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Alniss HY, Kemp BM, Holmes E, Hoffmann J, Ploch RM, Ramadan WS, Msallam YA, Al-Jubeh HM, Madkour MM, Celikkaya BC, Scott FJ, El-Awady R, Parkinson JA. Spectroscopic, biochemical and computational studies of bioactive DNA minor groove binders targeting 5'-WGWWCW-3' motif. Bioorg Chem 2024; 148:107414. [PMID: 38733748 DOI: 10.1016/j.bioorg.2024.107414] [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: 01/23/2024] [Revised: 04/18/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024]
Abstract
Spectroscopic, biochemical, and computational modelling studies have been used to assess the binding capability of a set of minor groove binding (MGB) ligands against the self-complementary DNA sequences 5'-d(CGCACTAGTGCG)-3' and 5'-d(CGCAGTACTGCG)-3'. The ligands were carefully designed to target the DNA response element, 5'-WGWWCW-3', the binding site for several nuclear receptors. Basic 1D 1H NMR spectra of the DNA samples prepared with three MGB ligands show subtle variations suggestive of how each ligand associates with the double helical structure of both DNA sequences. The variations among the investigated ligands were reflected in the line shape and intensity of 1D 1H and 31P-{1H} NMR spectra. Rapid visual inspection of these 1D NMR spectra proves to be beneficial in providing valuable insights on MGB binding molecules. The NMR results were consistent with the findings from both UV DNA denaturation and molecular modelling studies. Both the NMR spectroscopic and computational analyses indicate that the investigated ligands bind to the minor grooves as antiparallel side-by-side dimers in a head-to-tail fashion. Moreover, comparisons with results from biochemical studies offered valuable insights into the mechanism of action, and antitumor activity of MGBs in relation to their structures, essential pre-requisites for future optimization of MGBs as therapeutic agents.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Bryony M Kemp
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Elizabeth Holmes
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Joanna Hoffmann
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Rafal M Ploch
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Wafaa S Ramadan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hadeel M Al-Jubeh
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Moustafa M Madkour
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Bekir C Celikkaya
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Fraser J Scott
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK
| | - Raafat El-Awady
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - John A Parkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, UK.
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2
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Yin J, Wu S, Yang Y, Wang D, Ma Y, Zhao Y, Sheth S, Huang H, Song B, Chen Z. In Addition to Damaging the Plasma Membrane, Phenolic Monoterpenoid Carvacrol Can Bind to the Minor Groove of DNA of Phytopathogenic Fungi to Potentially Control Tea Leaf Spot Caused by Lasiodiplodia theobromae. PHYTOPATHOLOGY 2024; 114:700-716. [PMID: 37856707 DOI: 10.1094/phyto-07-23-0263-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Carvacrol expresses a wide range of biological activities, but the studies of its mechanisms focused on bacteria, mainly involving the destruction of the plasma membrane. In this study, carvacrol exhibited strong activities against several phytopathogenic fungi and demonstrated a novel antifungal mechanism against Lasiodiplodia theobromae. RNA sequencing indicated that many genes of L. theobromae hyphae were predominately induced by carvacrol, particularly those involved in replication and transcription. Hyperchromic, hypsochromic, and bathochromic effects in the UV-visible absorption spectrum were observed following titration of calf thymus DNA (ctDNA) and carvacrol, which indicated the formation of a DNA-carvacrol complex. Circular dichroism (CD) spectroscopy indicated that the response of DNA to carvacrol was similar to that of 4',6-diamidino-2-phenylindole (DAPI) but different from that of ethidium bromide (EB), implying the ionic bonds between carvacrol and ctDNA. Fluorescence spectrum (FS) analysis indicated that carvacrol quenched the fluorescence of double-stranded DNA (dsDNA) more than single-stranded DNA, indicating that carvacrol mainly bound to dsDNA. A displacement assay showed that carvacrol reduced the fluorescence intensity of the DNA-DAPI complex through competition with DAPI, but this did not occur for DNA-EB. The FS assay revealed that carvacrol bound to the AAA sequence on the minor groove of ds-oligonucleotides. The hydroxyl of carvacrol was verified to bind to ctDNA through a comparative test in which structural analogs of carvacrol, including thymol and 4-ethyl-1,2-dimethyl, were analyzed. The current study indicated carvacrol can destruct plasma membranes and bind to the minor groove of DNA, inhibiting fungal proliferation by disturbing the stability of dsDNA.
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Affiliation(s)
- Jiayu Yin
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Shuang Wu
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yongli Yang
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yue Ma
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China
| | - Yongtian Zhao
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, Guizhou, China
| | - Sujitraj Sheth
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
| | - Honglin Huang
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Baoan Song
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Zhuo Chen
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
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3
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Francesconi V, Rizzo M, Schenone S, Carbone A, Tonelli M. State-of-the-art Review on the Antiparasitic Activity of Benzimidazolebased Derivatives: Facing Malaria, Leishmaniasis, and Trypanosomiasis. Curr Med Chem 2024; 31:1955-1982. [PMID: 37718524 PMCID: PMC11071657 DOI: 10.2174/0929867331666230915093928] [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: 05/09/2023] [Revised: 06/19/2023] [Accepted: 08/27/2023] [Indexed: 09/19/2023]
Abstract
Protozoan parasites represent a significant risk for public health worldwide, afflicting particularly people in more vulnerable categories and cause large morbidity and heavy economic impact. Traditional drugs are limited by their toxicity, low efficacy, route of administration, and cost, reflecting their low priority in global health management. Moreover, the drug resistance phenomenon threatens the positive therapy outcome. This scenario claims the need of addressing more adequate therapies. Among the diverse strategies implemented, the medicinal chemistry efforts have also focused their attention on the benzimidazole nucleus as a promising pharmacophore for the generation of new drug candidates. Hence, the present review provides a global insight into recent progress in benzimidazole-based derivatives drug discovery against important protozoan diseases, such as malaria, leishmaniasis and trypanosomiasis. The more relevant chemical features and structure-activity relationship studies of these molecules are discussed for the purpose of paving the way towards the development of more viable drugs for the treatment of these parasitic infections.
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Affiliation(s)
- Valeria Francesconi
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Marco Rizzo
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
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4
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Ogbonna E, Paul A, Farahat AA, Terrell JR, Mineva E, Ogbonna V, Boykin DW, Wilson WD. X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences. ACS BIO & MED CHEM AU 2023; 3:335-348. [PMID: 37599788 PMCID: PMC10436263 DOI: 10.1021/acsbiomedchemau.3c00002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 08/22/2023]
Abstract
The rational design of small molecules that target specific DNA sequences is a promising strategy to modulate gene expression. This report focuses on a diamidinobenzimidazole compound, whose selective binding to the minor groove of AT DNA sequences holds broad significance in the molecular recognition of AT-rich human promoter sequences. The objective of this study is to provide a more detailed and systematized understanding, at an atomic level, of the molecular recognition mechanism of different AT-specific sequences by a rationally designed minor groove binder. The specialized method of X-ray crystallography was utilized to investigate how the sequence-dependent recognition properties in general, A-tract, and alternating AT sequences affect the binding of diamidinobenzimidazole in the DNA minor groove. While general and A-tract AT sequences give a narrower minor groove, the alternating AT sequences intrinsically have a wider minor groove which typically constricts upon binding. A strong and direct hydrogen bond between the N-H of the benzimidazole and an H-bond acceptor atom in the minor groove is essential for DNA recognition in all sequences described. In addition, the diamidine compound specifically utilizes an interfacial water molecule for its DNA binding. DNA complexes of AATT and AAAAAA recognition sites show that the diamidine compound can bind in two possible orientations with a preference for water-assisted hydrogen bonding at either cationic end. The complex structures of AAATTT, ATAT, ATATAT, and AAAA are bound in a singular orientation. Analysis of the helical parameters shows a minor groove expansion of about 1 Å across all the nonalternating DNA complexes. The results from this systematic approach will convey a greater understanding of the specific recognition of a diverse array of AT-rich sequences by small molecules and more insight into the design of small molecules with enhanced specificity to AT and mixed DNA sequences.
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Affiliation(s)
- Edwin
N. Ogbonna
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ananya Paul
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Abdelbasset A. Farahat
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Master
of Pharmaceutical Sciences Program, California
North State University, 9700 W Taron Dr., Elk Grove, California 95757, United States
| | - J. Ross Terrell
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ekaterina Mineva
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Victor Ogbonna
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - David W Boykin
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - W. David Wilson
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
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5
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El-Sayed SM, Ahmed SA, Gulia K, Lenhard JR, Hassan AHE, Farahat AA. Small Molecules Incorporating Privileged Amidine Moiety as Potential Hits Combating Antibiotic-Resistant Bacteria. Pharmaceuticals (Basel) 2023; 16:1040. [PMID: 37513951 PMCID: PMC10384254 DOI: 10.3390/ph16071040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The continuing need for the discovery of potent antibacterial agents against antibiotic-resistant pathogens is the driving force for many researchers to design and develop such agents. Herein, we report the design, synthesis, and biological evaluation of amidine derivatives as new antibacterial agents. Compound 13d was the most active in this study against a wide range of antibiotic-resistant, and susceptible, Gram-positive, and Gram-negative bacterial strains. Time-kill assay experiments indicated that compound 13d was an effective bactericidal compound against the tested organisms at the log-phase of bacterial growth. Docking simulations were performed to assess in silico its mode of action regarding UPPS, KARI, and DNA as potential bacterial targets. Results unveiled the importance of structural features of compound 13d in its biological activity including central thiophene ring equipped with left and right pyrrolo[2,3-b]pyridine and phenyl moieties and two terminal amidines cyclized into 4,5-dihydro-1H-imidazol-2-yl functionalities. Collectively, compound 13d represents a possible hit for future development of potent antibacterial agents.
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Affiliation(s)
- Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 35712, Egypt
| | - Samar A Ahmed
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Kanika Gulia
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Justin R Lenhard
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Medicinal Chemistry Laboratory, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Abdelbasset A Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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6
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Khan S, Ali A, Moinuddin, Mir AR, Khan RH, Alhumaydhi FA, Habib S. 4-Chloro-orthophenylenediamine alters DNA integrity and affects cell survival: inferences from a computational, biophysical/biochemical, microscopic and cell-based study. J Biomol Struct Dyn 2022; 40:14176-14187. [PMID: 34762004 DOI: 10.1080/07391102.2021.2001376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The deleterious impact of toxic constituents of hair dyes over the human health has gained immense attention in the recent past. Their oncogenicity, mutagenicity, role in protein modification, impact on cellular metabolism has been documented. There is little information on the mechanism of reactivity of hair dye components with the nucleic acids and its implications. This work, therefore, uses computational, biophysical/biochemical, microscopic and cell-based study to analyze the interaction of monocyclic aromatic amine and a hair dye component, 4-chloro-orthophenylenediamine (4-Cl-OPD) with the DNA, its impact on DNA structure and cell survival. The results suggest that 4-Cl-OPD binds with the DNA in minor groove of the duplex involving three base pairs preferentially the G-C residues, induces strand breaks and makes DNA thermally labile through loss of hydrogen bonding/base unstacking. 4-Cl-OPD causes fragmentation of DNA, reduction in size of the molecule, alters B-DNA conformation and disrupts its secondary structure. The modified DNA gives fragmented appearance, shows broken strands and aggregation in ultra-structural analysis. 4-Cl-OPD induces ROS generation in lymphocytes, increases the comet's average tail length and reduces the viability of lymphocytes. This study forms a base for establishing the direct toxicity of 4-Cl-OPD at the molecular and cellular level through direct production of superoxide radicalCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shifa Khan
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Asif Ali
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Moinuddin
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Abdul Rouf Mir
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Safia Habib
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
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7
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Rep V, Štulić R, Koštrun S, Kuridža B, Crnolatac I, Radić Stojković M, Paljetak HČ, Perić M, Matijašić M, Raić-Malić S. Novel tetrahydropyrimidinyl-substituted benzimidazoles and benzothiazoles: synthesis, antibacterial activity, DNA interactions and ADME profiling. RSC Med Chem 2022; 13:1504-1525. [PMID: 36561067 PMCID: PMC9749923 DOI: 10.1039/d2md00143h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/12/2022] [Indexed: 12/25/2022] Open
Abstract
A series of tetrahydropyrimidinyl-substituted benzimidazoles attached to various aliphatic or aromatic residues via phenoxymethylene were synthesised to investigate their antibacterial activities against selected Gram-positive and Gram-negative bacteria. The influence of the type of substituent at the C-3 and C-4 positions of the phenoxymethylene linker on the antibacterial activity was observed, showing that the aromatic moiety improved the antibacterial potency. Of all the evaluated compounds, benzoyl-substituted benzimidazole derivative 15a was the most active compound, particularly against the Gram-negative pathogens E. coli (MIC = 1 μg mL-1) and M. catarrhalis (MIC = 2 μg mL-1). Compound 15a also exhibited the most promising antibacterial activity against sensitive and resistant strains of S. pyogenes (MIC = 2 μg mL-1). Significant stabilization effects and positive induced CD bands strongly support the binding of the most biologically active benzimidazoles inside the minor grooves of AT-rich DNA, in line with docking studies. The predicted physico-chemical and ADME properties lie within drug-like space except for low membrane permeability, which needs further optimization. Our findings encourage further development of novel structurally related 5(6)-tetrahydropyrimidinyl substituted benzimidazoles in order to optimize their antibacterial effect against common respiratory pathogens.
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Affiliation(s)
- Valentina Rep
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| | - Rebeka Štulić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| | - Sanja Koštrun
- Selvita d.o.oPrilaz baruna Filipovića 2910000 ZagrebCroatia
| | - Bojan Kuridža
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Ivo Crnolatac
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Hana Čipčić Paljetak
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Mihaela Perić
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Mario Matijašić
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
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8
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Tentellino C, Tipping WJ, McGee LMC, Bain LM, Wetherill C, Laing S, Tyson-Hirst I, Suckling CJ, Beveridge R, Scott FJ, Faulds K, Graham D. Ratiometric imaging of minor groove binders in mammalian cells using Raman microscopy. RSC Chem Biol 2022; 3:1403-1415. [PMID: 36544571 PMCID: PMC9709774 DOI: 10.1039/d2cb00159d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/23/2022] [Indexed: 02/02/2023] Open
Abstract
Quantitative drug imaging in live cells is a major challenge in drug discovery and development. Many drug screening techniques are performed in solution, and therefore do not consider the impact of the complex cellular environment in their result. As such, important features of drug-cell interactions may be overlooked. In this study, Raman microscopy is used as a powerful technique for semi-quantitative imaging of Strathclyde-minor groove binders (S-MGBs) in mammalian cells under biocompatible imaging conditions. Raman imaging determined the influence of the tail group of two novel minor groove binders (S-MGB-528 and S-MGB-529) in mammalian cell models. These novel S-MGBs contained alkyne moieties which enabled analysis in the cell-silent region of the Raman spectrum. The intracellular uptake concentration, distribution and mechanism were evaluated as a function of the pK a of the tail group, morpholine and amidine, for S-MGB-528 and S-MGB-529, respectively. Although S-MGB-529 had a higher binding affinity to the minor groove of DNA in solution-phase measurements, the Raman imaging data indicated that S-MGB-528 showed a greater degree of intracellular accumulation. Furthermore, using high resolution stimulated Raman scattering (SRS) microscopy, the initial localisation of S-MGB-528 was shown to be in the nucleus before accumulation in the lysosome, which was demonstrated using a multimodal imaging approach. This study highlights the potential of Raman spectroscopy for semi-quantitative drug imaging studies and highlights the importance of imaging techniques to investigate drug-cell interactions, to better inform the drug design process.
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Affiliation(s)
- Christian Tentellino
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - William J. Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of StrathclydeGlasgow G1 1RDUK
| | - Leah M. C. McGee
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Laura M. Bain
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Corinna Wetherill
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Stacey Laing
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Izaak Tyson-Hirst
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde Glasgow G1 1XL UK
| | - Colin J. Suckling
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde Glasgow G1 1XL UK
| | - Fraser J. Scott
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
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9
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Synthesis and Evaluation of Novel DNA Minor Groove Binders as Antiamoebic Agents. Antibiotics (Basel) 2022; 11:antibiotics11070935. [PMID: 35884189 PMCID: PMC9312114 DOI: 10.3390/antibiotics11070935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
The free-living amoeba Acanthamoeba castellanii is responsible for the central nervous infection granulomatous amoebic encephalitis and sight-threatening infection Acanthamoeba keratitis. Moreover, no effective treatment is currently present, and a combination drug therapy is used. In this study, twelve DNA minor groove binders (MGBs) were synthesized and tested for their antiamoebic activity via amoebicidal, encystation, excystation, and cytopathogenicity assays. It was found that the compounds MGB3, MGB6, MGB22, MGB24, and MGB16 significantly reduce amoeba viability to 76.20%, 59.45%, 66.5%, 39.32%, and 43.21%, respectively, in amoebicidal assays. Moreover, the compounds MGB6, MGB20, MGB22, MGB28, MGB30, MGB32, and MGB16 significantly inhibit Acanthamoeba cysts, leading to the development of only 46.3%, 39%, 30.3%, 29.6%, 27.8%, 41.5%, and 45.6% cysts. Additionally, the compounds MGB3, MGB4, MGB6, MGB22, MGB24, MGB28, MGB32, and MGB16 significantly reduce the re-emergence of cysts to trophozoites, with viable trophozoites being only 64.3%, 47.3%, 41.4%, 52.9%, 55.4%, 40.6%, 62.1%, and 51.7%. Moreover, the compounds MGB3, MGB4, and MGB6 exhibited the greatest reduction in amoeba-mediated host-cell death, with cell death reduced to 41.5%, 49.4%, and 49.5%. With the following determined, future in vivo studies can be carried out to understand the effect of the compounds on animal models such as mice.
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Multitargeted anti-infective drugs: resilience to resistance in the antimicrobial resistance era. FUTURE DRUG DISCOVERY 2022; 4:FDD73. [PMID: 35600289 PMCID: PMC9112235 DOI: 10.4155/fdd-2022-0001] [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: 01/02/2022] [Accepted: 04/08/2022] [Indexed: 12/23/2022] Open
Abstract
The standard drug discovery paradigm of single molecule – single biological target – single biological effect is perhaps particularly unsuitable for anti-infective drug discovery. This is due to the rapid evolution of resistance likely to be observed with single target drugs. Multitargeted anti-infective drugs are likely to be superior due to their lower susceptibility to target-related resistance mechanisms. Strathclyde minor groove binders are a class of compounds which have been developed by adopting the multitargeted anti-infective drugs paradigm, and their effectiveness against a wide range of pathogenic organisms is discussed. The renaming of this class to Strathclyde nucleic acid binders is also presented due to their likely targets including both DNA and RNA.
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11
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Ruthenium(II) Polypyridyl Complexes and Their Use as Probes and Photoreactive Agents for G-quadruplexes Labelling. Molecules 2022; 27:molecules27051541. [PMID: 35268640 PMCID: PMC8912042 DOI: 10.3390/molecules27051541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/01/2023] Open
Abstract
Due to their optical and electrochemical properties, ruthenium(II) polypyridyl complexes have been used in a wide array of applications. Since the discovery of the light-switch ON effect of [Ru(bpy)2dppz]2+ when interacting with DNA, the design of new Ru(II) complexes as light-up probes for specific regions of DNA has been intensively explored. Amongst them, G-quadruplexes (G4s) are of particular interest. These structures formed by guanine-rich parts of DNA and RNA may be associated with a wide range of biological events. However, locating them and understanding their implications in biological pathways has proven challenging. Elegant approaches to tackle this challenge relies on the use of photoprobes capable of marking, reversibly or irreversibly, these G4s. Indeed, Ru(II) complexes containing ancillary π-deficient TAP ligands can create a covalently linked adduct with G4s after a photoinduced electron transfer from a guanine residue to the excited complex. Through careful design of the ligands, high selectivity of interaction with G4 structures can be achieved. This allows the creation of specific Ru(II) light-up probes and photoreactive agents for G4 labelling, which is at the core of this review composed of an introduction dedicated to a brief description of G-quadruplex structures and two main sections. The first one will provide a general picture of ligands and metal complexes interacting with G4s. The second one will focus on an exhaustive and comprehensive overview of the interactions and (photo)reactions of Ru(II) complexes with G4s.
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Kieswetter NS, Ozturk M, Hlaka L, Chia JE, Nichol RJO, Cross JM, McGee LMC, Tyson-Hirst I, Beveridge R, Brombacher F, Carter KC, Suckling CJ, Scott FJ, Guler R. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1061-1071. [PMID: 35084027 PMCID: PMC8969509 DOI: 10.1093/jac/dkac001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/20/2021] [Indexed: 11/14/2022] Open
Abstract
Background Objectives Methods Results Conclusions
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Affiliation(s)
- Nathan S. Kieswetter
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
- Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Mumin Ozturk
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
- Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lerato Hlaka
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
- Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Julius Ebua Chia
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
- Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Ryan J. O. Nichol
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Jasmine M. Cross
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Leah M. C. McGee
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Izaak Tyson-Hirst
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
- Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Katharine C. Carter
- Strathclyde Institute of Pharmacy of Biomedical Sciences, University of Strathclyde, Glasgow G4 0NR, Scotland
| | - Colin J. Suckling
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Fraser J. Scott
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, Scotland
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
- Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Corresponding author. E-mail:
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Guo P, Farahat AA, Paul A, Boykin DW, Wilson WD. Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove. Chem Sci 2021; 12:15849-15861. [PMID: 35024109 PMCID: PMC8672716 DOI: 10.1039/d1sc04720e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔT m, biosensor SPR with a K D of 4 nM, a similar K D from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central -CH of the benzodiimidazole is close to the -C[double bond, length as m-dash]O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.
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Affiliation(s)
- Pu Guo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - Abdelbasset A Farahat
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - David W Boykin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
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Transcriptional regulation of congocidine (netropsin) biosynthesis and resistance. Appl Environ Microbiol 2021; 87:e0138021. [PMID: 34586912 DOI: 10.1128/aem.01380-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The production of specialized metabolites by Streptomyces bacteria is usually temporally regulated. This regulation is complex and frequently involves both global and pathway-specific mechanisms. Streptomyces ambofaciens ATCC23877 produces several specialized metabolites, including spiramycins, stambomycins, kinamycins and congocidine. The production of the first three molecules has been shown to be controlled by one or several cluster-situated transcriptional regulators. However, nothing is known regarding the regulation of congocidine biosynthesis. Congocidine (netropsin) belongs to the family of pyrrolamide metabolites, which also includes distamycin and anthelvencins. Most pyrrolamides bind into the minor groove of DNA, specifically in A/T-rich regions, which gives them numerous biological activities, such as antimicrobial and antitumoral activities. We previously reported the characterization of the pyrrolamide biosynthetic gene clusters of congocidine (cgc) in S. ambofaciens ATCC23877, distamycin (dst) in Streptomyces netropsis DSM40846 and anthelvencins (ant) in Streptomyces venezuelae ATCC14583. The three gene clusters contain a gene encoding a putative transcriptional regulator, cgc1, dst1 and ant1 respectively. Cgc1, Dst1 and Ant1 present a high percentage of amino acid sequence similarity. We demonstrate here that Cgc1, an atypical orphan response regulator, activates the transcription of all cgc genes in the stationary phase of S. ambofaciens growth. We also show that the cgc cluster is constituted of eight main transcriptional units. Finally, we show that congocidine induces the expression of the transcriptional regulator Cgc1 and of the operon containing the resistance genes (cgc20 and cgc21, coding for an ABC transporter), and propose a model for the transcriptional regulation of the cgc gene cluster. Importance Understanding the mechanisms of regulation of specialized metabolite production can have important implications both at the level of specialized metabolism study (expression of silent gene clusters) and the biotechnological level (increase of the production of a metabolite of interest). We report here a study on the regulation of the biosynthesis of a metabolite from the pyrrolamide family, congocidine. We show that congocidine biosynthesis and resistance is controlled by Cgc1, a cluster-situated regulator. As the gene clusters directing the biosynthesis of the pyrrolamides distamycin and anthelvencin encode a homolog of Cgc1, our findings may be relevant for the biosynthesis of other pyrrolamides. In addition, our results reveal a new type of feed-forward induction mechanism, in which congocidine induces its own biosynthesis through the induction of the transcription of cgc1.
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15
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Brooke DP, McGee LMC, Giordani F, Cross JM, Khalaf AI, Irving C, Gillingwater K, Shaw CD, Carter KC, Barrett MP, Suckling CJ, Scott FJ. Truncated S-MGBs: towards a parasite-specific and low aggregation chemotype. RSC Med Chem 2021; 12:1391-1401. [PMID: 34447938 PMCID: PMC8372214 DOI: 10.1039/d1md00110h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/16/2021] [Indexed: 11/21/2022] Open
Abstract
This paper describes the design and synthesis of Strathclyde minor groove binders (S-MGBs) that have been truncated by the removal of a pyrrole ring in order to mimic the structure of the natural product, disgocidine. S-MGBs have been found to be active against many different organisms, however, selective antiparasitic activity is required. A panel of seven truncated S-MGBs was prepared and the activities examined against a number of clinically relevant organisms including several bacteria and parasites. The effect of the truncation strategy on S-MGB aggregation in aqueous environment was also investigated using 1H inspection and DOSY experiments. A lead compound, a truncated S-MGB, which possesses significant activity only against trypanosomes and Leishmania has been identified for further study and was also found to be less affected by aggregation compared to its full-length analogue.
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Affiliation(s)
- Daniel P Brooke
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde Glasgow UK
| | - Leah M C McGee
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde Glasgow UK
| | - Federica Giordani
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow UK
| | - Jasmine M Cross
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde Glasgow UK
| | - Abedawn I Khalaf
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde Glasgow UK
| | - Craig Irving
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde Glasgow UK
| | - Kirsten Gillingwater
- Parasite Chemotherapy Unit, Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute Basel Switzerland
- University of Basel Basel Switzerland
| | - Craig D Shaw
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde Glasgow UK
| | - Katharine C Carter
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde Glasgow UK
| | - Michael P Barrett
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow UK
| | - Colin J Suckling
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde Glasgow UK
| | - Fraser J Scott
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde Glasgow UK
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16
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Gotzmann C, Blacque O, Fox T, Alberto R. [Re(η
6
‐C
6
H
5
‐benzimidazole)
2
]
+
and Derivatives as Dye Mimics; Synthesis, UV Absorption Studies and DFT Calculations. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carla Gotzmann
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Olivier Blacque
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Thomas Fox
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Roger Alberto
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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17
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Godzieba M, Ciesielski S. Natural DNA Intercalators as Promising Therapeutics for Cancer and Infectious Diseases. Curr Cancer Drug Targets 2021; 20:19-32. [PMID: 31589125 DOI: 10.2174/1568009619666191007112516] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/11/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023]
Abstract
Cancer and infectious diseases are one of the greatest challenges of modern medicine. An unhealthy lifestyle, the improper use of drugs, or their abuse are conducive to the increase of morbidity and mortality caused by these diseases. The imperfections of drugs currently used in therapy for these diseases and the increasing problem of drug resistance have forced a search for new substances with therapeutic potential. Throughout history, plants, animals, fungi and microorganisms have been rich sources of biologically active compounds. Even today, despite the development of chemistry and the introduction of many synthetic chemotherapeutics, a substantial part of the new compounds being tested for treatment are still of natural origin. Natural compounds exhibit a great diversity of chemical structures, and thus possess diverse mechanisms of action and molecular targets. Nucleic acids seem to be a good molecular target for substances with anticancer potential in particular, but they may also be a target for antimicrobial compounds. There are many types of interactions of small-molecule ligands with DNA. This publication focuses on the intercalation process. Intercalators are compounds that usually have planar aromatic moieties and can insert themselves between adjacent base pairs in the DNA helix. These types of interactions change the structure of DNA, leading to various types of disorders in the functioning of cells and the cell cycle. This article presents the most promising intercalators of natural origin, which have aroused interest in recent years due to their therapeutic potential.
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Affiliation(s)
- Martyna Godzieba
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, ul. Sloneczna 45 G, 10-917 Olsztyn, Poland
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, ul. Sloneczna 45 G, 10-917 Olsztyn, Poland
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18
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Bisbenzimidazole Derivatives as Potential Antimicrobial Agents: Design, Synthesis, Biological Evaluation and Pharmacophore Analysis. Pharm Chem J 2021. [DOI: 10.1007/s11094-021-02389-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Ferger M, Ban Ž, Krošl I, Tomić S, Dietrich L, Lorenzen S, Rauch F, Sieh D, Friedrich A, Griesbeck S, Kenđel A, Miljanić S, Piantanida I, Marder TB. Bis(phenylethynyl)arene Linkers in Tetracationic Bis-triarylborane Chromophores Control Fluorimetric and Raman Sensing of Various DNAs and RNAs. Chemistry 2021; 27:5142-5159. [PMID: 33411942 PMCID: PMC8048639 DOI: 10.1002/chem.202005141] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/20/2020] [Indexed: 11/24/2022]
Abstract
We report four new luminescent tetracationic bis-triarylborane DNA and RNA sensors that show high binding affinities, in several cases even in the nanomolar range. Three of the compounds contain substituted, highly emissive and structurally flexible bis(2,6-dimethylphenyl-4-ethynyl)arene linkers (3: arene=5,5'-2,2'-bithiophene; 4: arene=1,4-benzene; 5: arene=9,10-anthracene) between the two boryl moieties and serve as efficient dual Raman and fluorescence chromophores. The shorter analogue 6 employs 9,10-anthracene as the linker and demonstrates the importance of an adequate linker length with a certain level of flexibility by exhibiting generally lower binding affinities than 3-5. Pronounced aggregation-deaggregation processes are observed in fluorimetric titration experiments with DNA for compounds 3 and 5. Molecular modelling of complexes of 5 with AT-DNA, suggest the minor groove as the dominant binding site for monomeric 5, but demonstrate that dimers of 5 can also be accommodated. Strong SERS responses for 3-5 versus a very weak response for 6, particularly the strong signals from anthracene itself observed for 5 but not for 6, demonstrate the importance of triple bonds for strong Raman activity in molecules of this compound class. The energy of the characteristic stretching vibration of the C≡C bonds is significantly dependent on the aromatic moiety between the triple bonds. The insertion of aromatic moieties between two C≡C bonds thus offers an alternative design for dual Raman and fluorescence chromophores, applicable in multiplex biological Raman imaging.
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Affiliation(s)
- Matthias Ferger
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Željka Ban
- Division of Organic Chemistry & BiochemistryRuđer Bošković Institute, Bijenička 5410000ZagrebCroatia
| | - Ivona Krošl
- Division of Organic Chemistry & BiochemistryRuđer Bošković Institute, Bijenička 5410000ZagrebCroatia
| | - Sanja Tomić
- Division of Organic Chemistry & BiochemistryRuđer Bošković Institute, Bijenička 5410000ZagrebCroatia
| | - Lena Dietrich
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Sabine Lorenzen
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Florian Rauch
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Daniel Sieh
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Alexandra Friedrich
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Stefanie Griesbeck
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Adriana Kenđel
- Division of Analytical ChemistryDepartment of Chemistry, Faculty of ScienceUniversity of Zagreb, Horvatovac 102a10000ZagrebCroatia
| | - Snežana Miljanić
- Division of Analytical ChemistryDepartment of Chemistry, Faculty of ScienceUniversity of Zagreb, Horvatovac 102a10000ZagrebCroatia
| | - Ivo Piantanida
- Division of Organic Chemistry & BiochemistryRuđer Bošković Institute, Bijenička 5410000ZagrebCroatia
| | - Todd B. Marder
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
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Controlling the reactivity of [Pd (II)(N^N^N)Cl] + complexes using 2,6-bis(pyrazol-2-yl)pyridine ligands for biological application: Substitution reactivity, CT-DNA interactions and in vitro cytotoxicity study. J Inorg Biochem 2020; 213:111261. [PMID: 33011625 DOI: 10.1016/j.jinorgbio.2020.111261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022]
Abstract
Four [(N^N^N)Pd(II)Cl]+ complexes [chloride-(2,2':6',2''-terpyridine)Pd(II)]Cl (PdL1), [chlorido(2,6-bis(N-pyrazol-2-yl)pyridine)Pd(II)]Cl (PdL2), [chlorido(2,6-bis(3,5-dimethyl-N-pyrazol-2-yl)pyridine)Pd(II)]Cl (PdL3) and [chlorido(2,6-bis(3,5-dimethyl-N-pyrazol-2-ylmethyl)pyridine)Pd(II)]BF4 (PdL4) were synthesized and characterized. The rates of substitution of these Pd(II) complexes with thiourea nucleophiles viz; thiourea (Tu), N,N'-dimethylthiourea (Dmtu) and N,N,N',N'-tetramethylthiourea (Tmtu) was investigated under pseudo first-order conditions as a function of nucleophile concentration [Nu] and temperature using the stopped-flow technique. The observed rate constants vary linearly with [Nu]; kobs = k2[Nu] and decreased in the order: PdL1 > PdL2 > PdL3 ≫ PdL4. The lower π-acceptability of the cis-coordinated N-pyrazol-2-yl groups (which coordinates via pyrazollic-N π-donor atoms) of the PdL2-4 significantly decelerates the reactivity relative to PdL1. Furthermore, the six-membered chelates having methylene bridge in PdL4 do not allow π-extension in the ligand and introduces steric hindrance further lowering the reactivity. Trends in DFT calculated data supported the observed reactivity trend. Spectrophotometric titration data of complexes with calf thymus DNA (CT-DNA) and viscosity measurements of the resultant mixtures suggested that associative interactions occur between the complexes and CT-DNA, likely through groove binding with high binding constants (Kb = 104 M-1). In vitro MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] cytotoxic activity data showed that PdL1 was the most potent complex against MCF7 breast cancer cells; its IC50 value is lower than that of cisplatin. The results demonstrate how modification of a spectator ligand can be used to slow down the reactivity of Pd(II) complexes. This is of special importance in controlling drug toxicity in both pharmaceutical and biomedical applications.
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Tessaro F, Scapozza L. How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids? Molecules 2020; 25:E2749. [PMID: 32545835 PMCID: PMC7355999 DOI: 10.3390/molecules25122749] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 11/16/2022] Open
Abstract
In this review, we retraced the '40-year evolution' of molecular docking algorithms. Over the course of the years, their development allowed to progress from the so-called 'rigid-docking' searching methods to the more sophisticated 'semi-flexible' and 'flexible docking' algorithms. Together with the advancement of computing architecture and power, molecular docking's applications also exponentially increased, from a single-ligand binding calculation to large screening and polypharmacology profiles. Recently targeting nucleic acids with small molecules has emerged as a valuable therapeutic strategy especially for cancer treatment, along with bacterial and viral infections. For example, therapeutic intervention at the mRNA level allows to overcome the problematic of undruggable proteins without modifying the genome. Despite the promising therapeutic potential of nucleic acids, molecular docking programs have been optimized mostly for proteins. Here, we have analyzed literature data on nucleic acid to benchmark some of the widely used docking programs. Finally, the comparison between proteins and nucleic acid targets docking highlighted similarity and differences, which are intrinsically related to their chemical and structural nature.
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Affiliation(s)
- Francesca Tessaro
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva CMU, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland;
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva CMU, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland;
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
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22
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Franco J, Scarone L, Comini MA. Novel distamycin analogues that block the cell cycle of African trypanosomes with high selectivity and potency. Eur J Med Chem 2020; 189:112043. [PMID: 31978782 DOI: 10.1016/j.ejmech.2020.112043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/03/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023]
Abstract
Polyamides-based compounds related to the Streptomycetal distamycin and netropsin are potent cytostatic molecules that bind to AT-rich regions of the minor groove of the DNA, hence interfering with DNA replication and transcription. Recently, derivatives belonging to this scaffold have been reported to halt the proliferation of deadly African trypanosomes by different and unrelated mechanisms. Here we describe the synthesis and preliminary characterization of the anti-trypanosomal mode of action of new potent and selective distamycin analogues. Two tri-heterocyclic derivatives containing a central N-methyl pyrrole ring (16 and 17) displayed high activity (EC50 < 20 nM) and selectivity (selectivity index >5000 with respect to mammalian macrophages) against the infective form of T. brucei. Both compounds caused cell cycle arrest by blocking the replication of the mitochondrial DNA but without affecting its integrity. This mode of action clearly differs from that reported for classical minor groove binder (MGB) drugs, which induce the degradation of the mitochondrial DNA. In line with this, in vitro assays suggest that 16 and 17 have a comparatively lower affinity for different template DNAs than the MGB drug diminazene. Therapeutic efficacy studies and stability assays suggest that the pharmacological properties of the hits should be optimized. The compounds can be rated as excellent scaffolds for the design of highly potent and selective anti-T. brucei agents.
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Affiliation(s)
- Jaime Franco
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay; Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Laura Scarone
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay.
| | - Marcelo A Comini
- Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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23
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Recent development of nucleic acid nanosensors to detect sequence-specific binding interactions: From metal ions, small molecules to proteins and pathogens. SENSORS INTERNATIONAL 2020; 1:100034. [PMID: 34766041 PMCID: PMC7434487 DOI: 10.1016/j.sintl.2020.100034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
DNA carries important genetic instructions and plays vital roles in regulating biological activities in living cells. Proteins such as transcription factors binds to DNA to regulate the biological functions of DNA, and similarly many drug molecules also bind to DNA to modulate its functions. Due to the importance of protein-DNA and drug-DNA binding, there has been intense effort in developing novel nanosensors in the same length scale as DNA, to effectively study these binding interactions in details. In addition, aptamers can be artificially selected to detect metal ions and pathogens such as bacteria and viruses, making nucleic acid nanosensors more versatile in detecting a large variety of analytes. In this minireview, we first explained the different types and binding modes of protein-DNA and drug-DNA interactions in the biological systems, as well as aptamer-target binding. This was followed by the review of five types of nucleic acid nanosensors based on optical or electrochemical detection. The five types of nucleic acid nanosensors utilizing colorimetric, dynamic light scattering (DLS), surface-enhanced Raman spectroscopy (SERS), fluorescence and electrochemical detections have been recently developed to tackle some of the challenges in high-throughput screening technology for large scale analysis, which is especially useful for drug development and mass screening for pandemic outbreak such as SARS or COVID-19.
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24
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Alniss HY, Witzel II, Semreen MH, Panda PK, Mishra YK, Ahuja R, Parkinson JA. Investigation of the Factors That Dictate the Preferred Orientation of Lexitropsins in the Minor Groove of DNA. J Med Chem 2019; 62:10423-10440. [DOI: 10.1021/acs.jmedchem.9b01534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hasan Y. Alniss
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Ini-Isabée Witzel
- Core Technology Platform, New York University of Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Pritam Kumar Panda
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
| | - Yogendra Kumar Mishra
- Functional Nanomaterials, Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Rajeev Ahuja
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
- Department of Materials and Engineering, Royal Institute of Technology (KTH), SE-10044 Stockholm Sweden
| | - John A. Parkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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25
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Nichol RJO, Khalaf AI, Sooda K, Hussain O, Griffiths HBS, Phillips R, Javid FA, Suckling CJ, Allison SJ, Scott FJ. Selective in vitro anti-cancer activity of non-alkylating minor groove binders. MEDCHEMCOMM 2019; 10:1620-1634. [PMID: 32952999 DOI: 10.1039/c9md00268e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/18/2019] [Indexed: 12/16/2022]
Abstract
Traditional cytotoxic agents which act through a DNA-alkylating mechanism are relatively non-specific, resulting in a small therapeutic window and thus limiting their effectiveness. In this study, we evaluate a panel of 24 non-alkylating Strathclyde Minor Groove Binders (S-MGBs), including 14 novel compounds, for in vitro anti-cancer activity against a human colon carcinoma cell line, a cisplatin-sensitive ovarian cancer cell line and a cisplatin-resistant ovarian cancer cell line. A human non-cancerous retinal epithelial cell line was used to measure selectivity of any response. We have identified several S-MGBs with activities comparable to cis-platin and carboplatin, but with better in vitro selectivity indices, particularly S-MGB-4, S-MGB-74 and S-MGB-317. Moreover, a comparison of the cis-platin resistant and cis-platin sensitive ovarian cancer cell lines reveals that our S-MGBs do not show cross resistance with cisplatin or carboplatin and that they likely have a different mechanism of action. Finally, we present an initial investigation into the mechanism of action of one compound from this class, S-MGB-4, demonstrating that neither DNA double strand breaks nor the DNA damage stress sensor protein p53 are induced. This indicates that our S-MGBs are unlikely to act through an alkylating or DNA damage response mechanism.
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Affiliation(s)
- Ryan J O Nichol
- Department of Biological and Geographical Sciences , School of Applied Sciences , University of Huddersfield , Huddersfield , UK
| | - Abedawn I Khalaf
- Department of Pure and Applied Chemistry , WestCHEM , University of Strathclyde , Glasgow , UK .
| | - Kartheek Sooda
- Department of Pharmacy , School of Applied Sciences , University of Huddersfield , Huddersfield , UK
| | - Omar Hussain
- Department of Pharmacy , School of Applied Sciences , University of Huddersfield , Huddersfield , UK
| | - Hollie B S Griffiths
- Department of Biological and Geographical Sciences , School of Applied Sciences , University of Huddersfield , Huddersfield , UK
| | - Roger Phillips
- Department of Pharmacy , School of Applied Sciences , University of Huddersfield , Huddersfield , UK
| | - Farideh A Javid
- Department of Pharmacy , School of Applied Sciences , University of Huddersfield , Huddersfield , UK
| | - Colin J Suckling
- Department of Pure and Applied Chemistry , WestCHEM , University of Strathclyde , Glasgow , UK .
| | - Simon J Allison
- Department of Biological and Geographical Sciences , School of Applied Sciences , University of Huddersfield , Huddersfield , UK
| | - Fraser J Scott
- Department of Pure and Applied Chemistry , WestCHEM , University of Strathclyde , Glasgow , UK .
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26
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Padroni G, Parkinson JA, Fox KR, Burley GA. Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides. Nucleic Acids Res 2019; 46:42-53. [PMID: 29194552 PMCID: PMC5758887 DOI: 10.1093/nar/gkx1211] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/28/2017] [Indexed: 01/05/2023] Open
Abstract
This manuscript reports the molecular basis for double-stranded DNA (dsDNA) binding of hairpin polyamides incorporating a 5-alkyl thiazole (Nt) unit. Hairpin polyamides containing an N-terminal Nt unit induce higher melting stabilisation of target dsDNA sequences relative to an archetypical hairpin polyamide incorporating an N-terminal imidazole (Im) unit. However, modification of the N-terminus from Im to Nt-building blocks results in an increase in dsDNA binding affinity but lower G-selectivity. A general G-selectivity trend is observed for Nt-containing polyamide analogues. G-selectivity increases as the steric bulk in the Nt 5-position increases. Solution-based NMR structural studies reveal differences in the modulation of the target DNA duplex of Nt-containing hairpin polyamides relative to the Im-containing archetype. A structural hallmark of an Nt polyamide•dsDNA complex is a more significant degree of major groove compression of the target dsDNA sequence relative to the Im-containing hairpin polyamide.
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Affiliation(s)
- Giacomo Padroni
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - John A Parkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Keith R Fox
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton SO17 1BJ, UK
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
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27
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Popov AB, Stolić I, Krstulović L, Taylor MC, Kelly JM, Tomić S, Tumir L, Bajić M, Raić-Malić S. Novel symmetric bis-benzimidazoles: Synthesis, DNA/RNA binding and antitrypanosomal activity. Eur J Med Chem 2019; 173:63-75. [PMID: 30986572 DOI: 10.1016/j.ejmech.2019.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/22/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
The novel benzimidazol-2-yl-fur-5-yl-(1,2,3)-triazolyl dimeric series with aliphatic and aromatic central linkers was successfully prepared with the aim of assessing binding affinity to DNA/RNA and antitrypanosomal activity. UV-Visible spectroscopy, thermal denaturation showed interaction of heterocyclic bis-amidines with ctDNA. Circular dichroism studies indicated uniform orientation of heterocyclic bis-amidines along the chiral double helix axis, revealing minor groove binding as the dominant binding mode. The amidino fragment and 1,4-bis(oxymethylene)phenyl spacer were the main determinants of activity against Trypanosoma brucei. The bis-benzimidazole imidazoline 15c, which had antitrypanosomal potency in the submicromolar range and DNA interacting properties, emerged as a candidate for further structural optimization to obtain more effective agents to combat trypanosome infections.
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Affiliation(s)
- A Bistrović Popov
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000, Zagreb, Croatia
| | - I Stolić
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000, Zagreb, Croatia
| | - L Krstulović
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000, Zagreb, Croatia
| | - M C Taylor
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - J M Kelly
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - S Tomić
- Division of Organic Chemistry and Biochemistry, Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10000, Zagreb, Croatia
| | - L Tumir
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Bijenička 54, HR-10000, Zagreb, Croatia
| | - M Bajić
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000, Zagreb, Croatia
| | - S Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000, Zagreb, Croatia.
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28
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Challenges and current status of computational methods for docking small molecules to nucleic acids. Eur J Med Chem 2019; 168:414-425. [PMID: 30831409 DOI: 10.1016/j.ejmech.2019.02.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 01/29/2023]
Abstract
Since the development of the first docking program in 1982, the use of docking-based in silico screening for potentially bioactive molecule discovery has become a common strategy in academia and pharmaceutical industry. Up until recently, application of docking programs has largely focused on drugs binding to proteins. However, with the discovery of promising drug targets in nucleic acids, including RNA riboswitches, DNA G-quadruplexes, and extended repeats in RNA, there has been greater interests in developing drugs for nucleic acids. However, due to major biochemical and physical differences in charges, binding pockets, and solvation, existing docking programs, developed for proteins, face difficulties when adopted directly for nucleic acids. In this review, we cover the current field of in silico docking to nucleic acids, available programs, as well as challenges faced in the field.
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29
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Lv M, Wang M, Lu K, Peng L, Zhao Y. DNA/Lysozyme-binding affinity study of novel peptides from TAT (47-57) and BRCA1 (782-786) in vitro by spectroscopic analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 209:109-117. [PMID: 30384016 DOI: 10.1016/j.saa.2018.10.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
SISLL-TAT and TAT-SISLL were synthesized by modifying the N- or C-termini of cell-penetrating peptides as transacting activator of transcription TAT (47-57) by attaching BRCA1 (782-786) (SISLL). The novel peptides were synthesized through Fmoc solid-phase synthesis procedures and characterized by LCQ Fleet MS, 1H NMR and 13C NMR. SISLL-TAT and TAT-SISLL displayed forceful antibacterial activities against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Salmonella typhimurium with low hemolysis. SISLL-TAT showed better antibacterial activity than TAT-SISLL, with the minimum inhibitory concentration (MIC) values of 10-33 μg·mL-1. The results of the DNA-binding activities showed that both SISLL-TAT and TAT-SISLL could interact with DNA via the minor groove mode, and the binding constants were 4.97 × 105 L·mol-1 and 4.42 × 105 L·mol-1 at 310 K, respectively. Circular dichroism analysis showed slight transformation of the lysozyme secondary structure caused by SISLL-TAT and TAT-SISLL. We also found that the novel peptides SISLL-TAT and TAT-SISLL targeted bacterial DNA resulting in cell death. This explains the antibacterial mechanism of SISLL-TAT and TAT-SISLL, and is a solid theoretical basis for further designing novel and highly effective antibiotics for clinical application.
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Affiliation(s)
- Mingxiu Lv
- School of Material and Chemical Engineering, Henan University of Engineering, Zhengzhou 450007, Henan, China; College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Mengwei Wang
- School of Material and Chemical Engineering, Henan University of Engineering, Zhengzhou 450007, Henan, China; College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Kui Lu
- School of Material and Chemical Engineering, Henan University of Engineering, Zhengzhou 450007, Henan, China; School of Chemical Engineering and Food Science, Zhengzhou Institute of Technology, Zhengzhou 450044, Henan, China.
| | - Lu Peng
- School of Material and Chemical Engineering, Henan University of Engineering, Zhengzhou 450007, Henan, China
| | - Yufen Zhao
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, Henan, China.
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30
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Giordani F, Khalaf AI, Gillingwater K, Munday JC, de Koning HP, Suckling CJ, Barrett MP, Scott FJ. Novel Minor Groove Binders Cure Animal African Trypanosomiasis in an in Vivo Mouse Model. J Med Chem 2019; 62:3021-3035. [DOI: 10.1021/acs.jmedchem.8b01847] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | - Abedawn I. Khalaf
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, Glasgow G1 1XL, U.K
| | - Kirsten Gillingwater
- Parasite Chemotherapy, Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4001, Switzerland
| | | | | | - Colin J. Suckling
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, Glasgow G1 1XL, U.K
| | | | - Fraser J. Scott
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, U.K
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31
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Arciszewska K, Pućkowska A, Wróbel A, Drozdowska D. Carbocyclic Analogues of Distamycin and Netropsin. Mini Rev Med Chem 2019; 19:98-113. [PMID: 30626311 DOI: 10.2174/1389557518666181009143203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 11/22/2022]
Abstract
The DNA as the depository of genetic information is a natural target for chemotherapy. A lot of anticancer and antimicrobial agents derive their biological activity from their selective interaction with DNA in the minor groove and from their ability to interfere with biological processes such as enzyme catalysis, replication and transcription. The discovery of the details of minor groove binding drugs, such as netropsin and distamycin A, oligoamides built of 4-amino-1-methylpyrrole-2-carboxylic acid residues, allowed to develop various DNA sequence-reading molecules, named lexitropsins, capable of interacting with DNA precisely, strongly and with a high specificity, and at the same time exhibiting significant cytotoxic potential. Among such compounds, lexitropsins built of carbocyclic sixmembered aromatic rings occupy a quite prominent place in drug research. This work is an attempt to present current findings in the study of carbocyclic lexitropins, their structures, syntheses and biological investigations such as DNA-binding and antiproliferative activity.
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Affiliation(s)
| | - Anna Pućkowska
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
| | - Agnieszka Wróbel
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
| | - Danuta Drozdowska
- Department of Organic Chemistry, Medical University, Bialystok 15-222, Mickiewicza Street 2c, Poland
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32
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Bellam R, Jaganyi D, Mambanda A, Robinson R, BalaKumaran MD. Seven membered chelate Pt(ii) complexes with 2,3-di(2-pyridyl)quinoxaline ligands: studies of substitution kinetics by sulfur donor nucleophiles, interactions with CT-DNA, BSA and in vitro cytotoxicity activities. RSC Adv 2019; 9:31877-31894. [PMID: 35530785 PMCID: PMC9072748 DOI: 10.1039/c9ra06488e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/18/2019] [Indexed: 11/21/2022] Open
Abstract
Dichloro platinum(ii) complexes coordinated with 2,3-di(2-pyridyl)quinoxaline ligands which form seven-membered chelates namely, bpqPtCl2, dmbpqPtCl2 and bbqPtCl2 (where bpq, dmbpq and bbq are 2,3-di(2-pyridyl)quinoxaline, 6,7-dimethyl-2,3-di(2-pyridyl)quinoxaline and 2,3-bis(2′pyriyl)benzo[g]quinoxaline, respectively) were synthesized, characterised and their respective hydrated product complexes namely, bpqPt(OH2)22+, dmbpqPt(OH2)22+ and bbqPt(OH2)22+ were prepared by chloride metathesis. The substitution kinetics of the aquated cations by thiourea nucleophiles indicated that the two aqua ligands are substituted simultaneously according to the rate law: kobs = k2[Nu]. This is followed by a forced dechelation of the ligands from the Pt (II) to form Pt(Nu)42+ species. The dechelation step is considerably slow to be monitored reliably. The rate of substitution is marginally enhanced by introducing two methyl groups and by extending the π-conjugation on the bpq core ligand. The reactivity order increased as bpqPt(OH2)22+ < dmbpqPt(OH2)22+ < bbqPt(OH2)22+. Reactivity trends were well supported by theoretical computed DFT electronic descriptors. The interactions of the Pt(ii) complexes with CT-DNA and BSA were also examined spectroscopically in tris buffers at pH 7.2. Spectroscopic and viscosity measurements suggested strong associative interactions between the Pt(ii) complexes and CT-DNA, most likely through groove binding. In silico theoretical binding studies showed energetically stable poses through associative non-covalent interactions. In vitro MTT cytotoxicity IC50 values of the Pt(ii) complexes on human liver carcinoma cells (HepG2) cancer cell lines revealed bbqPtCl2 as the least active. The fluorescence staining assays revealed the morphological changes suggested early apoptotic induction as well as non-specific necrosis. Dichloro platinum(ii) complexes coordinated with 2,3-di(2-pyridyl)quinoxaline ligands form seven-membered chelates were synthesized, characterised and their respective hydrated product complexes were prepared by chloride metathesis.![]()
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Affiliation(s)
- Rajesh Bellam
- School of Chemistry and Physics
- University of KwaZulu-Natal
- Pietermaritzburg 3209
- South Africa
| | - Deogratius Jaganyi
- School of Science
- College of Science and Technology
- University of Rwanda
- Kigali
- Rwanda
| | - Allen Mambanda
- School of Chemistry and Physics
- University of KwaZulu-Natal
- Pietermaritzburg 3209
- South Africa
| | - Ross Robinson
- School of Chemistry and Physics
- University of KwaZulu-Natal
- Pietermaritzburg 3209
- South Africa
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33
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Rahman A, O'Sullivan P, Rozas I. Recent developments in compounds acting in the DNA minor groove. MEDCHEMCOMM 2018; 10:26-40. [PMID: 30774852 DOI: 10.1039/c8md00425k] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022]
Abstract
The macromolecule that carries genetic information, DNA, is considered as an exceptional target for diseases depending on cellular division of malignant cells (i.e. cancer), microbes (i.e. bacteria) or parasites (i.e. protozoa). To aim for a comprehensive review to cover all aspects related to DNA targeting would be an impossible task and, hence, the objective of the present review is to present, from a medicinal chemistry point of view, recent developments of compounds targeting the minor groove of DNA. Accordingly, we discuss the medicinal chemistry aspects of heterocyclic small-molecules binding the DNA minor groove, as novel anticancer, antibacterial and antiparasitic agents.
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Affiliation(s)
- Adeyemi Rahman
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
| | - Patrick O'Sullivan
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
| | - Isabel Rozas
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
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34
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Ostrowska K, Maciejewska D, Cichowicz G, Dobrzycki Ł. Solid-state structure by X-ray and 13C CP/MAS NMR of new 6-acetyl-8-bromo-5-O-alkylamino-4,7-dimethylcoumarins. Struct Chem 2018. [DOI: 10.1007/s11224-018-1167-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Affiliation(s)
- Hasan Y. Alniss
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
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36
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Klimova RR, Momotyuk ED, Demidova NA, Chernoryzh YY, Koval VS, Ivanov AA, Zhuze AL, Kushch AA. [Dimeric bisbenzimidazoles suppress the herpes simplex virus and human cytomegalovirus infections in cell сultures]. Vopr Virusol 2018; 62:162-168. [PMID: 29733165 DOI: 10.18821/0507-4088-2017-62-4-162-168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/28/2017] [Indexed: 11/17/2022]
Abstract
Antiviral activity of new AТ-specific fluorescent symmetric dimeric bisbenzimidazoles of DBА(n) series was assessed in the cell models of infections caused by type 1 herpes simplex virus (HSV1) and human cytomegalovirus (CMV). In DBA(n) molecules bisbenzimidazole fragments are bound to an oligomethylene liner with varied number of methylene groups in the linker (n = 1, 3, 5, 7, 9, 11). In contrast to DB(n) dimeric bisbenzimidazoles, in DBA(n) series terminal fragments of macromolecules contain N-dimethylaminopropylcarboxamide groups instead of N-methylpiperazine groups. DBА(n) compounds better dissolve in water, pass across plasma and nuclear membrane, and stain DNA in living cells. DBA(1) and DBA(7) produced therapeutic effects in HSV1 infection; DBA(7) completely suppressed the infection. DBA(11) displayed in vitro therapeutic activity in HSV1 and CMV infections. In addition, DBA(7) and DBA(1) showed microbicidal activity. Thus, DBA(11), which is active against two viruses causing severe diseases with serious health consequences for immunodeficient individuals, should be further investigated. High antiviral activity of DBA(7) in all test models indicates that this compound is a promising active agent for innovative antiviral drugs.
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Affiliation(s)
- R R Klimova
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - E D Momotyuk
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation.,Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, 109473, Russian Federation
| | - N A Demidova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, 109473, Russian Federation
| | - Ya Yu Chernoryzh
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - V S Koval
- Engelhardt Institute of Molecular Biology, Moscow, 119991, Russian Federation.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russian Federation
| | - A A Ivanov
- Blokhin Russian Cancer Research Center, Research Institute of Carcinogenesis, Moscow, 115478, Russian Federation
| | - A L Zhuze
- Engelhardt Institute of Molecular Biology, Moscow, 119991, Russian Federation
| | - A A Kushch
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
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Non-covalent interaction between CA–TAT and calf thymus DNA: Deciphering the binding mode by in vitro studies. Int J Biol Macromol 2018; 114:1354-1360. [DOI: 10.1016/j.ijbiomac.2017.11.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 11/20/2022]
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38
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Hlaka L, Rosslee MJ, Ozturk M, Kumar S, Parihar SP, Brombacher F, Khalaf AI, Carter KC, Scott FJ, Suckling CJ, Guler R. Evaluation of minor groove binders (MGBs) as novel anti-mycobacterial agents and the effect of using non-ionic surfactant vesicles as a delivery system to improve their efficacy. J Antimicrob Chemother 2017; 72:3334-3341. [PMID: 28961913 PMCID: PMC5890746 DOI: 10.1093/jac/dkx326] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/31/2017] [Accepted: 08/05/2017] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES The slow development of major advances in drug discovery for the treatment of Mycobacterium tuberculosis (Mtb) infection suggests a compelling need for evaluation of more effective drug therapies against TB. New classes of drugs are constantly being evaluated for anti-mycobacterial activity with currently a very limited number of new drugs approved for TB treatment. Minor groove binders (MGBs) have previously revealed promising antimicrobial activity against various infectious agents; however, they have not yet been screened against Mtb. METHODS The mycobactericidal activity of 96 MGB compounds against Mtb was determined using an H37Rv-GFP microplate assay. MGB hits were screened for their intracellular mycobactericidal efficacy against the clinical Beijing Mtb strain HN878 in bone-marrow-derived macrophages using standard cfu counting. Cell viability was assessed by CellTiter-Blue assays. Selected MGBs were encapsulated into non-ionic surfactant vesicles (NIVs) for drug delivery system evaluation. RESULTS H37Rv-GFP screening yielded a hit-list of seven compounds at an MIC99 of between 0.39 and 1.56 μM. MGB-362 and MGB-364 displayed intracellular mycobactericidal activity against Mtb HN878 at an MIC50 of 4.09 and 4.19 μM, respectively, whilst being non-toxic. Subsequent encapsulation into NIVs demonstrated a 1.6- and 2.1-fold increased intracellular mycobacterial activity, similar to that of rifampicin when compared with MGB-alone formulation. CONCLUSIONS MGB anti-mycobacterial activities together with non-toxic properties indicate that MGB compounds constitute an important new class of drug/chemical entity, which holds promise in future anti-TB therapy. Furthermore, the ability of NIVs to better deliver entrapped MGB compounds to an intracellular Mtb infection suggests further preclinical evaluation is warranted.
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Affiliation(s)
- Lerato Hlaka
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Michael-Jon Rosslee
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Mumin Ozturk
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Santosh Kumar
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Suraj P Parihar
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Frank Brombacher
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
| | - Abedawn I Khalaf
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Katharine C Carter
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow G4 ORE, UK
| | - Fraser J Scott
- Department of Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Colin J Suckling
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Reto Guler
- University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa
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Guo P, Paul A, Kumar A, Harika NK, Wang S, Farahat AA, Boykin DW, Wilson WD. A modular design for minor groove binding and recognition of mixed base pair sequences of DNA. Chem Commun (Camb) 2017; 53:10406-10409. [PMID: 28880316 PMCID: PMC5616130 DOI: 10.1039/c7cc06246j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The design and synthesis of compounds that target mixed, AT/GC, DNA sequences is described. The design concept connects two N-methyl-benzimidazole-thiophene single GC recognition units with a flexible linker that lets the compound fit the shape and twist of the DNA minor groove while covering a full turn of the double helix.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Narinder K Harika
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Siming Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
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Picconi P, Hind C, Jamshidi S, Nahar K, Clifford M, Wand ME, Sutton JM, Rahman KM. Triaryl Benzimidazoles as a New Class of Antibacterial Agents against Resistant Pathogenic Microorganisms. J Med Chem 2017. [PMID: 28650661 DOI: 10.1021/acs.jmedchem.7b00108] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A new class of nontoxic triaryl benzimidazole compounds, derived from existing classes of DNA minor groove binders, were designed, synthesized, and evaluated for their antibacterial activity against multidrug resistant (MDR) Gram-positive and Gram-negative species. Molecular modeling experiments suggest that the newly synthesized class cannot be accommodated within the minor groove of DNA due to a change in the shape of the molecules. Compounds 8, 13, and 14 were found to be the most active of the series, with MICs in the range of 0.5-4 μg/mL against the MDR Staphylococci and Enterococci species. Compound 13 showed moderate activity against the MDR Gram-negative strains, with MICs in the range of 16-32 μg/mL. Active compounds showed a bactericidal mode of action, and a mechanistic study suggested the inhibition of bacterial gyrase as the mechanism of action (MOA) of this chemical class. The MOA was further supported by the molecular modeling study.
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Affiliation(s)
- Pietro Picconi
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Charlotte Hind
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - Shirin Jamshidi
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Kazi Nahar
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Melanie Clifford
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - Matthew E Wand
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - J Mark Sutton
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
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Abstract
Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes. Here we provide a thorough analysis of nucleic acid complexes containing either halogenated building blocks or halogenated ligands. We analyzed close contacts between halogens and electron-rich moieties. The phosphate backbone oxygen is clearly the most common halogen acceptor. We identified 21 X-bonds within known structures of nucleic acid complexes. A vast majority of the X-bonds is formed by halogenated nucleobases, such as bromouridine, and feature excellent geometries. Noncovalent ligands have been found to form only interactions with suboptimal interaction geometries. Hence, the first X-bonded nucleic acid binder remains to be discovered.
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Affiliation(s)
- Michal H Kolář
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia , Via del Liceo 1, I-06123 Perugia, Italy
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42
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Franco J, Medeiros A, Benítez D, Perelmuter K, Serra G, Comini MA, Scarone L. In vitro activity and mode of action of distamycin analogues against African trypanosomes. Eur J Med Chem 2016; 126:776-788. [PMID: 27951486 DOI: 10.1016/j.ejmech.2016.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/29/2016] [Accepted: 12/01/2016] [Indexed: 12/14/2022]
Abstract
Distamycin, a natural polyamide containing three heterocycle rings with a polar end, has inspired several groups to prepare synthetic analogues, which proved to have anti-trypanosomal and anti-tumoral activity. We describe the synthesis of bi and tri thiazoles amides that harbor different substitutions at their ends and the evaluation of their anti-Trypanosoma brucei activity. The most active compound 10b showed better biological activity (EC50 310 nM and selectivity index 16) than the control drug nifurtimox (EC50 15 μM and selectivity index 10). Studies on the mode of action show that the parasiticidal activity of 10b originates from disruption of lysosomal homeostasis, which is followed by release of redox active iron, an increase in oxidizing species and collapse of cell membrane integrity. In this respect, our study suggests that non-charged lipophylic distamycins destabilize cell membranes.
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Affiliation(s)
- Jaime Franco
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay; Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Andrea Medeiros
- Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Diego Benítez
- Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Karen Perelmuter
- Cell Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Gloria Serra
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Marcelo A Comini
- Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay.
| | - Laura Scarone
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay.
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Castaneda CH, Scuderi MJ, Edwards TG, Harris GD, Dupureur CM, Koeller KJ, Fisher C, Bashkin JK. Improved Antiviral Activity of a Polyamide Against High-Risk Human Papillomavirus Via N-Terminal Guanidinium Substitution. MEDCHEMCOMM 2016; 7:2076-2082. [PMID: 27840672 DOI: 10.1039/c6md00371k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the synthesis of two novel pyrrole-imidazole polyamides with N-terminal guanidinium or tetramethylguanidinium groups and evaluate their antiviral activity against three cancer-causing human papillomavirus strains. Introduction of guanidinium improves antiviral activity when compared to an unsubstituted analog, especially in IC90 values. These substitutions change DNA-binding preferences, while binding affinity remains unchanged.
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Affiliation(s)
- C H Castaneda
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - M J Scuderi
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - T G Edwards
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - G D Harris
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - C M Dupureur
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - K J Koeller
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - C Fisher
- NanoVir, LLC, Kalamazoo, MI 49008 (USA)
| | - J K Bashkin
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA; NanoVir, LLC, Kalamazoo, MI 49008 (USA)
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44
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Scott FJ, Puig-Sellart M, Khalaf AI, Henderson CJ, Westrop G, Watson DG, Carter K, Grant MH, Suckling CJ. An evaluation of Minor Groove Binders as anti-lung cancer therapeutics. Bioorg Med Chem Lett 2016; 26:3478-86. [DOI: 10.1016/j.bmcl.2016.06.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 11/30/2022]
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45
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Isouronium and N -hydroxyguanidinium derivatives as Cell growth inhibitors: A comparative study. Eur J Med Chem 2016; 117:269-82. [DOI: 10.1016/j.ejmech.2016.03.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 12/21/2022]
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Combination therapy with polymyxin B and netropsin against clinical isolates of multidrug-resistant Acinetobacter baumannii. Sci Rep 2016; 6:28168. [PMID: 27306928 PMCID: PMC4910107 DOI: 10.1038/srep28168] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/01/2016] [Indexed: 12/26/2022] Open
Abstract
Polymyxins are last-resort antibiotics for treating infections of Gram-negative bacteria. The recent emergence of polymyxin-resistant bacteria, however, urgently demands clinical optimisation of polymyxin use to minimise further evolution of resistance. In this study we developed a novel combination therapy using minimal concentrations of polymyxin B. After large-scale screening of Streptomyces secondary metabolites, we identified a reliable polymixin synergist and confirmed as netropsin using high-pressure liquid chromatography, nuclear magnetic resonance, and mass spectrometry followed by in vitro assays using various Gram-negative pathogenic bacteria. To evaluate the effectiveness of combining polymixin B and netropsin in vivo, we performed survival analysis on greater wax moth Galleria mellonella infected with colistin-resistant clinical Acinetobacter baumannii isolates as well as Escherichia coli, Shigella flexineri, Salmonella typhimuruim, and Pseudomonas aeruginosa. The survival of infected G. mellonella was significantly higher when treated with polymyxin B and netropsin in combination than when treated with polymyxin B or netropsin alone. We propose a netropsin combination therapy that minimises the use of polymyxin B when treating infections with multidrug resistant Gram-negative bacteria.
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47
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Scott FJ, Khalaf AI, Duffy S, Avery VM, Suckling CJ. Selective anti-malarial minor groove binders. Bioorg Med Chem Lett 2016; 26:3326-3329. [PMID: 27212070 DOI: 10.1016/j.bmcl.2016.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 10/21/2022]
Abstract
A set of 31 DNA minor groove binders (MGBs) with diverse structural features relating to both physical chemical properties and DNA binding sequence preference has been evaluated as potential drugs to treat Plasmodium falciparum infections using a chloroquine sensitive strain (3D7) and a chloroquine resistant strain (Dd2) in comparison with human embryonic kidney (HEK) cells as an indicator of mammalian cell toxicity. MGBs with an alkene link between the two N-terminal building blocks were demonstrated to be most active with IC50 values in the range 30-500nM and therapeutic ratios in the range 10->500. Many active compounds contained a C-alkylthiazole building block. Active compounds with logD7.4 values of approximately 3 or 7 were identified. Importantly the MGBs tested were essentially equally effective against both chloroquine sensitive and resistant strains. The results show that suitably designed MGBs have the potential for development into clinical candidates for antimalarial drugs effective against resistant strains of Plasmodia.
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Affiliation(s)
- Fraser J Scott
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Abedawn I Khalaf
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Sandra Duffy
- Discovery Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Vicky M Avery
- Discovery Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Colin J Suckling
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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48
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Ostrowska K, Maciejewska D, Dobrzycki Ł, Socha P. Solid state structure by X-ray and 13C CP/MAS NMR of new 5-[2-(N,N-dimethylamino)ethoxy]-4,7-dimethylcoumarins. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Harika NK, Paul A, Stroeva E, Chai Y, Boykin DW, Germann MW, Wilson WD. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition. Nucleic Acids Res 2016; 44:4519-27. [PMID: 27131382 PMCID: PMC4889958 DOI: 10.1093/nar/gkw353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/17/2016] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents.
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Affiliation(s)
- Narinder K Harika
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ekaterina Stroeva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Yun Chai
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
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50
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An evaluation of Minor Groove Binders as anti-Trypanosoma brucei brucei therapeutics. Eur J Med Chem 2016; 116:116-125. [PMID: 27060763 PMCID: PMC4872591 DOI: 10.1016/j.ejmech.2016.03.064] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 11/23/2022]
Abstract
A series of 32 structurally diverse MGBs, derived from the natural product distamycin, was evaluated for activity against Trypanosoma brucei brucei. Four compounds have been found to possess significant activity, in the nanomolar range, and represent hits for further optimisation towards novel treatments for Human and Animal African Trypanosomiases. Moreover, SAR indicates that the head group linking moiety is a significant modulator of biological activity.
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