Through our focused effort to discover new and effective agents against toxoplasmosis, a structure-based drug design approach was utilized to develop a series of potent inhibitors of the enoyl-acyl carrier protein (ACP) reductase (ENR) enzyme in Toxoplasma gondii (TgENR). Modifications to positions 5 and 4′ of the well-known ENR inhibitor triclosan afforded a series of 29 new analogs. Among the resulting compounds, many showed high potency and improved physicochemical properties in comparison with the lead. The most potent compounds 16a and 16c have IC50 values of 250 nM against Toxoplasma gondii tachyzoites without apparent toxicity to the host cells. Their IC50 values against the recombinant TgENR were 43 and 26 nM, respectively. Additionally, 11 other analogs in this series had IC50 values ranging from 17 to 130 nM in the enzyme-based assay.
With respect to their excellent in vitro activity as well as improved drug-like properties, the lead compounds 16a and 16c are deemed to be an excellent starting point for the development of new medicines to effectively treat Toxoplasma gondii infections.
Enoyl Reductase; Inhibitors; Medicinal Chemistry; Toxoplasma gondii; triclosan
A series of analogs of the adamantyl arotinoid (AdAr) chalcone 5 (MX781) having halogenated benzyloxy substituents at C2′ and heterocyclic derivatives replacing the chalcone group were found to inhibit IκBα kinase α (IKKα) and IκBα kinase β (IKKβ) activities. The growth inhibitory activity of some analogs against Jurkat T cells as well as prostate carcinoma cells (PC-3) and chronic myelogenous leukemia cells (K562), which contain elevated basal IKK activity, correlates with induction of apoptosis and increased inhibition of recombinant IKKα and IKKβ in vitro, pointing towards inhibition of IKK/NFκB signaling as the most likely target of the anticancer activities of these AdArs. While the chalcone functional group present in many dietary compounds has been shown to mediate interactions with IKKβ via Michael addition with cysteine residues, AdArs containing five-membered heterocyclic ring (isoxazoles and pyrazoles) in place of the chalcone of the parent system are potent inhibitors of IKKs as well, which suggests that other mechanisms for inhibition exist that do not depend on the presence of a reactive α,β-unsaturated ketone.
Adamantyl arotinoids; chalcones; synthesis; kinase activities; IKK
Disulfide bridges, which stabilize the native conformation of conotoxins impose a challenge in the synthesis of smaller analogs. In this work, we describe the synthesis of a minimized analog of the analgesic μ-conotoxin KIIIA that blocks two sodium channel subtypes, the neuronal NaV1.2 and skeletal muscle NaV1.4. Three disulfide-deficient analogs of KIIIA were initially synthesized in which the native disulfide bridge formed between either C1-C9, C2-C15 or C4-C16 was removed. Deletion of the first bridge only slightly affected the peptide’s bioactivity. To further minimize this analog, the N-terminal residue was removed and two non-essential Ser residues were replaced by a single 5-amino-3-oxapentanoic acid residue. The resulting “polytide” analog retained the ability to block sodium channels and to produce analgesia. Until now, the peptidomimetic approach applied to conotoxins has progressed only modestly at best; thus, the disulfide-deficient analogs containing backbone spacers provide an alternative advance toward the development of conopeptide-based therapeutics.
conopeptide; conotoxin; sodium channels; backbone spacers; disulfide bridges
The unwanted psychoactive effects of cannabinoid receptor agonists have limited their development as medicines. These CB1 mediated side effects are due to the fact that CB1 receptors are largely expressed in the Central Nervous System (CNS). Since it is known that CB1 receptors are also located peripherally, there is a growing interest in targeting cannabinoid receptors located outside the brain. A library of chromenopyrazoles designed in analogy to the classical cannabinoid cannabinol were synthesized, characterized and tested for cannabinoid activity. Radiolabeled binding assays were used to determine their affinities at CB1 and CB2 receptors. Structural features required for CB1/CB2 affinity and selectivity were explored using molecular modeling. Within the chromenopyrazoles series, some of them showed to be selective CB1 ligands. These modeling studies suggest that CB1 full selectivity over CB2 can be accounted for the presence of a pyrazole ring in the structure. The functional activities of selected chromenopyrazoles were evaluated in isolated tissues. Behavioral tests, in vivo, were then carried on the most effective CB1 cannabinoid agonist (13a). Chromenopyrazole 13a did not induce modifications in any of the tested parameters on the mouse cannabinoid tetrad, discarding CNS-mediated effects. This lack of agonistic activity in the CNS suggests that it does not readily cross the blood-brain barrier. Moreover, compound 13a can induce antinociception in a peripheral model of orofacial pain in rat. Taking into account the negative results obtained in the hot plate test, it could be suggested that the antinociception induced by 13a in the orofacial test may be mediated through peripheral mechanisms.
agonist; cannabinoid; peripheral; protein model; receptor
visible light; antiproliferation; singlet oxygen; organometallic complexes; rhenium
A facile hydroxyindole carboxylic acid-based focused amide library approach was designed to target both the PTP active site and a unique nearby pocket for enhanced affinity and selectivity. High throughput screening of the focused library let to the identification of a highly potent (Ki=50 nM) and selective (>100-fold against a large panel of PTPs) inhibitor 11a for mPTPB, an essential virulence factor for Mycobacterium tuberculosis. Importantly, 11a displayed highly efficacious cellular activity and was capable of reversing the altered immune responses induced by mPTPB in macrophages.
Focused amide library; HydroxyIndole carboxylic acid; PTP; mPTPB inhibitor; Tuberculosis
A reversible, reaction-based sensor for biological mobile zinc was designed, prepared, and characterized. The sensing mechanism of this probe is based on the zinc-induced, ring-opening reaction of spirobenzopyran to give a cyanine fluorophore that emits in the deep-red region of the electromagnetic spectrum. This probe is not activated by protons and operates efficiently in aqueous solution at pH 7 and high ionic strength. The mechanism of this reaction was studied by using a combination of kinetics experiments and DFT calculations. The biocompatibility of the probe was demonstrated in live HeLa cells.
Bioinorganic chemistry; Biosensors; Coordination chemistry; Spirobenzopyran
Recently, we described the aminothiazole lead (4-biphenyl-4-yl-thiazol-2-yl)-(6-methyl-pyridin-2-yl)-amine (1), which exhibits many desirable properties, including excellent stability in liver microsomes, oral bioavailability of ∼40% and high exposure in the brains of mice. Despite its good pharmacokinetic properties, compound 1 exhibited only modest potency in mouse neuroblastoma cells overexpressing the disease-causing prion protein PrPSc. Accordingly, we sought to identify analogs of 1 with improved antiprion potency in ScN2a-cl3 cells while retaining comparable or superior properties. We now report the discovery of improved lead compounds such as (6-methyl-pyridin-2-yl)-[4-(4-pyridin-3-yl-phenyl)-thiazol-2-yl]-amine (15) and cyclopropanecarboxylic acid (4-biphenyl-thiazol-2-yl)-amide (34), which exhibited brain exposure/EC50 ratios at least ten-fold greater than that of 1.
2-Aminothiazoles; neurological agents; pharmacokinetic optimization; prion disease; structure-activity relationships
The interaction of CXCR4 with CXCL12 (SDF-1) plays a critical role in cancer metastasis by facilitating the homing of tumor cells to metastatic sites. Based on our previously published work on CXCR4 antagonists, we have synthesized a series of aryl sulfonamides that inhibit the CXCR4/CXCL12 interaction. Analog bioactivities were assessed with binding affinity and Matrigel invasion assays. Computer modeling was employed to evaluate a selection of the new analogs docked into the CXCR4 X-ray structure and to rationalize discrepancies between the affinity and Matrigel in vitro assays. A lead compound 5a displays subnanomolar potency in the binding affinity assay (IC50 = 8.0 nM) and the Matrigel invasion assay (100% blockade of invasion at 10 nM). These data demonstrate that benzenesulfonamides are a unique class of CXCR4 antagonists with high potency.
CXCR4 inhibitors; metastasis; sulfonamides; inflammation
Malaria is a potentially fatal disease caused by Plasmodium parasites and poses a major medical risk in large parts of the world. The development of new, affordable antimalarial drugs is of vital importance as there are increasing reports of resistance to the currently available therapeutics. In addition, most of the current drugs used for chemoprophylaxis merely act on parasites already replicating in the blood. At this point, a patient might already be suffering from the symptoms associated with the disease and could additionally be infectious to an Anopheles mosquito. These insects act as a vector, subsequently spreading the disease to other humans. In order to cure not only malaria but prevent transmission as well, a drug must target both the blood- and pre-erythrocytic liver stages of the parasite. P. falciparum (Pf) enoyl acyl carrier protein (ACP) reductase (ENR) is a key enzyme of plasmodial type II fatty acid biosynthesis (FAS II). It has been shown to be essential for liver-stage development of Plasmodium berghei and is therefore qualified as a target for true causal chemoprophylaxis. Using virtual screening based on two crystal structures of PfENR, we identified a structurally novel class of FAS inhibitors. Subsequent chemical optimization yielded two compounds that are effective against multiple stages of the malaria parasite. These two most promising derivatives were found to inhibit blood-stage parasite growth with IC50 values of 1.7 and 3.0 µm and lead to a more prominent developmental attenuation of liver-stage parasites than the gold-standard drug, primaquine.
antimalarial agents; fatty acid biosynthesis; molecular modeling; multistage inhibitors; Plasmodium falciparum; virtual screening
The carboxylic acid functional group can be an important constituent of a pharmacophore, however, the presence of this moiety can also be responsible for significant drawbacks, including metabolic instability, toxicity, as well as limited passive diffusion across biological membranes. To avoid some of these shortcomings while retaining the desired attributes of the carboxylic acid moiety, medicinal chemists often investigate the use of carboxylic acid (bio)isosteres. The same type of strategy can also be effective for a variety other purposes, for example, to increase the selectivity of a biologically active compound or to create new intellectual property. Several carboxylic acid isosteres have been reported, however, the outcome of any isosteric replacement cannot be readily predicted as this strategy is generally found to be dependent upon the particular context (i.e., the characteristic properties of the drug and the drug–target). As a result, screening of a panel of isosteres is typically required. In this context, the discovery and development of novel carboxylic acid surrogates that could complement the existing palette of isosteres remains an important area of research. The goal of this Minireview is to provide an overview of the most commonly employed carboxylic acid (bio)isosteres and to present representative examples demonstrating the use and utility of each isostere in drug design.
bioisosteres; carboxylic acids; drug design; isosteric replacement
The reactivity of three cytotoxic trans-PtII complexes bearing aliphatic amine ligands, with transferrin and single-stranded oligonucleotides as DNA models, was investigated by ESI-MS and the results obtained are discussed in comparison with cisplatin. Tandem MS studies provided additional information on the preferential Pt binding sites. To determine whether trans-PtII complexes can migrate from a peptide to an oligonucleotide, transfer experiments were also performed using ESI-MS, and competitive binding of the trans-PtII complexes toward a model peptide and different oligonucleotides was also investigated. Significant differences in the reactivity of the trans complexes with respect to cisplatin were observed. In general, adduct formation with the selected peptide is favored for the trans compounds, whereas cisplatin shows a preference for oligonucleotides, especially if adjacent G–G residues are present. The results are discussed in relation to the possible mechanism of action of the trans-PtII complexes.
cancer; mass spectrometry; oligonucleotides; peptides; platinum
bioinformatics and chemoinformatics; chemical and biological space; drug design; physicochemical properties; neuroprotective agents
Chemogenomics methods seek to characterize the interaction between drugs and biological systems and are an important guide for the selection of screening compounds. The acid/base character of drugs has a profound influence on their affinity for the receptor, on their absorption, distribution, metabolism, excretion and toxicity (ADMET) profile and the way the drug can be formulated. In particular, the charge state of a molecule greatly influences its lipophilicity and biopharmaceutical characteristics.
This study investigates the acid/base profile of human small molecule drugs, chemogenomics datasets and screening compounds including a natural products set. We estimate the ionization constants (pKa values) of these compounds and determine the identity of the ionizable functional groups in each set. We find substantial differences in acid/base profiles of the chemogenomic classes. In many cases, these differences can be linked to the nature of the target binding site and the corresponding functional groups needed for recognition of the ligand. Clear differences are also observed between the acid/base characteristics of drugs and screening compounds. For example, the proportion of drugs containing a carboxylic acid was 20%, in stark contrast to a value of 2.4% for the screening set sample. The proportion of aliphatic amines was 27% for drugs and only 3.4% for screening compounds. This suggests that there is a mismatch between commercially available screening compounds and the compounds that are likely to interact with a given chemogenomic target family. Our analysis provides a guide for the selection of screening compounds to better target specific chemogenomic families with regard to the overall balance of acids, bases and pKa distributions.
Acid; Acidity; Base; Basicity; Chemogenomics; Drug discovery; Functional groups; GPCR; Ion channels; Ionization constant; Kinases; pKa
We investigated the derivation of non-natural peptide triazole dual receptor site antagonists of HIV-1 Env gp120 in order to establish a path for developing peptidomimetic antiviral agents. Previously, we found that the peptide triazole HNG-156 (R-I-N-N-I-X-W-S-E-A-M-M-CONH2, where X is ferrocenyltriazole-Pro (FtP)) had nanomolar binding affinity to gp120, inhibited gp120 binding to CD4 and the co-receptor surrogate mAb 17b and had potent antiviral activity in cell infection assays. Further, truncated variants of HNG-156, typified by UM-24 (Cit-N-N-I-X-W-S-CONH2) and containing the critical central stereospecific LX-LW cluster, retained the functional characteristics of the parent peptide triazole. In the current work, we examined the possibility to replace natural with unnatural residue components in UM-24 to the greatest extent possible. The analogue with the critical “hot spot” residue Trp 6 replaced with L-3-Benzothienylalanine (Bta) (KR-41), as well as a completely non-natural analogue containing D-amino acid substitutions outside the central cluster (KR-42, DCit-DN-DN-DI-X-Bta-DS-CONH2), retained the dual receptor site antagonism / antiviral activity signature. The results define differential functional roles of subdomains within the peptide triazole and provide a structural basis for designing metabolically stable peptidomimetic inhibitors of HIV-1 Env gp120.
Acquired Immune Deficiency Virus; HIV entry Inhibitors; Synthetic non-natural peptide triazoles; Surface Plasmon Resonance; Isothermal Titration Calorimetry
Three natural products have been assembled to obtain a new antimalarial hit. (+)-Usnic acid was used as scaffold to design and synthesize new products, that were tested on asexual development for P. falciparum and P. berghei. Among them, the ester of (+)-usnic acid-4-aminobutyric acid 14 with dihydroartemisinin shows considerable in vivo antimalarial activity against P. berghei in mice, similar to the synthetic drug artesunate. Compound 14 behaves as a delivery system for dihydroartemisinin and combine the effects of the endoperoxide with the redox properties of the phenolic portions of (+)-usnic acid.
antiprotozoal agents; drug discovery; Mannich bases; medicinal chemistry; usnic acid
Cyclooxygenase-2 (COX-2) inhibitors have been in the focus of medicinal chemistry for years and many compounds exhibiting high selectivity and affinity were developed. As carbaboranes represent interesting pharmacophores as phenyl mimetics in drug development, this paper presents the synthesis of carbaboranyl derivatives of COX-2-selective 2,3-disubstituted indoles. Despite the lability of carbaboranes under reducing conditions, 2-carbaborane-3-phenyl-1H-indoles could be synthesized by McMurry cyclization of the corresponding amides. While the meta-carbaboranyl-substituted derivatives (3a-c) lacked COX inhibition activity, the ortho-carbaboranyl analog (3d) was active but showed a selectivity shift towards COX-1.
Carbaboranes; Carboranes; COX inhibitor; Heterocycles; McMurry
APOBEC3G (A3G) is a single-stranded DNA cytosine deaminase that functions in innate immunity against retroviruses and retrotransposons. Although A3G can potently restrict Vif-deficient HIV-1 replication by catalyzing excessive levels of G-to-A hypermutation, sublethal levels of A3G-catalyzed mutation may contribute to the high level of HIV-1 fitness and its incurable prognosis. To chemically modulate A3G catalytic activity with the goal of reducing the HIV-1 genomic mutation rate, we synthesized and biochemically evaluated a class of 4-amino-1,2,4-triazole-3-thiol small molecule inhibitors that were identified by high-throughput screening. This class of compounds exhibits low micromolar (3.9 – 8.2 µm) inhibitory potency and remarkable specificity for A3G versus related deaminase APOBEC3A. Chemical modifications to inhibitors, A3G mutational screening, and thiol reactivity studies implicate C321, a residue proximal to the active site, as the critical A3G target for this class of molecules.
Drug Discovery; APOBEC3G; Heterocycles; Hypomutation; Antiviral Agents
A series of four stable synthetic bacteriochlorins was tested in vitro in HeLa cells for their potential in photodynamic therapy (PDT). The parent bacteriochlorin (BC), dicyano derivative (NC)2BC and corresponding zinc chelate (NC)2BC–Zn and palladium chelate (NC)2BC–Pd were studied. Direct dilution of a solution of bacteriochlorin in an organic solvent (N,N-dimethylacetamide) into serum-containing medium was compared with the dilution of bacteriochlorin in Cremophor EL (CrEL; polyoxyethylene glycerol triricinoleate) micelles into the same medium. CrEL generally reduced aggregation (as indicated by absorption and fluorescence) and increased activity up to tenfold (depending on bacteriochlorin), although it decreased cellular uptake. The order of PDT activity against HeLa human cancer cells after 24 h incubation and illumination with 10 J cm−2 of near-infrared (NIR) light is (NC)2BC–Pd (LD50 = 25 nm) > (NC)2BC > (NC)2BC–Zn ≈ BC. Subcellular localization was determined to be in the endoplasmic reticulum, mitochondria and lysosomes, depending on the bacteriochlorin. (NC)2BC–Pd showed PDT-mediated damage to mitochondria and lysosomes, and the greatest production of hydroxyl radicals as determined using a hydroxyphenylfluorescein probe. The incorporation of cyano substituents provides an excellent motif for the enhancement of the photoactivity and photostability of bacteriochlorins as PDT photosensitizers.
antitumor agents; Cremophor EL micelles; photodynamic therapy; photostability; reactive oxygen species; synthetic bacteriochlorins
Monoamine Transporters; Triple reuptake inhibitors; Pyran; Antidepressants
Successful Influenza A viral replication requires both viral proteins and host cellular factors. Here we utilized a cellular assay to screen for small molecules capable of interfering with any of such necessary viral or cellular components. We employed an established reporter assay assessing influenza viral replication by monitoring the activity of co-expressed luciferase. We screened a diverse chemical compound library, resulting in the identification of compound 7, inhibiting a novel yet elusive target. Quantitative real-time PCR studies confirmed the dose dependent inhibitory activity of compound 7 in a viral replication assay. Furthermore, we showed that compound 7 was effective in rescuing high dose influenza infection in an in vivo mouse model. As oseltamivir-resistant influenza strains emerge, compound 7 could be further investigated as a possible novel scaffold for the development of anti-influenza agents acting on novel targets.
Influenza virus; Drug discovery; Ugi reaction; tetrazole formation
Using a pyrrole-based scaffold, we developed a series of small molecules that mimic the three-dimensional arrangement of the polar and hydrophobic functional groups of the best cyclic-peptide inhibitor. Iterative optimization cycles of design, synthesis and kinetic testing has lead to an effective inhibitor of Wip1, that is selective for this phosphatase over others. The picture shows the structure of the best inhibitor bound to the active site of the enzyme.
Wip1; Inhibitor; Small Molecule
drug design; drug discovery; carbazoles; lansine; leishmaniasis
A series of (±)-6-alkyl-2,4-diaminopyrimidine-based inhibitors of bacterial dihydrofolate reductase (DHFR) have been prepared and evaluated for biological potency against Bacillus anthracis and Staphylococcus aureus. Biological studies reveal attenuated activity relative to earlier structures lacking substitution at C6 of the diaminopyrimidine moiety, though minimum inhibitory concentration (MIC) values are in the 0.125–8 μg/mL range for both organisms. This effect was rationalized from previous three-dimensional X-ray structure studies that indicate the presence of a side pocket containing two water molecules adjacent to the main binding pocket. Because of the hydrophobic nature of the substitutions at C6 the main interactions are with protein residues Leu20 and Leu28. These interactions lead to a minor conformational change in the protein, which opens the pocket containing these waters such that it is continuous with the main binding pocket. These water molecules are reported to play a critical role in the catalytic reaction. This highlights a new area for inhibitor expansion within the limited architectural variation at the catalytic site of bacterial DHFR.
6-Alkylpyrimidine-based antibiotics; DHFR inhibitors; Bacillus anthracis; Staphylococcus aureus
Ca2+-activated K+ channels (KCa) play a pivotal role in the physiology of a wide variety of tissues and disease states, including vascular endothelia, secretory epithelia, certain cancers, red blood cells (RBC), neurons and immune cells. Such widespread involvement has generated an intense interest in elucidating the function and regulation of these channels, with the goal of developing pharmacological strategies aimed at selective modulation of KCa channels in various disease states. Herein, we give an overview of the molecular and functional properties of these channels and their therapeutic importance as well as discuss the achievements made in designing pharmacological tools which control the function of KCa channels by modulating their gating properties. Moreover, this review discusses the recent advances in our understanding of KCa channel assembly and anterograde trafficking toward the plasma membrane, the microdomains in which these channels are expressed within the cell and finally the retrograde trafficking routes these channels take following endocytosis. As both the regulation of intracellular trafficking by agonists, as well as the protein-protein interactions that modify these events continue to be explored, we anticipate this will open up new therapeutic avenues for the targeting of these channels based on the pharmacological modulation of KCa channel density at the plasma membrane.
KCa3.1; KCa2.1; KCa2.2; KCa2.3; channel density; trafficking; pharmacological modulators