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Kotynia A, Krzyżak E, Żądło J, Witczak M, Szczukowski Ł, Mucha J, Świątek P, Marciniak A. Anti-Inflammatory and Antioxidant Pyrrolo[3,4- d]pyridazinone Derivatives Interact with DNA and Bind to Plasma Proteins-Spectroscopic and In Silico Studies. Int J Mol Sci 2024; 25:1784. [PMID: 38339061 PMCID: PMC10855066 DOI: 10.3390/ijms25031784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
From the point of view of the search for new pharmaceuticals, pyridazinone derivatives are a very promising group of compounds. In our previous works, we have proved that newly synthesized ligands from this group have desirable biological and pharmacokinetic properties. Therefore, we decided to continue the research evaluating the activity of pyrrolo[3,4-dpyridazinone derivatives. In this work, we focused on the interactions of five pyridazinone derivatives with the following biomolecules: DNA and two plasma proteins: orosomucoid and gamma globulin. Using several of spectroscopic methods, such as UV-Vis, CD, and fluorescence spectroscopy, we proved that the tested compounds form stable complexes with all biomacromolecules selected for analysis. These findings were also confirmed by the results obtained by molecular modeling. All tested pyridazinone derivatives bind to the ctDNA molecule via groove binding mechanisms. All these molecules can also be bound and transported by the tested plasma proteins; however, the stability of the complexes formed is lower than those formed with serum albumin.
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Affiliation(s)
- Aleksandra Kotynia
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
| | - Edward Krzyżak
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
| | - Julia Żądło
- “Biomolecule” Student Science Club, Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland; (J.Ż.); (M.W.)
| | - Maja Witczak
- “Biomolecule” Student Science Club, Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland; (J.Ż.); (M.W.)
| | - Łukasz Szczukowski
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland; (Ł.S.); (P.Ś.)
| | - Jakub Mucha
- Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland;
| | - Piotr Świątek
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wrocław, Poland; (Ł.S.); (P.Ś.)
| | - Aleksandra Marciniak
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
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2
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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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3
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Farahat AA, Kumar A, Wenzler T, Brun R, Paul A, Guo P, Wilson WD, Boykin DW. Investigation of the effect of structure modification of furamidine on the DNA minor groove binding and antiprotozoal activity. Eur J Med Chem 2023; 252:115287. [PMID: 36958267 PMCID: PMC10127280 DOI: 10.1016/j.ejmech.2023.115287] [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: 02/14/2023] [Revised: 03/05/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023]
Abstract
New analogs of the antiprotozoal agent Furamidine were prepared utilizing Stille coupling reactions and amidation of the bisnitrile intermediate using lithium bis-trimethylsilylamide. Both the phenyl groups and the furan moiety of furamidine were replaced by heterocycles including thiophene, selenophene, indole or benzimidazole. Based upon the ΔTm and the CD results, the new compounds showed strong binding to the DNA minor groove. The new analogues are also more active both in vitro and in vivo than furamidine. Compounds 7a, 7b, and 7f showed the highest activity in vivo by curing 75% of animals, and this merits further evaluation.
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Affiliation(s)
- Abdelbasset A Farahat
- Masters of Pharmaceutical Sciences Program, California Northstate University, Elk Grove, CA, 95757, USA; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Tanja Wenzler
- Swiss Tropical and Public Health Institute, Basel, 4002, Switzerland; University of Basel, Basel, 4003, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, Basel, 4002, Switzerland; University of Basel, Basel, 4003, Switzerland
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Pu Guo
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
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4
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Ogbonna EN, Paul A, Ross Terrell J, Fang Z, Chen C, Poon GMK, Boykin DW, Wilson WD. Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines. Bioorg Med Chem 2022; 68:116861. [PMID: 35661929 DOI: 10.1016/j.bmc.2022.116861] [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: 04/29/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of diverse diamidine derivatives with a 5'-GAATTC-3' binding site using a powerful array of methods including, biosensor-SPR methods, and X-ray crystallography. The benzimidazole-thiophene module provides an excellent minor groove recognition component. A central thiophene in a benzimidazole-thiophene-phenyl aromatic system provides essentially optimum curvature for matching the shape of the minor groove. Comparison of that structure to one with the benzimidazole replaced with an indole shows that the two structures are very similar, but have some interesting and important differences in electrostatic potential maps, the DNA minor groove binding structure based on x-ray crystallographic analysis, and inhibition of the major groove binding PU.1 transcription factor complex. The binding KD for both compounds is under 10 nM and both form amidine H-bonds to DNA bases. They both have bifurcated H-bonds from the benzimidazole or indole groups to bases at the center of the -AATT- binding site. Analysis of the comparative results provides an excellent understanding of how thiophene compounds recognize the minor groove and can act as transcription factor inhibitors.
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Affiliation(s)
- Edwin N Ogbonna
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - J Ross Terrell
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ziyuan Fang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Cen Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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5
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Arafa RK, Ismail MA, Wenzler T, Brun R, Paul A, Wilson WD, Alakhdar AA, Boykin DW. New antiparasitic flexible triaryl diamidines, their prodrugs and aza analogues: Synthesis, in vitro and in vivo biological evaluation, and molecular modelling studies. Eur J Med Chem 2021; 222:113625. [PMID: 34146914 DOI: 10.1016/j.ejmech.2021.113625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
Dicationic diamidines have been well established as potent antiparasitic agents with proven activity against tropical diseases like trypanosomiasis and malaria. This work presents the synthesis of new mono and diflexible triaryl amidines (6a-c, 13a,b and 17), their aza analogues (23 and 27) and respective methoxyamidine prodrugs (5, 7, 12a,b, 22 and 26). All diamidines were assessed in vitro against Trypanosoma brucei rhodesiense (T. b. r.) and Plasmodium falciparum (P. f.) where they displayed potent to moderate activities at the nanomolar level with IC50s = 11-378 nM for T. b. r. and 4-323 nM against P. f.. In vivo efficacy testing against T. b. r. STIB900 has shown the monoflexible diamidine 6c as the most potent derivative in this study eliciting 4/4 cures of infected mice for a treatment period of >60 days upon a 4 × 5 mg/kg dose i. p. treatment. Moreover, thermal melting analysis measurement ΔTm for this series of diamidines/poly (dA-dT) complexes fell between 0.5 and 19 °C with 6c showing the highest binding to the DNA minor groove. Finally, a 50 ns molecular dynamics study of an AT-rich DNA dodecamer with compound 6c revealed a strong binding complex supported by vdW and electrostatic interactions.
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Affiliation(s)
- Reem K Arafa
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Cairo, 12578, Egypt; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt.
| | - Mohamed A Ismail
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
| | - Tanja Wenzler
- Swiss Tropical and Public Health Institute, 4002, Basel, Switzerland; University of Basel, 4003, Basel, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, 4002, Basel, Switzerland; University of Basel, 4003, Basel, Switzerland
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, Georgia
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, Georgia
| | - Amira A Alakhdar
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Cairo, 12578, Egypt; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, Georgia
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6
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Doganc F, Celik I, Eren G, Kaiser M, Brun R, Goker H. Synthesis, in vitro antiprotozoal activity, molecular docking and molecular dynamics studies of some new monocationic guanidinobenzimidazoles. Eur J Med Chem 2021; 221:113545. [PMID: 34091216 DOI: 10.1016/j.ejmech.2021.113545] [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: 03/10/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 01/14/2023]
Abstract
A series of monocationic new guanidinobenzimidazole derivatives were prepared in a four step process starting from 2-nitro-1,4-phenylendiamine. Their antiparasitic activity against Plasmodium falciparum, Trypanosoma brucei rhodesiense, Trypanosoma cruzi and Leishmania donovani were evaluated in vitro. Two out of 20 tested monocationic compounds (7, 14) showed close activity with reference drug chloroquine against P. Falciparum. To understand the interactions between DNA minor groove and in vitro active compounds (7, 14) molecular docking studies were carried out. Stability and binding energies of DNA-ligand complexes formed by DNA with compounds 7 and 14 were measured by molecular dynamics simulations throughout 200 ns time. Root mean square deviation (RMSD) values of the ligands remained stable below 0.25 mm and root mean square fluctuation (RMSF) values of the active site residues with which it interacted decreased compared to the apo form. All compounds exhibited theoretical absorption, distribution, metabolism and excretion (ADME) profiles conforming to Lipinski's and Ghose's restrictive rules.
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Affiliation(s)
- Fatima Doganc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100, Tandogan, Ankara, Turkey
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38280, Yenidogan, Kayseri, Turkey
| | - Gokcen Eren
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330, Etiler, Ankara, Turkey
| | - Marcel Kaiser
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, Basel, CH, 4002, Switzerland; University of Basel, Basel, CH, 4001, Switzerland
| | - Reto Brun
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, Basel, CH, 4002, Switzerland; University of Basel, Basel, CH, 4001, Switzerland
| | - Hakan Goker
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100, Tandogan, Ankara, Turkey.
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7
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Al-Shun SA, El-Senduny FF, Ismail MA, El-Sayed WM, Badria FA, Youssef MM. Anticancer activity of new cationic arylthiophenes against hepatocellular carcinoma. Life Sci 2021; 269:119028. [PMID: 33444618 DOI: 10.1016/j.lfs.2021.119028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/25/2020] [Accepted: 12/31/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the second most common cancer-related death in the world. No effective curative option exists for the treatment of HCC. The available drugs exhibit severe toxic effects and low therapeutic index. AIM This work aimed to examine different monocationic arylthiophene derivatives for possible use as chemotherapeutic agents against HCC. METHODS The IC50 values for the compounds were determined. The mechanism of cytotoxicity was further investigated using different methods. RESULTS Compound 2j proved to retain the highest cytotoxicity in comparison to as a positive control. The selectivity index of compound 2j revealed the safety to normal cells. Moreover, compound 2j was able to inhibit HepG2 cells´ migration and division. The anticancer effect of compound 2j was found to be partially via cell cycle arrest, activation of the tumour suppressor p53 protein, and induction of apoptosis via both intrinsic and extrinsic pathways. Compound 2j has a potential sensitization activity and significantly reduced the IC50 values for the anticancer drugs doxorubicin, cisplatin, and taxol. CONCLUSION The tested arylthiophenes showed a potent cytotoxicity against HepG2 cells and were safe to normal cells. The most active compound 2j was found to be able to inhibit cell division and migration and also to induce apoptosis. Compound 2j also proved to have a sensitization effect on standard anticancer drugs.
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Affiliation(s)
- Sara A Al-Shun
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt.
| | - Fardous F El-Senduny
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt.
| | - Mohamed A Ismail
- Division of Organic Chemistry, Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt.
| | - Wael M El-Sayed
- Department of Zoology, Faculty of Science, Ain Shams University, Abbassia 11566, Cairo, Egypt.
| | - Farid A Badria
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Magdy M Youssef
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt.
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8
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Nafie MS, Arafa K, Sedky NK, Alakhdar AA, Arafa RK. Triaryl dicationic DNA minor-groove binders with antioxidant activity display cytotoxicity and induce apoptosis in breast cancer. Chem Biol Interact 2020; 324:109087. [PMID: 32294457 DOI: 10.1016/j.cbi.2020.109087] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
Despite advances in cancer treatment modalities, DNA still stands as one of the targets for anticancer agents. DNA minor groove binders (MGBs) represent an important investigational chemotherapeutic class with promising cytotoxic capacity. Herein this study reports the potent cytotoxic effect of a series of repurposed flexible bis-imidamides 1-4, triaryl bis-guanidine 5 and bis-N-substituted guanidines 6,7 having a 1,4-diphenoxybenzene scaffold backbone on MCF-7 and MDA-MB-231 breast cancer cell lines. Of these compounds, imidamide 4 was chosen for further in-vitro, in-vivo and molecular dynamics (MD) studies owing to its promising anti-tumor activity, with IC50 values on MCF-7 and MDA-MB-231 breast cancer cell lines of 1.9 and 2.08 μM, respectively. Annexin V/propidium iodide apoptosis assay revealed apoptosis induction on imidamide 4 treated MCF-7 cells. RT-PCR assay results demonstrated the proapoptotic effect of compound 4 through increase of mRNA levels of the pro-apoptotic genes; p53, PUMA, and Bax, and inhibiting the anti-apoptotic Bcl-2 gene expression in MCF-7 cells. Moreover, compound 4 induced a G0/G1 cell-cycle arrest in MCF-7 in a dose-dependent manner. Corroborating in-vivo experiments on Ehrlich ascites carcinoma (EAC)-bearing mice, reflected the anticancer strength of derivative 4. For further target validation, molecular dynamics (MD) studies demonstrated an energetically favorable binding of imidamide 4 with the DNA minor groove AT rich site. In effect, imidamide 4 can be viewed as a promising hit dicationic compound with good cytotoxic and apoptotic inducing activity against breast cancer that can be adopted for future optimization.
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Affiliation(s)
- Mohamed S Nafie
- Chemistry Department, Faculty of Science Suez Canal University, Ismailia, 41522, Egypt
| | - Kholoud Arafa
- Center for Materials Science, Zewail City of Science and Technology, 12578, Cairo, Egypt
| | - Nada K Sedky
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy, Sinai University, East Kantara Branch, New City, El Ismailia, 41611, Cairo, Egypt
| | - Amira A Alakhdar
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Cairo, Egypt
| | - Reem K Arafa
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Cairo, Egypt; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, 12578, Cairo, Egypt.
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9
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Farahat AA, Guo P, Shoeib H, Paul A, Boykin DW, Wilson WD. Small Sequence-Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove. Chemistry 2020; 26:4539-4551. [PMID: 31884714 PMCID: PMC7265973 DOI: 10.1002/chem.201904396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/10/2019] [Indexed: 12/24/2022]
Abstract
A series of small diamidines with thiophene and modified N-alkylbenzimidazole σ-hole module represent specific binding to single G⋅C base pair (bp) DNA sequence. The variation of N-alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3-amino-4-(alkyl- or phenyl-amino) benzonitriles. The final diamidines were synthesized using lithium bis-trimethylsilylamide (LiN[Si(CH3 )3 ]2 ) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor-SPR, fluorescence spectroscopy, DNA thermal melting, ESI-MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor-SPR. These small size single G⋅C bp highly specific binders extend the compound database for future biological applications.
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Affiliation(s)
- Abdelbasset A. Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Hadir Shoeib
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - David W. Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - W. David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
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10
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Depauw S, Lambert M, Jambon S, Paul A, Peixoto P, Nhili R, Morongiu L, Figeac M, Dassi C, Paul-Constant C, Billoré B, Kumar A, Farahat AA, Ismail MA, Mineva E, Sweat DP, Stephens CE, Boykin DW, Wilson WD, David-Cordonnier MH. Heterocyclic Diamidine DNA Ligands as HOXA9 Transcription Factor Inhibitors: Design, Molecular Evaluation, and Cellular Consequences in a HOXA9-Dependant Leukemia Cell Model. J Med Chem 2019; 62:1306-1329. [PMID: 30645099 PMCID: PMC6561105 DOI: 10.1021/acs.jmedchem.8b01448] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Most transcription factors were for a long time considered as undruggable targets because of the absence of binding pockets for direct targeting. HOXA9, implicated in acute myeloid leukemia, is one of them. To date, only indirect targeting of HOXA9 expression or multitarget HOX/PBX protein/protein interaction inhibitors has been developed. As an attractive alternative by inhibiting the DNA binding, we selected a series of heterocyclic diamidines as efficient competitors for the HOXA9/DNA interaction through binding as minor groove DNA ligands on the HOXA9 cognate sequence. Selected DB818 and DB1055 compounds altered HOXA9-mediated transcription in luciferase assays, cell survival, and cell cycle, but increased cell death and granulocyte/monocyte differentiation, two main HOXA9 functions also highlighted using transcriptomic analysis of DB818-treated murine Hoxa9-transformed hematopoietic cells. Altogether, these data demonstrate for the first time the propensity of sequence-selective DNA ligands to inhibit HOXA9/DNA binding both in vitro and in a murine Hoxa9-dependent leukemic cell model.
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Affiliation(s)
- Sabine Depauw
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Mélanie Lambert
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Samy Jambon
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Paul Peixoto
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Raja Nhili
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Laura Morongiu
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Martin Figeac
- Functional and Structural Genomic Platform, Lille University, F-59000 Lille, France
| | - Christelle Dassi
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Charles Paul-Constant
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Benjamin Billoré
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Abdelbasset A. Farahat
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed A. Ismail
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Ekaterina Mineva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Daniel P. Sweat
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30904, United States
| | - Chad E. Stephens
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30904, United States
| | - David W. Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
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11
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Guo P, Farahat AA, Paul A, Harika NK, Boykin DW, Wilson WD. Compound Shape Effects in Minor Groove Binding Affinity and Specificity for Mixed Sequence DNA. J Am Chem Soc 2018; 140:14761-14769. [PMID: 30353731 PMCID: PMC6399738 DOI: 10.1021/jacs.8b08152] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AT specific heterocyclic cations that bind in the DNA duplex minor groove have had major successes as cell and nuclear stains and as therapeutic agents which can effectively enter human cells. Expanding the DNA sequence recognition capability of the minor groove compounds could also expand their therapeutic targets and have an impact in many areas, such as modulation of transcription factor biological activity. Success in the design of mixed sequence binding compounds has been achieved with N-methylbenzimidazole ( N-MeBI) thiophenes which are preorganized to fit the shape of the DNA minor groove and H-bond to the -NH of G·C base pairs that project into the minor groove. Initial compounds bind strongly to a single G·C base pair in an AT context with a specificity ratio of 50 ( KD AT-GC/ KD AT) or less and this is somewhat low for biological use. We felt that modifications of compound shape could be used to probe local DNA microstructure in target mixed base pair sequences of DNA and potentially improve the compound binding selectivity. Modifications were made by increasing the size of the benzimidazole N-substituent, for example, by using N-isobutyl instead of N-Me, and by changing the molecular twist by introducing substitutions at specific positions on the aromatic core of the compounds. In both cases, we have been able to achieve a dramatic increase in binding specificity, including no detectible binding to pure AT sequences, without a significant loss in affinity to mixed base pair target sequences.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy , Mansoura University , Mansoura 35516 , Egypt
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - Narinder K Harika
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
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12
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Shigeno M, Fujii Y, Kajima A, Nozawa-Kumada K, Kondo Y. Catalytic Deprotonative α-Formylation of Heteroarenes by an Amide Base Generated in Situ from Tetramethylammonium Fluoride and Tris(trimethylsilyl)amine. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00247] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Masanori Shigeno
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Yuki Fujii
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Akihisa Kajima
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Kanako Nozawa-Kumada
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Yoshinori Kondo
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai 980-8578, Japan
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13
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Boulsourani Z, Geromichalos GD, Katsamakas S, Psycharis V, Raptopoulou CP, Hadjipavlou-Litina D, Sahpazidou D, Dendrinou-Samara C. Mononuclear copper(II) complexes with 2-thiophene carboxylate and N-N donors; DNA interaction, antioxidant/anti-inflammatory and antitumor activity. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2018; 94:493-508. [PMID: 30423734 DOI: 10.1016/j.msec.2018.09.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/10/2018] [Accepted: 09/22/2018] [Indexed: 12/22/2022]
Abstract
Redox-active compounds such as copper-phenanthroline are known as artificial/chemical nucleases with a great impact and potential for their applications as metallotherapeutics. In that vein, the mononuclear copper(II) complexes [Cu(L)2(bipy)] (1), [Cu(L)2(bipy)(H2O)] (2) and [Cu(L)2(phen)(H2O)] (3), where L = 2-thiophene carboxylate, bipy = 2,2΄-bipyridine and phen = 1,10-phenanthroline, have been prepared and pharmacochemically studied, while the crystal structure of 1 is also reported. All the tested complexes preferably bind to CT-DNA via minor groove as resulted from UV spectroscopy studies, luminescent titration, EB competition assays and viscosity measurements. Complexes 2 and 3 in aqua behave like a "light switch" for DNA. The intensity enhancement, with the increase of DNA concentration, reached about 3-fold for 2 and 10-fold for 3. In vitro antioxidant activity of compounds 1-3, was evaluated using two different antioxidant assays: a) interaction with 1,1-diphenyl-2-picryl-hydrazyl (DPPH) stable free radical and b) inhibition of lipid peroxidation. Moreover, their inhibitory activity on soybean lipoxygenase (LOX) was evaluated for their anti-inflammatory potency. The tested complexes showed good activity on both lipid peroxidation and soybean LOX inhibition while complex 2 exhibited the best antioxidant/anti-inflammatory activity. A computational analysis over the LOX protein structure 1JNQ was performed, in an effort to support their possible mode of action. The cytotoxicity of the complexes was determined and their efficacy against several human cancer cell lines (ovarian, OAW-42; lung, A549; colon, HT29; breast, MDA-MB-231; kidney, Caki-2; and cervical, Hela) and human non-tumor cell lines (lung, MRC-5; and breast, MTSV1-7) were evaluated. The best cytotoxic activity was appeared for complex 3. In silico, computational methods support antiestrogen activity of the administered complexes on normal breast cells.
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Affiliation(s)
- Z Boulsourani
- Lab of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - G D Geromichalos
- Lab of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; Cell Culture, Molecular Modeling and Drug Design Lab, Symeonidion Research Center, Theagenion Cancer Hospital, Thessaloniki, Greece
| | - S Katsamakas
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - V Psycharis
- Institute of Nanoscience and Nanotechnology NCSR "Demokritos",15310 Aghia Paraskevi Attikis, Greece
| | - C P Raptopoulou
- Institute of Nanoscience and Nanotechnology NCSR "Demokritos",15310 Aghia Paraskevi Attikis, Greece
| | - D Hadjipavlou-Litina
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - D Sahpazidou
- Cell Culture, Molecular Modeling and Drug Design Lab, Symeonidion Research Center, Theagenion Cancer Hospital, Thessaloniki, Greece
| | - C Dendrinou-Samara
- Lab of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
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14
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Grimmelsmann L, Marefat Khah A, Spies C, Hättig C, Nuernberger P. Ultrafast Dynamics of a Triazene: Excited-State Pathways and the Impact of Binding to the Minor Groove of DNA and Further Biomolecular Systems. J Phys Chem Lett 2017; 8:1986-1992. [PMID: 28426228 DOI: 10.1021/acs.jpclett.7b00472] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many synthetic DNA minor groove binders exhibit a strong increase in fluorescence when bound to DNA. The pharmaceutical-relevant berenil (diminazene aceturate) is an exception with an extremely low fluorescence quantum yield (on the order of 10-4). We investigate the ultrafast excited-state dynamics of this triazene by femtosecond time-resolved fluorescence experiments in water, ethylene glycol, and buffer and bound to the enzyme β-trypsin, the minor groove of AT-rich DNA, and G-quadruplex DNA. Ab initio calculations provide additional mechanistic insight. The complementing studies unveil that the excited-state motion initiated by ππ* excitation occurs in two phases: a subpicosecond phase associated with the lengthening of the central N═N double bond, followed by a bicycle-pedal-type motion of the triazene bridge, which is almost volume-conserving and can proceed efficiently within only a few picoseconds even under spatially confined conditions. Our results elucidate the excited-state relaxation mechanism of aromatic triazenes and explain the modest sensitivity of the fluorescence quantum yield of berenil even when it is bound to various biomolecules.
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Affiliation(s)
- Lena Grimmelsmann
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Alireza Marefat Khah
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Christian Spies
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Christof Hättig
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Patrick Nuernberger
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
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15
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Ismail MA, Youssef MM, Arafa RK, Al-Shihry SS, El-Sayed WM. Synthesis and antiproliferative activity of monocationic arylthiophene derivatives. Eur J Med Chem 2017; 126:789-798. [PMID: 27951487 DOI: 10.1016/j.ejmech.2016.12.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 10/20/2022]
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16
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Farahat AA, Bennett-Vaughn C, Mineva EM, Kumar A, Wenzler T, Brun R, Liu Y, Wilson WD, Boykin DW. Synthesis, DNA binding and antitrypanosomal activity of benzimidazole analogues of DAPI. Bioorg Med Chem Lett 2016; 26:5907-5910. [PMID: 27843114 DOI: 10.1016/j.bmcl.2016.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
Abstract
A series of novel benzimidazole diamidines were prepared from the corresponding dicyano analogues either by applying Pinner methodology (5a-c, 10 and 13a) or by making amidoximes intermediates that were reduced to the corresponding amidines (15a-c). The new amidines were evaluated in vitro against the protozoan parasite Trypanosoma brucei rhodesiense (T. b. r.). The thiophene analogue 5b and the N-methyl compound 15a showed superior antitrypanosomal activity compared to that of the parent I.
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Affiliation(s)
- Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | | | - Ekaterina M Mineva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Tanja Wenzler
- Swiss Tropical and Public Health Institute, Basel 4002, Switzerland; University of Basel, Basel 4003, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, Basel 4002, Switzerland; University of Basel, Basel 4003, Switzerland
| | - Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
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17
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Guo P, Paul A, Kumar A, Farahat AA, Kumar D, Wang S, Boykin DW, Wilson WD. The Thiophene "Sigma-Hole" as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove. Chemistry 2016; 22:15404-15412. [PMID: 27624927 PMCID: PMC5214980 DOI: 10.1002/chem.201603422] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/10/2022]
Abstract
In spite of its importance in cell function, targeting DNA is under-represented in the design of small molecules. A barrier to progress in this area is the lack of a variety of modules that recognize G⋅C base pairs (bp) in DNA sequences. To overcome this barrier, an entirely new design concept for modules that can bind to mixed G⋅C and A⋅T sequences of DNA is reported herein. Because of their successes in biological applications, minor-groove-binding heterocyclic cations were selected as the platform for design. Binding to A⋅T sequences requires hydrogen-bond donors whereas recognition of the G-NH2 requires an acceptor. The concept that we report herein uses pre-organized N-methylbenzimidazole (N-MeBI) thiophene modules for selective binding with mixed bp DNA sequences. The interaction between the thiophene sigma hole (positive electrostatic potential) and the electron-donor nitrogen of N-MeBI preorganizes the conformation for accepting an hydrogen bond from G-NH2 . The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that N-MeBI-thiophene monomer compounds can strongly and selectively recognize single G⋅C bp sequences. Replacing the thiophene with other moieties significantly reduces binding affinity and specificity, as predicted by the design concept. These results show that the use of molecular features, such as sigma-holes, can lead to new approaches for small molecules in biomolecular interactions.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dhiraj Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Siming Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA.
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18
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Karaaslan C, Kaiser M, Brun R, Göker H. Synthesis and potent antiprotozoal activity of mono/di amidino 2-anilinobenzimidazoles versus Plasmodium falciparum and Trypanosoma brucei rhodesiense. Bioorg Med Chem 2016; 24:4038-4044. [DOI: 10.1016/j.bmc.2016.06.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 10/21/2022]
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19
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Zhang Y, Zheng W, Luo Q, Zhao Y, Zhang E, Liu S, Wang F. Dual-targeting organometallic ruthenium(II) anticancer complexes bearing EGFR-inhibiting 4-anilinoquinazoline ligands. Dalton Trans 2016; 44:13100-11. [PMID: 26106875 DOI: 10.1039/c5dt01430a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have recently demonstrated that complexation with (η(6)-arene)Ru(II) fragments confers 4-anilinoquinazoline pharmacophores a higher potential for inducing cellular apoptosis while preserving the highly inhibitory activity of 4-anilinoquinazolines against EGFR and the reactivity of the ruthenium centre to 9-ethylguanine (Chem. Commun., 2013, 49, 10224-10226). Reported herein are the synthesis, characterisation and evaluation of the biological activity of a new series of ruthenium(ii) complexes of the type [(η(6)-arene)Ru(N,N-L)Cl]PF6 (arene = p-cymene, benzene, 2-phenylethanol or indane, L = 4-anilinoquinazolines). These organometallic ruthenium complexes undergo fast hydrolysis in aqueous solution. Intriguingly, the ligation of (arene)Ru(II) fragments with 4-anilinoquinazolines not only makes the target complexes excellent EGFR inhibitors, but also confers the complexes high affinity to bind to DNA minor grooves while maintaining their reactivity towards DNA bases, characterising them with dual-targeting properties. Molecular modelling studies reveal that the hydrolysis of these complexes is a favourable process which increases the affinity of the target complexes to bind to EGFR and DNA. In vitro biological activity assays show that most of this group of ruthenium complexes are selectively active inhibiting the EGF-stimulated growth of the HeLa cervical cancer cell line, and the most active complex [(η(6)-arene)Ru(N,N-L13)Cl]PF6 (, IC50 = 1.36 μM, = 4-(3'-chloro-4'-fluoroanilino)-6-(2-(2-aminoethyl)aminoethoxy)-7-methoxyquinazoline) is 29-fold more active than its analogue, [(η(6)-arene)Ru(N,N-ethylenediamine)Cl]PF6, and 21-fold more active than gefitinib, a well-known EGFR inhibitor in use clinically. These results highlight the strong promise to develop highly active ruthenium anticancer complexes by ligation of cytotoxic ruthenium pharmacophores with bioactive organic molecules.
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Affiliation(s)
- Yang Zhang
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, PR China.
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20
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Guggilapu SD, Prajapti SK, Nagarsenkar A, Lalita G, Naidu Vegi GM, Babu BN. MoO2Cl2 catalyzed efficient synthesis of functionalized 3,4-dihydropyrimidin-2(1H)-ones/thiones and polyhydroquinolines: recyclability, fluorescence and biological studies. NEW J CHEM 2016. [DOI: 10.1039/c5nj02444g] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
MoO2Cl2 catalyzed Biginelli, Hantzsch reactions exploring spectroscopic and biological properties of novel compounds.
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Affiliation(s)
- Sravanthi Devi Guggilapu
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- Hyderabad
- India
| | - Santosh Kumar Prajapti
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- Hyderabad
- India
| | - Atulya Nagarsenkar
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- Hyderabad
- India
| | - Guntuku Lalita
- Department of Pharmacology and Toxicology
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
| | - Ganga Modi Naidu Vegi
- Department of Pharmacology and Toxicology
- National Institute of Pharmaceutical Education and Research (NIPER)
- Hyderabad 500037
- India
| | - Bathini Nagendra Babu
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- Hyderabad
- India
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21
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Doan PH, Pitter DRG, Kocher A, Wilson JN, Goodson T. Two-Photon Spectroscopy as a New Sensitive Method for Determining the DNA Binding Mode of Fluorescent Nuclear Dyes. J Am Chem Soc 2015; 137:9198-201. [DOI: 10.1021/jacs.5b02674] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Phi H. Doan
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Demar R. G. Pitter
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Andrea Kocher
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James N. Wilson
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Theodore Goodson
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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22
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Berger ML, Maciejewska D, Vanden Eynde JJ, Mottamal M, Żabiński J, Kaźmierczak P, Rezler M, Jarak I, Piantanida I, Karminski-Zamola G, Mayence A, Rebernik P, Kumar A, Ismail MA, Boykin DW, Huang TL. Pentamidine analogs as inhibitors of [(3)H]MK-801 and [(3)H]ifenprodil binding to rat brain NMDA receptors. Bioorg Med Chem 2015; 23:4489-4500. [PMID: 26117647 DOI: 10.1016/j.bmc.2015.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 06/05/2015] [Accepted: 06/05/2015] [Indexed: 12/29/2022]
Abstract
The anti-protozoal drug pentamidine is active against opportunistic Pneumocystis pneumonia, but in addition has several other biological targets, including the NMDA receptor (NR). Here we describe the inhibitory potencies of 76 pentamidine analogs at 2 binding sites of the NR, the channel binding site labeled with [(3)H]MK-801 and the [(3)H]ifenprodil binding site. Most analogs acted weaker at the ifenprodil than at the channel site. The spermine-sensitivity of NR inhibition by the majority of the compounds was reminiscent of other long-chain dicationic NR blockers. The potency of the parent compound as NR blocker was increased by modifying the heteroatoms in the bridge connecting the 2 benzamidine moieties and also by integrating the bridge into a seven-membered ring. Docking of the 45 most spermine-sensitive bisbenzamidines to a recently described acidic interface between the N-terminal domains of GluN1 and GluN2B mediating polyamine stimulation of the NR revealed the domain contributed by GluN1 as the most relevant target.
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Affiliation(s)
- Michael L Berger
- Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| | - Dorota Maciejewska
- Department of Organic Chemistry, Medical University of Warsaw, Warsaw, Poland
| | | | | | - Jerzy Żabiński
- Department of Organic Chemistry, Medical University of Warsaw, Warsaw, Poland
| | - Paweł Kaźmierczak
- Department of Organic Chemistry, Medical University of Warsaw, Warsaw, Poland
| | - Mateusz Rezler
- Department of Organic Chemistry, Medical University of Warsaw, Warsaw, Poland
| | - Ivana Jarak
- Department of Organic Chemistry, University of Zagreb, Zagreb, Croatia
| | - Ivo Piantanida
- Department of Organic Chemistry, University of Zagreb, Zagreb, Croatia
| | | | - Annie Mayence
- College of Pharmacy, Xavier University of Louisiana, New Orleans, USA
| | - Patrick Rebernik
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Mohamed A Ismail
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Tien L Huang
- College of Pharmacy, Xavier University of Louisiana, New Orleans, USA
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23
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Design, synthesis, and structure–activity relationships of 1-ethylpyrazole-3-carboxamide compounds as novel hypoxia-inducible factor (HIF)-1 inhibitors. Bioorg Med Chem 2015; 23:1776-87. [DOI: 10.1016/j.bmc.2015.02.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/14/2015] [Accepted: 02/17/2015] [Indexed: 11/18/2022]
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Stolić I, Čipčić Paljetak H, Perić M, Matijašić M, Stepanić V, Verbanac D, Bajić M. Synthesis and structure–activity relationship of amidine derivatives of 3,4-ethylenedioxythiophene as novel antibacterial agents. Eur J Med Chem 2015; 90:68-81. [DOI: 10.1016/j.ejmech.2014.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 10/28/2014] [Accepted: 11/01/2014] [Indexed: 12/20/2022]
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25
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Geiger DK, Geiger HC, Deck JM. Structure determination of three furan-substituted benzimidazoles and calculation of π-π and C-H···π interaction energies. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2014; 70:1125-32. [PMID: 25471412 DOI: 10.1107/s205322961402405x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 10/31/2014] [Indexed: 11/10/2022]
Abstract
The synthesis and structural characterization of 2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzimidazole [C16H12N2O2, (I)], 2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzimidazol-3-ium chloride monohydrate [C16H13N2O2(+)·Cl(-)·H2O, (II)] and the hydrobromide salt 5,6-dimethyl-2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzimidazol-3-ium bromide [C18H17N2O2(+)·Br(-), (III)] are described. Benzimidazole (I) displays two sets of aromatic interactions, each of which involves pairs of molecules in a head-to-tail arrangement. The first, denoted set (Ia), exhibits both intermolecular C-H···π interactions between the 2-(furan-2-yl) (abbreviated as Fn) and 1-(furan-2-ylmethyl) (abbreviated as MeFn) substituents, and π-π interactions involving the Fn substituents between inversion-center-related molecules. The second, denoted set (Ib), involves π-π interactions involving both the benzene ring (Bz) and the imidazole ring (Im) of benzimidazole. Hydrated salt (II) exhibits N-H···OH2···Cl hydrogen bonding that results in chains of molecules parallel to the a axis. There is also a head-to-head aromatic stacking of the protonated benzimidazole cations in which the Bz and Im rings of one molecule interact with the Im and Fn rings of adjacent molecules in the chain. Salt (III) displays N-H···Br hydrogen bonding and π-π interactions involving inversion-center-related benzimidazole rings in a head-to-tail arrangement. In all of the π-π interactions observed, the interacting moieties are shifted with respect to each other along the major molecular axis. Basis set superposition energy-corrected (counterpoise method) interaction energies were calculated for each interaction [DFT, M06-2X/6-31+G(d)] employing atomic coordinates obtained in the crystallographic analyses for heavy atoms and optimized H-atom coordinates. The calculated interaction energies are -43.0, -39.8, -48.5, and -55.0 kJ mol(-1) for (Ia), (Ib), (II), and (III), respectively. For (Ia), the analysis was used to partition the interaction energies into the C-H···π and π-π components, which are 9.4 and 24.1 kJ mol(-1), respectively. Energy-minimized structures were used to determine the optimal interplanar spacing, the slip distance along the major molecular axis, and the slip distance along the minor molecular axis for 2-(furan-2-yl)-1H-benzimidazole.
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Affiliation(s)
- David K Geiger
- Department of Chemistry, SUNY-College at Geneseo, Geneseo, NY 14454, USA
| | - H Cristina Geiger
- Department of Chemistry, SUNY-College at Geneseo, Geneseo, NY 14454, USA
| | - Jared M Deck
- Department of Chemistry, SUNY-College at Geneseo, Geneseo, NY 14454, USA
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Ismail MA, Arafa RK, Youssef MM, El-Sayed WM. Anticancer, antioxidant activities, and DNA affinity of novel monocationic bithiophenes and analogues. DRUG DESIGN DEVELOPMENT AND THERAPY 2014; 8:1659-72. [PMID: 25302019 PMCID: PMC4189708 DOI: 10.2147/dddt.s68016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A series of 15 monocationic bithiophenes and isosteres were prepared and subjected to in vitro antiproliferative screening using the full National Cancer Institute (NCI)-60 cell line panel, representing nine types of cancer. Among the nine types of cancer involved in a five-dose screen, non-small cell lung and breast cancer cell lines were the most responsive to the antiproliferative effect of the tested compounds, especially cell lines A549/ATCC, NCI-H322M, and NCI-H460, whereas compounds 1a, 1c, 1d, and 7 exhibited potent activity, with GI50 values (drug concentration that causes 50% inhibition of cell growth) from less than 10 nM to 102 nM. In addition, compounds 1c and 1d gave GI50 values of 73 nM and 79 nM, respectively, against the MDA-MB-468 breast cancer cell line. Structure-activity relationship findings indicated that the mononitriles were far less active than their corresponding monoamidines and, within the amidines series, the bioisosteric replacement of a thiophene ring by a furan led to a reduction in antiproliferative activity. Also, molecular manipulations, involving substitution on the phenyl ring, or its replacement by a pyridyl, or alteration of the position of the amidine group, led to significant alteration in antiproliferative activity. On the other hand, DNA studies demonstrated that these monoamidine bichalcophenes have promising ability to cleave the genomic DNA. These monoamidines show a wide range of DNA affinities, as judged from their DNA cleavage effect, which are remarkably sensitive to all kinds of structural modifications. Finally, the novel bichalcophenes were tested for their antioxidant property by the ABTS (2,2'-azino- bis(3-ethylbenzthiazoline-6-sulfonic acid) diammonium salt) assay, as well as lipid and nitric oxide scavenging techniques, and were found to exhibit good-to-potent antioxidant abilities.
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Affiliation(s)
- Mohamed A Ismail
- Departments of Chemistry and Biological Sciences, College of Science, King Faisal University, Hofuf, Saudi Arabia ; Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Reem K Arafa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Magdy M Youssef
- Departments of Chemistry and Biological Sciences, College of Science, King Faisal University, Hofuf, Saudi Arabia ; Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Wael M El-Sayed
- Departments of Chemistry and Biological Sciences, College of Science, King Faisal University, Hofuf, Saudi Arabia ; Department of Zoology, Faculty of Science, University of Ain Shams, Abbassia, Cairo, Egypt
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27
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O'Sullivan P, Rozas I. Understanding the guanidine-like cationic moiety for optimal binding into the DNA minor groove. ChemMedChem 2014; 9:2065-73. [PMID: 25087855 DOI: 10.1002/cmdc.201402264] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 01/01/2023]
Abstract
Based on our previous positive results with bis-guanidine-like diaromatic compounds as DNA minor groove binders, we propose a new family: bis-2-amino-1,4,5,6-tetrahydropyrimidines. According to calculated parameters, these dicationic systems would have a more suitable size and lipophilicity for binding into the minor groove than previous series. Moreover, their DFT-optimised structures and docking into an AT oligomer model show that they would bind in the minor groove with good strength and without energy penalty. Hence, we prepared compounds 4 a-c and evaluated their binding to ssDNA and poly(dA-dT)2 by thermal denaturation experiments. The results showed that 4 a (CO) and 4 d (NH) were the best DNA binders. Compared to the previous series, 4 a-d are better binders than bis-guanidiniums but poorer than bis-2-aminoimidazolinium derivatives. Moreover, circular dichroism experiments using ssDNA and poly(dA-dT)2 confirmed binding into the minor groove. Based on our computational design as well as biophysical studies, we have been able to determine that the optimal interaction of guanidine-like dications in the minor grove occurs with bis-2-aminoimidazolinium systems.
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Affiliation(s)
- Patrick O'Sullivan
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College, University of Dublin, 152-160 Pearse St., Dublin 2 (Ireland)
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28
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Munde M, Wang S, Kumar A, Stephens CE, Farahat AA, Boykin DW, Wilson WD, Poon GMK. Structure-dependent inhibition of the ETS-family transcription factor PU.1 by novel heterocyclic diamidines. Nucleic Acids Res 2013; 42:1379-90. [PMID: 24157839 PMCID: PMC3902942 DOI: 10.1093/nar/gkt955] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ETS transcription factors mediate a wide array of cellular functions and are attractive targets for pharmacological control of gene regulation. We report the inhibition of the ETS-family member PU.1 with a panel of novel heterocyclic diamidines. These diamidines are derivatives of furamidine (DB75) in which the central furan has been replaced with selenophene and/or one or both of the bridging phenyl has been replaced with benzimidazole. Like all ETS proteins, PU.1 binds sequence specifically to 10-bp sites by inserting a recognition helix into the major groove of a 5′-GGAA-3′ consensus, accompanied by contacts with the flanking minor groove. We showed that diamidines target the minor groove of AT-rich sequences on one or both sides of the consensus and disrupt PU.1 binding. Although all of the diamidines bind to one or both of the expected sequences within the binding site, considerable heterogeneity exists in terms of stoichiometry, site–site interactions and induced DNA conformation. We also showed that these compounds accumulate in live cell nuclei and inhibit PU.1-dependent gene transactivation. This study demonstrates that heterocyclic diamidines are capable of inhibiting PU.1 by targeting the flanking sequences and supports future efforts to develop agents for inhibiting specific members of the ETS family.
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Affiliation(s)
- Manoj Munde
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA and Department of Pharmaceutical Sciences, Washington State University, Pullman, WA 99164-6534, USA
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29
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Nanjunda R, Wilson WD. Binding to the DNA minor groove by heterocyclic dications: from AT-specific monomers to GC recognition with dimers. ACTA ACUST UNITED AC 2013; Chapter 8:Unit8.8. [PMID: 23255206 DOI: 10.1002/0471142700.nc0808s51] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, have found extensive uses in biotechnology, and are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. This review focuses on the development of clinically useful heterocyclic diamidine minor groove binders. These compounds have shown us that the classical model for minor groove binding in AT DNA sequences must be expanded in several ways: compounds with nonstandard shapes can bind strongly to the groove, water can be directly incorporated into the minor groove complex in an interfacial interaction, and the compounds can form cooperative stacked dimers to recognize GC and mixed AT/GC base pair sequences.
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Affiliation(s)
- Rupesh Nanjunda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
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30
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Srivastava HK, Sastry GN. Efficient estimation of MMGBSA-based BEs for DNA and aromatic furan amidino derivatives. J Biomol Struct Dyn 2013; 31:522-37. [DOI: 10.1080/07391102.2012.703071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Wei D, Wilson WD, Neidle S. Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster. J Am Chem Soc 2013; 135:1369-77. [PMID: 23276263 DOI: 10.1021/ja308952y] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.
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Affiliation(s)
- DengGuo Wei
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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32
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Šípová H, Homola J. Surface plasmon resonance sensing of nucleic acids: a review. Anal Chim Acta 2013; 773:9-23. [PMID: 23561902 DOI: 10.1016/j.aca.2012.12.040] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 12/12/2022]
Abstract
Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.
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Affiliation(s)
- Hana Šípová
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic
| | - Jiří Homola
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic.
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33
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Nanjunda R, Musetti C, Kumar A, Ismail MA, Farahat AA, Wang S, Sissi C, Palumbo M, Boykin DW, Wilson WD. Heterocyclic dications as a new class of telomeric G-quadruplex targeting agents. Curr Pharm Des 2012; 18:1934-47. [PMID: 22380518 DOI: 10.2174/138161212799958422] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/28/2011] [Indexed: 11/22/2022]
Abstract
Small molecules that can induce and stabilize G-quadruplex DNA structures represent a novel approach for anti-cancer and anti-parasitic therapy and extensive efforts have been directed towards discovering lead compounds that are capable of stabilizing quadruplexes. The purpose of this study is to explore conformational modifications in a series of heterocyclic dications to discover structural motifs that can selectively bind and stabilize specific G-quadruplexes, such as those present in the human telomere. The G-quadruplex has various potential recognition sites for small molecules; however, the primary interaction site of most of these ligands is the terminal tetrads. Similar to duplex-DNA groove recognition, quadruplex groove recognition by small molecules offers the potential for enhanced selectivity that can be developed into a viable therapeutic strategy. The compounds investigated were selected based on preliminary studies with DB832, a bifuryl-phenyl diamidine with a unique telomere interaction. This compound provides a paradigm that can help in understanding the optimum compound-DNA interactions that lead to quadruplex groove recognition. DNA recognition by the DB832 derivatives was investigated by biophysical experiments such as thermal melting, circular dichroism, mass spectrometry and NMR. Biological studies were also performed to complement the biophysical data. The results suggest a complex binding mechanism which involves the recognition of grooves for some ligands as well as stacking at the terminal tetrads of the human telomeric G-quadruplex for most of the ligands. These molecules represent an excellent starting point for further SAR analysis for diverse modes of quadruplex recognition and subsequent structure optimization for drug development.
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Affiliation(s)
- Rupesh Nanjunda
- Dept. of Chemistry, Georgia State University, Atlanta GA 30303, USA
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34
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Nagle PS, Rodriguez F, Nguyen B, Wilson WD, Rozas I. High DNA affinity of a series of peptide linked diaromatic guanidinium-like derivatives. J Med Chem 2012; 55:4397-406. [PMID: 22497334 DOI: 10.1021/jm300296f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper we report the design and synthesis of a new family of asymmetric peptide linked diaromatic dications as potent DNA minor groove binders. These peptide-linked compounds, with a linear core, displayed a much larger affinity than other guanidinium-like derivatives from the same series with curved cores. As a first screening, the DNA affinity of these structures was evaluated by means of thermal denaturation experiments, finding that the nature of the cation (guanidinium vs 2-aminoimidazolinium) significantly influenced the binding strength. Their binding affinity was assessed by implementing further biophysical measurements such as surface plasmon resonance and circular dichroism. In particular, it was observed that compounds 6, 7, and 8 displayed both a strong binding affinity and significant selectivity for AT oligonucleotides. In addition, the thermodynamics of their binding was evaluated using isothermal titration calorimetry, indicating that the binding is derived from favorable enthalpic and entropic contributions.
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Affiliation(s)
- Padraic S Nagle
- School of Chemistry, Trinity Biomedical Sciences Institute, University of Dublin, Trinity College, Pearse St., Dublin 2, Ireland
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35
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Zhu Y, He J, Shi Q, Yang B, Tang M. Binding properties and conformational dynamics of reversible amidines with DNA from a theoretical view. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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36
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Ma DL, Chan DSH, Lee P, Kwan MHT, Leung CH. Molecular modeling of drug–DNA interactions: Virtual screening to structure-based design. Biochimie 2011; 93:1252-66. [PMID: 21514356 DOI: 10.1016/j.biochi.2011.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/01/2011] [Indexed: 12/11/2022]
Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
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37
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Liu Y, Kumar A, Depauw S, Nhili R, David-Cordonnier MH, Lee MP, Ismail MA, Farahat AA, Say M, Chackal-Catoen S, Batista-Parra A, Neidle S, Boykin DW, Wilson WD. Water-mediated binding of agents that target the DNA minor groove. J Am Chem Soc 2011; 133:10171-83. [PMID: 21627167 DOI: 10.1021/ja202006u] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecule complexes with DNA that incorporate linking water molecules are rare, and the DB921-DNA complex has provided a unique and well-defined system for analysis of water-mediated binding in the context of a DNA complex. DB921 has a benzimidazole-biphenyl system with terminal amidines that results in a linear conformation that does not possess the appropriate radius of curvature to match the minor groove shape and represents a new paradigm that does not fit the classical model of minor groove interactions. To better understand the role of the bound water molecule observed in the X-ray crystal structure of the DB921 complex, synthetic modifications have been made in the DB921 structure, and the interactions of the new compounds with DNA AT sites have been evaluated with an array of methods, including DNase I footprinting, biosensor-surface plasmon resonance, isothermal titration microcalorimetry, and circular dichroism. The interaction of a key compound, which has the amidine at the phenyl shifted from the para position in DB921 to the meta position, has also been examined by X-ray crystallography. The detailed structural, thermodynamic, and kinetic results provide valuable new information for incorporation of water molecules in the design of new lead scaffolds for targeting DNA in chemical biology and therapeutic applications.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, USA
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38
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QSAR study on the interactions between antibiotic compounds and DNA by a hybrid genetic-based support vector machine. MONATSHEFTE FUR CHEMIE 2011. [DOI: 10.1007/s00706-011-0493-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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39
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Novel diamidines with activity against Babesia divergens in vitro and Babesia microti in vivo. Antimicrob Agents Chemother 2011; 55:3439-45. [PMID: 21537025 DOI: 10.1128/aac.01482-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dicationic diamidines, such as diminazene and pentamidine, are well-studied chemotherapeutic agents with significant activity against parasitic diseases. The in vitro activities of novel diamidine compounds against the Babesia divergens strains 1903B and 4201 were investigated. The most potent compound, a diphenyl furan, had a 50% inhibitory concentration (IC(50)) of 1.5 ng/ml. In a murine model, several test compounds were effective enough to cure mice infected with Babesia microti at a dose of 12.5 and/or 25 mg/kg of body weight given by the subcutaneous route for 4 days. The best antibabesial properties were exhibited by terphenyls, benzimidazoles, diphenyl furans, pentamidine, and pentamidine analogues.
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40
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Biarnés X, Bongarzone S, Vargiu AV, Carloni P, Ruggerone P. Molecular motions in drug design: the coming age of the metadynamics method. J Comput Aided Mol Des 2011; 25:395-402. [PMID: 21327922 DOI: 10.1007/s10822-011-9415-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 01/28/2011] [Indexed: 01/25/2023]
Abstract
Metadynamics is emerging as a useful free energy method in physics, chemistry and biology. Recently, it has been applied also to investigate ligand binding to biomolecules of pharmacological interest. Here, after introducing the basic idea of the method, we review applications to challenging targets for pharmaceutical intervention. We show that this methodology, especially when combined with a variety of other computational approaches such as molecular docking and/or molecular dynamics simulation, may be useful to predict structure and energetics of ligand/target complexes even when the targets lack a deep binding cavity, such as DNA and proteins undergoing fibrillation in neurodegenerative diseases. Furthermore, the method allows investigating the routes of molecular recognition and the associated binding energy profiles, providing a molecular interpretation to experimental data.
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Affiliation(s)
- Xevi Biarnés
- International School for Advanced Studies, Trieste, Italy
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41
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Stolić I, Mišković K, Piantanida I, Lončar MB, Glavaš-Obrovac L, Bajić M. Synthesis, DNA/RNA affinity and antitumour activity of new aromatic diamidines linked by 3,4-ethylenedioxythiophene. Eur J Med Chem 2011; 46:743-55. [PMID: 21227551 DOI: 10.1016/j.ejmech.2010.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 12/04/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
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42
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Ismail MA, Bialy SAE, Brun R, Wenzler T, Nanjunda R, Wilson WD, Boykin DW. Dicationic phenyl-2,2'-bichalcophenes and analogues as antiprotozoal agents. Bioorg Med Chem 2010; 19:978-84. [PMID: 21194955 DOI: 10.1016/j.bmc.2010.11.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 11/16/2010] [Accepted: 11/22/2010] [Indexed: 11/29/2022]
Abstract
A series of phenyl-2,2'-bichalcophene diamidines 1a-h were synthesized from the corresponding dinitriles either via a direct reaction with LiN(TMS)₂, followed by deprotection with ethanolic HCl or through the bis-O-acetoxyamidoxime followed by hydrogenation in acetic acid and EtOH over Pd-C. These diamidines show a wide range of DNA affinities as judged from their ΔT(m) values which are remarkably sensitive to replacement of a furan unit with a thiophene one. These differences are explained in terms of the effect of subtle changes in geometry of the diamidines on binding efficacy. Five of the eight compounds were highly active (below 6 nM IC₅₀) in vitro against Trypanosoma brucei rhodesiense (T. b. r.) and four gave IC₅₀values less than 7 nM against Plasmodium falciparum (P. f.). Only one of the compounds was as effective as reference compounds in the T. b. r. mouse model for the acute phase of African trypanosomiasis.
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Branowska D, Farahat AA, Kumar A, Wenzler T, Brun R, Liu Y, Wilson WD, Boykin DW. Synthesis and antiprotozoal activity of 2,5-bis[amidinoaryl]thiazoles. Bioorg Med Chem 2010; 18:3551-8. [PMID: 20403703 PMCID: PMC2892117 DOI: 10.1016/j.bmc.2010.03.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 03/23/2010] [Accepted: 03/24/2010] [Indexed: 10/19/2022]
Abstract
Seven novel diamidino 2,5-bis(aryl)thiazoles (5a-g) were synthesized and evaluated against Trypanosoma brucei rhodensiense (T. b. r.) and Plasmodium falciparum (P. f.). The diamidines were obtained directly from the corresponding bis-nitriles (4a-g) by the action of lithium bis(trimethylsilyl)amide. The bis-nitriles 4a-f were synthesized in four steps starting with the Stille coupling of 2-tributyltinthiazole with the appropriate cyanoaryl halide. The bis-nitrile 5g was obtained by the palladium facilitated coupling of the mixed tin-silyl reagent 2-trimethylsilyl-5-trimethyltinthiazole with 2-bromo-5-cyanopyridine. The amidoxime potential prodrugs 6a-e, 6g were obtained by the reaction of hydroxylamine with the bis-nitriles. O-Methylation of the amidoximes gave the corresponding N-methoxyamidines 7a-c, 7e, 7g. The diamidines showed strong DNA binding affinity as reflected by DeltaT(m) measurements. Four of the diamidines 5a, 5b, 5d and 5e were highly active in vitro against P. f. giving IC(50) values between 1.1 and 2.5nM. The same four diamidines showed IC(50) values between 4 and 6nM against T. b. r. The selectivity indices ranged from 233 to 9175. One diamidine 5a produced one of four cures at an ip dose of 4x5mg/kg in the STIB900 mouse model for acute African trypanosomiasis. The amidoxime and N-methoxyamidine of 5a were the only produgs to provide cures (1/4 cures) in the same mouse model on oral dosage at 4x25mg/kg.
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Affiliation(s)
- Danuta Branowska
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
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Palladium-Catalysed Direct Arylation of Heteroaromatics Bearing Unprotected Hydroxyalkyl Functions using Aryl Bromides. Adv Synth Catal 2010. [DOI: 10.1002/adsc.200900793] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Tevis DS, Kumar A, Stephens CE, Boykin DW, Wilson WD. Large, sequence-dependent effects on DNA conformation by minor groove binding compounds. Nucleic Acids Res 2009; 37:5550-8. [PMID: 19578063 PMCID: PMC2760788 DOI: 10.1093/nar/gkp558] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To determine what topological changes antiparasitic heterocyclic dications can have on kinetoplast DNA, we have constructed ligation ladders, with phased A5 and ATATA sequences in the same flanking sequence context, as models. Bending by the A5 tract is observed, as expected, while the ATATA sequence bends DNA very little. Complexes of these DNAs with three diamidines containing either furan, thiophene or selenophene groups flanked by phenylamidines were investigated along with netropsin. With the bent A5 ladder the compounds caused either a slight increase or decrease in the bending angle. Surprisingly, however, with ATATA all of the compounds caused significant bending, to values close to or even greater than the A5 bend angle. Results with a mixed cis sequence, which has one A5 and one ATATA, show that the compounds bend ATATA in the same direction as a reference A5 tract, that is, into the minor groove. These results are interpreted in terms of a groove structure for A5 which is largely pre-organized for a fit to the heterocyclic amidines. With ATATA the groove is intrinsically wider and must close to bind the compounds tightly. The conformational change at the binding site then leads to significant bending of the alternating DNA sequence.
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Affiliation(s)
- Denise S Tevis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
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46
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Spitzer GM, Wellenzohn B, Markt P, Kirchmair J, Langer T, Liedl KR. Hydrogen-bonding patterns of minor groove-binder-DNA complexes reveal criteria for discovery of new scaffolds. J Chem Inf Model 2009; 49:1063-9. [PMID: 19275189 DOI: 10.1021/ci800455f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Minor groove-binding ligands are able to control gene expression and are of great interest for therapeutic applications. We extracted hydrogen-bonding geometries from all available structures of minor groove-binder-DNA complexes of two noncovalent binding modes, namely 1:1 (including hairpin and cyclic ligands) and 2:1 ligand/DNA binding. Positions of the ligand atoms involved in hydrogen bonding deviate from idealized hydrogen bond geometries and do not exploit the possibilities indicated by water molecules. Therefore, we suggest the inclusion of shape-based descriptors rather than hydrogen-bond patterns in virtual screening protocols for the identification of innovative minor groove-binding scaffolds.
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Affiliation(s)
- Gudrun M Spitzer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
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47
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Synthesis and affinity to DNA of phenylbenzoimidazoles and benzoimidazo[1,2-c]quinazolines. Eur J Med Chem 2009; 44:3305-12. [PMID: 19349097 PMCID: PMC7115644 DOI: 10.1016/j.ejmech.2009.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 03/02/2009] [Accepted: 03/06/2009] [Indexed: 01/12/2023]
Abstract
Novel N-(benzoimidazophenyl)dialkylaminoalkylamides and 6-dialkylaminoalkylbenzoimidazo[1,2-c]quinazolines were prepared as potential interferon inducers and antiviral agents. They were screened for the DNA affinity by the ethidium bromide displacement assay. It was shown that the lg Ka values of the compounds containing tetracyclic benzoimidazo[1,2-c]quinazoline fragment are approximately one order magnitude greater than those of the corresponding acyclic phenylbenzoimidazole derivatives.
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48
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Effect of 3,4-ethylenedioxy-extension of thiophene core on the DNA/RNA binding properties and biological activity of bisbenzimidazole amidines. Bioorg Med Chem 2009; 17:2544-54. [PMID: 19231203 DOI: 10.1016/j.bmc.2009.01.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 01/20/2009] [Accepted: 01/22/2009] [Indexed: 11/22/2022]
Abstract
Novel bisbenzimidazoles (4-6), characterized by 3,4-ethylenedioxy-extension of thiophene core, revealed pronounced affinity and strong thermal stabilization effect toward ds-DNA. They interact within ds-DNA grooves as dimmers or even oligomers and agglomerate along ds-RNA. Compounds 4-6 have shown moderate to strong antiproliferative effect toward panel of eight carcinoma cell lines. Compound 5 displayed the best inhibitory potential and in equitoxic concentration (IC(50)=1 x 10(-6)M) induced accumulation of cells in G2/M phase after 48 h of incubation. Fluorescence microscopy showed that 5 entered into live HeLa cells within 30 min, but did not accumulate in nuclei even after 2.5h. Compound 5 inhibited the growth of Trypanosome cruzi epimastigotes (IC(50)=4.3 x 10(-6)M).
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49
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Nguyen B, Neidle S, Wilson WD. A role for water molecules in DNA-ligand minor groove recognition. Acc Chem Res 2009; 42:11-21. [PMID: 18798655 DOI: 10.1021/ar800016q] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting the minor groove of DNA through binding to a small molecule has long been considered an important molecular-recognition strategy in biology. A wide range of synthetic heterocyclic molecules bind noncovalently in the minor groove of the double helix and are also effective against a number of human and animal diseases. A classic structural concept, the isohelicity principle, has guided much of this work: such heterocyclic molecules require a shape that complements the convex surface of the minor groove. Researchers have used this principle to design molecules that can read DNA sequences. This principle also predicts that molecules that lack the complementary shape requirement would only bind weakly to DNA. Recently, however, researchers have unexpectedly found that some essentially linear compounds, which do not have this feature, can have high DNA affinity. In this Account, we discuss an alternative recognition concept based on these new findings. We demonstrate that highly structured water molecules can play a key role in mediating between the ligand and DNA minor groove without loss of binding affinity. Combined structural and thermodynamic approaches to understanding the behavior of these molecules have shown that there are different categories of bound water in their DNA complexes. For example, application of this water-bridging concept to the phenylamidine platform has resulted in the discovery of molecules with high levels of biological activity and low nonspecific toxicity. Some of these molecules are now in advanced clinical trials.
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Affiliation(s)
- Binh Nguyen
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302
| | - Stephen Neidle
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, U.K
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302
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Boer DR, Canals A, Coll M. DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes. Dalton Trans 2008:399-414. [PMID: 19122895 DOI: 10.1039/b809873p] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine and Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Barcelona, Spain
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