Computational Studies and Biosynthesis of Natural Products with Promising Anticancer Properties

We present an overview of computational approaches for the prediction of metabolic pathways by which plants biosynthesise compounds, with a focus on selected very promising anticancer secondary metabolites from floral sources. We also provide an overview of databases for the retrieval of useful genomic data, discussing the strengths and limitations of selected prediction software and the main computational tools (and methods), which could be employed for the investigation of the uncharted routes towards the biosynthesis of some of the identified anticancer metabolites from plant sources, eventually using specific examples to address some knowledge gaps when using these approaches

Investigation of some plant stilbenoids and their fragments for the identification of inhibitors of SARS-CoV-2 viral spike/ACE2 protein binding

In silico binding studies were conducted on the known plant-derived polyphenolic tetrameric stilbenoids, (–)-hopeaphenol (1), vaticanol B (2) and vatalbinoside A (3) and their monomeric derivative resveratrol (8), identified from several plant species. The natural products (NPs) 1–3 had been previously evaluated against the SARS-CoV-2 protein targets responsible for viral transmission and infection. The two isomeric compounds (–)-hopeaphenol and vaticanol B had displayed a high affinity for blocking the binding of the SARS-CoV-2 viral spike with the human angiotensin-converting enzyme 2 (ACE2). Molecular docking and molecular dynamics simulations have been used to attempt to explain the affinity of the compounds to the spike/ACE2 complex. The hydrophobic properties of the respective target sites were computed and compared with the physicochemical properties of the NPs to explain the affinity of each compound toward the target site. Molecular docking and computed ADMET/DMPK profiles were also used to demonstrate the potential of the NPs and their fragments as possible lead compounds for antiviral discovery. These results support the experimental data obtained to date on 1–3 and clearly identify the stilbenoid structure class as one worthy of future studies during chemical biology and/or drug discovery antiviral efforts

An evaluation of spirooxindoles as blocking agents of SARS-CoV-2 spike/ACE2 interaction : synthesis, biological evaluation and computational analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gained significant public health attention owing to its devastating effects on lives and livelihoods worldwide. Due to difficult access to vaccines in many developing countries and the inefficiency of vaccines in providing complete protection even with fully vaccinated persons, there remains the need for the development of novel drugs to combat the disease. This study describes the in vitro activity of a library of fifty-five spiro-fused tetrahydroisoquinoline–oxindole hybrids (spirooxindoles) as potential blocking agents of the interaction between the SARS-CoV-2 viral spike and the human angiotensin-converting enzyme 2 (ACE2) receptor, essential for viral transmission. The synthesis was conducted by the Pictet-Spengler condensation of phenethylamine and isatin derivatives, while the screening against spike-ACE2 interaction was done using our previously described AlphaScreen fluorescent assay. The in vitro screening identified compound (11j) as the most active, showing a 50% inhibitory concentration (IC50) of 3.6 μM against SARS-CoV-2 spike/ACE2 interaction. Structure-activity relationships explained via molecular docking studies and the computation of binding free energy of each compound with respect to the spike/ACE2 protein-protein interaction showed that the most active compound possesses a bulky naphthyl group, which addresses voluminous hydrophobic regions of the ACE2 binding site and interacts with the hydrophobic residues of the target. Therefore, these compounds could be potentially useful in searching for SARS-CoV-2 spike/ACE2 interaction blocking agents

5-chloro-3-(2-(2,4-dinitrophenyl) hydrazono)indolin-2-one: synthesis, characterization, biochemical and computational screening against SARS-CoV-2

Chemical prototypes with broad-spectrum antiviral activity are important toward developing new therapies that can act on both existing and emerging viruses. Binding of the SARS-CoV-2 spike protein to the host angiotensin-converting enzyme 2 (ACE2) receptor is required for cellular entry of SARS-CoV-2. Toward identifying new chemical leads that can disrupt this interaction, including in the presence of SARS-CoV-2 adaptive mutations found in variants like omicron that can circumvent vaccine, immune, and therapeutic antibody responses, we synthesized 5-chloro-3-(2-(2,4-dinitrophenyl)hydrazono)indolin-2-one (H2L) from the condensation reaction of 5-chloroisatin and 2,4-dinitrophenylhydrazine in good yield. H2L was characterised by elemental and spectral (IR, electronic, Mass) analyses. The NMR spectrum of H2L indicated a keto–enol tautomerism, with the keto form being more abundant in solution. H2L was found to selectively interfere with binding of the SARS-CoV-2 spike receptor-binding domain (RBD) to the host angiotensin-converting enzyme 2 receptor with a 50% inhibitory concentration (IC50) of 0.26 μM, compared to an unrelated PD-1/PD-L1 ligand–receptor-binding pair with an IC50 of 2.06 μM in vitro (Selectivity index = 7.9). Molecular docking studies revealed that the synthesized ligand preferentially binds within the ACE2 receptor-binding site in a region distinct from where spike mutations in SARS-CoV-2 variants occur. Consistent with these models, H2L was able to disrupt ACE2 interactions with the RBDs from beta, delta, lambda, and omicron variants with similar activities. These studies indicate that H2L-derived compounds are potential inhibitors of multiple SARS-CoV-2 variants, including those capable of circumventing vaccine and immune responses

Binding Free Energy (BFE) Calculations and Quantitative Structure–Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 (smHDAC8) Inhibitors

Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC50 values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors

Case studies on computer-based identification of natural products as lead molecules

AbstractThe development and application of computer-aided drug design/discovery (CADD) techniques (such as structured-base virtual screening, ligand-based virtual screening and neural networks approaches) are on the point of disintermediation in the pharmaceutical drug discovery processes. The application of these CADD methods are standing out positively as compared to other experimental approaches in the identification of hits. In order to venture into new chemical spaces, research groups are exploring natural products (NPs) for the search and identification of new hits and more efficient leads as well as the repurposing of approved NPs. The chemical space of NPs is continuously increasing as a result of millions of years of evolution of species and these data are mainly stored in the form of databases providing access to scientists around the world to conduct studies using them. Investigation of these NP databases with the help of CADD methodologies in combination with experimental validation techniques is essential to identify and propose new drug molecules. In this chapter, we highlight the importance of the chemical diversity of NPs as a source for potential drugs as well as some of the success stories of NP-derived candidates against important therapeutic targets. The focus is on studies that applied a healthy dose of the emerging CADD methodologies (structure-based, ligand-based and machine learning).</jats:p

Compounds from African Medicinal Plants with Activities against Protozoal Diseases: Schistosomiasis, Trypanosomiasis and Leishmaniasis

Parasitic diseases continue represent a threat on a global scale, particularly among the poorest countries in the world. This is particularly because of the absence of vaccines, and in some cases, resistance against available drugs, currently being used for their treatment. In this review emphasis is laid on natural products and scaffolds from African medicinal plants (AMPs) for lead drug discovery and possible further development of drugs for the treatment of parasitic diseases. In the discussion, emphasis has been laid on alkaloids, terpenoids, quinones, flavonoids and narrower compound classes of compounds with micromolar range activities against Schistosoma, Trypanosoma and Leishmania species. Suggestions for future drug development from African medicinal plants have also been provided.</jats:p

Compounds from African Medicinal Plants with Activities Against Selected Parasitic Diseases: Schistosomiasis, Trypanosomiasis and Leishmaniasis

Abstract Parasitic diseases continue to represent a threat on a global scale, particularly among the poorest countries in the world. This is particularly because of the absence of vaccines, and in some cases, resistance against available drugs, currently being used for their treatment. In this review emphasis is laid on natural products and scaffolds from African medicinal plants (AMPs) for lead drug discovery and possible further development of drugs for the treatment of parasitic diseases. In the discussion, emphasis has been laid on alkaloids, terpenoids, quinones, flavonoids and narrower compound classes of compounds with micromolar range activities against Schistosoma, Trypanosoma and Leishmania species. In each subparagraph, emphasis is laid on the compound subclasses with most promising in vitro and/or in vivo activities of plant extracts and isolated compounds. Suggestions for future drug development from African medicinal plants have also been provided. This review covering 167 references, including 82 compounds, provides information published within two decades (1997–2017). Graphical Abstrac

A Bioactivity Versus Ethnobotanical Survey of Medicinal Plants from Nigeria, West Africa

Traditional medicinal practices play a key role in health care systems in countries with developing economies. The aim of this survey was to validate the use of traditional medicine within local Nigerian communities. In this review, we examine the ethnobotanical uses of selected plant species from the Nigerian flora and attempt to correlate the activities of the isolated bioactive principles with known uses of the plant species in African traditional medicine. Thirty-three (33) plant species were identified and about 100 out of the 120 compounds identified with these plants matched with the ethnobotanical uses of the plants