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Ghorab, M. M., M. S. Alsaid, M. S. Alsaid, and R. K. Arafa, "Cytotoxic activity of some novel sulfonamide derivatives.", Acta poloniae pharmaceutica, vol. 72, issue 1, pp. 79-87, 2015 Jan-Feb. Abstract

The versatile synthons 2-chloro-N-(4-sulfamoylphenyl)acetamides la,b were used as a key intermediates for the synthesis of sulfonamide derivatives with adamantyl 2, indene 3, morpholinophenyl 4, pipronyl 5, benzothiazole 6-8, pyrazole 9, thiadiazole 10,11, quinoline 12, isoquinoline 13, thiazoles 14-19, acrylamides 20-24 and benzochromene 25 moieties via reaction with several nitrogen nucleophiles. The newly synthesized compounds were screened in vitro for their anticancer activity against breast cancer (MDA-MB-231) and colon cancer (HT-29) cell lines. Compound 17 was found to be the most potent against breast cancer cell lines with IC55 value 66.6 μM compared with the reference drug 5-fluorouracil with IC50 value 77.28 μM.

Ghorab, M. M., M. S. Al-Said, and R. K. Arafa, "Design, synthesis and potential anti-proliferative activity of some novel 4-aminoquinoline derivatives.", Acta pharmaceutica (Zagreb, Croatia), vol. 64, issue 3, pp. 285-97, 2014 Sep. Abstract

Novel nineteen compounds based on a 4-aminoquinoline scaffold were designed and synthesized as potential antiproliferative agents. The new compounds were N-substituted at the 4-position by aryl or heteroaryl (1-9), quinolin- 3-yl (10), 2-methylquinolin-3-yl (11), thiazol-2-yl (12), and dapsone moieties (13, 14 and 18). Bis-compounds 15, 16 and 19 were also synthesized to assess their biological activity. All the newly synthesized comounds were tested for in vitro antiproliferative activity against the MCF-7 breast cancer cell line. Seventeen of the novel compounds showed higher activity than the reference drug doxorubicin. The corresponding 7-(trifluoromethyl)-N-(3,4,5-trimethoxyphenyl)quinolin-4- amine 1, N-(7-(trifluoromethyl)quinolin-4-yl)quinolin- 3- amine (10), 2-methyl-N-(7-trifluorome-thyl)quinolin-4-yl) quinolin-3-amine (11) and N-(4-(4-aminophenylsulfonyl) phenyl)-7-chloroquinolin-4-amine (13) were almost twice to thrice as potent as doxorubicin. Biological screening of the tested compounds could offer an encouraging framework in this field that may lead to the discovery of potent anticancer agents.

Bashandy, M. S., M. S. Alsaid, R. K. Arafa, and M. M. Ghorab, "Design, synthesis and molecular docking of novel N,N-dimethylbenzenesulfonamide derivatives as potential antiproliferative agents.", Journal of enzyme inhibition and medicinal chemistry, vol. 29, issue 5, pp. 619-27, 2014 Oct. Abstract

Novel pyridine, thiophene, thiazole, chromene and benzochromene derivatives bearing a N,N-dimethylbenzenesulfonamide moiety 6-20 were synthesized. The target compounds were obtained through employing a series of heterocyclization reactions utilizing the key intermediate hydrazide hydrazone derivative 3. The structures of the newly synthesized compounds were confirmed by elemental analyses, IR, (1)H-NMR and (13)C-NMR spectral data. All the newly synthesized compounds were evaluated for their in vitro antiproliferative activity against the human breast cancer cell line MCF-7. Biological screening results showed that sulfonamides 6, 9, 11, 16 and 17 with IC50 values 21.81, 25.50, 20.60, 25.83 and 31.20 μM, respectively, possessed higher antiproliferative activity compared to doxorubicin, IC50 value 32.00 μM, as position control. Molecular docking study was also performed to assess the binding mode of the synthesized sulfonamides with their potential biomolecular target, carbonic anhydrase IX (CA IX), which is usually highly expressed in some types of cancer cells.

Ghorab, M. M., M. Ceruso, M. S. Alsaid, Y. M. Nissan, R. K. Arafa, and C. T. Supuran, "Novel sulfonamides bearing pyrrole and pyrrolopyrimidine moieties as carbonic anhydrase inhibitors: Synthesis, cytotoxic activity and molecular modeling.", European journal of medicinal chemistry, vol. 87, pp. 186-96, 2014 Nov 24. Abstract

Novel pyrrole and pyrrolopyrimidine scaffold-based sulfonamides were designed and synthesized. The carbonic anhydrase (CA) inhibition ability of all derivatives was assessed against the human (h) cytosolic isoforms hCA I and II and the transmembrane, tumor-associated isoforms hCA IX and XII. Some of these sulfonamides were 6-8 fold more potent than the reference drug acetazolamide (AZA, Ki = 5.7 nM)) against hCA XII showing subnanomolar activity. The in vitro cytotoxicity of these derivatives was evaluated against MCF-7, where some derivatives were more cytotoxic than doxorubicin (IC50 = 8.02 μM) displaying IC50 values between 6.46 and 7.56 μM. Docking of these sulfonamides with CA XII was performed and their binding modes were comparable with that of AZA.

Ghorab, M. M., M. Higgins, M. S. Alsaid, R. K. Arafa, A. A. Shahat, and A. T. Dinkova-Kostova, "Synthesis, molecular modeling and NAD(P)H:quinone oxidoreductase 1 inducer activity of novel cyanoenone and enone benzenesulfonamides.", Journal of enzyme inhibition and medicinal chemistry, vol. 29, issue 6, pp. 840-5, 2014 Dec. Abstract

UNLABELLED: Abstract In biological systems, the Keap1/Nrf2/antioxidant response element pathway determines the ability of mammalian cells to adapt and survive conditions of oxidative, electrophilic and inflammatory stress by regulating the production of cytoprotective enzymes

NAD(P)H: quinone oxidoreductase 1 (NQO1, EC being one of them. Novel biologically active benzenesulfonamides 2, 3, 5-7, penta-2,4-dienamide 4 and chromene-2-carboxamide 8 structurally augmented with an electron-deficient Michael acceptor enone or cyanoenone functionalities were prepared. A new biological activity was conferred to these molecules, that of induction of NQO1. The potency of induction was increased by incorporation of a nitrile group adjacent to the enone and the dinitrophenyl derivative 3 was the most promising inducer. Also, molecular docking of the new compounds in the Nrf2-binding site of Keap1 was performed to assess their ability to inhibit Keap1 which biologically leads to a consequent Nrf2 accumulation and enhanced gene expression of NQO1. Docking results showed considerable interactions between the new molecules and essential binding site amino acids.

Ismail, M. A., R. K. Arafa, M. M. Youssef, and W. M. El-Sayed, "Anticancer, antioxidant activities, and DNA affinity of novel monocationic bithiophenes and analogues.", Drug design, development and therapy, vol. 8, pp. 1659-72, 2014. 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.

Arafa, R. K., M. S. Nour, and N. A. El-Sayed, "Novel heterocyclic-fused pyrimidine derivatives: synthesis, molecular modeling and pharmacological screening.", European journal of medicinal chemistry, vol. 69, pp. 498-507, 2013 Nov. Abstract

Novel heterocyclic-fused pyrimidines viz pyrrolo[1,2-c]pyrimidines 4-8, pyrimido[5,4-e]pyrrolo[1,2-c]pyrimidines 9-14, pyrimido[4',5':4,5]pyrimido[1,6-a]azepines 16-18, pyrrolo[1',2':1,6]pyrimido[4,5-d][1,3]thiazines 19a,b and 1,3-thiazino[4',5':4,5]pyrimido[1,6-a]-azepine 19c were designed and synthesized as potential anticancer agents. In this investigation all the newly synthesized compounds were subjected to cytotoxic screening against MCF-7 breast cancer cell line. Moreover, kinase inhibitory assay was done for compounds 5, 7, 9 and 18 against the non-receptor and receptor tyrosine kinases c-Src and VEGFR, respectively. The tested compounds were more potent against c-Src than VEGFR, and the highest activity was observed for 18 showing 81% c-Src activity inhibition. Finally, molecular docking was performed with c-Src and VEGFR in an attempt to simulate and understand the possible binding interactions underlying the association between these small molecules and the kinase enzyme ATP binding pocket essential amino acids.

Arafa, R. K., G. H. Hegazy, G. A. Piazza, and A. H. Abadi, "Synthesis and in vitro antiproliferative effect of novel quinoline-based potential anticancer agents.", European journal of medicinal chemistry, vol. 63, pp. 826-32, 2013 May. Abstract

Several derivatives with a quinoline scaffold and a flexible, semi-flexible or rigid side chains at position 8 of the quinoline ring were synthesized and assessed for their in vitro activity versus the human colon cancer cell line HT29 and the human breast cancer cell line MDA-MB231. The HT29 cell line was more refractory to the cytotoxic activity of some compounds, meanwhile all the quinoline derivatives except one displayed high to moderate activity against MDA-MB231 with IC50 values ranging between 4.6 and 48.2 μM. The most active derivative in this study against both tested cell lines was the Schiff's base 4e with IC50 of 4.7 and 4.6 μM against HT29 and MDA-MB231, respectively.

Ismail, M. A., S. Al-Shihry, R. K. Arafa, and U. El-Ayaan, "Synthesis, antimicrobial activity and molecular modeling study of substituted 5-aryl-pyrimido[5,4-c]quinoline-2,4-diones.", Journal of enzyme inhibition and medicinal chemistry, vol. 28, issue 3, pp. 530-8, 2013 Jun. Abstract

A series of pyrimido[5,4-c]quinoline-2,4-dione derivatives 5a-k were synthesized in moderate yields via a thermolysis reaction of equimolar ratio of 5-arylidine-1,3-dimethylbarbituric acid derivatives 3a-d with aniline derivatives 4a-d at 150-180 °C for 1-2 h. Eight of the synthesized compounds were chosen for a primary in vitro one-dose anticancer assay performed using the full NCI 60 cell panel. Only compound 5b showed moderate GI% at the used dose (10 μM) against four of the tested cell lines corresponding to leukemia SR (GI%: 51), non small-cell lung cancer HOP-92 (GI%: 63), melanoma UACC-62 (GI%: 53) and renal cancer UO-31 (GI%: 69). On the other hand, antimicrobial screening of the whole set of the synthesized compounds was performed against three Gram +ve and two Gram -ve bacterial strains. Results of the antimicrobial screening showed that compounds 5d, 5e, 5f, 5h and 5k have broad-spectrum antibacterial efficacy being moderately active against all the tested Gram +ve and two Gram -ve bacteria. Also, compound 5a showed interesting results being only active against Streptococcus faecalis and both tested Gram -ve strains viz. E. coli and P. aeruginosa. In order to compare the binding mode of the most active compounds 5e and 5f along with the inactive compound 5c we docked these compounds into the empty binding site of topoisomerase II DNA gyrase (PDB ID: 1KZN), and results were compared with the bound inhibitor Clorobiocin.

Patrick, D. A., M. A. Ismail, R. K. Arafa, T. Wenzler, X. Zhu, T. Pandharkar, S. K. Jones, K. A. Werbovetz, R. Brun, D. W. Boykin, et al., "Synthesis and antiprotozoal activity of dicationic m-terphenyl and 1,3-dipyridylbenzene derivatives.", Journal of medicinal chemistry, vol. 56, issue 13, pp. 5473-94, 2013 Jul 11. Abstract

4,4″-Diamidino-m-terphenyl (1) and 36 analogues were prepared and assayed in vitro against T rypanosoma brucei rhodesiense , Trypanosoma cruzi , Plasmodium falciparum , and Leishmania amazonensis . Twenty-three compounds were highly active against T. b. rhodesiense or P. falciparum. Most noteworthy were amidines 1, 10, and 11 with IC50 of 4 nM against T. b. rhodesiense, and dimethyltetrahydropyrimidinyl analogues 4 and 9 with IC50 values of ≤ 3 nM against P. falciparum. Bis-pyridylimidamide derivative 31 was 25 times more potent than benznidazole against T. cruzi and slightly more potent than amphotericin B against L. amazonensis. Terphenyldiamidine 1 and dipyridylbenzene analogues 23 and 25 each cured 4/4 mice infected with T. b. rhodesiense STIB900 with four daily 5 mg/kg intraperitoneal doses, as well as with single doses of ≤ 10 mg/kg. Derivatives 5 and 28 (prodrugs of 1 and 25) each cured 3/4 mice with four daily 25 mg/kg oral doses.

Hunt, R. A., M. Munde, A. Kumar, M. A. Ismail, A. A. Farahat, R. K. Arafa, M. Say, A. Batista-Parra, D. Tevis, D. W. Boykin, et al., "Induced topological changes in DNA complexes: influence of DNA sequences and small molecule structures.", Nucleic acids research, vol. 39, issue 10, pp. 4265-74, 2011 May. Abstract

Heterocyclic diamidines are compounds with antiparasitic properties that target the minor groove of kinetoplast DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structures are likely to be involved. In this study, we have developed a polyacrylamide gel electrophoresis-based screening method to determine topological effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and ATATA. The AAAAA and AAATT sequences have the largest intrinsic bend, whereas the TTTAA and ATATA sequences are relatively straight. The changes caused by binding of the compounds are sequence dependent, but generally the topological effects on AAAAA and AAATT are similar as are the effects on TTTAA and ATATA. A total of 13 compounds with a variety of structural differences were evaluated for topological changes to DNA. All compounds decrease the mobility of the ATATA sequence that is consistent with decreased minor groove width and bending of the relatively straight DNA into the minor groove. Similar, but generally smaller, effects are seen with TTTAA. The intrinsically bent AAAAA and AAATT sequences, which have more narrow minor grooves, have smaller mobility changes on binding that are consistent with increased or decreased bending depending on compound structure.

Arafa, R. K., T. Wenzler, R. Brun, Y. Chai, and D. W. Wilson, "Molecular modeling study and synthesis of novel dicationic flexible triaryl guanidines and imidamides as antiprotozoal agents.", European journal of medicinal chemistry, vol. 46, issue 12, pp. 5852-60, 2011 Dec. Abstract

A new series of fourteen dicationic flexible triaryl bis-guanidines 3a,b, bis-N-substituted guanidines 7a,b and 8a,b as well as bis-imidamides 9-12a,b having a 1,3- or 1,4-diphenoxybenzene scaffold backbone were synthesized. The in vitro activity of the novel dications as antiprotozoal agents against Trypanosoma brucei rhodesiense (T.b.r.) and Plasmodium falciparum (P.f.) was assessed. Interestingly, six of the newly synthesized dications viz 3a,b, 7a,b and 8a,b were more active against P.f. than the reference drug pentamidine. Also, some of the dications showed moderate antitrypanosomal activity. Thermal melting analysis of the novel dications was performed to determine their ligand-DNA relative binding affinities. Finally, docking of the dications with an AT rich DNA oligonucleotide was executed to understand their binding mode with the minor groove.

Ghorab, M. M., F. A. Ragab, H. I. Heiba, R. K. Arafa, and E. M. El-Hossary, "In vitro anticancer screening and radiosensitizing evaluation of some new quinolines and pyrimido[4,5-b]quinolines bearing a sulfonamide moiety.", European journal of medicinal chemistry, vol. 45, issue 9, pp. 3677-84, 2010 Sep. Abstract

Sulfonamide bearing compounds possess many types of biological activities and have recently been reported to show substantial antitumor activity in vitro and/or in vivo. There are a variety of mechanisms for the anticancer activity, and the most prominent mechanism is the inhibition of carbonic anhydrase (CA) isozymes. The present work reports the synthesis of twenty novel quinoline and pyrimido[4,5-b]quinoline derivatives bearing a sulfonamide moiety. The new synthesized compounds were designed in compliance with the general pharmacophoric requirements for CA inhibiting anticancer drugs, as this may play a role in their anticancer activity. All the newly synthesized compounds were evaluated for their in vitro anticancer activity against human breast cancer cell line (MCF7). Compounds 6, 9 and 18 showed IC(50) values (72.9 microM, 72.1 microM and 71.9 microM, respectively) comparable to that of the reference drug doxorubicin (IC(50) = 71.8 microM). On the other hand, compound 8 exhibited better activity than doxorubicin with an IC(50) value of 64.5 microM. Additionally, the most potent compounds 8 and 18 were evaluated for their ability to enhance the cell killing effect of gamma-radiation.

Gillingwater, K., A. Kumar, M. A. Ismail, R. K. Arafa, C. E. Stephens, D. W. Boykin, R. R. Tidwell, and R. Brun, "In vitro activity and preliminary toxicity of various diamidine compounds against Trypanosoma evansi.", Veterinary parasitology, vol. 169, issue 3-4, pp. 264-72, 2010 May 11. Abstract

Trypanosoma evansi is an animal pathogenic protozoan, causing a wasting disease called Surra, which is broadly distributed in a wide range of mammalian hosts. Chemotherapy is the most efficient control method, which depends on four drugs. Unfortunately, with the appearance of resistance to these drugs, their effective use is threatened, emphasising a need to find new drugs. Diamidines bind to the minor groove of DNA at AT-rich sites and exert their anti-trypanosomal activity by inhibiting one or more DNA dependent enzymes or by directly impeding the transcription process. In total, 67 novel diamidine compounds were tested in vitro to determine activity against an animal pathogenic Chinese kinetoplastic T. evansi strain. In comparison, a human pathogenic Trypanosoma brucei rhodesiense strain and a P2 transporter knock out of a Trypanosoma brucei brucei strain were also tested. All diamidine compounds tested in this study against T. evansi produced inhibitory concentration (IC(50)) values below 50 nM. The results demonstrate that these compounds are highly active against T. evansi in vitro. In addition, preliminary in vivo toxicity tests were performed on all 67 diamidines with 69% of the compounds showing no acute toxicity at an intra-peritoneal dose of 100mg/kg.

Hu, L., R. K. Arafa, M. A. Ismail, A. Patel, M. Munde, D. W. Wilson, T. Wenzler, R. Brun, and D. W. Boykin, "Synthesis and activity of azaterphenyl diamidines against Trypanosoma brucei rhodesiense and Plasmodium falciparum.", Bioorganic & medicinal chemistry, vol. 17, issue 18, pp. 6651-8, 2009 Sep 15. Abstract

A series of azaterphenyl diamidines has been synthesized and evaluated for in vitro antiprotozoal activity against both Trypanosoma brucei rhodesiense (T. b. r.) and Plasmodium falciparum (P. f.) and in vivo efficacy in the STIB900 acute mouse model for T. b. r. Six of the 13 compounds showed IC(50) values less than 7 nM against T. b. r. Twelve of those exhibited IC(50) values less than 6 nM against P. f. and six of those showed IC(50) values 0.6 nM, which are more than 25-fold as potent as furamidine. Moreover, two of them showed more than 40-fold selectivity for P. f. versus T. b. r. Three compounds 15b, 19d and 19e exhibited in vivo efficacy against T. b. r. much superior to furamidine, and equivalent to or better than azafuramidine. The antiparasitic activity of these diamidines depends on the ring nitrogen atom(s) location relative to the amidine groups and generally correlates with DNA binding affinity.

Hassan, G. S., N. A. Farag, G. H. Hegazy, and R. K. Arafa, "Design and synthesis of novel benzopyran-2-one derivatives of expected antimicrobial activity through DNA gyrase-B inhibition.", Archiv der Pharmazie, vol. 341, issue 11, pp. 725-33, 2008 Nov. Abstract

In an attempt to find a new class of antibacterial agents, we have synthesized thirty new coumarin (2H-benzopyran-2-one) analogues. These derivatives include substituted azetidin-2-ones (beta-lactam) 3a-f, pyrrolidin-2-ones 4a-f, 2H-1,3,4-oxadiazoles 5a-f, and thiazolidin-4-ones 6a-f attached to 4-phenyl-2H-benzopyran-2-one through an oxyacetamido or an oxymethyl bridge. The target compounds were synthesized starting from 2-oxo-4-phenyl-2H-benzo[b]pyran-7-yl-oxyacetic acid hydrazides 2a-f. The new compounds were evaluated as DNA gyrase-B inhibitors through molecular modeling and docking techniques using the Molsoft ICM 3.4-8C program. The synthesized compounds were also screened for antibacterial activity against four different species of Gram-positive and Gram-negative bacteria; as well as screening against C. albicans for antifungal activity. The molecular modeling data were in accordance with the antimicrobial screening results.

Ismail, M. A., R. K. Arafa, T. Wenzler, R. Brun, F. A. Tanious, D. W. Wilson, and D. W. Boykin, "Synthesis and antiprotozoal activity of novel bis-benzamidino imidazo[1,2-a]pyridines and 5,6,7,8-tetrahydro-imidazo[1,2-a]pyridines.", Bioorganic & medicinal chemistry, vol. 16, issue 2, pp. 683-91, 2008 Jan 15. Abstract

The key dinitrile intermediates 4a-d were synthesized by reaction of phenacyl bromide 1 and the appropriate 2-amino-5-bromopyridines to yield 3a-d. Suzuki coupling of 3a-d with 4-cyanophenylboronic acid yielded the 2,6-bis(4-cyanophenyl)-imidazo[1,2-a]pyridine derivatives 4a-d. The bis-amidoximes 5a-d, obtained from 4a-d by the action of hydroxylamine, were converted to the bis-O-acetoxyamidoximes which on catalytic hydrogenation in a mixture of ethanol/ethyl acetate gave the acetate salts of 2,6-bis[4-(amidinophenyl)]-imidazo[1,2-a]pyridines 7a-d. In contrast, catalytic hydrogenation of the bis-O-acetoxyamidoxime of 5a in glacial acetic acid gave the saturated analogue 2,6-bis[4-(amidinophenyl)]-5,6,7,8-tetrahydro-imidazo[1,2-a]pyridine 8. O-Methylation of the amidoximes 5a-d gave the N-methoxyamidines 6a-d. The diamidines showed strong DNA binding affinity, were very active in vitro against T. b. r. exhibiting IC(50) values between 7 and 38nM, but were less effective against P. f. with IC(50) values between 23 and 92nM. Two of the diamidines 7c and 7d were slightly more active than furamidine but less active than azafuramidine in the T. b. r. STIB900 mouse model. Only one prodrug 6b showed moderate activity in the same mouse model.

Hu, L., R. K. Arafa, M. A. Ismail, T. Wenzler, R. Brun, M. Munde, D. W. Wilson, S. Nzimiro, S. Samyesudhas, K. A. Werbovetz, et al., "Azaterphenyl diamidines as antileishmanial agents.", Bioorganic & medicinal chemistry letters, vol. 18, issue 1, pp. 247-51, 2008 Jan 1. Abstract

Eighteen diamidino azaterphenyls and analogues were evaluated as anti-leishmanials; nine of the compounds gave IC50 values less than 1 microM, five exhibited values less than 0.40 microM, and two gave values less than 0.10 microM in a Leishmania donovani axenic amastigote assay. The activity of the diamidines strongly depends on the ring N-atom location relative to the amidine groups and correlates with DNA affinity. Transmission electron microscopy studies showed a dramatic dilation of the mitochondrion and evidence of disintegration of the kinetoplast of the amastigotes.

Arafa, R. K., M. A. Ismail, M. Munde, D. W. Wilson, T. Wenzler, R. Brun, and D. W. Boykin, "Novel linear triaryl guanidines, N-substituted guanidines and potential prodrugs as antiprotozoal agents.", European journal of medicinal chemistry, vol. 43, issue 12, pp. 2901-8, 2008 Dec. Abstract

A series of triaryl guanidines and N-substituted guanidines designed to target the minor groove of DNA were synthesized and evaluated as antiprotozoal agents. Selected carbamate prodrugs of these guanidines were assayed for their oral efficacy. The linear triaryl bis-guanidines 6a,b were prepared from their corresponding diamines 4a,b through the intermediate BOC protected bis-guanidines 5a,b followed by acid catalyzed deprotection. The N-substituted guanidino analogues 9c-f were obtained in three steps starting by reacting the diamines 4a,b with ethyl isothiocyanatoformate to give the carbamoyl thioureas 7a,b. Subsequent condensation of 7a,b with various amines in the presence of EDCI provided the carbamoyl N-substituted guanidine intermediates 8a-f which can also be regarded as potential prodrugs for the guanidino derivatives. Compounds 9c-f were obtained via the base catalyzed decarbamoylation of 8a-f. The DNA binding affinities for the target dicationic bis-guanidines were assessed by DeltaT(m) values. In vitro antiprotozoal screening of the new compounds showed that derivatives 6a, 9c and 9e possess high to moderate activity against Trypanosoma brucei rhodesiense (T.b.r.) and Plasmodium falciparum (P.f.). While the prodrugs did not yield cures upon oral administration in the antitrypanosomal STIB900 mouse model, compounds 8a and 8c prolonged the survival of the treated mice.

Munde, M., M. A. Ismail, R. Arafa, P. Peixoto, C. J. Collar, Y. Liu, L. Hu, M. - H. David-Cordonnier, A. Lansiaux, C. Bailly, et al., "Design of DNA minor groove binding diamidines that recognize GC base pair sequences: a dimeric-hinge interaction motif.", Journal of the American Chemical Society, vol. 129, issue 44, pp. 13732-43, 2007 Nov 7. Abstract

The classical model of DNA minor groove binding compounds is that they should have a crescent shape that closely fits the helical twist of the groove. Several compounds with relatively linear shape and large dihedral twist, however, have been found recently to bind strongly to the minor groove. These observations raise the question of how far the curvature requirement could be relaxed. As an initial step in experimental analysis of this question, a linear triphenyl diamidine, DB1111, and a series of nitrogen tricyclic analogues were prepared. The goal with the heterocycles is to design GC binding selectivity into heterocyclic compounds that can get into cells and exert biological effects. The compounds have a zero radius of curvature from amidine carbon to amidine carbon but a significant dihedral twist across the tricyclic and amidine-ring junctions. They would not be expected to bind well to the DNA minor groove by shape-matching criteria. Detailed DNase I footprinting studies of the sequence specificity of this set of diamidines indicated that a pyrimidine heterocyclic derivative, DB1242, binds specifically to a GC-rich sequence, -GCTCG-. It binds to the GC sequence more strongly than to the usual AT recognition sequences for curved minor groove agents. Other similar derivatives did not exhibit the GC specificity. Biosensor-surface plasmon resonance and isothermal titration calorimetry experiments indicate that DB1242 binds to the GC sequence as a highly cooperative stacked dimer. Circular dichroism results indicate that the compound binds in the minor groove. Molecular modeling studies support a minor groove complex and provide an inter-compound and compound-DNA hydrogen-bonding rational for the unusual GC binding specificity and the requirement for a pyrimidine heterocycle. This compound represents a new direction in the development of DNA sequence-specific agents, and it is the first non-polyamide, synthetic compound to specifically recognize a DNA sequence with a majority of GC base pairs.

Munde, M., M. Lee, S. Neidle, R. Arafa, D. W. Boykin, Y. Liu, C. Bailly, and D. W. Wilson, "Induced fit conformational changes of a "reversed amidine" heterocycle: optimized interactions in a DNA minor groove complex.", Journal of the American Chemical Society, vol. 129, issue 17, pp. 5688-98, 2007 May 2. Abstract

To better understand the molecular basis for recognition of the DNA minor groove by heterocyclic cations, a series of "reversed amidine" substituted heterocycles has been prepared. Amidine derivatives for targeting the minor groove have the amidine carbon linked to a central heterocyclic system, whereas in the reverse orientation, an amidine nitrogen provides the link. The reverse system has a larger dihedral angle as well as a modified spatial relationship with the groove relative to amidines. Because of the large dihedral, the reversed amidines should have reduced binding to DNA relative to similar amidines. Such a reduction is observed in footprinting, circular dichroism (CD), biosensor-surface plasmon resonance (SPR), and isothermal titration calorimetric (ITC) experiments with DB613, which has a central phenyl-furan-phenyl heterocyclic system. The reduction is not seen when a pyrrole (DB884) is substituted for the furan. Analysis of a number of derivatives defines the pyrrole and a terminal phenyl substituent on the reversed amidine groups as critical components in the strong binding of DB884. ITC and SPR comparisons showed that the better binding of DB884 was due to a more favorable binding enthalpy and that it had exceptionally slow dissociation from DNA. Crystallographic analysis of DB884 bound to an AATT site shows that the compound was bound in the minor groove in a 1:1 complex as suggested by CD solution studies. Surprisingly, unlike the amidine derivative, the pyrrole -NH of DB884 formed an H-bond with a central T of the AATT site and this accounts for the enthalpy-driven strong binding. The structural results and molecular modeling studies provide an explanation for the differences in binding affinities for related amidine and reversed amidine analogues.

Ismail, M. A., R. K. Arafa, R. Brun, T. Wenzler, Y. Miao, D. W. Wilson, C. Generaux, A. Bridges, J. E. Hall, and D. W. Boykin, "Synthesis, DNA affinity, and antiprotozoal activity of linear dications: Terphenyl diamidines and analogues.", Journal of medicinal chemistry, vol. 49, issue 17, pp. 5324-32, 2006 Aug 24. Abstract

Diamidines 10a-g and 18a,b were obtained from dinitriles 9a-g and 15a,b by treatment with lithium trimethylsilylamide or upon hydrogenation of bis-O-acetoxyamidoximes. Dinitriles 9a-g were prepared via Suzuki reactions between arylboronic acids and arylnitriles. Potential prodrugs 12a-f and 17 were prepared via methylation of the diamidoximes 11a-f and 16a. Significant DNA affinities for rigid-rod molecules were observed. Compounds 10a, 10b, 10d, 18a, and 18b show IC50 values of 5 nM or less against Trypanosoma brucei rhodesiense (T. b. r.) and 10a, 10b, 10e, 18a, and 18b gave similar ones against Plasmodium falciparum (P.f.). The dications, 10a, 10d, 10f, and 10g are more active than furamidine in vivo. The prodrugs are only moderately effective on oral administration. Mouse liver microsome bioconversion of the methamidoxime prodrugs is significantly reduced from that of pafuramidine and suggests that the in vivo efficacy of these prodrugs is, in part, due to poor bioconversion.

Bailly, C., R. K. Arafa, F. A. Tanious, W. Laine, C. Tardy, A. Lansiaux, P. Colson, D. W. Boykin, and D. W. Wilson, "Molecular determinants for DNA minor groove recognition: design of a bis-guanidinium derivative of ethidium that is highly selective for AT-rich DNA sequences.", Biochemistry, vol. 44, issue 6, pp. 1941-52, 2005 Feb 15. Abstract

The phenanthridinium dye ethidium bromide is a prototypical DNA intercalating agent. For decades, this anti-trypanosomal agent has been known to intercalate into nucleic acids, with little preference for particular sequences. Only polydA-polydT tracts are relatively refractory to ethidium intercalation. In an effort to tune the sequence selectivity of known DNA binding agents, we report here the synthesis and detailed characterization of the mode of binding to DNA of a novel ethidium derivative possessing two guanidinium groups at positions 3 and 8. This compound, DB950, binds to DNA much more tightly than ethidium and exhibits distinct DNA-dependent absorption and fluorescence properties. The study of the mode of binding to DNA by means of circular and electric linear dichroism revealed that, unlike ethidium, DB950 forms minor groove complexes with AT sequences. Accurate quantification of binding affinities by surface plasmon resonance using A(n)T(n) hairpin oligomer indicated that the interaction of DB950 is over 10-50 times stronger than that of ethidium and comparable to that of the known minor groove binder furamidine. DB950 interacts weakly with GC sites by intercalation. DNase I footprinting experiments performed with different DNA fragments established that DB950 presents a pronounced selectivity for AT-rich sites, identical with that of furamidine. The replacement of the amino groups of ethidium with guanidinium groups has resulted in a marked gain of both affinity and sequence selectivity. DB950 provides protection against DNase I cleavage at AT-containing sites which frequently correspond to regions of enhanced cleavage in the presence of ethidium. Although DB950 maintains a planar phenanthridinium chromophore, the compound no longer intercalates at AT sites. The guanidinium groups of DB950, just like the amidinium group of furamidine (DB75), are the critical determinants for recognition of AT binding sites in DNA. The chemical modulation of the ethidium exocyclic amines is a profitable option to tune the nucleic acid recognition properties of phenylphenanthridinium dyes.

Arafa, R. K., R. Brun, T. Wenzler, F. A. Tanious, D. W. Wilson, C. E. Stephens, and D. W. Boykin, "Synthesis, DNA affinity, and antiprotozoal activity of fused ring dicationic compounds and their prodrugs.", Journal of medicinal chemistry, vol. 48, issue 17, pp. 5480-8, 2005 Aug 25. Abstract

Dicationic guanidine, N-alkylguanidine, and reversed amidine derivatives of fused ring systems have been synthesized from their corresponding bis-amines. DNA binding studies suggest that the diguanidines and the N-alkyl diguanidines fluorenes bind in the minor groove in a manner similar to that of the previously reported dicationic carbazole derivatives. The diguanidines and the N-alkyl diguanidines showed promising in vitro activity against both Trypanosoma brucei rhodesiense and Plasmodium falciparum. Promising in vivo biological results were obtained for the dicationic N-isopropylguanidino-9H-fluorene, giving 4/4 cures of the treated animals in the STIB900 animal model for African trypanosomiasis. The N-methyl analogue showed high activity as well. In addition, with the goal of enhancing the oral bioavailability, two novel classes of potential guanidine prodrugs were prepared. The N-alkoxyguanidine derivatives were not effective as prodrugs. In contrast, a number of the carbamates showed promising activity. The value of the carbamate prodrugs was clearly demonstrated by the results, which gave 4/4 cures on oral administration in the STIB900 mouse model.