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
multicomponent reaction; drug discovery; protein-protein interaction; p53-Mdm2; fluorine
glucagon-like peptide-1 (GLP-1); human pancreatic islets; insulinotropic effects; receptor agonists; vitamin B12
The synthesis of halogenated analogs of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (1), known commonly as bexarotene, and their evaluation for retinoid-X-receptor (RXR)-specific agonist performance is described. Compound 1 is FDA approved to treat cutaneous T-cell lymphoma (CTCL); however, bexarotene treatment can induce hypothyroidism and elevated triglyceride levels, presumably by disrupting RXR heterodimer pathways for other nuclear receptors. The novel halogenated analogs in this study were modeled and assessed for their ability to bind to RXR and stimulate RXR homodimerization in an RXRE-mediated transcriptional assay as well as an RXR mammalian-2-hybrid assay. In an array of 8 novel compounds, 4 analogs were discovered to promote RXR-mediated transcription with comparable EC50 values as 1 and are selective RXR agonists. Our approach also uncovered a periodic trend of increased binding and homodimerization of RXR when substituting a halogen atom for a proton ortho to the carboxylic acid on 1.
Bexarotene; Cutaneous T Cell Lymphoma; Retinoic Acid Receptor; Retinoid X Receptor; Rexinoid
Microtubule stabilizers are powerful anti-mitotic compounds and represent a proven cancer treatment strategy. Several classes of compounds in clinical use or trials, such as the taxanes and epothilones, bind to the same region of β-tubulin. Determining how these molecules interact with tubulin and stabilize microtubules is important both for understanding the mechanism of action and enhancing chemotherapeutic potential, e.g. reducing side effects, increasing solubility, and overcoming resistance. Structural studies using nonpolymerized tubulin or stabilized polymers have produced different models of epothilone binding. Here, we used directed mutagenesis of the binding site on Saccharomyces cerevisiae β-tubulin to analyze interactions between Epothilone B and its biologically relevant substrate, dynamic microtubules. Five engineered amino acid changes contributed to a 125-fold increase in Epothilone B cytotoxicity independent of inherent microtubule stability. The mutagenesis of endogenous β-tubulin was done in otherwise isogenic strains. This facilitated the correlation of amino acid substitutions with altered cytotoxicity using molecular mechanics simulations. The results, which are based on the interaction between Epothilone B and dynamic microtubules, most strongly support the binding mode determined by NMR spectroscopy-based studies. This work establishes a system for discriminating between potential binding modes and among various compounds and/or analogues using a sensitive biological activity-based readout.
epothilone; microtubule; tubulin; taxol binding site; microtubule stabilizer; drug design; antitumor agents
flavonoid; naringenin; resveratrol; abyssinone II; antitubercular; antibacterial mechanistic study
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
Acivicin analogues with an increased affinity for CTP synthetase (CTPS) were designed as potential new trypanocidal agents. The inhibitory activity against CTPS can be improved by increasing the molecular complexity, by inserting groups able to establish additional interaction with the binding pocket of the enzyme. This strategy has been pursued with the synthesis of α-amino-substituted analogues of Acivicin and N1-substituted-pyrazoline derivatives. In general, there is a direct correlation between the enzymatic activity and the in vitro anti-trypanosomal efficacy of the derivatives studied here. However, this cannot be taken as a general rule, since other important factors may play a role, notably the ability of uptake / diffusion of the molecules into the trypanosomes.
CTP synthetase; Trypanosoma; Amino acid; Isoxazoline; Pyrazoline
Pathogenicity of Yersinia pestis (Y. pestis) relies on several effector proteins, including YopH, a protein-tyrosine phosphatase. Previously, we screened a library of analogues based on the ubiquitous PTP substrate, p-nitrophenylphosphate (pNPP) and found that incorporation of a 3-phenyl substituent (6-nitro-[1,1'-biphenyl]-3-yl dihydrogen phosphate (1)) enhanced affinity. The current study reports the conversion of 1 from a substrate to inhibitor by replacing the hydrolysable phosphoryl group with a 3-isoxazolecarboxylic acid moiety and by introduction of an aminooxy group and subsequent diversification using oxime-based click chemistry. As reported herein, this approach led to the identification of non-promiscuous low micromolar affinity bidentate YopH inhibitors.
Substrate screening; Aminooxy platform; Oxime-based click chemistry; YopH inhibitors; In silico docking studies
Can we consider cancer as a “metabolic disease”? Tumors are the result of a metabolic selection, forming tissues composed of heterogeneous cells that generally express an overactive metabolism as a common feature. In fact, cancer cells have to deal with increased needs for both energy and biosynthetic intermediates, in order to support their growth and invasiveness. However, their high proliferation rate often generates regions that are not sufficiently oxygenated. Therefore, their carbohydrate metabolism has to rely mostly on a glycolytic process that is uncoupled from oxidative phosphorylation. This metabolic switch, also known as the “Warburg Effect”, constitutes a fundamental adaptation of the tumor cells to a relatively hostile environment, and supports the evolution of aggressive and metastatic phenotypes. As a result, tumor glycolysis may constitute an attractive target for cancer therapy. This approach has often raised concerns that anti-glycolytic agents may cause serious side effects on normal cells. Actually, the key for a selective action against cancer cells can be found in their hyperbolic addiction to glycolysis, which may be exploited to generate new anti-cancer drugs showing minimal toxicity. In fact, there is growing evidence that supports many glycolytic enzymes and transporters as suitable candidate targets for cancer therapy. Herein we review some of the most relevant anti-glycolytic agents that have been investigated so far for the treatment of cancer.
anticancer agents; glycolysis; inhibitors; tumor metabolism; warburg effect