Synthesis and activity of ß-carboline antimalarials targeting the Plasmodium falciparum heat shock 90 protein.

A collection of ß-carbolines based on the natural product harmine, a compound known to target the heat shock 90 protein of Plasmodium falciparum, was synthesized and tested for antimalarial activity and potential toxicity. Several of these novel compounds display promising bioactivity, providing a new potential therapeutic with a mode of action that differs versus any currently available clinical treatment.

Identification of Plasmodium falciparum heat shock 90 inhibitors via molecular docking.

A virtual screen was performed to identify anti-malarial compounds targeting Plasmodium falciparum heat shock 90 protein by applying a series of drug-like and commercial availability filters to compounds in the ZINC database, resulting in a virtual library of more than 13 million candidates. The goal of the virtual screen was to identify novel compounds which could serve as a starting point for the development of antimalarials with a mode of action different from anything currently used in the clinic. The screen targeted the ATP binding pocket of the highly conserved Plasmodium heat shock 90 protein, as this protein is critical to the survival of the parasite and has several significant structural differences from the human homolog. The top twelve compounds from the virtual screen were tested in vitro, with all twelve showing no antiproliferative activity against the human fibroblast cell line and three compounds exhibiting single digit or better micromolar antiproliferative activity against the chloroquine-sensitive P. falciparum 3D7 strain.

Antimalarial activity of 2,6-dibenzylidenecyclohexanone derivatives.

Malaria remains one of the deadliest infectious diseases worldwide and continues to infect hundreds of millions of individuals each year. Here we report the discovery and derivatization of a series of 2,6-dibenzylidenecyclohexanones targeting the chloroquine-sensitive 3D7 strain of Plasmodium falciparum . While the initial lead compound displayed significant toxicity in a human cell proliferation assay, we were able to identify a derivative with no detectable toxicity and sub-micromolar potency.

Structure guided development of potent piperazine-derived hydroxamic acid inhibitors targeting falcilysin.

The protozoan parasite Plasmodium falciparum causes the most severe form of human malaria and is estimated to kill 400,000 people a year. The parasite infects and replicates in host red blood cells (RBCs), where it expresses an array of proteases to carry out multiple essential processes. We are investigating the function of falcilysin (FLN), a protease known to be required for parasite development in the RBC. We previously developed a piperazine-based hydroxamic acid scaffold to generate the first inhibitors of FLN, and the current study reports the optimization of the lead compound from that series. A range of substituents were tested at the N1 and N4 positions of the piperazine core, and inhibitors with significantly improved potency against purified FLN and cultured P. falciparum were identified. Computational studies were also performed to understand the mode of binding for these compounds, and predicted a binding model consistent with the biochemical data and the distinctive SAR observed at both the N1 and N4 positions.

Antimalarial activity of tetrahydro-ß-carbolines targeting the ATP binding pocket of the Plasmodium falciparum heat shock 90 protein.

A series of tetrahydro-ß-carboline derivatives of a lead compound known to target the heat shock 90 protein of Plasmodium falciparum were synthesized and assayed for both potency against the parasite and toxicity against a human cell line. Using a rationalized structure based design strategy, a new lead compound with a potency two orders of magnitude greater than the original lead compound was found. Additional modeling of this new lead compound suggests multiple avenues to further increase potency against this target, potentially paving the path for a therapeutic with a mode of action different than any current clinical treatment.

In vitro and in vivo anti-malarial activity of novel harmine-analog heat shock protein 90 inhibitors: a possible partner for artemisinin.

BACKGROUND: The emergence of artemisinin-resistant Plasmodium falciparum strains poses a serious challenge to the control of malaria. This necessitates the development of new anti-malarial drugs. Previous studies have shown that the natural beta-carboline alkaloid harmine is a promising anti-malarial agent targeting the P. falciparum heat-shock protein 90 (PfHsp90). The aim of this study was to test the anti-malarial activity of harmine analogues. METHODS: Forty-two harmine analogues were synthesized and the binding of these analogues to P. falciparum heat shock protein 90 was investigated. The in vitro anti-malarial activity of two of the analogues, 17A and 21A, was evaluated using a 72-h growth inhibition assay. The in vivo anti-malarial activity was tested in Plasmodium berghei infection of BALB/c mice. The potential of 21A for a combination treatment with artemisinin was evaluated using in vivo combination study with dihydro-artemisinin in BALB/c mice. Cytotoxicity of the harmine analogues was tested in vitro using HepG2 and HeLa cell lines. RESULTS: 17A and 21A bound to PfHsp90 with average IC50 values of 12.2 ± 2.3 and 23.1 ± 8.8 µM, respectively. They also inhibited the P. falciparum W2 strain with average IC50 values of 4.2 ± 1.3 and 5.7 ± 1.7 µM, respectively. In vivo, three daily injections of P. berghei-infected BALB/c mice with 100 mg/kg of either 17A or 21A showed significant reduction in parasitaemia with a 51.5 and 56.1% reduction, respectively. Mice treated with 17A and 21A showed a median survival time of 11 and 14 days, respectively, while the vehicle control mice survived a median of only 8.5 days. A dose-ranging experiment with 21A showed that the compound has a dose-dependent anti-malarial effect. Furthermore, treatment of infected mice with a combination of 21A and dihydroartemisinin (DHA) showed a dramatic reduction in parasitaemia compared to treatment with DHA alone. CONCLUSION: A novel and non-toxic harmine analogue has been synthesized which binds to PfHsp90 protein, inhibits P. falciparum in vitro at micromolar concentration, reduces parasitaemia and prolongs survival of P. berghei-infected mice with an additive anti-malarial effect when combined with DHA.

Reaction of InCl3 with various reducing agents: InCl3-NaBH4-mediated reduction of aromatic and aliphatic nitriles to primary amines.

While alternative methods of preparing dichloroindium hydride (HInCl(2)) via the in situ reduction of InCl(3) using lithium amino borohydride (LAB) were explored, generation of HInCl(2) from the reduction of InCl(3) by sodium borohydride (NaBH(4)) was also re-evaluated for comparison. The reductive capability of the InCl(3)/NaBH(4) system was found to be highly dependent on the solvent used. Investigation by (11)B NMR spectroscopic analyses indicated that the reaction of InCl(3) with NaBH(4) in THF generates HInCl(2) along with borane-tetrahydrofuran (BH(3)·THF) in situ. Nitriles underwent reduction to primary amines under optimized conditions at 25 °C using 1 equiv of anhydrous InCl(3) with 3 equiv of NaBH(4) in THF. A variety of aromatic, heteroaromatic, and aliphatic nitriles were reduced to their corresponding primary amine in 70-99% isolated yields. Alkyl halide and nitrile functional groups were reduced in tandem by utilizing the reductive capabilities of both HInCl(2) and BH(3)·THF in a one-pot reaction. Finally, the selective reduction of the carbon bromine bond in the presence of nitriles was achieved by generating HInCl(2) via the reduction InCl(3) with NaBH(4) in CH(3)CN or with lithium dimethylaminoborohydride (MeLAB) in THF.

Mild and expedient asymmetric reductions of α,ß-unsaturated alkenyl and alkynyl ketones by TarB-NO2 and mechanistic investigations of ketone reduction.

A facile and mild reduction procedure is reported for the preparation of chiral allylic and propargyl alcohols in high enantiomeric purity. Under optimized conditions, alkynyl and alkenyl ketones were reduced by TarB-NO2 and NaBH4 at 25 °C in 1 h to produce chiral propargyl and allylic alcohols with enantiomeric excesses and yields up to 99%. In the case of α,ß-unsaturated alkenyl ketones, α-substituted cycloalkenones were reduced with up to 99% ee, while more substituted and acyclic derivatives exhibited lower induction. For α,ß-ynones, it was found that highly branched aliphatic ynones were reduced with optimal induction up to 90% ee, while reduction of aromatic and linear aliphatic derivatives resulted in more modest enantioselectivity. Using the (L)-TarB-NO2 reagent derived from (L)-tartaric acid, we routinely obtained highly enantioenriched chiral allylic and propargyl alcohols with (R) configuration. Since previous models and a reduction of a saturated analogue predicted propargyl products of (S) configuration, a series of new mechanistic studies were conducted to determine the likely orientation of aromatic, alkenyl, and alkynyl ketones in the transition state.

Evaluation of consensus scoring methods for AutoDock Vina, smina and idock.

We investigated the application of consensus scoring using the freely available and open source structure-based virtual screening docking programs AutoDock Vina, smina and idock. These individual programs and several simple consensus scoring methods were tested for their ability to identify hits against 20 DUD-E benchmark targets using the AUC and EF1 metrics. We found that all of the consensus scoring methods, however normalized, fared worse, on average, than simply using the output from a single program, smina. Additionally, the effect of a significant increase in the run time of all three programs was tested to find if a longer run time yielded improved results. Our results indicated that a longer run time than the default had little impact on the performance of these three programs or on consensus scoring methods based on their output. Thus, we have found that using the smina program alone at default settings is the best approach for researchers that do not have access to a suite of commercial docking software packages.

Synthesis and Structure-Activity Relationship of Dual-Stage Antimalarial Pyrazolo[3,4-b]pyridines.

Malaria remains one of the most deadly infectious diseases, causing hundreds of thousands of deaths each year, primarily in young children and pregnant mothers. Here, we report the discovery and derivatization of a series of pyrazolo[3,4-b]pyridines targeting Plasmodium falciparum, the deadliest species of the malaria parasite. Hit compounds in this series display sub-micromolar in vitro activity against the intraerythrocytic stage of the parasite as well as little to no toxicity against the human fibroblast BJ and liver HepG2 cell lines. In addition, our hit compounds show good activity against the liver stage of the parasite but little activity against the gametocyte stage. Parasitological profiles, including rate of killing, docking, and molecular dynamics studies, suggest that our compounds may target the Qo binding site of cytochrome bc1.

Reductions of aliphatic and aromatic nitriles to primary amines with diisopropylaminoborane.

Diisopropylaminoborane [BH(2)N(iPr)(2)] in the presence of a catalytic amount of lithium borohydride (LiBH(4)) reduces a large variety of aliphatic and aromatic nitriles in excellent yields. BH(2)N(iPr)(2) can be prepared by two methods: first by reacting diisopropylamineborane [(iPr)(2)N:BH(3)] with 1.1 equiv of n-butyllithium (n-BuLi) followed by methyl iodide (MeI), or reacting iPrN:BH(3) with 1 equiv of n-BuLi followed by trimethylsilyl chloride (TMSCl). BH(2)N(iPr)(2) prepared with MeI was found to reduce benzonitriles to the corresponding benzylamines at ambient temperatures, whereas diisopropylaminoborane prepared with TMSCl does not reduce nitriles unless a catalytic amount of a lithium ion source, such as LiBH(4) or lithium tetraphenylborate (LiBPh(4)), is added to the reaction. The reductions of benzonitriles with one or more electron-withdrawing groups on the aromatic ring generally occur much faster with higher yields. For example, 2,4-dichlorobenzonitrile was successfully reduced to 2,4-dichlorobenzylamine in 99% yield after 5 h at 25 degrees C. On the other hand, benzonitriles containing electron-donating groups on the aromatic ring require refluxing in tetrahydrofuran (THF) for complete reduction. For instance, 4-methoxybenzonitrile was successfully reduced to 4-methoxybenzylamine in 80% yield. Aliphatic nitriles can also be reduced by the BH(2)N(iPr)(2)/cat. LiBH(4) reducing system. Benzyl cyanide was reduced to phenethylamine in 83% yield. BH(2)N(iPr)(2) can also reduce nitriles in the presence of unconjugated alkenes and alkynes such as the reduction of 2-hexynenitrile to hex-5-yn-1-amine in 80% yield. Unfortunately, selective reduction of a nitrile in the presence of an aldehyde is not possible as aldehydes are reduced along with the nitrile. However, selective reduction of the nitrile group at 25 degrees C in the presence of an ester is possible as long as the nitrile group is activated by an electron-withdrawing substituent. It should be pointed out that lithium aminoborohydrides (LABs) do not reduce nitriles under ambient conditions and behave as bases with aliphatic nitriles as well as nitriles containing acidic alpha-protons. Consequently, both LABs and BH(2)N(iPr)(2) are complementary to each other and offer methods for the selective reductions of multifunctional compounds.

Microwave-Assisted Preparation of 1-Aryl-1H-pyrazole-5-amines.

A synthetic process for the preparation of a variety of 1-aryl-1H-pyrazole-5-amines was developed. The microwave-mediated nature of this method makes it efficient in both time and resources and utilizes water as the solvent. 3-Aminocrotononitrile or an appropriate α-cyanoketone is combined with an aryl hydrazine and dissolved in 1 M HCl. The mixture is then heated in a microwave reactor at 150 °C, typically for 10-15 min. The product can be readily obtained by basifying the solution with 10% NaOH and isolating the desired compound with a simple vacuum filtration. The use of water as a solvent in this reaction lends to its ease and utility in production, and this method is easily reproducible with a variety of functional groups. Typical isolated yields range from 70-90%, and reactions can be performed on the milligram to gram scale with little to no change in observed yields. Some of the applications of these molecules and their derivatives include pesticides, anti-malarials, and chemotherapeutics, among many others.

Identification of potential Zika virus NS2B-NS3 protease inhibitors via docking, molecular dynamics and consensus scoring-based virtual screening.

The Zika virus has recently become a subject of acute interest after the discovery of the link between viral infection and microcephaly in infants. Though a number of treatments are under active investigation, there are currently no approved treatments for the disease. To address this critical need, we screened more than 7 million compounds targeting the NS2B-NS3 protease in an attempt to identify promising inhibitor candidates. Starting with commercially and freely available compounds, we identified six hits utilizing an exhaustive consensus screening protocol, followed by molecular dynamics simulation and binding energy estimation using MM/GBSA and MM/PBSA methods. These compounds feature a variety of cores and functionalities, and all are predicted to have good pharmacokinetic profiles, making them promising candidates for screening assays. Graphical abstract Virtual screen of potential Zika virus NS2B-NS3 protease inhibitors.