Islamic University Malaysia, 25200, Kuantan, Pahang, Malaysia.
| | - Khattab Al-Khafaji
- Department of Environmental Science, College of Energy and Environmental Science, Al-Karkh, University of Science, Baghdad, 10081, Iraq
| | - Bidu Pal
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj, 8100, Bangladesh
| | - Partha Biswas
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Manoj Mandal
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj, 8100, Bangladesh.
| | - Md Nazmul Hasan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
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15
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Verma J, Vashisth H. Structural Models for a Series of Allosteric Inhibitors of IGF1R Kinase. Int J Mol Sci 2024; 25:5368. [PMID: 38791406 PMCID: PMC11121299 DOI: 10.3390/ijms25105368] [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: 04/07/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
The allosteric inhibition of insulin-like growth factor receptor 1 kinase (IGF1RK) is a potential strategy to overcome selectivity barriers for targeting receptor tyrosine kinases. We constructed structural models of a series of 12 indole-butyl-amine derivatives that have been reported as allosteric inhibitors of IGF1RK. We further studied the dynamics and interactions of each inhibitor in the allosteric pocket via all-atom explicit-solvent molecular dynamics (MD) simulations. We discovered that a bulky carbonyl substitution at the R1 indole ring is structurally unfavorable for inhibitor binding in the IGF1RK allosteric pocket. Moreover, we found that the most potent derivative (termed C11) acquires a distinct conformation: forming an allosteric pocket channel with better shape complementarity and interactions with the receptor. In addition to a hydrogen-bonding interaction with V1063, the cyano derivative C11 forms a stable hydrogen bond with M1156, which is responsible for its unique binding conformation in the allosteric pocket. Our findings show that the positioning of chemical substituents with different pharmacophore features at the R1 indole ring influences molecular interactions and binding conformations of indole-butyl-amine derivatives and, hence, dramatically affects their potencies. Our results provide a structural framework for the design of allosteric inhibitors with improved affinities and specificities against IGF1RK.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA;
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA;
- Department of Chemistry, University of New Hampshire, Durham, NH 03824, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824, USA
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16
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Verma J, Vashisth H. Structural Models for a Series of Allosteric Inhibitors of IGF1R Kinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588115. [PMID: 38617226 PMCID: PMC11014618 DOI: 10.1101/2024.04.04.588115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The allosteric inhibition of Insulin-like Growth Factor Receptor 1 Kinase (IGF1RK) is a potential strategy to overcome selectivity barriers in targeting receptor tyrosine kinases. We constructed structural models of a series of 12 indole-butyl-amine derivatives which have been reported as allosteric inhibitors of IGF1RK. We further studied dynamics and interactions of each inhibitor in the allosteric pocket via all-atom explicit-solvent molecular dynamics (MD) simulations. We discovered that a bulky carbonyl substitution at the R1 indole ring is structurally unfavorable for inhibitor binding in the IGF1RK allosteric pocket. Moreover, we found that the most potent derivative (termed C11) acquires a distinct conformation, forming an allosteric pocket channel with better shape complementarity and interactions with the receptor. In addition to a hydrogen bonding interaction with V1063, the cyano derivative C11 forms a stable hydrogen bond with M1156, which is responsible for its unique binding conformation in the allosteric pocket. Our findings show that the position of chemical substituents at the R1 indole ring with different pharmacophore features influences molecular interactions and binding conformations of the indole-butyl-amine derivatives, hence dramatically affecting their potencies. Our results provide a structural framework for the design of allosteric inhibitors with improved affinities and specificities against IGF1RK.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA
- Department of Chemistry, University of New Hampshire, Durham, NH 03824, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824, USA
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17
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Jiao F, Cui W, Wang P, Tong HHY, Guo J, Tao J. Synergistic inhibition mechanism of quinazolinone and piperacillin on penicillin-binding protein 2a: a promising approach for combating methicillin-resistant Staphylococcus aureus. J Biomol Struct Dyn 2024:1-13. [PMID: 38497736 DOI: 10.1080/07391102.2024.2330708] [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: 01/21/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
The production of penicillin-binding protein 2a (PBP2a), a cell wall synthesis protein, is primarily responsible for the high-level resistance observed in methicillin-resistant Staphylococcus aureus (MRSA). PBP2a exhibits a significantly reduced affinity for most β-lactam antibiotics owing to its tightly closed active site. Quinazolinones (QNE), a novel class of non-β-lactam antibiotics, could initiate the allosteric regulation of PBP2a, resulting in the opening of the initially closed active pocket. Based on our previous study, we have a basic understanding of the dual-site inhibitor ceftaroline (CFT) induced allosteric regulation of PBP2a. However, there are still limitations in the knowledge of how combining medicines, QNE and piperacillin (PIP), induce the allosteric response of PBP2a and inhibit its function. Herein, molecular dynamics (MD) simulations were performed to elucidate the intricate mechanisms underlying the combination mode of QNE and PIP. Our study successfully captured the opening process of the active pocket upon the binding of the QNE at the allosteric site, which alters the signaling pathways with a favorable transmission to the active site. Subsequent docking experiments with different conformational states of the active pocket indicated that all three inhibitors, PIP, QNE, and CFT, exhibited higher docking scores and more favorable docking poses to the open active pocket. These findings reveal the implied mechanism of QNE-mediated allostery underlying combination therapy and provide novel insights into developing innovative therapeutic modalities against MRSA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fangfang Jiao
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Weirong Cui
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Pinkai Wang
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Henry H Y Tong
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
- Engineering Research Centre of Applied Technology on Machine Translation and Artificial Intelligence, Macao Polytechnic University, Macao, China
| | - Jun Tao
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
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18
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Moetlediwa MT, Jack BU, Mazibuko-Mbeje SE, Pheiffer C, Titinchi SJJ, Salifu EY, Ramharack P. Evaluating the Therapeutic Potential of Curcumin and Synthetic Derivatives: A Computational Approach to Anti-Obesity Treatments. Int J Mol Sci 2024; 25:2603. [PMID: 38473849 DOI: 10.3390/ijms25052603] [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: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Natural compounds such as curcumin, a polyphenolic compound derived from the rhizome of turmeric, have gathered remarkable scientific interest due to their diverse metabolic benefits including anti-obesity potential. However, curcumin faces challenges stemming from its unfavorable pharmacokinetic profile. To address this issue, synthetic curcumin derivatives aimed at enhancing the biological efficacy of curcumin have previously been developed. In silico modelling techniques have gained significant recognition in screening synthetic compounds as drug candidates. Therefore, the primary objective of this study was to assess the pharmacokinetic and pharmacodynamic characteristics of three synthetic derivatives of curcumin. This evaluation was conducted in comparison to curcumin, with a specific emphasis on examining their impact on adipogenesis, inflammation, and lipid metabolism as potential therapeutic targets of obesity mechanisms. In this study, predictive toxicity screening confirmed the safety of curcumin, with the curcumin derivatives demonstrating a safe profile based on their LD50 values. The synthetic curcumin derivative 1A8 exhibited inactivity across all selected toxicity endpoints. Furthermore, these compounds were deemed viable candidate drugs as they adhered to Lipinski's rules and exhibited favorable metabolic profiles. Molecular docking studies revealed that both curcumin and its synthetic derivatives exhibited favorable binding scores, whilst molecular dynamic simulations showed stable binding with peroxisome proliferator-activated receptor gamma (PPARγ), csyclooxygenase-2 (COX2), and fatty acid synthase (FAS) proteins. The binding free energy calculations indicated that curcumin displayed potential as a strong regulator of PPARγ (-60.2 ± 0.4 kcal/mol) and FAS (-37.9 ± 0.3 kcal/mol), whereas 1A8 demonstrated robust binding affinity with COX2 (-64.9 ± 0.2 kcal/mol). In conclusion, the results from this study suggest that the three synthetic curcumin derivatives have similar molecular interactions to curcumin with selected biological targets. However, in vitro and in vivo experimental studies are recommended to validate these findings.
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Affiliation(s)
- Marakiya T Moetlediwa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Department of Biochemistry, North-West University, Mmabatho 2745, South Africa
| | - Babalwa U Jack
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | | | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Salam J J Titinchi
- Department of Chemistry, Faculty of Natural Science, University of the Western Cape, Bellville 7535, South Africa
| | - Elliasu Y Salifu
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | - Pritika Ramharack
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
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19
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Bjarnason S, McIvor JAP, Prestel A, Demény KS, Bullerjahn JT, Kragelund BB, Mercadante D, Heidarsson PO. DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2. Nat Commun 2024; 15:1445. [PMID: 38365983 PMCID: PMC10873366 DOI: 10.1038/s41467-024-45847-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.
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Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Jordan A P McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Andreas Prestel
- Department of Biology, REPIN and Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Kinga S Demény
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Jakob T Bullerjahn
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Birthe B Kragelund
- Department of Biology, REPIN and Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland.
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20
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Erba F, Mei G, Minicozzi V, Sabatucci A, Di Venere A, Maccarrone M. Conformational Dynamics of Lipoxygenases and Their Interaction with Biological Membranes. Int J Mol Sci 2024; 25:2241. [PMID: 38396917 PMCID: PMC10889196 DOI: 10.3390/ijms25042241] [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: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Lipoxygenases (LOXs) are a family of enzymes that includes different fatty acid oxygenases with a common tridimensional structure. The main functions of LOXs are the production of signaling compounds and the structural modifications of biological membranes. These features of LOXs, their widespread presence in all living organisms, and their involvement in human diseases have attracted the attention of the scientific community over the last decades, leading to several studies mainly focused on understanding their catalytic mechanism and designing effective inhibitors. The aim of this review is to discuss the state-of-the-art of a different, much less explored aspect of LOXs, that is, their interaction with lipid bilayers. To this end, the general architecture of six relevant LOXs (namely human 5-, 12-, and 15-LOX, rabbit 12/15-LOX, coral 8-LOX, and soybean 15-LOX), with different specificity towards the fatty acid substrates, is analyzed through the available crystallographic models. Then, their putative interface with a model membrane is examined in the frame of the conformational flexibility of LOXs, that is due to their peculiar tertiary structure. Finally, the possible future developments that emerge from the available data are discussed.
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Affiliation(s)
- Fulvio Erba
- Department of Clinical Science and Translational Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Giampiero Mei
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Velia Minicozzi
- Department of Physics and INFN, Tor Vergata University of Rome, Via Della Ricerca Scientifica 1, 00133 Rome, Italy;
| | - Annalaura Sabatucci
- Department of Biosciences and Technology for Food Agriculture and Environment, University of Teramo, Via Renato Balzarini 1, 64100 Teramo, Italy;
| | - Almerinda Di Venere
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito, 67100 L’Aquila, Italy
- European Center for Brain Research (CERC), Santa Lucia Foundation IRCCS, 00143 Rome, Italy
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Kocanova S, Raynal F, Goiffon I, Oksuz BA, Baú D, Kamgoué A, Cantaloube S, Zhan Y, Lajoie B, Marti-Renom MA, Dekker J, Bystricky K. Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells. Life Sci Alliance 2024; 7:e202302154. [PMID: 37989525 PMCID: PMC10663337 DOI: 10.26508/lsa.202302154] [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: 05/12/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023] Open
Abstract
The genome is organized in functional compartments and structural domains at the sub-megabase scale. How within these domains interactions between numerous cis-acting enhancers and promoters regulate transcription remains an open question. Here, we determined chromatin folding and composition over several hundred kb around estrogen-responsive genes in human breast cancer cell lines after hormone stimulation. Modeling of 5C data at 1.8 kb resolution was combined with quantitative 3D analysis of multicolor FISH measurements at 100 nm resolution and integrated with ChIP-seq data on transcription factor binding and histone modifications. We found that rapid estradiol induction of the progesterone gene expression occurs in the context of preexisting, cell type-specific chromosomal architectures encompassing the 90 kb progesterone gene coding region and an enhancer-spiked 5' 300 kb upstream genomic region. In response to estradiol, interactions between estrogen receptor α (ERα) bound regulatory elements are reinforced. Whereas initial enhancer-gene contacts coincide with RNA Pol 2 binding and transcription initiation, sustained hormone stimulation promotes ERα accumulation creating a regulatory hub stimulating transcript synthesis. In addition to implications for estrogen receptor signaling, we uncover that preestablished chromatin architectures efficiently regulate gene expression upon stimulation without the need for de novo extensive rewiring of long-range chromatin interactions.
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Affiliation(s)
- Silvia Kocanova
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Flavien Raynal
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Isabelle Goiffon
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Betul Akgol Oksuz
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Davide Baú
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Alain Kamgoué
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Sylvain Cantaloube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Ye Zhan
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Bryan Lajoie
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
- Genome Biology Program, Centre de Regulació Genòmica (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Job Dekker
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Kerstin Bystricky
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
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22
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Petgrave M, Ramgoolam SD, Ganesan A. Deciphering the Molecular Association of Human CRIP1a with an Agonist-Bound Cannabinoid Receptor 1. J Chem Inf Model 2024; 64:499-517. [PMID: 38159053 DOI: 10.1021/acs.jcim.3c01579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cannabinoid receptor 1 (CB1) is a class A G-protein-coupled receptor that plays important roles in several physiological and pathophysiological processes. Therefore, targeted regulation of CB1 activity is a potential therapeutic strategy for several diseases, including neurological disorders. Apart from cannabinoid ligands, CB1 signaling can also be regulated by different CB1-associated proteins. In particular, the cannabinoid receptor interacting protein 1a (CRIP1a) associates with an activated CB1 receptor and alters the G-protein selectivity, thereby reducing the agonist-mediated signal transduction of the CB1 receptor. Experimental evidence suggests that two peptides corresponding to the distal and central C-terminal segments of CB1 could interact with CRIP1a. However, our knowledge of the molecular basis of CB1-CRIP1a recognition is still limited. In this work, we use an extensive combination of computational methods to build the first comprehensive atomistic model human CB1-CRIP1a complex. Our model provides novel structural insights into the interactions of CRIP1a with a membrane-embedded, complete, agonist-bound CB1 receptor in humans. Our results highlight the key residues that stabilize the CB1-CRIP1a complex, which will be useful to guide in vitro mutagenesis experiments. Furthermore, our human CB1-CRIP1a complex presents a model system for structure-based drug design to target this physiologically important complex for modulating CB1 activity.
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Affiliation(s)
- Maya Petgrave
- ArGan'sLab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, Ontario N2G 1C5, Canada
| | - Shubham Devesh Ramgoolam
- ArGan'sLab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, Ontario N2G 1C5, Canada
| | - Aravindhan Ganesan
- ArGan'sLab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, Ontario N2G 1C5, Canada
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23
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Calderón JC, Plut E, Keller M, Cabrele C, Reiser O, Gervasio FL, Clark T. Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors. J Chem Inf Model 2024; 64:205-218. [PMID: 38150388 DOI: 10.1021/acs.jcim.3c01574] [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: 12/29/2023]
Abstract
A metadynamics protocol is presented to characterize the binding and unbinding of peptide ligands to class A G-protein-coupled receptors (GPCRs). The protocol expands on the one previously presented for binding and unbinding small-molecule ligands to class A GPCRs and accounts for the more demanding nature of the peptide binding-unbinding process. It applies to almost all class A GPCRs. Exemplary simulations are described for subtypes Y1R, Y2R, and Y4R of the neuropeptide Y receptor family, vasopressin binding to the vasopressin V2 receptor (V2R), and oxytocin binding to the oxytocin receptor (OTR). Binding free energies and the positions of alternative binding sites are presented and, where possible, compared with the experiment.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, Erlangen 91052, Germany
| | - Eva Plut
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg D-93040, Germany
| | - Chiara Cabrele
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany
| | - Oliver Reiser
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany
| | | | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, Erlangen 91052, Germany
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24
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Güner E, Özkan Ö, Yalcin-Ozkat G, Ölgen S. Determination of Novel SARS-CoV-2 Inhibitors by Combination of Machine Learning and Molecular Modeling Methods. Med Chem 2024; 20:153-231. [PMID: 37957860 DOI: 10.2174/0115734064265609231026063624] [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: 06/25/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
INTRODUCTION Within the scope of the project, this study aimed to find novel inhibitors by combining computational methods. In order to design inhibitors, it was aimed to produce molecules similar to the RdRp inhibitor drug Favipiravir by using the deep learning method. METHODS For this purpose, a Trained Neural Network (TNN) was used to produce 75 molecules similar to Favipiravir by using Simplified Molecular Input Line Entry System (SMILES) representations. The binding properties of molecules to Viral RNA-dependent RNA polymerase (RdRp) were studied by using molecular docking studies. To confirm the accuracy of this method, compounds were also tested against 3CL protease (3CLpro), which is another important enzyme for the progression of SARS-CoV-2. Compounds having better binding energies and RMSD values than favipiravir were searched with similarity analysis on the ChEMBL drug database in order to find similar structures with RdRp and 3CLpro inhibitory activities. RESULTS A similarity search found new 200 potential RdRp and 3CLpro inhibitors structurally similar to produced molecules, and these compounds were again evaluated for their receptor interactions with molecular docking studies. Compounds showed better interaction with RdRp protease than 3CLpro. This result presented that artificial intelligence correctly produced structures similar to favipiravir that act more specifically as RdRp inhibitors. In addition, Lipinski's rules were applied to the molecules that showed the best interaction with RdRp, and 7 compounds were determined to be potential drug candidates. Among these compounds, a Molecular Dynamic simulation study was applied for ChEMBL ID:1193133 to better understand the existence and duration of the compound in the receptor site. CONCLUSION The results confirmed that the ChEMBL ID:1193133 compound showed good Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), hydrogen bonding, and remaining time in the active site; therefore, it was considered that it could be active against the virus. This compound was also tested for antiviral activity, and it was determined that it did not delay viral infection, although it was cytotoxic between 5mg/mL-1.25mg/mL concentrations. However, if other compounds could be tested, it might provide a chance to obtain activity, and compounds should also be tested against the enzymes as well as the other types of viruses.
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Affiliation(s)
- Ersin Güner
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, 34010 Topkapı, İstanbul, Turkey
| | - Özgür Özkan
- Teknokent Arı, Pinticks Software Company, Istanbul Technical University, Reşitpaşa Mah. Katar Street, No:4/B204 Sarıyer, İstanbul, Turkey
| | - Gözde Yalcin-Ozkat
- Bioengineering Department, Faculty of Engineering and Architecture, Recep Tayyip Erdogan University, 53100 Rize, Turkey
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Süreyya Ölgen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, 34010 Topkapı, İstanbul, Turkey
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25
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Issa AA, Ibraheem HH, El-Sayed DS. Computational innovation of in situ metallic elements with zirconia as a novel possible carrier for chemotherapeutic medication. J Mol Model 2023; 30:14. [PMID: 38148383 DOI: 10.1007/s00894-023-05815-x] [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: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023]
Abstract
CONTEXT Electronic sustainable behavior on the material surface and in situ metal configuration were accompted with some metal atoms like Li, Na, and K elements. Metal-doped ZrO2 crystal exported modified characteristics related to electronic conduction and exhibited some dynamic modification around the surface of the metal oxide. Computational perturbations were considered to discuss the modification behavior in addition to the studied Li, Na, and K metals. Optimization of the three doping systems was achieved followed by generating DOS and electronic band structure maps. A dynamic simulation was performed with temperature over 2000 k: the presence of the metal on the surface and prediction of its ZrO2 inclusion leading to access adsorption behavior, besides generating predictive designed models described the adsorption affinity on the solid-state surface. It cannot be neglected the importance of various metals as a main role in chemotherapy. Molecular docking investigation was considered to predict the binding behavior of the studied metal ZrO2 carrier system as an anticancer agent. Also, docking affinity was helpful in comparing the active sites binding for the studied metals, resulting in a notable binding affinity for both Li- and Na-zirconia incorporation. METHODS The program PWSCF, which is a component of the quantum ESPRESSO suite for quantum simulation of materials, was used to construct geometric systems. The generalized gradient approximation in the Perdew-Burke-Ernzerhof (GGA/PBE) function with D3 correction (Becke-Jonson damping) was applied to the exchange-correlation energy. As the last step in the DFT postulation and design, adsorption locator annealing was carried out on the convergent models using the Materials Studio simulation package. The main roles played by metal atoms are in protein binding and the suppression of bio-active regions. For the docking process, the protein was produced using AutoDock 4.2 and Discovery Studio software in accordance with the usual methodology. Chimera and Discovery Studio were used to examine the docking data that was processed after generating specific grid box dimensions for 7BTN.
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Affiliation(s)
- Ali Abdullah Issa
- Department of Applied Sciences, University of Technology, Baghdad, Iraq
| | - Hiba H Ibraheem
- Department of Applied Sciences, University of Technology, Baghdad, Iraq
| | - Doaa S El-Sayed
- Chemistry Department, Faculty of Science, Alexandria University, Baghdad Street, Moharam Bey, P.O. Box 21511, Alexandria, Egypt.
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26
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Piot L, Heroven C, Bossi S, Zamith J, Malinauskas T, Johnson C, Wennagel D, Stroebel D, Charrier C, Aricescu AR, Mony L, Paoletti P. GluD1 binds GABA and controls inhibitory plasticity. Science 2023; 382:1389-1394. [PMID: 38060673 DOI: 10.1126/science.adf3406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 10/25/2023] [Indexed: 12/23/2023]
Abstract
Fast synaptic neurotransmission in the vertebrate central nervous system relies primarily on ionotropic glutamate receptors (iGluRs), which drive neuronal excitation, and type A γ-aminobutyric acid receptors (GABAARs), which are responsible for neuronal inhibition. However, the GluD1 receptor, an iGluR family member, is present at both excitatory and inhibitory synapses. Whether and how GluD1 activation may affect inhibitory neurotransmission is unknown. In this work, by using a combination of biochemical, structural, and functional analyses, we demonstrate that GluD1 binds GABA, a previously unknown feature of iGluRs. GluD1 activation produces long-lasting enhancement of GABAergic synaptic currents in the adult mouse hippocampus through a non-ionotropic mechanism that is dependent on trans-synaptic anchoring. The identification of GluD1 as a GABA receptor that controls inhibitory synaptic plasticity challenges the classical dichotomy between glutamatergic and GABAergic receptors.
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Affiliation(s)
- Laura Piot
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | | | - Simon Bossi
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | - Joseph Zamith
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Chris Johnson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Doris Wennagel
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | - David Stroebel
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | - Cécile Charrier
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | | | - Laetitia Mony
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
| | - Pierre Paoletti
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Université PSL, CNRS, INSERM, F-75005 Paris, France
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27
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Adewumi AT, Mosebi S. Characteristic Binding Landscape of Estrogen Receptor-α36 Protein Enhances Promising Cancer Drug Design. Biomolecules 2023; 13:1798. [PMID: 38136668 PMCID: PMC10741999 DOI: 10.3390/biom13121798] [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: 11/10/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Breast cancer (BC) remains the most common cancer among women worldwide, and estrogen receptor-α expression is a critical diagnostic factor for BC. Estrogen receptor (ER-α36) is a dominant-negative effector of ER-α66-mediated estrogen-responsive gene pathways. ER-α36 is a novel target that mediates the non-genomic estrogen signaling pathway. However, the crystallized structure of ER-α36 remains unavailable for molecular studies. ER-positive and triple-negative BC tumors aggressively resist the FDA-approved drugs; therefore, highly potent structure-based inhibitors with preeminent benefits over toxicity will preferably replace the current BC treatment. Broussoflanol B (BFB), a B. papyrifera bark compound, exhibits potent growth inhibitory activity in ER-negative BC cells by inducing cell cycle arrest. For the first time, we unravel the comparative dynamic events of the enzymes' structures and the binding mechanisms of BFB when bound to the ER-α36 and ER-α66 ligand-binding domain using an all-atom molecular dynamics simulations approach and MM/PBSA-binding-free energy calculations. The dynamic findings have revealed that ER-α36 and ER-α66 LBD undergo timescale "coiling", opening and closing conformations favoring the high-affinity BFB-bound ER-α36 (ΔG = -52.57 kcal/mol) compared to the BFB-bound ER-α66 (ΔG = -42.41 kcal/mol). Moreover, the unbound (1.260 Å) and bound ER-α36 (1.182 Å) exhibit the highest flexibilities and atomistic motions relative to the ER-α66 systems. The RMSF (Å) of the unbound ER-α36 and ER-α66 exhibit lesser stabilities than the BFB-bound systems, resulting in higher structural flexibilities and atomistic motions than the bound variants. These findings present a model that describes the mechanisms by which the BFB compound induces downregulation-accompanied cell cycle arrest at the Gap0 and Gap1 phases.
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Affiliation(s)
| | - Salerwe Mosebi
- Department of Life and Consumer Sciences, University of South Africa, Private Bag X06, Florida 1710, South Africa;
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28
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Jiao F, Bao Y, Li M, Zhang Y, Zhang F, Wang P, Tao J, Tong HHY, Guo J. Unraveling the mechanism of ceftaroline-induced allosteric regulation in penicillin-binding protein 2a: insights for novel antibiotic development against methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0089523. [PMID: 37971241 PMCID: PMC10720500 DOI: 10.1128/aac.00895-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) acquires high-level resistance against β-lactam antibiotics by expressing penicillin-binding protein 2a (PBP2a). PBP2a is a cell wall-synthesizing protein whose closed active site exhibits a reduced binding affinity toward β-lactam antibiotics. Ceftaroline (CFT), a fifth-generation cephalosporin, can effectively inhibit the PBP2a activity by binding to an allosteric site to trigger the active site opening, allowing a second CFT to access the active site. However, the essential mechanism behind the allosteric behavior of PBP2a remains unclear. Herein, computational simulations are employed to elucidate how CFT allosterically regulates the conformation and dynamics of the active site of PBP2a. While CFT stabilizes the allosteric domain surrounding it, it simultaneously enhances the dynamics of the catalytic domain. Specifically, the study successfully captured the opening process of the active pocket in the allosteric CFT-bound systems and discovered that CFT alters the potential signal-propagating pathways from the allosteric site to the active site. These findings reveal the implied mechanism of the CFT-mediated allostery in PBP2a and provide new insights into dual-site drug design or combination therapy against MRSA targeting PBP2a.
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Affiliation(s)
- Fangfang Jiao
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Yiqiong Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengrong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Zhang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Pinkai Wang
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Tao
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Henry H. Y. Tong
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
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29
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Onyenaka C, Idowu KA, Ha NP, Graviss EA, Olaleye OA. Anti-Tuberculosis Potential of OJT008 against Active and Multi-Drug-Resistant Mycobacterium Tuberculosis: In Silico and In Vitro Inhibition of Methionine Aminopeptidase. Int J Mol Sci 2023; 24:17142. [PMID: 38138972 PMCID: PMC10742973 DOI: 10.3390/ijms242417142] [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: 09/21/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Despite the recent progress in the diagnosis of tuberculosis (TB), the chemotherapeutic management of TB continues to be challenging. Mycobacterium tuberculosis (Mtb), the etiological agent of TB, is classified as the 13th leading cause of death globally. In addition, 450,000 people were reported to develop multi-drug-resistant TB globally. The current project focuses on targeting methionine aminopeptidase (MetAP), an essential protein for the viability of Mtb. MetAP is a metalloprotease that catalyzes the excision of the N-terminal methionine (NME) during protein synthesis, allowing the enzyme to be an auspicious target for the development of novel therapeutic agents for the treatment of TB. Mtb possesses two MetAP1 isoforms, MtMetAP1a and MtMetAP1c, which are vital for Mtb viability and, hence, a promising chemotherapeutic target for Mtb therapy. In this study, we cloned and overexpressed recombinant MtMetAP1c. We investigated the in vitro inhibitory effect of the novel MetAP inhibitor, OJT008, on the cobalt ion- and nickel ion-activated MtMetAP1c, and the mechanism of action was elucidated through an in silico approach. The compound's potency against replicating and multi-drug-resistant (MDR) Mtb strains was also investigated. The induction of the overexpressed recombinant MtMetAP1c was optimized at 8 h with a final concentration of 1 mM Isopropyl β-D-1-thiogalactopyranoside. The average yield from 1 L of Escherichia coli culture for MtMetAP1c was 4.65 mg. A preliminary MtMetAP1c metal dependency screen showed optimum activation with nickel and cobalt ions occurred at 100 µM. The half-maximal inhibitory concentration (IC50) values of OJT008 against MtMetAP1c activated with CoCl2 and NiCl2 were 11 µM and 40 µM, respectively. The in silico study showed OJT008 strongly binds to both metal-activated MtMetAP1c, as evidenced by strong molecular interactions and a higher binding score, thereby corroborating our result. This in silico study validated the pharmacophore's metal specificity. The potency of OJT008 against both active and MDR Mtb was <0.063 µg/mL. Our study reports OJT008 as an inhibitor of MtMetAP1c, which is potent at low micromolar concentrations against both active susceptible and MDR Mtb. These results suggest OJT008 is a potential lead compound for the development of novel small molecules for the therapeutic management of TB.
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Affiliation(s)
- Collins Onyenaka
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA (K.A.I.)
| | - Kehinde A. Idowu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA (K.A.I.)
| | - Ngan P. Ha
- Center for Infectious Disease Research, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Edward A. Graviss
- Center for Infectious Disease Research, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Omonike A. Olaleye
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA (K.A.I.)
- Center for Infectious Disease Research, Houston Methodist Research Institute, Houston, TX 77030, USA
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30
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Jiang HW, Wu HY, Wang CH, Yang CH, Ko JT, Ho HC, Tsai MD, Bryant DA, Li FW, Ho MC, Ho MY. A structure of the relict phycobilisome from a thylakoid-free cyanobacterium. Nat Commun 2023; 14:8009. [PMID: 38049400 PMCID: PMC10696076 DOI: 10.1038/s41467-023-43646-9] [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: 04/27/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been challenging to test this hypothesis because ancestral species are generally inaccessible. Here we use spectroscopy and cryo-electron microscopy to reveal a structure of a "paddle-shaped" PBS from a thylakoid-free cyanobacterium that likely retains ancestral traits. This PBS lacks rods and specialized ApcD and ApcF subunits, indicating relict characteristics. Other features include linkers connecting two chains of five phycocyanin hexamers (CpcN) and two core subdomains (ApcH), resulting in a paddle-shaped configuration. Energy transfer calculations demonstrate that chains are less efficient than rods. These features may nevertheless have increased light absorption by elongating PBS before multilayered thylakoids with hemidiscoidal PBS evolved. Our results provide insights into the evolution and diversification of light-harvesting strategies before the origin of thylakoids.
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Affiliation(s)
- Han-Wei Jiang
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Jui-Tse Ko
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Han-Chen Ho
- Department of Anatomy, Tzu Chi University, Hualien, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan.
| | - Ming-Yang Ho
- Department of Life Science, National Taiwan University, Taipei, Taiwan.
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
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Birkic N, Visentin D, Svedružić Ž, Reynolds CA. Binding interactions of fatty acyl lipid mediators within the vanilloid pocket of TRPV1: A molecular dynamics study. Prostaglandins Other Lipid Mediat 2023; 169:106771. [PMID: 37657597 PMCID: PMC10841302 DOI: 10.1016/j.prostaglandins.2023.106771] [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: 02/28/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
The transient receptor potential vanilloid 1 (TRPV1) channel is a ligand-gated, nonselective cation channel expressed in primary sensory neurons, which has a role in nociception. The channel is activated by noxious heat, pH, capsaicin and other endogenous vanilloids, including lipid mediators (LMs) enzymatically derived from polyunsaturated fatty acids (PUFA). Although capsaicin binding to TRPV1 has been well characterized, the molecular mechanism by which endogenous LM ligands bind the channel is not well understood. In this study, we characterized the binding interactions for 13 endogenous LM ligands, within the vanilloid pocket of TRPV1 using a molecular dynamics (MD) approach. We observed that LM ligands can be grouped based on their structure and affinity for the vanilloid pocket. Furthermore, the position as well as the number of the polar groups on the LM ligand directly impact binding stability through various polar interactions with the protein. As an additional control we performed docking experiments of the PUFA precursor molecules linoleic acid and arachidonic acid which failed to form stable interactions within the vanilloid pocket. While LM ligands with similar structures displayed similar binding interactions, there were notable exceptions in the case of 20-HETE, 9-HODE, and 9,10-DiHOME. Our study offers new insights into the mechanisms involved in TRPV1 activation by endogenous LM ligands. The observed binding interactions may assist in the interpretation of in vivo and in vitro pharmacodynamics studies.
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Affiliation(s)
- Nada Birkic
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - David Visentin
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Željko Svedružić
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Christian A Reynolds
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia; Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI, USA.
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Elyasi-Ebli P, Yazdanparast R, Gharaghani S, Barzegari E. Insights on the conformation and appropriate drug-target sites on retinal IMPDH1 using the 604-aa isoform lacking the C-terminal extension. Res Pharm Sci 2023; 18:638-647. [PMID: 39005562 PMCID: PMC11246115 DOI: 10.4103/1735-5362.389951] [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: 01/02/2023] [Revised: 04/05/2023] [Accepted: 08/19/2023] [Indexed: 07/16/2024] Open
Abstract
Background and purpose Retinitis pigmentosa (RP) accounts for 2 percent of global cases of blindness. The RP10 form of the disease results from mutations in isoform 1 of inosine 5'-monophosphate dehydrogenase (IMPDH1), the rate-limiting enzyme in the de novo purine nucleotide synthesis pathway. Retinal photoreceptors contain specific isoforms of IMPDH1 characterized by terminal extensions. Considering previously reported significantly varied kinetics among retinal isoforms, the current research aimed to investigate possible structural explanations and suitable functional sites for the pharmaceutical targeting of IMPDH1 in RP. Experimental approach A recombinant 604-aa IMPDH1 isoform lacking the carboxyl-terminal peptide was produced and underwent proteolytic digestion with α-chymotrypsin. Dimer models of wild type and engineered 604-aa isoform were subjected to molecular dynamics simulation. Findings/Results The IMPDH1 retinal isoform lacking C-terminal peptide was shown to tend to have more rapid proteolysis (~16% digestion in the first two minutes). Our computational data predicted the potential of the amino-terminal peptide to induce spontaneous inhibition of IMPDH1 by forming a novel helix in a GTP binding site. On the other hand, the C-terminal peptide might block the probable inhibitory role of the N-terminal extension. Conclusion and implications According to the findings, augmenting IMPDH1 activity by suppressing its filamentation is suggested as a suitable strategy to compensate for its disrupted activity in RP. This needs specific small molecule inhibitors to target the filament assembly interface of the enzyme.
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Affiliation(s)
- Parisa Elyasi-Ebli
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Razieh Yazdanparast
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sajjad Gharaghani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ebrahim Barzegari
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Abouleisa RRE, Miller JM, Gebreil A, Salama ABM, Dwenger M, Abdelhafez H, Wahid RM, Adewumi AT, Soliman ME, Abo-Dya NE, Mohamed TMA. A novel small molecule inhibitor of p38⍺ MAP kinase augments cardiomyocyte cell cycle entry in response to direct cell cycle stimulation. Br J Pharmacol 2023; 180:3271-3289. [PMID: 37547998 PMCID: PMC10726296 DOI: 10.1111/bph.16209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND AND PURPOSE Myocardial infarction (MI) is the leading cause of mortality globally due in part to the limited ability of cardiomyocytes (CMs) to regenerate. Recently, we demonstrated that overexpression of four-cell cycle factors, CDK1, CDK4, cyclin B1 and cyclin D1 (4F), induced cell division in ~20% of the post-mitotic CMs overexpressed 4F. The current study aims to identify a small molecule that augments 4F-induced CM cycle induction. EXPERIMENTAL APPROACH, KEY RESULTS Screening of small molecules with a potential to augment 4F-induced cell-cycle induction in 60-day-old mature human induced pluripotent cardiomyocytes (hiPS-CMs) revealed N-(4,6-Dimethylpyridin-2-yl)-4-(pyridine-4-yl)piperazine-1-carbothioamide (NDPPC), which activates cell cycle progression in 4F-transduced hiPS-CMs. Autodock tool and Autodock vina computational methods showed that NDPPC has a potential interaction with the binding site at the human p38⍺ mitogen-activated protein kinase (p38⍺ MAP kinase), a critical negative regulator of the mammalian cell cycle. A p38 MAP kinase activity assay showed that NDPPC inhibits p38⍺ with 5-10 times lower IC50 compared to the other P38 isoforms in a dose-dependent manner. Overexpression of p38⍺ MAP kinase in CMs inhibited 4F cell cycle induction, and treatment with NDPPC reversed the cell cycle inhibitory effect. CONCLUSION AND IMPLICATIONS NDPPC is a novel inhibitor for p38 MAP kinase and is a promising drug to augment CM cell cycle response to the 4F. NDPPC could become an adjunct treatment with other cell cycle activators for heart failure treatment.
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Affiliation(s)
- Riham R E Abouleisa
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Jessica M. Miller
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Ahmad Gebreil
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Abou Bakr M. Salama
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
- Department of Cardiovascular Medicine, Faculty of Medicine, Zagazig University, Egypt
| | - Marc Dwenger
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Hania Abdelhafez
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Reham M. Wahid
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
- Physiology Department, Faculty of Medicine, Zagazig University, Egypt
| | - Adeniyi T. Adewumi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E.S. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Nader E. Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Tamer M A Mohamed
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
- Division of Environmental Medicine, Department of Medicine, University of Louisville, Louisville, KY
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Moten D, Batsalova T, Apostolova D, Mladenova T, Dzhambazov B, Teneva I. In Silico Design of a New Epitope-Based Vaccine against Grass Group 1 Allergens. Adv Respir Med 2023; 91:486-503. [PMID: 37987298 PMCID: PMC10660545 DOI: 10.3390/arm91060036] [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: 08/31/2023] [Revised: 10/09/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
Allergic diseases are a global public health problem that affects up to 30% of the population in industrialized societies. More than 40% of allergic patients suffer from grass pollen allergy. Grass pollen allergens of group 1 and group 5 are the major allergens, since they induce allergic reactions in patients at high rates. In this study, we used immunoinformatic approaches to design an effective epitope-based vaccine against the grass group 1 allergens. After the alignment of all known pollen T-cell and B-cell epitopes from pollen allergens available in the public databases, the epitope GTKSEVEDVIPEGWKADTSY was identified as the most suitable for further analyses. The target sequence was subjected to immunoinformatics analyses to predict antigenic T-cell and B-cell epitopes. Population coverage analysis was performed for CD8+ and CD4+ T-cell epitopes. The selected T-cell epitopes (VEDVIPEGW and TKSEVEDVIPEGWKA) covered 78.87% and 98.20% of the global population and 84.57% and 99.86% of the population of Europe. Selected CD8+, CD4+ T-cell and B-cell epitopes have been validated by molecular docking analysis. CD8+ and CD4+ T-cell epitopes showed a very strong binding affinity to major histocompatibility complex (MHC) class I (MHC I) molecules and MHC class II (MHC II) molecules with global energy scores of -72.1 kcal/mol and -89.59 kcal/mol, respectively. The human IgE-Fc (PDB ID 4J4P) showed a lower affinity with B-cell epitope (ΔG = -34.4 kcal/mol), while the Phl p 2-specific human IgE Fab (PDB ID 2VXQ) had the lowest binding with the B-cell epitope (ΔG = -29.9 kcal/mol). Our immunoinformatics results demonstrated that the peptide GTKSEVEDVIPEGWKADTSY could stimulate the immune system and we performed ex vivo tests showed that the investigated epitope activates T cells isolated from patients with grass pollen allergy, but it is not recognized by IgE antibodies specific for grass pollen allergens. This confirms the importance of such studies to establish universal epitopes to serve as a basis for developing an effective vaccine against a particular group of allergens. Further in vivo studies are needed to validate the effectiveness of such a vaccine against grass pollen allergens.
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Affiliation(s)
- Dzhemal Moten
- Department of Developmental Biology, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.M.); (T.B.); (D.A.); (B.D.)
| | - Tsvetelina Batsalova
- Department of Developmental Biology, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.M.); (T.B.); (D.A.); (B.D.)
| | - Desislava Apostolova
- Department of Developmental Biology, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.M.); (T.B.); (D.A.); (B.D.)
| | - Tsvetelina Mladenova
- Department of Botany and Biological Education, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria;
| | - Balik Dzhambazov
- Department of Developmental Biology, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.M.); (T.B.); (D.A.); (B.D.)
| | - Ivanka Teneva
- Department of Botany and Biological Education, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria;
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Nur MA, Islam M, Biswas S, Hasan MN, Rahman MM, Uddin MJ, Satter MA, Amin MZ. Determination of biological activities of malabar spinach ( Basellaalba) fruit extracts and molecular docking against COX-II enzyme. Heliyon 2023; 9:e21568. [PMID: 38027774 PMCID: PMC10663853 DOI: 10.1016/j.heliyon.2023.e21568] [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: 05/08/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
To achieve the health benefit from the natural of Basella. Albafruit. This study intended to figure out the bioactive compounds in the two varieties of B. alba (native and hybrid) fruit extract and measurement its biological activities like antioxidant, anti-inflammatory, cytotoxic activities and a molecular docking were performed to observed the pharmaceutical impact on the anti-inflammatory Cyclooxygenase-2 (COX-2) enzyme. The cold extractions along with GC-MS were used for the extraction of and analysis of phytoconstituents from B. alba fruit. The hemolytic inhibitory and BSA (Bovine serum albumin)-denaturation assay, DPPH(2,2-diphenyl-1-picrylhydrazyl) and H2O2-free radical scavenging analysis, and brine shrimp lethalness test were performed to measure the biological activities of the extracted The biological activities assay results showed that the ethanol extract of native malabar spinach exhibited dose-dependent antioxidant activity. The IC50 value 21.55 ± 1.51 μg/mL was for DPPH scavenging assay and 23.36 ± 0.36 μg/mL was for H2O2 scavenging analysis. In anti-inflammatory activity assessment study, the IC50 values of the ethanol extracts were 20.52 ± 0.91 μg/mL for BSA inhibition and 20.43 ± 1.30 μg/mL for RBC hemolytic inhibitory study. In this study, cytotoxicity test results reveal that aqueous extract exhibited no cytotoxicity as compared to ethanol and ethyl acetate extract (LD50 = 875.27 μg/mL). Conversely, the current study insist the in silico analysis, to find out the anti-inflammatory activity of the investigated two fruit varieties due to pharmacokinetics analysis, toxicity properties analysis, ADMETand molecular docking. The result of this study signified that both (native and hybrid) malabar spinach fruit varieties contain phytoconstituents with potent antioxidant, anti-inflammatory, and cytotoxic action.Moreover, the in vitro and in silico results suggest that the native and hybrid fruit varieties of the extracts could be a superior striver for future appraisal as a prospective therapeutically active ingredient.
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Affiliation(s)
- M. Ashaduzzaman Nur
- Dept. of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore-7408, Bangladesh
| | - Mubenul Islam
- Dept. of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore-7408, Bangladesh
| | - Sangram Biswas
- Dept. of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore-7408, Bangladesh
| | - M. Nahid Hasan
- Dept. of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore-7408, Bangladesh
| | - M. Mashiar Rahman
- Dept. of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore-7408, Bangladesh
| | - M. Jashim Uddin
- Dept. of Pharmacy, Jashore University of Science and Technology, Jashore-7408, Bangladesh
| | - Mohammed A. Satter
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Qudrat-I-Khuda Road, Dhanmondhi, Dhaka-1205, Bangladesh
| | - M. Ziaul Amin
- Dept. of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore-7408, Bangladesh
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Upendra N, Kavya KM, Krishnaveni S. Molecular dynamics simulation study on Bacillus subtilis EngA: the presence of Mg 2+ at the active-sites promotes the functionally important conformation. J Biomol Struct Dyn 2023; 41:9219-9231. [PMID: 36444972 DOI: 10.1080/07391102.2022.2151513] [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: 08/16/2022] [Accepted: 11/20/2022] [Indexed: 11/30/2022]
Abstract
EngA, a GTPase contains two GTP binding domains [GD1, GD2], and the C-terminal KH domain shown to be involved in the later stages of ribosome maturation. Association of EngA to the ribosomal subunit in the intermediate stage of maturation is essential for complete ribosome maturation. However, this association was shown to be dependent on the nucleotide bound combinations. This nucleotide dependent association tendency is attributed to the conformational changes that occur among different nucleotide bound combinations. Therefore, to explore the conformational changes, all-atom molecular dynamics simulations for Bacillus subtilis EngA in different nucleotide bound combinations along with the presence or absence of Mg2+ in the active-sites were carried out. The presence of Mg2+ along with the bound nucleotide at the GD2 active-site dictates the GD2-Sw-II mobility, but the GD1-Sw-II mobility has not shown any nucleotide or Mg2+ dependent movement. However, the GD1-Sw-II secondary conformations are shown to be influenced by the GD2 nucleotide bound state. This allosteric connection between the GD2 active-site and the GD1-Sw-II is also observed through the dynamic network analysis. Further, the exploration of the GD1-KH interface interactions exhibited a more attractive tendency when GD1 is bound to GTP-Mg2+. In addition, the presence of Mg2+ stabilizes active-site water and also increases the distances between the α- and γ- phosphates of the bound GTP. Curiously, three water molecules in the GD1 active-site and only one water molecule in the GD2 active-site are stabilized. This indicates that the probability of GTP hydrolysis is more in GD1 compared to GD2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- N Upendra
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | - K M Kavya
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | - S Krishnaveni
- Department of Studies in Physics, University of Mysore, Mysuru, India
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Chen T, Pu M, Subramanian S, Kearns D, Rowe-Magnus D. PlzD modifies Vibrio vulnificus foraging behavior and virulence in response to elevated c-di-GMP. mBio 2023; 14:e0153623. [PMID: 37800901 PMCID: PMC10653909 DOI: 10.1128/mbio.01536-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Many free-swimming bacteria propel themselves through liquid using rotary flagella, and mounting evidence suggests that the inhibition of flagellar rotation initiates biofilm formation, a sessile lifestyle that is a nearly universal surface colonization paradigm in bacteria. In general, motility and biofilm formation are inversely regulated by the intracellular second messenger bis-(3´-5´)-cyclic dimeric guanosine monophosphate (c-di-GMP). Here, we identify a protein, PlzD, bearing a conserved c-di-GMP binding PilZ domain that localizes to the flagellar pole in a c-di-GMP-dependent manner and alters the foraging behavior, biofilm, and virulence characteristics of the opportunistic human pathogen, Vibrio vulnificus. Our data suggest that PlzD interacts with components of the flagellar stator to decrease bacterial swimming speed and changes in swimming direction, and these activities are enhanced when cellular c-di-GMP levels are elevated. These results reveal a physical link between a second messenger (c-di-GMP) and an effector (PlzD) that promotes transition from a motile to a sessile state in V. vulnificus.
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Affiliation(s)
- Tianyi Chen
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Meng Pu
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Dan Kearns
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Dean Rowe-Magnus
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Bloomington, Indiana, USA
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Li Z, Ren L, Wang X, Chen M, Wang T, Dai R, Wang Z. Anaerobic hydrolysis of recalcitrant tetramethylammonium from semiconductor wastewater: Performance and mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132239. [PMID: 37567140 DOI: 10.1016/j.jhazmat.2023.132239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The treatment of tetramethylammonium hydroxide (TMAH)-bearing wastewater, generated in the electronic and semiconductor industries, raises significant concerns due to the neurotoxic, recalcitrant, and bio-inhibiting effects of TMAH. In this study, we proposed the use of an anaerobic hydrolysis bioreactor (AHBR) for TMAH removal, achieving a high removal efficiency of approximately 85%, which greatly surpassed the performance of widely-used advanced oxidation processes (AOPs). Density functional theory calculations indicated that the unexpectedly poor efficiency (5.8-8.0%) of selected AOPs can be attributed to the electrostatic repulsion between oxidants and the tightly bound electrons of TMAH. Metagenomic analyses of the AHBR revealed that Proteobacteria and Euryarchaeota played a dominant role in the transformation of TMAH through processes such as methyl transfer, methanogenesis, and acetyl-coenzyme A synthesis, utilizing methyl-tetrahydromethanopterin as a substrate. Moreover, several potential functional genes (e.g., mprF, basS, bcrB, sugE) related to TMAH resistance have been identified. Molecular docking studies between five selected proteins and tetramethylammonium further provided evidence supporting the roles of these potential functional genes. This study demonstrates the superiority of AHBR as a pretreatment technology compared to several widely-researched AOPs, paving the way for the proper design of treatment processes to abate TMAH in semiconductor wastewater.
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Affiliation(s)
- Zhouyan Li
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Lehui Ren
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xueye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Mei Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Tianlin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ruobin Dai
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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Sinha S, Li J, Tam B, Wang SM. Classification of PTEN missense VUS through exascale simulations. Brief Bioinform 2023; 24:bbad361. [PMID: 37843401 DOI: 10.1093/bib/bbad361] [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: 06/29/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Phosphatase and tensin homolog (PTEN), a tumor suppressor with dual phosphatase properties, is a key factor in PI3K/AKT signaling pathway. Pathogenic germline variation in PTEN can abrogate its ability to dephosphorylate, causing high cancer risk. Lack of functional evidence lets numerous PTEN variants be classified as variants of uncertain significance (VUS). Utilizing Molecular Dynamics (MD) simulations, we performed a thorough evaluation for 147 PTEN missense VUS, sorting them into 66 deleterious and 81 tolerated variants. Utilizing replica exchange molecular dynamic (REMD) simulations, we further assessed the variants situated in the catalytic core of PTEN's phosphatase domain and uncovered conformational alterations influencing the structural stability of the phosphatase domain. There was a high degree of agreement between our results and the variants classified by Variant Abundance by Massively Parallel Sequencing, saturation mutagenesis, multiplexed functional data and experimental assays. Our extensive analysis of PTEN missense VUS should benefit their clinical applications in PTEN-related cancer. SIGNIFICANCE STATEMENT Classification of PTEN variants affecting its lipid phosphatase activity is important for understanding the roles of PTEN variation in the pathogenesis of hereditary and sporadic malignancies. Of the 3000 variants identified in PTEN, 1296 (43%) were assigned as VUS. Here, we applied MD and REMD simulations to investigate the effects of PTEN missense VUS on the structural integrity of the PTEN phosphatase domain consisting the WPD, P and TI active sites. We classified a total of 147 missense VUS into 66 deleterious and 81 tolerated variants by referring to the control group comprising 54 pathogenic and 12 benign variants. The classification was largely in concordance with these classified by experimental approaches.
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Affiliation(s)
- Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau S.A.R, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau S.A.R, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau S.A.R, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau S.A.R, China
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Hassan MA, Elmageed GMA, El-Qazaz IG, El-Sayed DS, El-Samad LM, Abdou HM. The Synergistic Influence of Polyflavonoids from Citrus aurantifolia on Diabetes Treatment and Their Modulation of the PI3K/AKT/FOXO1 Signaling Pathways: Molecular Docking Analyses and In Vivo Investigations. Pharmaceutics 2023; 15:2306. [PMID: 37765275 PMCID: PMC10535482 DOI: 10.3390/pharmaceutics15092306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
This study was aimed at probing the modulatory influence of polyflavonoids extracted from Citrus aurantifolia, lemon peel extract (LPE-polyflavonoids), on attenuating diabetes mellitus (DM) and its complications. HPLC investigations of the LPE exhibited the incidence of five flavonoids, including diosmin, biochanin A, hesperidin, quercetin, and hesperetin. The in silico impact on ligand-phosphatidylinositol 3-kinase (PI3K) interaction was investigated in terms of polyflavonoid class to explore the non-covalent intakes and binding affinity to the known protein active site. The drug likeness properties and pharmacokinetic parameters of the LPE-polyflavonoids were investigated to assess their bioavailability in relation to Myricetin as a control. Remarkably, the molecular docking studies demonstrated a prominent affinity score of all these agents together with PI3K, implying the potency of the extract to orchestrate PI3K, which is the predominant signal for lessening the level of blood glucose. To verify these findings, in vivo studies were conducted, utilizing diabetic male albino rats treated with LPE-polyflavonoids and other groups treated with hesperidin and diosmin as single flavonoids. Our findings demonstrated that the LPE-polyflavonoids significantly ameliorated the levels of glucose, insulin, glycogen, liver function, carbohydrate metabolizing enzymes, G6Pd, and AGEs compared to the diabetic rats and those exposed to hesperidin and diosmin. Furthermore, the LPE-polyflavonoids regulated the TBARS, GSH, CAT, TNF-α, IL-1β, IL-6, and AFP levels in the pancreatic and hepatic tissues, suggesting their antioxidant and anti-inflammatory properties. In addition, the pancreatic and hepatic GLUT4 and GLUT2 were noticeably increased in addition to the pancreatic p-AKT in the rats administered with the LPE-polyflavonoids compared to the other diabetic rats. Remarkably, the administration of LPE-polyflavonoids upregulated the expression of the pancreatic and hepatic PI3K, AMPK, and FOXO1 genes, emphasizing the efficiency of the LPE in orchestrating all the signaling pathways necessitated to reduce the diabetes mellitus. Notably, the histopathological examinations of the pancreatic and hepatic tissues corroborated the biochemical results. Altogether, our findings accentuated the potential therapeutic role of LPE-polyflavonoids in controlling diabetes mellitus.
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Affiliation(s)
- Mohamed A. Hassan
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Egypt
| | - Ghada M. Abd Elmageed
- Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21321, Egypt; (G.M.A.E.); (I.G.E.-Q.); (L.M.E.-S.)
| | - Ibtehal G. El-Qazaz
- Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21321, Egypt; (G.M.A.E.); (I.G.E.-Q.); (L.M.E.-S.)
| | - Doaa S. El-Sayed
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt;
| | - Lamia M. El-Samad
- Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21321, Egypt; (G.M.A.E.); (I.G.E.-Q.); (L.M.E.-S.)
| | - Heba M. Abdou
- Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21321, Egypt; (G.M.A.E.); (I.G.E.-Q.); (L.M.E.-S.)
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41
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Cele ZED, Matshe W, Mdlalose L, Setshedi K, Malatji K, Mkhwanazi NP, Ntombela T, Balogun M. Cationic Chitosan Derivatives for the Inactivation of HIV-1 and SARS-CoV-2 Enveloped Viruses. ACS OMEGA 2023; 8:31714-31724. [PMID: 37692209 PMCID: PMC10483524 DOI: 10.1021/acsomega.3c02143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023]
Abstract
Cationic chitosan derivatives have been widely studied as potential antimicrobial agents. However, very little is known about their antiviral activity and mode of action against enveloped viruses. We investigated the ability of hydroxypropanoic acid-grafted chitosan (HPA-CS) and N-(2-hydroxypropyl)-3-trimethylammonium chitosan chloride (HTCC) to inactivate enveloped viruses like the human immunodeficiency virus (HIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The membrane-disrupting potential of the chitosan derivatives was initially investigated in a hemolysis assay. At 1.0 mg/mL, about 80% hemolysis was observed for the cationic chitosan derivatives, which was significant when compared to almost no membrane-disrupting activity by the unmodified chitosan. Virus inhibition was evaluated using the luciferase-based antiviral assay against the HIV-1 NL4.3 virus (400 TCID). The IC50 of HPA-CS was 4.109 mg/mL, while the HTCC showed a higher antiviral activity at an IC50 = 0.225 mg/mL. For practical application, the antiviral efficacies of the HTCC-coated and uncoated nonmedical masks were evaluated for SARS- CoV-2 virus capture. The coated masks demonstrated an almost excellent performance with nearly 100% viral inhibition compared to less than 60% inhibition by the uncoated masks. Molecular docking predictions suggest that the HTCC polymers interact with the viral spike protein, blocking the coronavirus interaction with the target host cell's angiotensin-converting enzyme 2 cellular receptors.
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Affiliation(s)
- Zamani E. D. Cele
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - William Matshe
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Lindani Mdlalose
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Katlego Setshedi
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Kanyane Malatji
- Emerging
Research Area Platform, Next Generation Health Cluster, Council for Scientific and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Nompumelelo Prudence Mkhwanazi
- College
of Health Science, School of Laboratory Medicine and Medical Science,
HIV Pathogenesis Programme, University of
KwaZulu-Natal, Durban, KwaZulu-Natal 4041 South Africa
| | - Thandokuhle Ntombela
- Faculty
of Science, School of Chemistry, University
of the Witwatersrand, Johannesburg 00000, South Africa
| | - Mohammed Balogun
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
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42
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Das T, Mukhopadhyay C. Comparison and Possible Binding Orientations of SARS-CoV-2 Spike N-Terminal Domain for Gangliosides GM3 and GM1. J Phys Chem B 2023; 127:6940-6948. [PMID: 37523476 DOI: 10.1021/acs.jpcb.3c02286] [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: 08/02/2023]
Abstract
SARS-CoV-2 spike glycoprotein is anchored by gangliosides. The sialic acid in the ganglioside headgroup is responsible for virus attachment and entry into host cells. We used coarse-grained (CG) molecular dynamics simulations to expand on our previous study of GM1 interaction with two different orientations of the SARS-CoV-2 S1 subunit N-terminal domain (NTD) and to confirm the role of sialic acid receptors in driving the viral receptor; GM3 was used as another ganglioside on the membrane. Because of the smaller headgroup, sialic acid is crucial in GM3 interactions, whereas GM1 interacts with NTD via both the sialic acid and external galactose. In line with our previous findings for NTD orientations in GM1 binding, we identified two orientations, "compact" and "distributed", comprising sugar receptor-interacting residues in GM3-embedded lipid bilayers. Gangliosides in closer proximity to the compact NTD orientation might cause relatively greater restrictions to penetrate the bilayer. However, the attachment of a distributed NTD orientation with more negative interaction energies appears to facilitate GM1/GM3 to move quickly across the membrane. Our findings likely shed some light on the orientations that the NTD receptor acquires during the early phases of interaction with GM1 and GM3 in a membrane environment.
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Affiliation(s)
- Tanushree Das
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
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43
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Muñoz-Muñoz PLA, Mares-Alejandre RE, Meléndez-López SG, Ramos-Ibarra MA. Structural Insights into the Giardia lamblia Target of Rapamycin Homolog: A Bioinformatics Approach. Int J Mol Sci 2023; 24:11992. [PMID: 37569368 PMCID: PMC10418948 DOI: 10.3390/ijms241511992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
TOR proteins, also known as targets of rapamycin, are serine/threonine kinases involved in various signaling pathways that regulate cell growth. The protozoan parasite Giardia lamblia is the causative agent of giardiasis, a neglected infectious disease in humans. In this study, we used a bioinformatics approach to examine the structural features of GTOR, a G. lamblia TOR-like protein, and predict functional associations. Our findings confirmed that it shares significant similarities with functional TOR kinases, including a binding domain for the FKBP-rapamycin complex and a kinase domain resembling that of phosphatidylinositol 3-kinase-related kinases. In addition, it can form multiprotein complexes such as TORC1 and TORC2. These results provide valuable insights into the structure-function relationship of GTOR, highlighting its potential as a molecular target for controlling G. lamblia cell proliferation. Furthermore, our study represents a step toward rational drug design for specific anti-giardiasis therapeutic agents.
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Affiliation(s)
| | - Rosa E. Mares-Alejandre
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, Mexico; (P.L.A.M.-M.); (S.G.M.-L.); (M.A.R.-I.)
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44
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Plut E, Calderón JC, Stanojlović V, Gattor AO, Höring C, Humphrys LJ, Konieczny A, Kerres S, Schubert M, Keller M, Cabrele C, Clark T, Reiser O. Stereochemistry-Driven Interactions of α,γ-Peptide Ligands with the Neuropeptide Y Y 4-Receptor. J Med Chem 2023. [PMID: 37440703 DOI: 10.1021/acs.jmedchem.3c00363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The G-protein-coupled Y4-receptor (Y4R) and its endogenous ligand, pancreatic polypeptide (PP), suppress appetite in response to food intake and, thus, are attractive drug targets for body-weight control. The C-terminus of human PP (hPP), T32-R33-P34-R35-Y36-NH2, penetrates deep into the binding pocket with its tyrosine-amide and di-arginine motif. Here, we present two C-terminally amidated α,γ-hexapeptides (1a/b) with sequence Ac-R31-γ-CBAA32-R33-L34-R35-Y36-NH2, where γ-CBAA is the (1R,2S,3R)-configured 2-(aminomethyl)-3-phenylcyclobutanecarboxyl moiety (1a) or its mirror image (1b). Both peptides bind the Y4R (Ki of 1a/b: 0.66/12 nM) and act as partial agonists (intrinsic activity of 1a/b: 50/39%). Their induced-fit binding poses in the Y4R pocket are unique and build ligand-receptor contacts distinct from those of the C-terminus of the endogenous ligand hPP. We conclude that energetically favorable interactions, although they do not match those of the native ligand hPP, still guarantee high binding affinity (with 1a rivaling hPP) but not the maximum receptor activation.
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Affiliation(s)
- Eva Plut
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Jacqueline C Calderón
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Vesna Stanojlović
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Carina Höring
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Laura J Humphrys
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Adam Konieczny
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Sabine Kerres
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Chiara Cabrele
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Oliver Reiser
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
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Maiti A, Buffalo CZ, Saurabh S, Montecinos-Franjola F, Hachey JS, Conlon WJ, Tran GN, Hassan B, Walters KJ, Drobizhev M, Moerner WE, Ghosh P, Matsuo H, Tsien RY, Lin JY, Rodriguez EA. Structural and photophysical characterization of the small ultra-red fluorescent protein. Nat Commun 2023; 14:4155. [PMID: 37438348 PMCID: PMC10338489 DOI: 10.1038/s41467-023-39776-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
The small Ultra-Red Fluorescent Protein (smURFP) represents a new class of fluorescent protein with exceptional photostability and brightness derived from allophycocyanin in a previous directed evolution. Here, we report the smURFP crystal structure to better understand properties and enable further engineering of improved variants. We compare this structure to the structures of allophycocyanin and smURFP mutants to identify the structural origins of the molecular brightness. We then use a structure-guided approach to develop monomeric smURFP variants that fluoresce with phycocyanobilin but not biliverdin. Furthermore, we measure smURFP photophysical properties necessary for advanced imaging modalities, such as those relevant for two-photon, fluorescence lifetime, and single-molecule imaging. We observe that smURFP has the largest two-photon cross-section measured for a fluorescent protein, and that it produces more photons than organic dyes. Altogether, this study expands our understanding of the smURFP, which will inform future engineering toward optimal FPs compatible with whole organism studies.
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Affiliation(s)
- Atanu Maiti
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Cosmo Z Buffalo
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Saumya Saurabh
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | | | - Justin S Hachey
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - William J Conlon
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Geraldine N Tran
- Department of Radiology, Boston University, Boston, MA, 02118, USA
| | - Bakar Hassan
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Partho Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroshi Matsuo
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Roger Y Tsien
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
- Howard Hughes Medical Institute, La Jolla, CA, 92093, USA
| | - John Y Lin
- Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, 7000, Australia
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
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46
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Nishimura T, Lazzeri G, Mizushima N, Covino R, Tooze SA. Unique amphipathic α helix drives membrane insertion and enzymatic activity of ATG3. SCIENCE ADVANCES 2023; 9:eadh1281. [PMID: 37352354 PMCID: PMC10289646 DOI: 10.1126/sciadv.adh1281] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/22/2023] [Indexed: 06/25/2023]
Abstract
Autophagosome biogenesis requires a localized perturbation of lipid membrane dynamics and a unique protein-lipid conjugate. Autophagy-related (ATG) proteins catalyze this biogenesis on cellular membranes, but the underlying molecular mechanism remains unclear. Focusing on the final step of the protein-lipid conjugation reaction, the ATG8/LC3 lipidation, we show how the membrane association of the conjugation machinery is organized and fine-tuned at the atomistic level. Amphipathic α helices in ATG3 proteins (AHATG3) have low hydrophobicity and contain less bulky residues. Molecular dynamics simulations reveal that AHATG3 regulates the dynamics and accessibility of the thioester bond of the ATG3~LC3 conjugate to lipids, enabling the covalent lipidation of LC3. Live-cell imaging shows that the transient membrane association of ATG3 with autophagic membranes is governed by the less bulky-hydrophobic feature of AHATG3. The unique properties of AHATG3 facilitate protein-lipid bilayer association, leading to the remodeling of the lipid bilayer required for the formation of autophagosomes.
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Affiliation(s)
- Taki Nishimura
- PRESTO, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076, Japan
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gianmarco Lazzeri
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, Frankfurt am Main 60438, Germany
- Goethe University, Frankfurt am Main 60438, Germany
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Roberto Covino
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, Frankfurt am Main 60438, Germany
- Goethe University, Frankfurt am Main 60438, Germany
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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47
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Kashif M, Alsaiari AA, Kumar B, Asalam M, Khan MI, Ahmad A, Lone RA, Almehmadi M, Zamzami MA, Akhtar MS. Recombinant expression and preliminary characterization of Peptidyl-prolyl cis/trans-isomerase Rrd1 from Saccharomyces cerevisiae. PLoS One 2023; 18:e0282749. [PMID: 37310980 DOI: 10.1371/journal.pone.0282749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/22/2023] [Indexed: 06/15/2023] Open
Abstract
Sacchromycescerevisiae Peptidyl-prolylcis/trans-isomerase Rrd1 has been linked to DNA repair, bud morphogenesis, advancement of the G1 phase, DNA replication stress, microtubule dynamics and is also necessary for the quick decrease in Sgs1p levels in response to rapamycin. In present study, Rrd1 gene was amplified by standard PCR and subsequently cloned downstream to bacteriophage T7 inducible promoter and lac operator of expression vector pET21d(+). Additionally, immobilized metal affinity chromatography (IMAC) was used to purify the protein upto its homogeneity, and its homogeneous purity was further confirmed through western blotting. Size exclusion chromatography implies that Rrd1 is existing as monomer in its natural state. Foldwise Rrd1 protein belongs to PTPA-like protein superfamily. Rrd1 showed characteristic negative minima at 222 and 208 nm represent protein typically acquired α helix in the far-UV CD spectra. Fluorescence spectra showed properly folded tertiary structures of Rrd1 at physiological conditions. Rrd1protein can be identified from different species using a fingerprint created by PIPSA analysis. The protein's abundance could aid in its crystallization, biophysical characterization and identification of other-interacting partners of Rrd1 protein.
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Affiliation(s)
- Mohd Kashif
- Center for Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Bhupendra Kumar
- Center for Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Mohd Asalam
- CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, India
| | | | - Abrar Ahmad
- Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rayees Ahmad Lone
- Center for Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Sohail Akhtar
- CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, India
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Hsieh JY, Chen KC, Wang CH, Liu GY, Ye JA, Chou YT, Lin YC, Lyu CJ, Chang RY, Liu YL, Li YH, Lee MR, Ho MC, Hung HC. Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration. Commun Biol 2023; 6:548. [PMID: 37217557 DOI: 10.1038/s42003-023-04930-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
Human mitochondrial NAD(P)+-dependent malic enzyme (ME2) is well-known for its role in cell metabolism, which may be involved in cancer or epilepsy. We present potent ME2 inhibitors based on cyro-EM structures that target ME2 enzyme activity. Two structures of ME2-inhibitor complexes demonstrate that 5,5'-Methylenedisalicylic acid (MDSA) and embonic acid (EA) bind allosterically to ME2's fumarate-binding site. Mutagenesis studies demonstrate that Asn35 and the Gln64-Tyr562 network are required for both inhibitors' binding. ME2 overexpression increases pyruvate and NADH production while decreasing the cell's NAD+/NADH ratio; however, ME2 knockdown has the opposite effect. MDSA and EA inhibit pyruvate synthesis and thus increase the NAD+/NADH ratio, implying that these two inhibitors interfere with metabolic changes by inhibiting cellular ME2 activity. ME2 silence or inhibiting ME2 activity with MDSA or EA decreases cellular respiration and ATP synthesis. Our findings suggest that ME2 is crucial for mitochondrial pyruvate and energy metabolism, as well as cellular respiration, and that ME2 inhibitors could be useful in the treatment of cancer or other diseases that involve these processes.
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Affiliation(s)
- Ju-Yi Hsieh
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Kun-Chi Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan ROC
| | - Guang-Yaw Liu
- Institute of Medicine, College of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan ROC
| | - Jie-An Ye
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
- Institute of Medicine, College of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan ROC
| | - Yu-Tung Chou
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Yi-Chun Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Cheng-Jhe Lyu
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Rui-Ying Chang
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Yi-Liang Liu
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Yen-Hsien Li
- Instrument Center, Office of Research and Development, National Chung Hsing University, Taichung, 40227, Taiwan ROC
- Department of Chemistry, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Mau-Rong Lee
- Department of Chemistry, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan ROC.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan ROC.
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC.
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, 402, Taiwan ROC.
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan ROC.
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan ROC.
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49
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Kladova OA, Tyugashev TE, Mikushina ES, Kuznetsov NA, Novopashina DS, Kuznetsova AA. The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain. Cells 2023; 12:cells12091300. [PMID: 37174699 PMCID: PMC10177036 DOI: 10.3390/cells12091300] [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: 03/31/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
To maintain the integrity of the genome, there is a set of enzymatic systems, one of which is base excision repair (BER), which includes sequential action of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases. Normally, BER works efficiently, but the enzymes themselves (whose primary function is the recognition and removal of damaged bases) are subject to amino acid substitutions owing to natural single-nucleotide polymorphisms (SNPs). One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA with complementary dNMPs. It is known that many SNPs can cause an amino acid substitution in this enzyme and a significant decrease in the enzymatic activity. In this study, the activity of four natural variants of Polβ, containing substitution E154A, G189D, M236T, or R254I in the transferase domain, was analyzed using molecular dynamics simulations and pre-steady-state kinetic analyses. It was shown that all tested substitutions lead to a significant reduction in the ability to form a complex with DNA and with incoming dNTP. The G189D substitution also diminished Polβ catalytic activity. Thus, a decrease in the activity of studied mutant forms may be associated with an increased risk of damage to the genome.
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Affiliation(s)
- Olga A Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Daria S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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Nim YS, Fong IYH, Deme J, Tsang KL, Caesar J, Johnson S, Pang LTH, Yuen NMH, Ng TLC, Choi T, Wong YYH, Lea SM, Wong KB. Delivering a toxic metal to the active site of urease. SCIENCE ADVANCES 2023; 9:eadf7790. [PMID: 37083535 PMCID: PMC10121161 DOI: 10.1126/sciadv.adf7790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Urease is a nickel (Ni) enzyme that is essential for the colonization of Helicobacter pylori in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the cytoplasm, cells have evolved metal carrier proteins, or metallochaperones, to deliver the toxic ions to specific protein complexes. Ni delivery requires urease to form an activation complex with the urease accessory proteins UreFD and UreG. Here, we determined the cryo-electron microscopy structures of H. pylori UreFD/urease and Klebsiella pneumoniae UreD/urease complexes at 2.3- and 2.7-angstrom resolutions, respectively. Combining structural, mutagenesis, and biochemical studies, we show that the formation of the activation complex opens a 100-angstrom-long tunnel, where the Ni ion is delivered through UreFD to the active site of urease.
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Affiliation(s)
- Yap Shing Nim
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ivan Yu Hang Fong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Justin Deme
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Ka Lung Tsang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Caesar
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Longson Tsz Hin Pang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Nicholas Man Hon Yuen
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tin Long Chris Ng
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tung Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yakie Yat Hei Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Susan M. Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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