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issn:0968-0.96
1.  Semisynthetic Studies Identify Mitochondria Poisons from Botanical Dietary Supplements – Geranyloxycoumarins from Aegle marmelos 
Bioorganic & medicinal chemistry  2013;21(7):1795-1803.
Bioassay-guided isolation and subsequent structure elucidation of a Bael tree Aegle marmelos lipid extract yielded two unstable acylated geranyloxycoumarin mixtures (1–2), six geranyloxycoumarins (3–8), (+)-9′-isovaleroxylariciresinol (9), and dehydromarmeline (10). In a T47D cell-based reporter assay, 1 and 2 potently inhibited hypoxia-induced HIF-1 activation (IC50 values 0.18 and 1.10 μg mL−1, respectively). Insufficient material and chemical instability prevented full delineation of the fatty acyl side chain olefin substitution patterns in 1 and 2. Therefore, five fatty acyl geranyloxycoumarin ester derivatives (11–15) were prepared from marmin (3) and commercial fatty acyl chlorides by semisynthesis. The unsaturated C-6′ linoleic acid ester derivative 14 that was structurally most similar to 1 and 2, inhibited HIF-1 activation with comparable potency (IC50 0.92 μM). The octanoyl (11) and undecanoyl (12) ester derivatives also suppressed HIF-1 activation (IC50 values 3.1 and 0.87 μM, respectively). Mechanistic studies revealed that these geranyloxycoumarin derivatives disrupt mitochondrial respiration, primarily at complex I. Thus, these compounds may inhibit HIF-1 activation by suppressing mitochondria-mediated hypoxic signaling. One surprising observation was that, while less potent, the purported cancer chemopreventive agent auraptene (8) was found to act as a mitochondrial poison that disrupts HIF-1 signaling in tumors.
doi:10.1016/j.bmc.2013.01.048
PMCID: PMC3602229  PMID: 23434131
Botanical Dietary Supplements; Mitochondrial Poisons; Geranyloxycoumarin; Auraptene; Hypoxia-Inducible Factor-1 (HIF-1)
2.  Synthesis and biological activity of 5-chloro-N4-substituted phenyl-9H-pyrimido[4,5-b]indole-2,4-diamines as vascular endothelial growth factor receptor-2 inhibitors and antiangiogenic agents1 
Bioorganic & medicinal chemistry  2013;21(7):1857-1864.
Inhibition of receptor tyrosine kinase (RTK) signaling pathways is an important area for the development of novel anticancer agents. Numerous multikinase inhibitors (MKIs) have been recently approved for the treatment of cancer. Vascular endothelial growth factor receptor-2 (VEGFR-2) is the principal mediator of tumor angiogenesis. In an effort to develop ATP-competitive VEGFR-2 selective inhibitors the 5-chloro-N4-substituted phenyl-9H-pyrimido[4,5-b]indole-2,4-diamine scaffold was designed. The synthesis of the target compounds involved N-(4,5-dichloro-9H-pyrimido[4,5-b]indol-2-yl)-2,2-dimethylpropanamide) as a common intermediate. A nucleophilic displacement of the 4-chloro group of the common intermediate by appropriately substituted anilines afforded the target compounds. Biological evaluation indicated that compound 5 is a potent and selective VEGFR-2 inhibitor comparable to sunitinib and semaxinib.
doi:10.1016/j.bmc.2013.01.040
PMCID: PMC3602277  PMID: 23434139
Receptor tryosine kinase inhibitors; Pyrimido[4; 5-b]indol synthesis; Cytotoxicity; VEGFR-2 inhibitors
3.  Two-component covalent inhibitor 
Bioorganic & medicinal chemistry  2013;21(7):1988-1991.
Inhibitors that covalently damage proteins or nucleic acids offer great potency, but are difficult to rationally design and suffer from poor specificity. Here we outline a general concept for constructing covalent inhibitors, called the two-component covalent inhibitor (TCCI). The approach takes advantage of two ligand analogs equipped with pre-reactive groups. Binding of the analogs to the adjacent sites of a target biopolymer brings the pre-reactive groups in close proximity and causes their interaction followed by covalent damage of the target. In the present study we used light-activated pre-reactive groups to inactivate a DNA polymerase. It was found that the efficiency of a traditional single-component inhibitor was greatly reduced in the presence of a non-target protein, while the TCCI was not significantly affected. Our findings suggest that TCCI approach has advantages in inactivation of biopolymers in complex multi-component systems.
doi:10.1016/j.bmc.2013.01.021
PMCID: PMC3602336  PMID: 23411398
Covalent inhibitors; irreversible inhibitors; drug design; DNA polymerase; enzymes; nucleotide analogs; aryl azide; pyrene
4.  Novel Inhibitors of Bacterial Virulence: Development of 5,6-dihydrobenzo[h]quinazolin-4(3H)-ones for the Inhibition of Group A Streptococcal Streptokinase Expression 
Bioorganic & medicinal chemistry  2013;21(7):1880-1897.
Resistance to antibiotics is an increasingly dire threat to human health that warrants the development of new modes of treating infection. We recently identified 1 (CCG-2979) as an inhibitor of the expression of streptokinase, a critical virulence factor in Group A Streptococcus that endows blood-borne bacteria with fibrinolytic capabilities. In this report, we describe the synthesis and biological evaluation of a series of novel 5,6-dihydrobenzo[h]quinazolin-4(3H)-one analogs of 1 undertaken with the goal of improving the modest potency of the lead. In addition to achieving an over 35-fold increase in potency, we identified structural modifications that improve the solubility and metabolic stability of the scaffold. The efficacy of two new compounds 12c (CCG-203592) and 12k (CCG-205363) against biofilm formation in Staphylococcus aureus represents a promising additional mode of action for this novel class of compounds.
doi:10.1016/j.bmc.2013.01.046
PMCID: PMC3605901  PMID: 23433668
Group A Streptococcus; virulence inhibitor; antibiotic; streptokinase; antibiotic resistance; metabolic oxidation; biofilm; antivirulence
5.  6-Oxo and 6-Thio Purine Analogs as Antimycobacterial Agents 
Bioorganic & medicinal chemistry  2013;21(7):1685-1695.
6–Oxo and 6–thio purine analogs were prepared based on the initial activity screening of a small, diverse purine library against Mycobacterium tuberculosis (Mtb). Certain analogs showed moderate to good inhibitory activity. N9-substitution apparently enhances the antimycobacterial activity in the purine series described herein. Several 2-amino and 2-chloro purine analogs were also synthesized that showed moderate inhibitory activity against Mtb.
doi:10.1016/j.bmc.2013.01.054
PMCID: PMC3612542  PMID: 23434367
Mycobacterium tuberculosis; Purines; Antimycobacterial agents
6.  Small-Molecule Inhibition of the uPAR·uPA Interaction: Synthesis, Biochemical, Cellular, in vivo Pharmacokinetics and Efficacy Studies in Breast Cancer Metastasis 
Bioorganic & medicinal chemistry  2013;21(7):2145-2155.
The uPAR·uPA protein-protein interaction (PPI) is involved in signaling and proteolytic events that promote tumor invasion and metastasis. A previous study had identified 4 (IPR-803) from computational screening of a commercial chemical library and shown that the compound inhibited uPAR·uPA PPI in competition biochemical assays and invasion cellular studies. Here, we synthesize 4 to evaluate in vivo pharmacokinetic (PK) and efficacy studies in a murine breast cancer metastasis model. First, we show, using fluorescence polarization and saturation transfer difference (STD) NMR, that 4 binds directly to uPAR with sub-micromolar affinity of 0.2 μM. We show that 4 blocks invasion of breast MDA-MB-231, and inhibits matrix metalloproteinase (MMP) breakdown of the extracellular matrix (ECM). Derivatives of 4 also inhibited MMP activity and blocked invasion in a concentration-dependent manner. 4 also impaired MDA-MB-231 cell adhesion and migration. Extensive in vivo PK studies in NOD-SCID mice revealed a half-life of nearly 5 hours and peak concentration of 5 μM. Similar levels of the inhibitor were detected in tumor tissue up to 10 hours. Female NSG mice inoculated with highly malignant TMD-MDA-MB-231 in their mammary fat pads showed that 4 impaired metastasis to the lungs with only four of the treated mice showing severe or marked metastasis compared to ten for the untreated mice. Compound 4 is a promising template for the development of compounds with enhanced PK parameters and greater efficacy.
doi:10.1016/j.bmc.2012.12.047
PMCID: PMC3625246  PMID: 23411397
7.  Design and synthesis of glycoprotein-based multivalent glyco-ligands for influenza hemagglutinin and human galectin-3 
Bioorganic & medicinal chemistry  2013;21(7):2037-2044.
We report a facile synthesis of glycoprotein-based glyco-ligands and their binding with influenza hemagglutinin and human galectin-3. Human serum albumin (HSA) was used as the scaffold and an Asn-linked complex type N-glycan prepared from chicken eggs was used as the glycan building block. It was found that Cu(I)-catalyzed alkyne–azide cycloaddition reaction (click chemistry) between the alkyne-labeled glycan and the azide-tagged HSA led to an efficient formation of the glycoconjugates. The density of glycan ligands on the protein scaffold was readily varied by changing the molar ratios of the two reactants. Binding studies indicated that the sialylated and desialylated multivalent glycoligands could selectively bind to influenza hemagglutinin and human galectin-3, respectively, with high affinity. In the two glycan–lectin interactions, a clear multivalent effect was observed. Moreover, a cell-based assay showed that the synthetic multivalent glyco-ligands could efficiently inhibit the attachment of galectin-3 to human prostate cancer and lung cancer cell lines. This study suggests that the synthetic glycoprotein-based glyco-ligands can be useful for different applications, including blocking the function of galectin-3 in cancer metastasis.
doi:10.1016/j.bmc.2013.01.028
PMCID: PMC3737422  PMID: 23411399
Glycoprotein; Conjugation; Glyco-ligand; Galectin-3; Hemagglutinin; Multivalent inhibitor; Influenza; Cancer metastasis
8.  Fluorescent schweinfurthin B and F analogues with anti-proliferative activity 
Bioorganic & medicinal chemistry  2010;18(18):6734-6741.
The natural tetracyclic schweinfurthins are potent and selective inhibitors of cell growth in the National Cancer Institute’s 60-cell line screen. Most of the natural schweinfurthins display unique and potent activity in the 60 cell-line screen of the National Cancer Institute. At this time, the mechanism or cellular target that underlies this activity has not yet been identified, and efforts to illuminate the schweinfurthins’ mode of action would benefit from development of potent fluorescent analogues that could be readily visualized within cells. This report describes the synthesis of fluorescent analogues of schweinfurthins B and F, and demonstrates that these compounds retain the potent and differentially toxic activities against select human cancer cells that are characteristic of the natural schweinfurthins. In addition, the synthesis of control compounds that maintain parallel fluorescent properties, but lack the potent activity of the natural schweinfurthin is described. Use of fluorescence microscopy shows differences between the localization of the active and re latively inactive schweinfurthin analogues. The active compounds localize in peripheral puncta which may identify the site (or sites) of activity.
doi:10.1016/j.bmc.2010.07.056
PMCID: PMC3967504  PMID: 20724169
9.  Improved synthesis of 17β-hydroxy-16α-iodo-wortmannin, 17β-hydroxy-16α-iodoPX866, and the [131I] analogue as useful PET tracers for PI3-kinase 
Bioorganic & medicinal chemistry  2013;21(17):5182-5187.
An improved method for the synthesis of 17β-hydroxy-16α-iodo-wortmannin along with the first synthesis of 17β-hydroxy-16α-iodoPX866 and [131I] radiolabeled 17β-hydroxy-16α-[131I]iodo-wortmannin, as potential PET tracers for PI3K was also described. The differences between wortmannin and its iodo analogue were compared by covalently docking each structure to L833 in PI3K.
doi:10.1016/j.bmc.2013.06.036
PMCID: PMC3960976  PMID: 23859776
PI3 kinase; Positron emission tomography (PET); imaging; 17β-Hydroxy-16α-iodowortmannin; 17β-Hydroxy-16α-iodoPX866; 17β-Hydroxy-16α-[131I]iodowortmannin
10.  INSIGHTS TOWARDS SULFONAMIDE DRUG SPECIFICITY IN α-CARBONIC ANHYDRASES 
Bioorganic & medicinal chemistry  2012;21(6):1526-1533.
Carbonic anhydrases (CAs, EC 4.2.1.1) are a group of metalloenzymes that play important roles in carbon metabolism, pH regulation, CO2 fixation in plants, ion transport etc., and are found in all eukaryotic and many microbial organisms. This family of enzymes catalyzes the interconversion of CO2 and HCO3−. There are at least 16 different CA isoforms in the alpha structural class (α-CAs) that have been isolated in higher vertebrates, with CA isoform II (CA II) being ubiquitously abundant in all human cell types. CA inhibition has been exploited clinically for decades for various classes of diuretics and anti-glaucoma treatment. The characterization of the overexpression of CA isoform IX (CA IX) in certain tumors has raised interest in CA IX as a diagnostic marker and drug target for aggressive cancers and therefore the development of CA IX specific inhibitors. An important goal in the field of CA is to identify, rationalize, and design potential compounds that will preferentially inhibit CA IX over all other isoforms of CA. The variations in the active sites between isoforms of CA are subtle and this causes non-specific CA inhibition which leads to various side effects. In the case of CA IX inhibition, CA II along with other isoforms of CA provide off-target binding sites which is undesirable for cancer treatment. The focus of this article is on CA IX inhibition and two different structural approaches to CA isoform specific drug designing: tail approach and fragment addition approach.
doi:10.1016/j.bmc.2012.08.019
PMCID: PMC3593968  PMID: 22985956
11.  3-Phenyl substituted 6,7-dimethoxyisoquinoline derivatives as FtsZ-targeting antibacterial agents 
Bioorganic & medicinal chemistry  2012;20(24):7012-7029.
The emergence of multidrug-resistant bacteria has created an urgent need for antibiotics with a novel mechanism of action. The bacterial cell division protein FtsZ is an attractive target for the development of novel antibiotics. The benzo[c]phenanthridinium sanguinarine and the dibenzo[a,g]quinolizin-7-ium berberine are two structurally similar plant alkaloids that alter FtsZ function. The presence of a hydrophobic functionality at either the 1-position of 5-methylbenzo[c]phenanthridinium derivatives or the 2-position of dibenzo[a,g]quinolizin-7-ium derivatives is associated with significantly enhanced antibacterial activity. 3-Phenylisoquinoline represents a subunit within the ring-systems of both of these alkaloids. Several 3-phenylisoquinolines and 3-phenylisoquinolinium derivatives have been synthesized and evaluated for antibacterial activity against Staphylococcus aureus and Enterococcus faecalis, including multidrug-resistant strains of methicillin-resistant S. aureus (MRSA) and vancomycin-resistant E. faecalis (VRE). A number of derivatives were found to have activity against both MRSA and VRE. The binding of select compounds to S. aureus FtsZ (SaFtsZ) was demonstrated and characterized using fluorescence spectroscopy. In addition, the compounds were shown to act as stabilizers of SaFtsZ polymers and concomitant inhibitors of SaFtsZ GTPase activity. Toxicological assessment of select compounds revealed minimal cross-reaction mammalian β-tubulin as well as little or no human cytotoxicity.
doi:10.1016/j.bmc.2012.10.009
PMCID: PMC3947851  PMID: 23127490
Antibacterial; Isoquinoline; FtsZ-targeting; Cytotoxicity; Staphylococcus aureus; Enterococcus faecalis
12.  Evaluation of adamantane hydroxamates as botulinum neurotoxin inhibitors: synthesis, crystallography, modeling, kinetic and cellular based studies 
Bioorganic & medicinal chemistry  2012;21(5):1344-1348.
Botulinum neurotoxins (BoNTs) are the most lethal biotoxins known to mankind and are responsible for the neuroparalytic disease botulism. Current treatments for botulinum poisoning are all protein based and thus have a limited window of treatment opportunity. Inhibition of the BoNT light chain protease (LC) has emerged as a therapeutic strategy for the treatment of botulism as it may provide an effective post exposure remedy. Using a combination of crystallographic and modeling studies a series of hydroxamates derived from 1-adamantylacetohydroxamic acid (3a) were prepared. From this group of compounds, an improved potency of about 17-fold was observed for two derivatives. Detailed mechanistic studies on these structures revealed a competitive inhibition model, with a Ki = 27 nM, which makes these compounds some of the most potent small molecule, non-peptidic BoNT/A LC inhibitors reported to date.
doi:10.1016/j.bmc.2012.12.001
PMCID: PMC3574188  PMID: 23340139
Botulinum neurotoxin; Protease inhibitor; Adamantane derivatives; Small molecule inhibitor; Zinc-dependent metalloprotease
13.  Cyclopropyl- and Methyl-Containing Inhibitors of Neuronal Nitric Oxide Synthase 
Bioorganic & medicinal chemistry  2012;21(5):1333-1343.
Inhibitors of neuronal nitric oxide synthase have been proposed as therapeutics for the treatment of different types of neurological disorders. On the basis of a cis-3,4-pyrrolidine scaffold, a series of trans-cyclopropyl- and methyl-containing nNOS inhibitors have been synthesized. The insertion of a rigid electron-withdrawing cyclopropyl ring decreases the basicity of the adjacent amino group, which resulted in decreased inhibitory activity of these inhibitors compared to the parent compound. Nonetheless, three of them exhibited double-digit nanomolar inhibition with high nNOS selectivity on the basis of in vitro enzyme assays. Crystal structures of nNOS and eNOS with these inhibitors bound provide a basis for detailed structure-activity relationship (SAR) studies. The conclusions from these studies will be used as a guide in the future development of selective NOS inhibitors.
doi:10.1016/j.bmc.2012.12.019
PMCID: PMC3574199  PMID: 23352768
Neuronal nitric oxide synthase; inhibition; isozyme selectivity; cyclopropyl analogues; X-ray crystallography
14.  N2-Trimethylacetyl substituted and unsubstituted-N4-phenylsubstituted-6-(2-pyridin-2-ylethyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamines: Design, cellular receptor tyrosine kinase inhibitory activities and in vivo evaluation as antiangiogenic, antimetastatic and antitumor agents 
Bioorganic & medicinal chemistry  2013;21(5):1312-1323.
Six novel N4-phenylsubstituted-6-(2-pyridin-2-ylethyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamines and their N2-trimethylacetyl substituted analogs were synthesized as receptor tyrosine kinase (RTK) inhibitors. A microwave-mediated Sonogashira reaction was used as a key step for the synthesis of these compounds. Biological evaluation, in whole cell assays, showed that some analogs had remarkable inhibitory activity against a variety of RTKs and in particular cytotoxic activity against A431 tumor cells in culture. The inhibitory data against RTKs in this study demonstrated that variation of the 4-anilino substituents of thse analogs dictates both potency and specificity of inhibitory activity against various RTKs. The study also supported the hypothesis that interaction of substituents on the 2-amino group with hydrophobic site-II provides an increase in potency. Compound 8 of this series was selected for evaluation in vivo in a B16-F10 syngeneic mouse tumor model and exhibited significant reduction in tumor growth rate, in tumor vascular density and in metastases to the lung compared to the control.
doi:10.1016/j.bmc.2012.12.045
PMCID: PMC3574204  PMID: 23375090
15.  Secondary Amines Containing One Aromatic Nitro Group: Preparation, Nitrosation, Sustained Nitric Oxide Release, and the Synergistic Effects of Released Nitric Oxide and an Arginase Inhibitor on Vascular Smooth Muscle Cell Proliferation 
Bioorganic & medicinal chemistry  2013;21(5):1123-1135.
Atherosclerosis, a leading cause of death worldwide, is associated with the excessive proliferation of vascular smooth muscle cells. Nitrogen monoxide, more commonly known as nitric oxide, inhibits this uncontrolled proliferation. Herein we report the preparation of two families of nitric oxide donors; beginning with the syntheses of secondary amine precursors, obtained through the reaction between two equivalents of various monoamines with 2,4 or 2,6-difluoronitrobenzene. The purified secondary amines were nitrosated then subjected to a Griess reagent test to examine the slow and sustained nitric oxide release rate for each compound in both the absence and presence of reduced glutathione. The release rate profiles of these two isomeric families of NO-donors were strongly dependent on the number of side chain methylene units and the relative orientations of the nitro groups with respect to the N-nitroso moieties. The nitrosated compounds were then added to human aortic smooth muscle cell cultures, individually and in tandem with S-2-amino-6-boronic acid (ABH), a potent arginase inhibitor. Cell viability studies indicated a lack of toxicity of the amine precursors, in addition to anti-proliferative effects exhibited by the nitrosated compounds, which were enhanced in the presence of ABH.
doi:10.1016/j.bmc.2012.12.043
PMCID: PMC3574223  PMID: 23375096
Sustained Nitric Oxide Release; Cell Culture Study; Smooth Muscle Cell Proliferation Inhibition
16.  Synthesis of 5,7-disubstituted-4-methyl-7H-pyrrolo[2, 3-d]pyrimidin-2-amines as microtubule inhibitors 
Bioorganic & medicinal chemistry  2013;21(5):1180-1189.
Compounds 1-4 were previously reported as potent antimitotic and antitumor agents with Pgp modulatory effects. Compounds 5-18 have been synthesized in an attempt to optimize the various activities of 1-4. Compounds 5-10 explored the influence of methoxy substitutions on the 7-benzyl moiety in 1, while 11-18 investigated the influence of incorporation of a sulfur linker at C5 compared to 1-3. Compounds 5-10 demonstrated potent single-digit micromolar tumor cell cytotoxicity, Pgp modulation and microtubule inhibition. Compound 7 of this series was the most potent and showed GI50 values in the nanomolar range against several human tumor cell lines in the standard NCI preclinical in vitro screen. Antitumor activity and Pgp modulatory effects were found to decrease for the 5-phenylthio compounds 11-14 compared to their 5-phenylethyl analogs 2-4 and the standard compound Taxol. Incorporation of methoxy substitutions on the 7-benzyl moiety improved antitumor activity for the 5-phenylthio compounds 16 and 17. Compounds 16 and 17 demonstrated single to two-digit micromolar inhibition of tumor cells.
doi:10.1016/j.bmc.2012.12.029
PMCID: PMC3582361  PMID: 23352482
Pyrrolo[2,3-d]pyrimidines; Microtubule inhibitors; Microwave assisted organic synthesis
17.  Selection of heptapeptides that bind helix 69 of bacterial 23S ribosomal RNA 
Bioorganic & medicinal chemistry  2013;21(5):1240-1247.
Helix 69 of E. coli 23S rRNA has important roles in specific steps of translation, such as subunit association, translocation, and ribosome recycling. An M13 phage library was used to identify peptide ligands with affinity for helix 69. One selected sequence, NQVANHQ, was shown through a bead assay to interact with helix 69. Electrospray ionization mass spectroscopy revealed an apparent dissociation constant for the amidated peptide and helix 69 in the low micromolar range. This value is comparable to that of aminoglycoside antibiotics binding to the A site of 16S rRNA or helix 69. Helix 69 variants (human) and unrelated RNAs (helix 31 or A site of 16S rRNA) showed two- to four-fold lower affinity for NQVANHQ-NH2. These results suggest that the peptide has desirable features for development as a lead compound for novel antimicrobials.
doi:10.1016/j.bmc.2012.12.048
PMCID: PMC3594512  PMID: 23375098
RNA; modified nucleotides; pseudouridine; antibiotics; phage display
18.  Development of a new class of aromatase inhibitors: Design, synthesis and inhibitory activity of 3-phenylchroman-4-one (isoflavanone) derivatives 
Bioorganic & medicinal chemistry  2012;20(8):2603-2613.
Aromatase (CYP19) catalyzes the aromatization reaction of androgen substrates to estrogens, the last and rate-limiting step in estrogen biosynthesis. Inhibition of aromatase is a new and promising approach to treat hormone-dependent breast cancer. We present here the design and development of isoflavanone derivatives as potential aromatase inhibitors. Structural modifications were performed on the A and B rings of isoflavanones via microwave-assisted, gold-catalyzed annulation reactions of hydroxyaldehydes and alkynes. The in vitro aromatase inhibition of these compounds was determined by fluorescence-based assays utilizing recombinant human aromatase (baculovirus/insect cell-expressed). The compounds 3-(4-phenoxyphenyl)chroman-4-one (1h), 6-methoxy-3-phenylchroman-4-one (2a) and 3-(pyridin-3-yl)chroman-4-one (3b) exhibited potent inhibitory effects against aromatase with IC50 values of 2.4 μM, 0.26 μM and 5.8 μM, respectively. Docking simulations were employed to investigate crucial enzyme/inhibitor interactions such as hydrophobic interactions, hydrogen bonding and heme iron coordination. This report provides useful information on aromatase inhibition and serves as a starting point for the development of new flavonoid aromatase inhibitors.
doi:10.1016/j.bmc.2012.02.042
PMCID: PMC3933949  PMID: 22444875
Breast cancer; Aromatase inhibitors; Isoflavanones
19.  Probing the steric requirements of the γ-aminobutyric acid aminotransferase active site with fluorinated analogues of vigabatrin 
Bioorganic & medicinal chemistry  2012;21(4):903-911.
We have synthesized three analogues of 4-amino-5-fluorohexanoic acids as potential inactivators of γ-aminobutyric acid aminotransferase (GABA-AT), which were designed to combine the potency of their shorter chain analogue, 4-amino-5-fluoropentanoic acid (AFPA), with the greater enzyme selectivity of the antiepileptic vigabatrin (Sabril®). Unexpectedly, these compounds failed to inactivate or inhibit the enzyme, even at high concentrations. On the basis of molecular modeling studies, we propose that the GABA-AT active site has an accessory binding pocket that accommodates the vinyl group of vigabatrin and the fluoromethyl group of AFPA, but is too narrow to support the extra width of one distal methyl group in the synthesized analogues.
doi:10.1016/j.bmc.2012.12.009
PMCID: PMC3563932  PMID: 23306054
γ-Aminobutyric acid aminotransferase; Vigabatrin; 4-amino-5-fluoropentanoic acid; enzyme inhibition; Molecular dynamics
20.  Synthesis of N4-(Substituted phenyl)-N4-alkyl/desalkyl-9H-pyrimido[4,5-b]indole-2,4-diamines and Identification of New Microtubule Disrupting Compounds that are Effective against Multidrug Resistant Cells1 
Bioorganic & medicinal chemistry  2012;21(4):891-902.
A series of fourteen N4-(substituted phenyl)-N4-methyl/desmethyl-9H-pyrimido[4,5-b]indole-2,4-diamines was synthesized as potential microtubule targeting agents. The synthesis involved a Fisher indole cyclization of 2-amino-6-hydrazinylpyrimidin-4(3H)-one with cyclohexanone, followed by oxidation, chlorination and displacement with appropriate anilines. Compounds 6, 14 and 15 had low nanomolar potency against MDA-MB-435 tumor cells and depolymerized microtubules. Compound 6 additionally had nanomolar GI50 values against 57 of the NCI 60-tumor panel cell lines. Mechanistic studies showed that 6 inhibited tubulin polymerization and [3H]colchicine binding to tubulin. The most potent compounds were all effective in cells expressing P-glycoprotein or the βIII isotype of tubulin, which have been associated with clinical drug reisistence. Modeling studies provided the potential interactions of 6, 14 and 15 within the colchicine site.
doi:10.1016/j.bmc.2012.12.010
PMCID: PMC3572549  PMID: 23332369
21.  QSAR study on maximal inhibition (Imax) of quaternary ammonium antagonists for S-(−)-nicotine-evoked dopamine release from dopaminergic nerve terminals in rat striatum 
Bioorganic & medicinal chemistry  2009;17(13):4477-4485.
Maximal inhibition (Imax) of the agonist effect is an important pharmacological property of inhibitors that interact with multiple receptor subtypes that are activated by the same agonist and which elicit the same functional response. This report represents the first QSAR study on a set of 66 mono- and bis-quaternary ammonium salts that act as antagonists at neuronal nicotinic acetylcholine receptors mediating nicotine-evoked dopamine release, conducted using multi-linear regression (MLR) and neural network (NN) analysis with the maximal inhibition (Imax) values of the antagonists as target values. The statistical results for the generated MLR model were: r2 = 0.89, rmsd = 9.01, q2 = 0.83 and loormsd = 11.1; the statistical results for the generated NN model were: r2 = 0.89, rmsd = 8.98, q2 = 0.83 and loormsd = 11.2. The maximal inhibition values of the compounds exhibited a good correlation with the predictions made by the QSAR models developed, which provide a basis for rationalizing selection of compounds for synthesis in the discovery of effective and selective second generation inhibitors of nAChRs mediating nicotine-evoked dopamine release.
doi:10.1016/j.bmc.2009.05.010
PMCID: PMC3914672  PMID: 19477134
QSAR study; Nicotinic receptors; Antagonists; Maximal inhibition
22.  Structure-based drug design and potent anti-cancer activity of tricyclic 5:7:5-fused diimidazo[4,5-d:4′,5′-f][1,3]diazepines 
Bioorganic & medicinal chemistry  2012;21(3):618-631.
Judicial structural modifications of 5:7-fused ring-expanded nucleosides (RENs), based on molecular modeling studies with one of its known targets, human RNA helicase (hDDX3), led to the lead, novel, 5:7-5-fused tricyclic heterocycle (1). The latter exhibited promising broad-spectrum in vitro anticancer activity against a number of cancer cell lines screened. This paper describes our systematic, albeit limited, structure-activity relationship (SAR) studies on this lead compound, which produced a number of analogs with broad-spectrum in vitro anticancer activities against lung, breast, prostate, and ovarian cancer cell lines, in particular compounds 15i, 15j, 15m and 15n which showed IC50 values in submicromolar to micromolar range, and are worthy of further explorations. The SAR data also enabled us to propose a tentative SAR model for future SAR efforts for ultimate realization of optimally active and minimally toxic anticancer compounds based on the diimidazo[4,5-d:4′,5′-f][1,3]diazepine structural skeleton of the lead compound 1.
doi:10.1016/j.bmc.2012.11.050
PMCID: PMC3546142  PMID: 23290252
Organic synthesis and medicinal chemistry; Diimidazo[4, 5-d:4′, 5′-f][1, 3]diazepines; Anti-cancer activity; Lung, breast, prostate and ovarian cancers; In vitro screening; Structure-activity relationship (SAR) studies; DDX3 as potential target
23.  Synthesis and Biological Evaluation of N-Alkyl-N-(4-methoxyphenyl)pyridin-2-amines as a New Class of Tubulin Polymerization Inhibitors 
Bioorganic & medicinal chemistry  2012;21(3):632-642.
Based on our prior antitumor hits, 32 novel N-alkyl-N-substituted phenylpyridin-2-amine derivatives were designed, synthesized and evaluated for cytotoxic activity against A549, KB, KBVIN, and DU145 human tumor cell lines (HTCL). Subsequently, three new leads (6a, 7g, and 8c) with submicromolar GI50 values of 0.19 to 0.41 μM in the cellular assays were discovered, and these compounds also significantly inhibited tubulin assembly (IC50 1.4–1.7 μM) and competitively inhibited colchicine binding to tubulin with effects similar to those of the clinical candidate CA-4 in the same assays. These promising results indicate that these tertiary diarylamine derivatives represent a novel class of tubulin polymerization inhibitors targeting the colchicine binding site and showing significant anti-proliferative activity.
doi:10.1016/j.bmc.2012.11.047
PMCID: PMC3546147  PMID: 23274123
N-alkyl-N-phenylpyridin-2-amines; cytotoxicity; tubulin polymerization inhibitors; colchicine binding site
24.  Enhanced Bioactivity of Silybin B Methylation Products 
Bioorganic & medicinal chemistry  2012;21(3):742-747.
Flavonolignans from milk thistle (Silybum marianum) have been investigated for their cellular modulatory properties, including cancer chemoprevention and hepatoprotection, as an extract (silymarin), as partially purified mixtures (silibinin and isosilibinin), and as pure compounds (a series of seven isomers). One challenge with the use of these compounds in vivo is their relatively short half-life due to conjugation, particularly glucuronidation. In an attempt to generate analogues with improved in vivo properties, particularly reduced metabolic liability, a semi-synthetic series was prepared in which the hydroxy groups of silybin B were alkylated. A total of five methylated analogues of silybin B were synthesized using standard alkylation conditions (dimethyl sulfate and potassium carbonate in acetone), purified using preparative HPLC, and elucidated via spectroscopy and spectrometry. Of the five, one was monomethylated (3), one was dimethylated (4), two were trimethylated (2 and 6), and one was tetramethylated (5). The relative potency of all compounds was determined in a 72 hr growth-inhibition assay against a panel of three prostate cancer cell lines (DU-145, PC-3, and LNCaP) and a human hepatoma cell line (Huh7.5.1) and compared to natural silybin B. Compounds also were evaluated for inhibition of both cytochrome P450 2C9 (CYP2C9) activity in human liver microsomes and hepatitis C virus infection in Huh7.5.1 cells. The monomethyl and dimethyl analogues were shown to have enhanced activity in terms of cytotoxicity, CYP2C9 inhibitory potency, and antiviral activity (up to 6-fold increased potency) compared to the parent compound, silybin B. In total, these data suggested that methylation of flavonolignans can increase bioactivity.
doi:10.1016/j.bmc.2012.11.035
PMCID: PMC3630461  PMID: 23260576
Silybin B; Milk thistle; Silybum marianum; Flavonolignans; Methylation
25.  Synthesis and Cellular Studies of Polyamine Conjugates of a Mercaptomethyl-carboranylporphyrin1 
Bioorganic & medicinal chemistry  2012;21(2):485-495.
Seven polyamine conjugates of a tri(p-carboranylmethylthio)tetrafluorophenylporphyrin were prepared in high yields by sequential substitution of the p-phenyl fluoride of tetrakis(pentafluorophenyl)porphyrin (TPPF), and investigated as boron delivery agents for boron neutron capture therapy (BNCT). The polyamines used were derivatives of the natural-occurring spermine with different lengths of the carbon chains, terminal primary amine groups and, in two of the conjugates, additional aminoethyl moieties. A tri(polyethylene glycol) conjugate was also synthesized for comparison purposes. The polyamine conjugates showed low dark cytotoxicity (IC50 > 400 μM) and low phototoxicity (IC50 > 40 μM at 1.5 J/cm2). All polyamine conjugates, with one exception, showed higher uptake into human glioma T98G cells (up to 12-fold) than the PEG conjugate, and localized preferentially in the cell ER, Golgi and the lysosomes. Our results show that spermine derivatives can serve as effective carriers of boronated porphyrins for the BNCT of tumors.
doi:10.1016/j.bmc.2012.11.007
PMCID: PMC3547609  PMID: 23219853
BNCT; polyamine; PDT; carborane; porphyrin

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