In silico pharmacophore modeling and simulation studies for searching potent antileishmanials targeted against Leishmania donovani nicotinamidase

Nicotinamidase is a key enzyme for the salvage pathway catalyzing the first step for the conversion of nicotinamide (NAm) to nicotinic acid (NA) required for the synthesis of Nicotinamide Adenine Dinucleotide (NAD⁺) in the subsequent steps. Leishmania protozoan parasites are NAD⁺ auxotrophs and need precursors (nicotinamide, nicotinic acid, nicotinamide riboside) from their host environment to synthesize NAD⁺ for their survival. Interestingly, absence of this enzyme in higher eukaryotes and its absolute requirement in the developmental cycle of Leishmania has led nicotinamidase an attractive drug target towards leishmaniasis. Hence, we report some potential inhibitors for nicotinamidase screened based on 3-D pharmacophore model consisting of “ML”, “Hyd|Aro”, “Acc” and “Excl vol” features. Subsequently, dynamics simulation studies validate the proposed pharmacophore model suggesting its reliability for future studies. Furthermore, these essential site-specific features will help in enhancing the inhibition of nicotinamidase activity. Results of our study suggest that blocking of active site of nicotinamidase by the identified lead inhibitor will have major impact on the infectious processes and the survival of the parasite. Furthermore, due to the structural homology in the enzyme among L. donovani, L. infantum, L. major, we anticipate that our study would help to design more potent drug candidates against leshmaniasis for these three species.     

Drug search for leishmaniasis: a virtual screening approach by grid computing

The trypanosomatid protozoa Leishmania is endemic in ~100 countries, with infections causing ~2 million new cases of leishmaniasis annually. Disease symptoms can include severe skin and mucosal ulcers, fever, anemia, splenomegaly, and death. Unfortunately, therapeutics approved to treat leishmaniasis are associated with potentially severe side effects, including death. Furthermore, drug-resistant Leishmania parasites have developed in most endemic countries. To address an urgent need for new, safe and inexpensive anti-leishmanial drugs, we utilized the IBM World Community Grid to complete computer-based drug discovery screens (Drug Search for Leishmaniasis) using unique leishmanial proteins and a database of 600,000 drug-like small molecules. Protein structures from different Leishmania species were selected for molecular dynamics (MD) simulations, and a series of conformational “snapshots” were chosen from each MD trajectory to simulate the protein’s flexibility. A Relaxed Complex Scheme methodology was used to screen ~2000 MD conformations against the small molecule database, producing >1 billion protein-ligand structures. For each protein target, a binding spectrum was calculated to identify compounds predicted to bind with highest average affinity to all protein conformations. Significantly, four different Leishmania protein targets were predicted to strongly bind small molecules, with the strongest binding interactions predicted to occur for dihydroorotate dehydrogenase (LmDHODH; PDB:3MJY). A number of predicted tight-binding LmDHODH inhibitors were tested in vitro and potent selective inhibitors of Leishmania panamensis were identified. These promising small molecules are suitable for further development using iterative structure-based optimization and in vitro/in vivo validation assays.     

An Overview on Target-Based Drug Design against Kinetoplastid Protozoan Infections: Human African Trypanosomiasis,Chagas Disease and Leishmaniases

The protozoan diseases Human African Trypanosomiasis (HAT), Chagas disease (CD), and leishmaniases span worldwide and therefore their impact is a universal concern. The present regimen against kinetoplastid protozoan infections is poor and insufficient. Target-based design expands the horizon of drug design and development and offers novel chemical entities and potential drug candidates to the therapeutic arsenal against the aforementioned neglected diseases. In this review, we report the most promising targets of the main kinetoplastid parasites, as well as their corresponding inhibitors. This overview is part of the Special Issue, entitled “Advances of Medicinal Chemistry against Kinetoplastid Protozoa (Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp.) Infections: Drug Design, Synthesis and Pharmacology”.     

Synthesis of Polycyclic Ether-Benzopyrans and In Vitro Inhibitory Activity against Leishmania tarentolae

Construction of a focused library of polycyclic ether-benzopyrans was undertaken in order to discover new therapeutic compounds that affect Leishmania growth and infectivity. This is especially of interest since there are few drug therapies for leishmaniasis that do not have serious drawbacks such high cost, side effects, and emerging drug resistance. The construction of these polycyclic ether-benzopyrans utilized an acetoxypyranone-alkene [5+2] cycloaddition and the Suzuki-Miyaura cross-coupling. The multi-gram quantity of the requisite aryl bromide was obtained followed by effective Pd-catalyzed coupling with boronic acid derivatives. Compounds were tested in vitro using the parasitic protozoan, Leishmania tarentolae. Effects of concentration, time, and exposure to light were evaluated. In addition, the effects on secreted acid phosphatase activity and nitric oxide production were investigated, since both have been implicated in parasite infectivity. The data presented herein are indicative of disruption of the Leishmania tarentolae and thus provide impetus for the development and testing of a more extensive library.     

Identification of Kaurane-Type Diterpenes as Inhibitors of Leishmania Pteridine Reductase I

The current treatments against Leishmania parasites present high toxicity and multiple side effects, which makes the control and elimination of leishmaniasis challenging. Natural products constitute an interesting and diverse chemical space for the identification of new antileishmanial drugs. To identify new drug options, an in-house database of 360 kauranes (tetracyclic diterpenes) was generated, and a combined ligand- and structure-based virtual screening (VS) approach was performed to select potential inhibitors of Leishmania major (Lm) pteridine reductase I (PTR1). The best-ranked kauranes were employed to verify the validity of the VS approach through LmPTR1 enzyme inhibition assay. The half-maximal inhibitory concentration (IC₅₀) values of selected bioactive compounds were examined using the random forest (RF) model (i.e., 2β-hydroxy-menth-6-en-5β-yl ent-kaurenoate (135) and 3α-cinnamoyloxy-ent-kaur-16-en-19-oic acid (302)) were below 10 μM. A compound similar to 302, 3α-p-coumaroyloxy-ent-kaur-16-en-19-oic acid (302a), was also synthesized and showed the highest activity against LmPTR1. Finally, molecular docking calculations and molecular dynamics simulations were performed for the VS-selected, most-active kauranes within the active sites of PTR1 hybrid models, generated from three Leishmania species that are known to cause cutaneous leishmaniasis in the new world (i.e., L. braziliensis, L. panamensis, and L. amazonensis) to explore the targeting potential of these kauranes to other species-dependent variants of this enzyme.     

Co-feeding with DME: An effective way to enhance gasoline production via low temperature aromatization of LPG

The aromatization of light alkenes in liquefied petroleum gas (LPG) with and without dimethyl ether (DME) addition in the feed was investigated on a modified ZSM-5 catalyst. The results showed that under the given reaction conditions the selectivity of alkenes to high-octane gasoline blending components was markedly enhanced and the formation of propane and butanes was greatly suppressed with the addition of DME. It was also found that the distribution of C₅₊ components was changed a lot with DME addition into the LPG feed. The formation of branched hydrocarbons (mainly C₆?C₈ i-paraffin) and multi-methyl substituted aromatics, which are high octane number gasoline blending components, was promoted significantly, while the content of n-paraffins and olefins in C₅₊ components was decreased obviously, indicating that in addition to the oligomerization, cracking, hydrogen-transfer and dehydrogenation-cyclization of alkenes, the methylation of the formed aromatics and olefins intermediates also plays an important role in determining the product distribution due to the high reactivity of surface methoxy groups formed by DME. And this process, in combination with the syngas-to-methanol/DME technology, provides an alternative way to the production of high-octane gasoline from coal, natural gas or renewable raw materials.     

A facile procedure for synthesis of 3-[2-(N,N-dialkylamino)ethyl]-3-fluorooxindoles by direct fluorination of N,N-dialkyltryptamines

A practical procedure for the synthesis of 3-fluorooxindole derivatives having basic amine moieties was developed, which involves Selectfluor™-mediated oxidative fluorination of N,N-dialkyltryptamines in the presence of Lewis acid. This procedure was applied to an antimigraine drug, rizatriptan, to afford the corresponding 3-fluorooxindole, which is a potential fluorine-containing drug candidate.     

Synthesis and evaluation of glucosamine-6-phosphate analogues as activators of glmS riboswitch

The glmS riboswitch is a ribozyme found in numerous Gram-positive bacteria and responds to the cellular concentrations of glucosamine 6-phosphate (GlcN6P). Given the importance of GlcN6P for cell wall biosynthesis, the glmS riboswitch has become a new drug target for the development of antibiotics. Herein, we describe the efficient synthesis of three GlcN6P analogues and their evaluation on inducing self-cleavage of the glmS riboswitch from Bacillus subtilis. Our results provide valuable information for further elucidation of the structure-activity relationships and drug design for glmS riboswitch antibiotics.     

In Silico Insights into the Mechanism of Action of Epoxy-α-Lapachone and Epoxymethyl-Lawsone in Leishmania spp.

Epoxy-α-lapachone (Lap) and Epoxymethyl-lawsone (Law) are oxiranes derived from Lapachol and have been shown to be promising drugs for Leishmaniases treatment. Although, it is known the action spectrum of both compounds affect the Leishmania spp. multiplication, there are gaps in the molecular binding details of target enzymes related to the parasite’s physiology. Molecular docking assays simulations were performed using DockThor server to predict the preferred orientation of both compounds to form stable complexes with key enzymes of metabolic pathway, electron transport chain, and lipids metabolism of Leishmania spp. This study showed the hit rates of both compounds interacting with lanosterol C-14 demethylase (−8.4 kcal/mol to −7.4 kcal/mol), cytochrome c (−10.2 kcal/mol to −8.8 kcal/mol), and glyceraldehyde-3-phosphate dehydrogenase (−8.5 kcal/mol to −7.5 kcal/mol) according to Leishmania spp. and assessed compounds. The set of molecular evidence reinforces the potential of both compounds as multi-target drugs for interrupt the network interactions between parasite enzymes, which can lead to a better efficacy of drugs for the treatment of leishmaniases.     

Rational Approaches for Drug Designing Against Leishmaniasis

Leishmaniasis has been ignored for many years mainly because it plagues remote and poor areas. However, recently, it has drawn attention of several investigators, and active research is going on for antileishmanial drug discovery. The current available drugs have high failure rates and significant side effects. Recently, liposomal preparations of amphotericin B are available and have proved to be a better drug, but they are very expensive. Miltefosine is one of the few orally administered drugs that are effective against Leishmania. However, it has exhibited teratogenicity, hence, should not be administered to pregnant women. Thus, the search for novel and improved antileishmanial drugs continue. A rational approach to design and develop new antileishmanials can be to identify several metabolic and biochemical differences between host and parasite that can be exploited as drug target. Moreover, many natural products also have significant antileishmanial activity and are yet to be exploited. In the current review, we aim to bring together various drug targets of Leishmania, recent development in the field, future prospects, and hope in the area.     

Corrosion Behavior of Steel A3 Influenced by Thiobacillus Ferrooxidans

The electrochemical measurement and surface analysis methods were employed to investigate the corrosion behavior of steel A3 influenced by Thiobacillus ferrooxidans (T.f). Polarization curve results indicated that the presence of Thiobacillus ferrooxidans resulted in higher corrosion potential of the electrode and obviously accelerated the corrosion current density. Atomic force microscope (AFM) results showed that asymmetric biofilms adhered to the surface of steel A3 after 7 days of exposure. The scanning electron microscopy (SEM) results showed that pitting appeared on the surface of steel A3 after 7 days of exposure in T.f solution, which was induced by the metabolism of bacteria and the morphology of the deposit. Pitting holes of steel A3 in T.f solution were deeper after 20 days of exposure. The presence of Thiobacillus ferrooxidans aggravated the localized corrosion of A3 steel.     

Synthesis of potential bisubstrate inhibitors of Leishmania elongating α-d-mannosyl phosphate transferase

Synthesis of a potential mechanism-based bisubstrate inhibitor 1 of the elongating α-d-mannosyl phosphate transferase in Leishmania, comprising a guanosine subunit bound to the synthetic acceptor substrate through the methylenebisphosphonate linker, as well as its analogues 2 and 3 has been successfully accomplished.     

Novel aromatics bearing 4-O-methylglucose unit isolated from the oriental crude drug Bombyx Batryticatus

Oriental crude drug, Bombyx Batryticatus, is dried silkworm larva, Bombyx mori L., which are dead and stiffened due to a Beauveria bassiana infection. In traditional Japanese, Korean, and Chinese medicine, it is employed as analgesic and anticonvulsant. We investigated the constituents of Bombyx Batryticatus and isolated four novel aromatics bearing 4-O-methylglucose moiety, BB-1, 2, 3, and 4 (1-4). It is speculated that these compounds are produced by an interaction between plants, insects, and microorganisms.     

Alkyl-Resorcinol Derivatives as Inhibitors of GDP-Mannose Pyrophosphorylase with Antileishmanial Activities

Leishmaniasis is a vector-borne disease caused by the protozoan parasite Leishmania found in tropical and sub-tropical areas, affecting 12 million people around the world. Only few treatments are available against this disease and all of them present issues of toxicity and/or resistance. In this context, the development of new antileishmanial drugs specifically directed against a therapeutic target appears to be a promising strategy. The GDP-Mannose Pyrophosphorylase (GDP-MP) has been previously shown to be an attractive therapeutic target in Leishmania. In this study, a chemical library of 5000 compounds was screened on both L. infantum (LiGDP-MP) and human (hGDP-MP) GDP-MPs. From this screening, oncostemonol D was found to be active on both GDP-MPs at the micromolar level. Ten alkyl-resorcinol derivatives, of which oncostemonols E and J (2 and 3) were described for the first time from nature, were then evaluated on both enzymes as well as on L. infantum axenic and intramacrophage amastigotes. From this evaluation, compounds 1 and 3 inhibited both GDP-MPs at the micromolar level, and compound 9 displayed a three-times lower IC₅₀ on LiGDP-MP, at 11 µM, than on hGDP-MP. As they displayed mild activities on the parasite, these compounds need to be further pharmacomodulated in order to improve their affinity and specificity to the target as well as their antileishmanial activity.     

Agariblazeispirols A and B, an unprecedented skeleton from the cultured mycelia of the fungus, Agaricus blazei

Agariblazeispirols A and B, which have a unique steroidal skeleton, have been isolated from the cultured mycelia of Agaricus blazei (Agaricaceae). The absolute structure of Agariblazeispirol A was established to be (20S,22R,23R,24S)-13β,22:22,25-diepoxy-5-methoxy-14β-methyl-18-nor-des-A-ergosta-5,7,9,11-tetraen-23-ol by extensive 1D and 2D NMR spectral data, and X-ray analysis. The structure of Agariblazeispirol B was elucidated to be a stereoisomer of agariblazeispirol A at its carbon 22, (20S,22S,23R,24S)-13β,22:22,25-diepoxy-5-methoxy-14β-methyl-18-nor-des-A-ergosta-5,7,9,11-tetraen-23-ol by comparison of extensive 1D and 2D NMR spectral data with those of agariblazeispirol A. Both compounds showed a moderate circumvention of drug resistance on mouse leukemia P388/VCR cells.     

Surface plasmon resonance detection of oligonucleotide sequences of the rpoB genes of Mycobacterium tuberculosis

Oligonucleotide sequences related to the normal and mutated rpoB genes of Mycobacterium tuberculosis are detected using a surface plasmon resonance (SPR) biosensor system. A bioselective element was prepared by immobilizing the thiol-modified oligonucleotides of the selected sequence (the capture probe P2) that contains the mutated TCG → TTG codon 531 (evoking drug resistance) of the rpoB gene of M. tuberculosis on a gold sensor surface. Specific hybridization between immobilized probe P2 and complementary target T2 gave the highest sensor response, single-base mismatched oligonucleotide TN (corresponding to the normal gene sequence) produced somewhat smaller response and no response was observed at injection of noncomplementary oligonucleotide TC. The P2-T2 hybridization efficiency is calculated ca. 30% (5 × 10¹² molecules cm⁻²), and the lowest detection limit of T2 was 10 nM. An extended T2E oligonucleotide sequence consisting of T2 sequence and additional 24 nucleotides was shown to cause more pronounced sensor response (at least 5 nM T2E was easily detected). Injection into the sensor cell of the oligonucleotides complementary to the free additional part of T2E after P2-T2E hybridization gave a significant additional SPR response, thus showing that the sandwich hybridization format further improves the sensor sensitivity and decreases the lowest detection limit. The experimental results on surface hybridization between the studied oligonucleotides were in good agreement with thermodynamic parameters of the hybridization calculated for solution conditions. The described approach could be proposed as a basis for creating a biosensor for real-time and label-free diagnostics of drug resistant tuberculosis.     

Fourier transform infrared spectroscopy and solid-state nuclear magnetic resonance studies of octadecyl modified metal oxides obtained from different silane precursors

Octadecyl (C₁₈) modified metal oxide substrates, including titania, zirconia, hafnia, and alumina, are prepared using two types of silylating reagents, n-octadecyltrihydridosilane and n-octadecyltrichlorosilane. Fourier transform infrared (FTIR) and solid-state ²⁹Si nuclear magnetic resonance (NMR) measurements are performed to examine the cross-linking of the silanes. Solid-state ¹³C NMR spectroscopy provides information about the conformation and mobility of surface-immobilized alkyl chains. Variable temperature FTIR investigations are carried out to study the influence of the organosilane precursors and metal oxides on the conformational order of the alkyl modified systems. It is found that grafting by means of n-octadecyltrichlorosilane yields higher grafting densities than surface modification with n-octadecyltrihydridosilane. Combined pyridine adsorption and diffuse reflectance infrared Fourier transform (DRIFT) measurements are performed on the titania and hafnia substrates to evaluate potential surface heterogeneities, i.e. Lewis and Brønsted sites. Differences in the alkyl chain conformational order within the series of C₁₈ modified metal oxides are explained by the presence of island structures. The reduced C₁₈ conformational order for the samples grafted with n-octadecyltrihydridosilane is traced back to the lower grafting density which in turn points to a lower reactivity of this silylating reagent. The most striking result is the higher conformational order of the C₁₈ chains grafted in the present surface modified metal oxides when compared with silica-based systems. This finding is attributed to the lower porosity of the metal oxide supports along with more closely packed chains on the surface.     

Identification and enantioselective gas chromatographic mass-spectrometric separation of O-desmethylnaproxen,the main metabolite of the drug naproxen,as a new environmental contaminant

O-Desmethylnaproxen (2-(6-hydroxynaphthalen-2-yl)propanoic acid) was identified in 10 different water samples from Germany and Pakistan. In the Pakistan samples it was found in all samples, surface water and effluents, exhibiting estimated concentrations between 0.04 and 1.36 μg/L. In Germany it was only encountered in the STP-effluent with an average concentration of 0.23 μg/L. Furthermore, enantioselective GC analyses revealed differences in the enantiomeric ratios found in Germany and Pakistan. To the best of our knowledge this is the first report on the identification of O-desmethylnaproxen, the main metabolite of the drug naproxen, in environmental samples.     

First synthesis and characterization of SRR/RSS-Ezetimibe

The two stereoisomers, SRR-Ezetimibe 2 and RSS-Ezetimibe 3 are related substances of the cholesterol absorption inhibitor drug Ezetimibe 1. Herein, we present an efficient and practical synthesis approach to deliver these two stereoisomers for the first time, and a proof of SRR-Ezetimibe 2 by single-crystal X-ray analysis. Our research will be of immense help for organic chemists to study the impurity profile of Ezetimibe 1.