Conformational analysis of rhazinilam and three-dimensional quantitative structure–activity relationships of rhazinilam analogues

Applications of QSAR study in drug design of tubulin binding inhibitors

New drug discovery is recognized as a complicated, costly, time-consuming, and difficult process. Computer-aided drug discovery has developed as a potent and promising method for faster, cheaper, and more effective drug creation. Recently, the rapid rise of computational methods for drug discovery, including anticancer medicines, had a substantial and exceptional impact on anticancer drug design, as well as providing beneficial insights into the field of cancer therapy. In this paper, we discussed the quantitative structure-activity relationship (QSAR), which is a significant in-silico tool in rational drug design. The QSAR method is used to optimize the existing leads to improve their biological activities, and physicochemical properties and to predict the biological activities of untested and sometimes unavailable compounds, so QSAR is a significant method in drug designing. This article is a comprehensive review of various QSAR studies conducted which help to create new and potent inhibitors for targeting tubulin, a crucial target in cancer treatment. It particularly focuses on studies that provide structural insights into the compounds targeting tubulin. It should prioritize continually researching specific scaffolds, with a focus on important attachment regions, to gather more powerful molecular data and enhance models. This will lead to a better understanding of drug interactions and the development of improved cancer-targeting inhibitors for tubulin.Communicated by Ramaswamy H. Sarma.

Extended Connectivity Fingerprints as a Chemical Reaction Representation for Enantioselective Organophosphorus-Catalyzed Asymmetric Reaction Prediction

Predicting the outcomes of organic reactions using data-driven approaches aids in the acceleration of research. In laboratory-scale experiments, only a small number of reaction data can be accessed for machine learning model construction, where reaction representations play a pivotal role in the success of model construction. Nevertheless, representation comparison for a small data set is not adequate. Herein, focusing on the enantioselectivity of phosphoric-acid-catalyzed reactions, various two-dimensional and three-dimensional reaction representations (descriptors) were compared. Overall, the concatenated form of the extended connectivity fingerprints showed the best predictive capability for the two types of data sets: high-throughput experimental data and manually collected literature data sets. Furthermore, highlighting the substructure contribution to the prediction outcome was shown to be informative for guiding catalyst development.

Evaluation of the antimicrobial activities of ultrasonicated spinach leaf extracts using RAPD markers and electron microscopy

Spinach (Spinacia oleracea L.) leaves represent an important dietary source of nutrients, antioxidants and antimicrobials. As such, spinach leaves play an important role in health and have been used in the treatment of human diseases since ancient times. Here, the aims were to optimize the extraction methods for recovering antimicrobial substances of spinach leaves, determine the minimum inhibitory concentrations (MICs) of the antimicrobial substances against Escherichia coli and Staphylococcus aureus and, finally, evaluate the effects of spinach leaves' antimicrobials on bacterial DNA using central composite face-centered methods. The effect of the extracts on both Gram-positive and Gram-negative bacterial models was examined by scanning electron microscopy (SEM) and random amplification of polymorphic (bacterial) DNA (RAPD). The optimal extraction conditions were at 45 °C, ultrasound power of 44% and an extraction time of 23 min. The spinach extracts exhibited antimicrobial activities against both bacteria with MICs in the 60-100 mg/ml range. Interestingly, SEM showed that the treated bacterial cells appear damaged with a reduction in cell number. RAPD analysis of genomic DNA showed that the number and sizes of amplicons were decreased by treatments. Based on these results, it was inferred that spinach leaf extracts exert bactericidal activities by both inducing mutations in DNA and causing cell wall disruptions.

Antiparasitic Indole Alkaloids from Aspidosperma desmanthum and A. spruceanum from the Peruvian Amazonia

Twenty-three indole alkaloids were isolated from Aspidosperma desmanthum and A. spruceanum. Alkaloids 1-4 were isolated from the leaves, 5-8 from the stem bark and 9-15 from the root bark of A. desmanthum. Alkaloids 5, 11, 16, 17 and 19 were isolated from the stem bark, 18 and 20-22 from the root bark and 23 from the flowers of A. spruceanum. Compounds 4, 14, and 15 have not been previously reported as natural products while 16 and 20 have been isolated for the first time from the genus Aspidosperma. Their structures were determined by spectroscopic techniques including 1D and 2D NMR experiments (COSY, NOESY, HSQC, HMBC). The antiparasitic activity of these compounds was tested against Trypanosoma cruzi and Leishmania infantum and their non-specific cytotoxicity on mammalian cells. The most active compounds were 10, 12, 13, and 14 from A. desmanthum, and 19, 21 and 22 from A. spruceanum. Aspidolimine (10) aspidocarpine (12) and tubotaiwine (21) showed selective activity against L. infantum.

Probing interactions of tubulin with small molecules, peptides, and protein fragments by solution nuclear magnetic resonance

The description of the molecular mechanisms of interaction between tubulin or microtubules and partners at atomic scale is expected to have critical impacts on the understanding of basic physiological processes. This information will also help the design of future drug candidates that may be used to fight various pathologies such as cancer or neurological diseases. For these reasons, this aspect of tubulin research has been tackled since the seventies using many different methods and at different scales. NMR appears as a unique approach to provide, with atomic resolution, the solution structure and dynamical properties of tubulin/microtubule partners in free and bound states. Though tubulin is not directly amenable to solution NMR, the NMR ligand-based experiments allow one to obtain valuable data on the molecular mechanisms that sustain structure-function relationship, in particular atomic details on the partner binding site. We will first describe herein some basic principles of solution NMR spectroscopy that should not be missed for a comprehensive reading of NMR reports. A series of results will then be presented to illustrate the wealth and variety of NMR experiments and how this approach enlightens tubulin/microtubules interaction with partners.

Rhazinilam and quebrachamine derivatives from Yunnan Kopsia arborea

Three new rhazinilam-derived alkaloids, kopsiyunnanines C1, C2, and C3, and a new quebrachamine-type alkaloid, kopsiyunnanine D, which possess an unusual methoxymethyl or ethoxymethyl function, were isolated from the aerial parts of Yunnan Kopsia arborea. This is the first report of the presence of these functions in natural alkaloids. The structures and absolute configurations of the alkaloids were determined by spectroscopic methods and confirmed by semisynthesis.

A new synthetic approach to biaryls of the rhazinilam type. Application to synthesis of three novel phenylpyridine-carbamate analogues

The synthesis of three novel racemic phenylpyridine-carbamate analogues of rhazinilam and their biological evaluation as inhibitors of microtubule assembly and disassembly by interaction with tubulin are described. The sterically hindered ortho-disubstituted biaryl unit as the challenging key structural element is first obtained by a sequential regiocontrolled nucleophilic addition of a lithium ortho-lithiohomobenzylic alkoxide species to 3-bromo-5-oxazolyl pyridine as the electrophile and a subsequent oxidation step. The incorporation of the amino group by replacement of the bromide has been achieved using a Buchwald-Hartwig amination coupling. Ultimate deprotection steps furnished free-amino and free-hydroxyl appendages which were connected by phosgenation to furnish the nine-membered median carbamate ring.

A Review on Recent Developments in Syntheses of the post-Secodine Indole Alkaloids. Part II: Modified Alkaloid Types

The second part of the planned review on developments in the field of total and formal total synthesis of the post-secodine indole alkaloids concentrates on modified alkaloid types, i.e. those skeletons derived from primary types by formation of additional and/or rupture of existing bonds, while connectivities next to indol(e)ine moiety remain intact. It thus reviews the synthesis of alkaloids of quebrachamine/cleavamine type including VLB-bis-indoles, rhazinilam type, aspidofractinine/kopsane and kopsifoline type, as well as kopsijasminilam alkaloids, lapidilectine B and danuphylline. It covers the literature of from 1991-1992 up to approximately end 2006. A review with 174 references.