1
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Wan L, He A, Li J, Guo P, Han D. High-Resolution NMR Structures of Intrastrand Hairpins Formed by CTG Trinucleotide Repeats. ACS Chem Neurosci 2024; 15:868-876. [PMID: 38319692 DOI: 10.1021/acschemneuro.3c00769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
The CAG and CTG trinucleotide repeat expansions cause more than 10 human neurodegenerative diseases. Intrastrand hairpins formed by trinucleotide repeats contribute to repeat expansions, establishing them as potential drug targets. High-resolution structural determination of CAG and CTG hairpins poses as a long-standing goal to aid drug development, yet it has not been realized due to the intrinsic conformational flexibility of repetitive sequences. We herein investigate the solution structures of CTG hairpins using nuclear magnetic resonance (NMR) spectroscopy and found that four CTG repeats with a clamping G-C base pair was able to form a stable hairpin structure. We determine the first solution NMR structure of dG(CTG)4C hairpin and decipher a type I folding geometry of the TGCT tetraloop, wherein the two thymine residues form a T·T loop-closing base pair and the first three loop residues continuously stack. We further reveal that the CTG hairpin can be bound and stabilized by a small-molecule ligand, and the binding interferes with replication of a DNA template containing CTG repeats. Our determined high-resolution structures lay an important foundation for studying molecular interactions between native CTG hairpins and ligands, and benefit drug development for trinucleotide repeat expansion diseases.
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Affiliation(s)
- Liqi Wan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Axin He
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jinxing Li
- ReviR Therapeutics, Shenzhen Bay Hi-Tech Ecological Park, Nanshan District, Shenzhen, Guangdong 518067, China
| | - Pei Guo
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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2
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Sakthikumar K, Kabuyaya Isamura B, Krause RWM. Exploring the antioxidant, antimicrobial, cytotoxic and biothermodynamic properties of novel morpholine derivative bioactive Mn(ii), Co(ii) and Ni(ii) complexes - combined experimental and theoretical measurements towards DNA/BSA/SARS-CoV-2 3CL Pro. RSC Med Chem 2023; 14:1667-1697. [PMID: 37731703 PMCID: PMC10508264 DOI: 10.1039/d2md00394e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/07/2022] [Indexed: 09/22/2023] Open
Abstract
A novel class of bioactive complexes (1-3) [MII(L)2(bpy)], where, L = 2-(4-morpholinobenzylideneamino)phenol, bpy = 2,2'-bipyridine, MII = Mn (1), Co (2) or Ni (3), were assigned to octahedral geometry based on analytical and spectral measurements. Gel electrophoresis showed that complex (2) demonstrated significant DNA cleavage activity compared to the other complexes under the action of oxidation agent (H2O2). The DNA binding constant properties measured by various techniques were in the following sequence: (2) > (3) > (1) > (HL), which suggests that the complexes might intercalate DNA, a possibility that is also supported by their biothermodynamic characteristics. The binding constant results for BSA from electronic absorption and fluorometric titrations demonstrate that complex (2) exhibits the highest binding effectiveness among them all, which means that all the compounds could interact with BSA through a static approach, additionally supported by FRET measurements. DFT and docking calculations were employed to realize the electronic structure, reactivity, and interaction capability of all substances with DNA, BSA, and the SARS-CoV-2 main protease. These binding energies fell within the ranges -7.7 to -8.5, -8.2 to -10.1 and -6.7 to -9.3 kcal mol-1, respectively. The higher reactivity of the complexes than the ligand is supported by FMO theory. The in vitro antibacterial, cytotoxicity, and radical scavenging characteristics revealed that complexes (2-3) have better biological efficacy than the others. The cytotoxicity and binding properties also show good correlation with the partition coefficient (log P), which is encouraging because all of the experimental findings are closely correlated with the theoretical measurements.
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Affiliation(s)
- Karunganathan Sakthikumar
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
| | - Bienfait Kabuyaya Isamura
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
- Department of Chemistry, The University of Manchester Manchester M13 9PL UK
| | - Rui Werner Maçedo Krause
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
- Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa +27 741622674 +27 46 603 7030
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3
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Satange R, Chang CC, Li L, Lin SH, Neidle S, Hou MH. Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects. Nucleic Acids Res 2023; 51:3540-3555. [PMID: 36919604 PMCID: PMC10164580 DOI: 10.1093/nar/gkad156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Combination cancer chemotherapy is one of the most useful treatment methods to achieve a synergistic effect and reduce the toxicity of dosing with a single drug. Here, we use a combination of two well-established anticancer DNA intercalators, actinomycin D (ActD) and echinomycin (Echi), to screen their binding capabilities with DNA duplexes containing different mismatches embedded within Watson-Crick base-pairs. We have found that combining ActD and Echi preferentially stabilised thymine-related T:T mismatches. The enhanced stability of the DNA duplex-drug complexes is mainly due to the cooperative binding of the two drugs to the mismatch duplex, with many stacking interactions between the two different drug molecules. Since the repair of thymine-related mismatches is less efficient in mismatch repair (MMR)-deficient cancer cells, we have also demonstrated that the combination of ActD and Echi exhibits enhanced synergistic effects against MMR-deficient HCT116 cells and synergy is maintained in a MMR-related MLH1 gene knockdown in SW620 cells. We further accessed the clinical potential of the two-drug combination approach with a xenograft mouse model of a colorectal MMR-deficient cancer, which has resulted in a significant synergistic anti-tumour effect. The current study provides a novel approach for the development of combination chemotherapy for the treatment of cancers related to DNA-mismatches.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung402, Taiwan
| | - Chih-Chun Chang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung402, Taiwan
| | - Long‐Yuan Li
- Department of Life Sciences, National Chung Hsing University, Taichung402, Taiwan
| | - Sheng-Hao Lin
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Division of Chest Medicine, Changhua Christian Hospital, Changhua City, Taiwan
- Departement of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung402, Taiwan
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4
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Satange R, Rode AB, Hou MH. Revisiting recent unusual drug-DNA complex structures: Implications for cancer and neurological disease diagnostics and therapeutics. Bioorg Med Chem 2022; 76:117094. [PMID: 36410206 DOI: 10.1016/j.bmc.2022.117094] [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: 09/14/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
DNA plays a crucial role in various biological processes such as protein production, replication, recombination etc. by adopting different conformations. Targeting these conformations by small molecules is not only important for disease therapy, but also improves our understanding of the mechanisms of disease development. In this review, we provide an overview of some of the most recent ligand-DNA complexes that have diagnostic and therapeutic applications in neurological diseases caused by abnormal repeat expansions and in cancer associated with mismatches. In addition, we have discussed important implications of ligands targeting higher-order structures, such as four-way junctions, G-quadruplexes and triplexes for drug discovery and DNA nanotechnology. We provide an overview of the results and perspectives of such structural studies on ligand-DNA interactions.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics National Chung Hsing University, Taichung 402, Taiwan; Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Ambadas B Rode
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics National Chung Hsing University, Taichung 402, Taiwan; Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
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5
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Yamada T, Furuita K, Sakurabayashi S, Nomura M, Kojima C, Nakatani K. NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA. Nucleic Acids Res 2022; 50:9621-9631. [PMID: 36095126 PMCID: PMC9508812 DOI: 10.1093/nar/gkac740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/02/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
Trinucleotide repeat (TNR) diseases are caused by the aberrant expansion of CXG (X = C, A, G and T) sequences in genomes. We have reported two small molecules binding to TNR, NCD, and NA, which strongly bind to CGG repeat (responsible sequence of fragile X syndrome) and CAG repeat (Huntington's disease). The NMR structure of NA binding to the CAG/CAG triad has been clarified, but the structure of NCD bound to the CGG/CGG triad remained to be addressed. We here report the structural determination of the NCD-CGG/CGG complex by NMR spectroscopy and the comparison with the NA-CAG/CAG complex. While the NCD-CGG/CGG structure shares the binding characteristics with that of the NA-CAG/CAG complex, a significant difference was found in the overall structure caused by the structural fluctuation at the ligand-bound site. The NCD-CGG/CGG complex was suggested in the equilibrium between stacked and kinked structures, although NA-CAG/CAG complex has only the stacked structures. The dynamic fluctuation of the NCD-CGG/CGG structure at the NCD-binding site suggested room for optimization in the linker structure of NCD to gain improved affinity to the CGG/CGG triad.
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Affiliation(s)
- Takeshi Yamada
- Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Kyoko Furuita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuhei Sakurabayashi
- Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Makoto Nomura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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6
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Estrella-Parra EA, Arreola R, Álvarez-Sánchez ME, Torres-Romero JC, Rojas-Espinosa O, De la Cruz-Santiago JA, Martinez-Benitez MB, López-Camarillo C, Lara-Riegos JC, Arana-Argáez VE, Ramírez-Camacho MA. Natural marine products as antiprotozoal agents against amitochondrial parasites. Int J Parasitol Drugs Drug Resist 2022; 19:40-46. [PMID: 35636129 PMCID: PMC9157375 DOI: 10.1016/j.ijpddr.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/15/2022]
Abstract
The goal of this work is to compile and discuss molecules of marine origin reported in the scientific literature with anti-parasitic activity against Trichomonas, Giardia, and Entamoeba, parasites responsible for diseases that are major global health problems, and Microsporidial parasites as an emerging problem. The presented data correspond to metabolites with anti-parasitic activity in human beings that have been isolated by chromatographic techniques from marine sources and structurally elucidated by spectroscopic and spectrometric procedures. We also highlight some semi-synthetic derivatives that have been successful in enhancing the activity of original compounds. The biological oceanic reservoir offers the possibility to discover new biologically active molecules as lead compounds to develop new drug candidates. The molecular variety is extensive and must be correctly explored and managed. Also, it will be necessary to take some actions to preserve the source species from extinction or overharvest (e.g., by cryopreservation of coral spermatozoa, oocytes, embryos, and larvae) and coordinate appropriate exploitation to increase the chemical knowledge of the natural products generated in the oceans. Additional initiatives such as the total synthesis of complex natural products and their derivatives can help to prevent overharvest of the marine ecosystems and at the same time contribute to the discovery of new molecules. Natural active components of marine organisms have specific biological properties. The marine compounds have multiple anti-parasitic activity. The semi-synthetic derivatives of natural active components of marine organism are candidates for new drugs.
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Affiliation(s)
- Edgar Antonio Estrella-Parra
- Laboratorio de Fitoquímica, UBIPRO, FES-Iztacala, Unidad Nacional Autónoma de México, Av. De los Barrios No.1, Los Reyes Iztacala, Tlalnepantla, 54090, Estado de México, Mexico
| | - Rodrigo Arreola
- Psychiatric Genetics Department, Clinical Research Branch, National Institute of Psychiatry, Ramón de la Fuente, Calzada México-Xochimilco 101, Colonia San Lorenzo Huipulco, Tlalpan, 14370, México City, DF, Mexico
| | - Maria Elizbeth Álvarez-Sánchez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), San Lorenzo 290, Col. Del Valle, 03100, Mexico City, Mexico.
| | | | - Oscar Rojas-Espinosa
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), 11340, Ciudad de México, Mexico
| | - José Alberto De la Cruz-Santiago
- Psychiatric Genetics Department, Clinical Research Branch, National Institute of Psychiatry, Ramón de la Fuente, Calzada México-Xochimilco 101, Colonia San Lorenzo Huipulco, Tlalpan, 14370, México City, DF, Mexico
| | - Máximo Berto Martinez-Benitez
- Psychiatric Genetics Department, Clinical Research Branch, National Institute of Psychiatry, Ramón de la Fuente, Calzada México-Xochimilco 101, Colonia San Lorenzo Huipulco, Tlalpan, 14370, México City, DF, Mexico
| | - Cesar López-Camarillo
- Psychiatric Genetics Department, Clinical Research Branch, National Institute of Psychiatry, Ramón de la Fuente, Calzada México-Xochimilco 101, Colonia San Lorenzo Huipulco, Tlalpan, 14370, México City, DF, Mexico
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7
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Satange R, Kao SH, Chien CM, Chou SH, Lin CC, Neidle S, Hou MH. Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism. Nucleic Acids Res 2022; 50:8867-8881. [PMID: 35871296 PMCID: PMC9410880 DOI: 10.1093/nar/gkac629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/24/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022] Open
Abstract
The use of multiple drugs simultaneously targeting DNA is a promising strategy in cancer therapy for potentially overcoming single drug resistance. In support of this concept, we report that a combination of actinomycin D (ActD) and echinomycin (Echi), can interact in novel ways with native and mismatched DNA sequences, distinct from the structural effects produced by either drug alone. Changes in the former with GpC and CpG steps separated by a A:G or G:A mismatch or in a native DNA with canonical G:C and C:G base pairs, result in significant asymmetric backbone twists through staggered intercalation and base pair modulations. A wobble or Watson–Crick base pair at the two drug-binding interfaces can result in a single-stranded ‘chair-shaped’ DNA duplex with a straight helical axis. However, a novel sugar-edged hydrogen bonding geometry in the G:A mismatch leads to a ‘curved-shaped’ duplex. Two non-canonical G:C Hoogsteen base pairings produce a sharply kinked duplex in different forms and a four-way junction-like superstructure, respectively. Therefore, single base pair modulations on the two drug-binding interfaces could significantly affect global DNA structure. These structures thus provide a rationale for atypical DNA recognition via multiple DNA intercalators and a structural basis for the drugs’ potential synergetic use.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
| | - Shih-Hao Kao
- Institute of Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
| | - Ching-Ming Chien
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University , Taichung 402, Taiwan
| | - Chi-Chien Lin
- Institute of Biomedical Science, National Chung Hsing University , Taichung 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London , London WC1N 1AX, United Kingdom
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
- Institute of Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
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8
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Erlandson A, Gade P, Menikpurage IP, Kim CY, Mera PE. The UvrA-like protein Ecm16 requires ATPase activity to render resistance against echinomycin. Mol Microbiol 2022; 117:1434-1446. [PMID: 35534931 PMCID: PMC9328131 DOI: 10.1111/mmi.14918] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 12/02/2022]
Abstract
Bacteria use various strategies to become antibiotic resistant. The molecular details of these strategies are not fully understood. We can increase our understanding by investigating the same strategies found in antibiotic‐producing bacteria. In this work, we characterize the self‐resistance protein Ecm16 encoded by echinomycin‐producing bacteria. Ecm16 is a structural homolog of the nucleotide excision repair protein UvrA. Expression of ecm16 in the heterologous system Escherichia coli was sufficient to render resistance against echinomycin. Ecm16 binds DNA (double‐stranded and single‐stranded) using a nucleotide‐independent binding mode. Ecm16’s binding affinity for DNA increased by 1.7‐fold when the DNA is intercalated with echinomycin. Ecm16 can render resistance against echinomycin toxicity independently of the nucleotide excision repair system. Similar to UvrA, Ecm16 has ATPase activity, and this activity is essential for Ecm16’s ability to render echinomycin resistance. Notably, UvrA and Ecm16 were unable to complement each other's function. Together, our findings identify new mechanistic details of how a refurbished DNA repair protein Ecm16 can specifically render resistance to the DNA intercalator echinomycin.
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Affiliation(s)
- Amanda Erlandson
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Molecular Biology Program, New Mexico State University, Las Cruces, NM, USA
| | - Priyanka Gade
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, USA
| | - Inoka P Menikpurage
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chu-Young Kim
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, USA.,Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, USA
| | - Paola E Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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9
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Chen C, Chen X, Ren B, Guo H, Abdel-Mageed WM, Liu X, Song F, Zhang L. Characterization of Streptomyces sp. LS462 with high productivity of echinomycin, a potent antituberculosis and synergistic antifungal antibiotic. J Ind Microbiol Biotechnol 2021; 48:kuab079. [PMID: 34661655 PMCID: PMC8788810 DOI: 10.1093/jimb/kuab079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/12/2021] [Indexed: 02/05/2023]
Abstract
A biologically active microbial strain, designated as "LS462," was isolated from a soil sample collected from Yaoli Virgin Forest of Jiangxi Province, China. The strain was able to produce a high yield of echinomycin (172 mg/l) even under nonoptimized culture conditions and is proposed to serve as a promising source of echinomycin. In this study, echinomycin exhibited strong anti-Mycobacterium tuberculosis H37Rv activity and synergistic antifungal effect with a greatly reduced dosage of posaconazole on Candida albicans SC5314. The strain belongs to the genus Streptomyces according to its morphological and 16S rDNA phylogenetic analysis. The 16S rDNA was found to have the highest sequence identity with Streptomyces fuscichromogenes (99.37% similarity). Extensive nuclear magnetic resonance and mass spectroscopic data were used to determine the structure of echinomycin. The strain S. fuscichromogenes has not been previously reported to produce echinomycin. Strain LS462 may be exploited as a new potential source for the commercial production of echinomycin. Also, this work is the first to report the new synergistic antifungal activity of echinomycin and further study of the synergistic mechanism will be helpful to guide the development of antifungal agents.
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Affiliation(s)
- Caixia Chen
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Xiangyin Chen
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Biao Ren
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- West China Hospital of Stomatology, Sichuan University, Sichuan 610041, P. R. China
| | - Hui Guo
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Wael M Abdel-Mageed
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Fuhang Song
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, P. R. China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
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10
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He M, Wang Y, Huang S, Zhao N, Cheng M, Zhang X. Computational exploration of natural peptides targeting ACE2. J Biomol Struct Dyn 2021; 40:8018-8029. [PMID: 33826484 DOI: 10.1080/07391102.2021.1905555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Interaction between the SARS-COV-2 (2019 novel coronavirus) spike protein and ACE2 receptors expressed on cellular surfaces initialises viral attachment and consequent infection. Blocking this interaction shows promise for blocking or ameliorating the virus' pathological effects on the body. By contrast to work focusing on the coronavirus, which has significant potential diversity through possible accumulation of mutations during transmission, targeting the conserved ACE2 protein expressed on human cells offers an attractive alternative route to developing pharmacological prophylactics against viral invasion. In this study, we screened a virtual database of natural peptides in silico, with ACE2 as the target, and performed structural analyses of the interface region in the SARS-COV-2 RBD/ACE2 complex. These analyses have identified 15 potentially effective compounds. Analyses of ACE2/polypeptide interactions suggest that these peptides can block viral invasion of cells by stably binding in the ACE2 active site pocket. Molecular simulation results for Complestatin and Valinomycin indicate that they may share this mechanism. The discovery of this probable binding mechanism provides a frame of reference for further optimization, and design of high affinity ACE2 inhibitors that could serve as leads for production of drugs with preventive and therapeutic effects against SARS-COV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Meixi He
- CAS Key Laboratory of Separation Sciences of Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Wang
- CAS Key Laboratory of Separation Sciences of Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuai Huang
- CAS Key Laboratory of Separation Sciences of Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Nan Zhao
- CAS Key Laboratory of Separation Sciences of Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
| | - Mengchun Cheng
- CAS Key Laboratory of Separation Sciences of Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China
| | - Xiaozhe Zhang
- CAS Key Laboratory of Separation Sciences of Analytical Chemistry, Dalian Institute of Chemical Physics, Dalian, China.,Partner Group of Max Planck Society, Dalian, China
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11
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Synthesis and Structure-Chirality Relationship Analysis of Steroidal Quinoxalines to Design and Develop New Chiral Drugs. CHEMISTRY 2021. [DOI: 10.3390/chemistry3010030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Of the utmost importance of chirality in organic compounds and drugs, the present work reports structure-chirality relationship of three steroidal quinoxalines, which were synthesised by condensing diaminobenzenes with cholestenone. All the compounds were purified and characterised by varying analytical tools prior to their chiroptical analysis by circular dichroism (CD) technique. The substituent groups on quinoxalines contributed to determining the chiroptical properties of the compounds. The positive Cotton effects have been observed in the CD spectra of unsubstituted and methyl-substituted quinoxalines, which indicated their P helicity. Importantly, chloro-substituent on quinoxalines produced different CD behaviour, which can be attributed to the presence of three lone pairs of electrons on Cl atom. The present work provides guidelines for determining the chiral properties of steroidal quinoxalines, which can be useful to design and develop potential molecules of biological importance.
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Chien CM, Wu PC, Satange R, Chang CC, Lai ZL, Hagler LD, Zimmerman SC, Hou MH. Structural Basis for Targeting T:T Mismatch with Triaminotriazine-Acridine Conjugate Induces a U-Shaped Head-to-Head Four-Way Junction in CTG Repeat DNA. J Am Chem Soc 2020; 142:11165-11172. [PMID: 32478511 DOI: 10.1021/jacs.0c03591] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The potent DNA-binding compound triaminotriazine-acridine conjugate (Z1) functions by targeting T:T mismatches in CTG trinucleotide repeats that are responsible for causing neurological diseases such as myotonic dystrophy type 1, but its binding mechanism remains unclear. We solved a crystal structure of Z1 in a complex with DNA containing three consecutive CTG repeats with three T:T mismatches. Crystallographic studies revealed that direct intercalation of two Z1 molecules at both ends of the CTG repeat induces thymine base flipping and DNA backbone deformation to form a four-way junction. The core of the complex unexpectedly adopts a U-shaped head-to-head topology to form a crossover of each chain at the junction site. The crossover junction is held together by two stacked G:C pairs at the central core that rotate with respect to each other in an X-shape to form two nonplanar minor-groove-aligned G·C·G·C tetrads. Two stacked G:C pairs on both sides of the center core are involved in the formation of pseudo-continuous duplex DNA. Four metal-mediated base pairs are observed between the N7 atoms of G and CoII, an interaction that strongly preserves the central junction site. Beyond revealing a new type of ligand-induced, four-way junction, these observations enhance our understanding of the specific supramolecular chemistry of Z1 that is essential for the formation of a noncanonical DNA superstructure. The structural features described here serve as a foundation for the design of new sequence-specific ligands targeting mismatches in the repeat-associated structures.
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Affiliation(s)
| | | | | | | | | | - Lauren D Hagler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Satange R, Chuang CY, Neidle S, Hou MH. Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Nucleic Acids Res 2019; 47:8899-8912. [PMID: 31361900 PMCID: PMC6895262 DOI: 10.1093/nar/gkz653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/06/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn–syn, water mediated anti–syn and syn–syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5′ intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chien-Ying Chuang
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
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Satange R, Chang CK, Hou MH. A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic Acids Res 2019; 46:6416-6434. [PMID: 29945186 PMCID: PMC6061790 DOI: 10.1093/nar/gky561] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
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Abstract
A hypoxic environment can be defined as a region of the body or the whole body that is deprived of oxygen. Hypoxia is a feature of many diseases, such as cardiovascular disease, tissue trauma, stroke, and solid cancers. A loss of oxygen supply usually results in cell death; however, when cells gradually become hypoxic, they may survive and continue to thrive as described for conditions that promote metastatic growth. The role of hypoxia in these pathogenic pathways is therefore of great interest, and understanding the effect of hypoxia in regulating these mechanisms is fundamentally important. This chapter gives an extensive overview of these mechanisms. Moreover, given the challenges posed by tumor hypoxia we describe the current methods to simulate and detect hypoxic conditions followed by a discussion on current and experimental therapies that target hypoxic cells.
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Affiliation(s)
- Elizabeth Bowler
- College of Medicine and Health, University of Exeter Medical School, Exeter, UK.
| | - Michael R Ladomery
- Faculty Health and Applied Sciences, University of the West of England, Bristol, UK
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Alshaer W, Zraikat M, Amer A, Nsairat H, Lafi Z, Alqudah DA, Al Qadi E, Alsheleh T, Odeh F, Alkaraki A, Zihlif M, Bustanji Y, Fattal E, Awidi A. Encapsulation of echinomycin in cyclodextrin inclusion complexes into liposomes: in vitro anti-proliferative and anti-invasive activity in glioblastoma. RSC Adv 2019; 9:30976-30988. [PMID: 35529392 PMCID: PMC9072562 DOI: 10.1039/c9ra05636j] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 09/20/2019] [Indexed: 02/03/2023] Open
Abstract
Echinomycin, a DNA bis-intercalator peptide antibiotic, was complexed with γCD and loaded into PEGylated liposomes. The liposomes encapsulating echinomycin showed potent anti-proliferative and anti-invasive effect against U-87 MG glioblastoma cells.
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Yamada T, Miki S, Ni L, Nakatani K. CGG repeat DNA assisted dimerization of CGG/CGG binding molecule through intermolecular disulfide formation. Chem Commun (Camb) 2018; 54:13072-13075. [PMID: 30280156 DOI: 10.1039/c8cc06757k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new DNA binding small molecule, NCD-CC is reported. NCD-CC has a NCD domain, which recognizes the G-G mismatch in a CGG/CGG triad, and a cysteinylcystein (CC) moiety. Dimerization of NCD-CC through intermolecular disulfide bond formation was accelerated in the presence of CGG repeat DNA.
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Affiliation(s)
- Takeshi Yamada
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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