Application of Amino Acids in the Structural Modification of Natural Products: A Review

Design, synthesis, and in vivo and in vitro biological screening of pseudolaric acid B derivatives as potential anti-tumor agents

Pseudolaric Acid B (PAB), a natural product with remarkable anti-tumor activity, is a starting point for new anticancer therapeutics. We designed and synthesized 27 PAB derivatives and evaluated their anti-proliferative activities against four cancer cell lines: MCF-7, HCT-116, HepG2, and A549. Compared with unmodified PAB, the PAB derivatives showed stronger anti-proliferative activity. The ability of compound D3 (IC50 = 0.21 μM) to inhibit HCT-116 cells was approximately 5.3 times that of PAB (IC50 = 1.11 μM) and the antiproliferative action was unrelated to cytotoxicity (SI=20.38), indicating its superior safety profile (PAB; SI=0.95). Compound D3 effectively suppressed the EdU-positive rate and reduced colony formation, arrested HCT-116 cells in the S and G2/M phases and induced apoptosis. In vivo experiments further demonstrated low toxicity of compound D3 while suppressing tumor growth in mice. In summary, given its strong anti-proliferative effect and relative safety, further development of compound D3 is warranted.

Synthesis of Novel Planar-Chiral Charge-Compensated nido-Carborane-Based Amino Acid

Amino acids with unusual types of chirality and their derivatives have recently attracted attention as precursors in the synthesis of chiral catalysts and peptide analogues with unique properties. In this study, we have synthesized a new nido-carborane-based planar-chiral amino acid, in the molecule of which the amino group is directly bonded to the B(3) atom, and the carboxyl group is attached to the B(9) atom through the CH2S+(Me) fragment. 3-Amino-9-dimethylsulfonio-nido-carborane, prepared in three steps from 3-amino-closo-carborane in a high yield, was a key intermediate in the synthesis of the target planar-chiral amino acid. The carboxymethyl group at the sulfur atom was introduced by the demethylation reaction of the dimethylsulfonio derivative, followed by S-alkylation. The structure of new 3,9-disubstituted nido-carboranes was studied for the first time using NMR spectroscopy. The resonances of all boron atoms in the 11B NMR spectrum of 3-amino-9-dimethylsulfonio-nido-carborane were assigned based on the 2D NMR correlation experiments. The nido-carborane-based planar-chiral amino acid and related compounds are of interest as a basis for peptide-like compounds and chiral ligands.

Exploring the solubility and intermolecular interactions of biologically significant amino acids l-serine and L-cysteine in binary mixtures of H2O + DMF, H2O + DMSO and H2O + ACN in temperature range from T = 288.15 K to 308.15 K

In the presented work, a study on the solubility and intermolecular interactions of l-serine and L-cysteine was carried out in binary mixtures of H2O + dimethylformamide (DMF), H2O + dimethylsulfoxide (DMSO), and H2O + acetonitrile (ACN) in the temperature range of T = 288.15 K to 308.15 K. l-serine exhibited the highest solubility in water, while L-cysteine was more soluble in water-DMF. The solvation process was assessed through standard Gibbs energy calculations, indicating the solvation stability order: water-ACN > water-DMSO > water-DMF for l-serine, and water-DMF > water-DMSO > water-ACN for L-cysteine. This study also explored the influence of these amino acids on solvent-solvent interactions, revealing changes in chemical entropies and self-association patterns within the binary solvent mixtures.

Design, Synthesis, and Antitumor Activity of Isoliquiritigenin Amino Acid Ester Derivatives

Isoliquiritigenin (ISL) is a chalcone that has shown great potential in the treatment of cancer. However, its relatively weak activity and low water solubility limit its clinical application. In this study, we designed and synthesized 21 amino acid ester derivatives of ISL and characterized the compounds using 1H NMR and 13C NMR. Among them, compound 9 (IC50 = 14.36 μM) had a better inhibitory effect on human cervical cancer (Hela) than ISL (IC50 = 126.5 μM), and it was superior to the positive drug 5-FU (IC50 = 33.59 μM). The mechanism of the action experiment showed that compound 9 could induce Hela cell apoptosis and autophagy through the PI3K/Akt/mTOR pathway.

Design, synthesis, and evaluation of novel arecoline-linked amino acid derivatives for insecticidal and antifungal activities

A series of arecoline derivatives with amino acid moieties were designed and synthesised using an acylamide condensation strategy, taking arecoline as the foundational structure. The insecticidal efficacy of these compounds against Aphis craccivora and Tetranychus cinnabarinus was evaluated. Notably, derivatives 3h and 3i demonstrated superior insecticidal activity compared with arecoline. Additionally, 3h and 3i showed good fungicidal effectiveness against two types of plant fungi. Moreover, molecular docking analyses suggested that 3h and 3i could affect the nervous systems of A. craccivora and T. cinnabarinus by binding to neuronal nicotinic acetylcholine receptors. These findings suggest that compounds 3h and 3i represent promising leads for further development in insecticide and fungicide research.

Natural products in osteoarthritis treatment: bridging basic research to clinical applications

Osteoarthritis (OA) is the most prevalent degenerative musculoskeletal disease, severely impacting the function of patients and potentially leading to disability, especially among the elderly population. Natural products (NPs), obtained from components or metabolites of plants, animals, microorganisms etc., have gained significant attention as important conservative treatments for various diseases. Recently, NPs have been well studied in preclinical and clinical researches, showing promising potential in the treatment of OA. In this review, we summed up the main signaling pathways affected by NPs in OA treatment, including NF-κB, MAPKs, PI3K/AKT, SIRT1, and other pathways, which are related to inflammation, anabolism and catabolism, and cell death. In addition, we described the therapeutic effects of NPs in different OA animal models and the current clinical studies in OA patients. At last, we discussed the potential research directions including in-depth analysis of the mechanisms and new application strategies of NPs for the OA treatment, so as to promote the basic research and clinical transformation in the future. We hope that this review may allow us to get a better understanding about the potential bioeffects and mechanisms of NPs in OA therapy, and ultimately improve the effectiveness of NPs-based clinical conservative treatment for OA patients.

Evaluation of Antitumor Activity of Xanthones Conjugated with Amino Acids

Cancer is a complex disease characterized by several alterations, which confer, to the cells, the capacity to proliferate uncontrollably and to resist cellular death. Multiresistance to conventional chemotherapy drugs is often the cause of treatment failure; thus, the search for natural products or their derivatives with therapeutic action is essential. Chiral derivatives of xanthones (CDXs) have shown potential inhibitory activity against the growth of some human tumor cell lines. This work reports the screening of a library of CDXs, through viability assays, in different cancer cell lines: A375-C5, MCF-7, NCI-H460, and HCT-15. CDXs' effect was analyzed based on several parameters of cancer cells, and it was also verified if these compounds were substrates of glycoprotein-P (Pgp), one of the main mechanisms of resistance in cancer therapy. Pgp expression was evaluated in all cell lines, but no expression was observed, except for HCT-15. Also, when a humanized yeast expressing the human gene MDR1 was used, no conclusions could be drawn about CDXs as Pgp substrates. The selected CDXs did not induce significant differences in the metabolic parameters analyzed. These results show that some CDXs present promising antitumor activity, but other mechanisms should be triggered by these compounds.

Amino acids modified nanoscale zero-valent iron: Density functional theory calculations, experimental synthesis and application in the Fenton-like degradation of organic solvents

To improve the adsorption and catalytic performance of heterogeneous Fenton-like catalysts for oil wastes, amino acids were used to modify nanoscale zero-valent iron (AA@Fe0), which were applied in the Fenton-like degradation of organic solvents (tributyl phosphate and n-dodecane, named TBP and DD). Twelve amino acids, i.e., glycine (Gly), alanine (Ala), leucine (Leu), proline (Pro), phenylalanine (Phe), methionine (Met), cysteine (Cys), asparagine (Asn), serine (Ser), glutamic acid (Glu), lysine (Lys) and arginine (Arg), were selected and calculated by density functional theory (DFT). The optimized structure, charge distribution, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), interaction region indicator (IRI) isosurface map and adsorption energy of AA@Fe0, AA@Fe0-TBP and AA@Fe0-DD were studied, which indicated that Fe is more likely to approach and charge transfer with -COO and -NH3 on the α-carbon of amino acids. There is strong attraction between Fe and -COO, and Van der Waals force between Fe and -NH3, respectively. In the interaction of AA@Fe0 with TBP and DD, Van der Waal force plays an important role. AA@Fe0 was synthesized in laboratory and characterized to investigate physicochemical properties. In Fenton-like degradation of organic solvents, the change of COD in water phase during the degradation process as well as the volume of the organic phase after the reaction were investigated. The results of calculations combined with experiments showed that Ser-modified Fe0 performed the best in these amino acids, with 98% removal of organic solvents. A possible catalytic mechanism was proposed in which amino acids acted a linking role between Fe and organic solvents, activating H2O2 to generate hydroxyl radicals for the degradation of organic solvents.

Bioactivities and Structure-Activity Relationships of Usnic Acid Derivatives: A Review

Usnic acid has a variety of biological activities, and has been widely studied in the fields of antibacterial, immune stimulation, antiviral, antifungal, anti-inflammatory and antiparasitic. Based on this, usnic acid is used as the lead compound for structural modification. In order to enhance the biological activity and solubility of usnic acid, scholars have carried out a large number of structural modifications, and found some usnic acid derivatives to be of more potential research value. In this paper, the structural modification, biological activity and structure-activity relationship of usnic acid were reviewed to provide reference for the development of usnic acid derivatives.

Development of trisubstituted thiophene-3-arboxamide selenide derivatives as novel EGFR kinase inhibitors with cytotoxic activity

Overexpression of EGFR is one of the eminent oncogenic drivers detected in the development of several human cancers. The increasing incidences of mutation-based resistance in the tyrosine kinase domain call upon the need for the development of a newer class of small-molecule TK inhibitors. Accordingly, a new series of symmetrical trisubstituted thiophene-3-carboxamide selenide derivatives was developed via the hybridization of complementary pharmacophores. Most of the compounds showed a modest to excellent antiproliferative action at 20 μM concentration. The utmost antiproliferative activity was portrayed by compound 16e on the selected cancer cell lines with IC50 < 9 μM, the lowest being 3.20 ± 0.12 μM in the HCT116 cell line. Further, it also displayed an impressive EGFR kinase inhibition with an IC50 value of 94.44 ± 2.22 nM concentration. As a corollary of the reported EGFR inhibition, the nature, energy, and stability of the binding interactions were contemplated via in silico studies.

Natural Products-Pyrazine Hybrids: A Review of Developments in Medicinal Chemistry

Pyrazine is a six-membered heterocyclic ring containing nitrogen, and many of its derivatives are biologically active compounds. References have been downloaded through Web of Science, PubMed, Science Direct, and SciFinder Scholar. The structure, biological activity, and mechanism of natural product derivatives containing pyrazine fragments reported from 2000 to September 2023 were reviewed. Publications reporting only the chemistry of pyrazine derivatives are beyond the scope of this review and have not been included. The results of research work show that pyrazine-modified natural product derivatives have a wide range of biological activities, including anti-inflammatory, anticancer, antibacterial, antiparasitic, and antioxidant activities. Many of these derivatives exhibit stronger pharmacodynamic activity and less toxicity than their parent compounds. This review has a certain reference value for the development of heterocyclic compounds, especially pyrazine natural product derivatives.

Recent Review on the Extraction and Qualitative Assay of Cysteine and Other Amino Acids from Vellore Feather Waste and Molecular Docking Studies of Cysteine for Pharmacological Applications

Products produced from waste are a relatively recent innovation. Feather substrates are abundant in keratin content and improper disposal can cause ecosystem contamination. However, these pollutants can be transformed into value-added products for industrial application. Physical, chemical and cutting-edge microbiological methods were utilized for decomposing keratin and aid in the identification and estimation of amino acids from poultry feather wastes. These beneficial approaches are receiving more attention due to their retrieval of harmless and value added byproducts. These keratin-based compounds are used widely in pharmaceutical, livestock feed, fertilizer, and a variety of other industrial sectors. Since keratin is primarily consisting of amino acids, it can be utilized to affirm and estimate the amino acids in these feather substrates. This study primarily highlights the various methodologies employed for the qualitative estimation of amino acids in feather waste samples and the inhibitory activity of keratinase enzyme by EDTA and pepstatin in order to accumulate amino acids for drug delivery purpose and their importance in various pharmaceutical industries. In addition to that, molecular docking studies of cysteine with many standard pharmaceutical drugs like acetaminophen, pethidine, methylphenidate, carbamazepine, cillin and amlodipine were performed using autodock to demonstrate how cysteine greatly reduces conventional drug toxicity and its side effects.

Synthesis and Antitumor Activity of Panaxadiol Pyrazole and Isooxazole Derivatives

In this study, we designed and synthesized 19 nitrogen-containing heterocyclic derivatives of panaxadiol (PD). We first reported the antiproliferative activity of these compounds against four different tumor cells. The results of the MTT assay showed that the PD pyrazole derivative (compound 12b) had the best antitumor activity and could significantly inhibit the proliferation of four tested tumor cells. For A549 cells, the IC50 value was as low as 13.44±1.23 μM. Western blot analysis showed that the PD pyrazole derivative was a bifunctional regulator. On the one hand, it can down-regulate the expression of HIF-1α by acting on PI3 K/AKT signaling pathway in A549 cells. On the other hand, it can induce the decrease of CDKs protein family and E2F1 protein expression levels, thus playing a crucial role in cell cycle arrest. According to the results of molecular docking, we found that multiple hydrogen bonds were formed between the PD pyrazole derivative and two related proteins, and the docking score of the derivative was also significantly higher than that of the crude drug. In summary, the study of the PD pyrazole derivative laid a foundation for the development of ginsenoside as an antitumor agent.

2',4'-Dihydroxy-6'‑methoxy-3',5'-dimethylchalcone and its amino acid-conjugated derivatives induce G0/G1 cell cycle arrest and apoptosis via BAX/BCL2 ratio upregulation and in silico insight in SiHa cell lines

We modified the chemical structure of 2',4'-dihydroxy-6'‑methoxy-3',5'-dimethylchalcone (DMC, 1), a phytochemical found in the seed of Syzygium nervosum A.Cunn. ex DC., by conjugation with the amino acid L-alanine (compound 3a) or L-valine (compound 3b) to enhance anticancer activity and water solubility. Compounds 3a and 3b had antiproliferative activity in human cervical cancer cell lines (C-33A, SiHa and HeLa), with half-maximal inhibitory concentrations (IC₅₀) of 7.56 ± 0.27 and 8.24 ± 0.14 µM, respectively in SiHa cells; these values were approximately two-fold greater than DMC. We investigated the biological activities of compounds 3a and 3b based on a wound healing assay, a cell cycle assay and messenger RNA (mRNA) expression analysis to determine the possible mechanism of anticancer activity. Compounds 3a and 3b inhibited SiHa cell migration in the wound healing assay. After treatment with compounds 3a and 3b, there was an increase in SiHa cells in the G1 phase, indicative of cell cycle arrest. Moreover, compound 3a showed potential anticancer activity by upregulating TP53 and CDKN1A that resulted in upregulation of BAX and downregulation of CDK2 and BCL2, leading to apoptosis and cell cycle arrest. The BAX/BCL2 expression ratio was increased after treatment with compound 3avia the intrinsic apoptotic pathway. In silico molecular dynamics simulation and binding free energy calculation shed light on how these DMC derivatives interact with the HPV16 E6 protein, a viral oncoprotein associated with cervical cancer. Our findings suggest that compound 3a is a potential candidate for anti-cervical cancer drug development.

Modular Synthesis of Unnatural Peptides via Rh(III)-Catalyzed Diastereoselective Three-Component Carboamidation Reaction

Herein we report a modular peptide ligation methodology that couples dioxazolones, arylboronic acids, and acrylamides to construct amide bonds in a diastereoselective manner under mild conditions, facilitated by Rh(III) catalysis. By converting the C-terminus of one peptide into a dioxazolone and the N-terminus of a second peptide into an acrylamide, the two pieces can be bridged by an arylboronic acid to construct unnatural phenylalanine, tyrosine, and tryptophan residues at the junction point with diastereoselectivity for their corresponding d-stereocenters. The reaction exhibits excellent functional group tolerance with a large substrate scope and is compatible with a wide array of protected amino acid residues that are utilized in Fmoc solid phase peptide synthesis. The methodology is applied to the synthesis of six diastereomeric proteasome inhibitor analogs, as well as the ligation of two 10-mer oligopeptides to construct a 21-mer polypeptide with an unnatural phenylalanine residue at the center.

Synthesis and Antioxidant Evaluation of O-Methylated Emodacidamides: Starting from Parietin, a Secondary Metabolite of Lichen Xanthoria parietina

Polyhydroxy-anthraquinones bearing amino acids are found rather seldom in nature. Emodacidamides, isolated from a marine-derived fungus, Penicillium sp. SCSIO sof101 by Luo et al. (2017) are the first natural example of amino acid conjugated anthraquinone. In this study, O-methylated emodacidamides and emodinic acid-anilides were synthesized starting from parietin, extracted from the lichen Xanthoria parietina (L.) Th. Fr. The structural elucidations of prepared compounds were confirmed by 1D and 2D NMR analyses including HSQC and HMBC techniques. In addition, all newly synthesized compounds were evaluated for the antioxidant activities with free radical 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging. The synthesized compounds showed low to moderate antioxidant and DPPH scavenging activities. The antioxidant activities were supported within quantum chemical calculations using the DFT-B3LYP/6-311++G(d,p) level of theory. It is observed that the antioxidant activity of emodacidamides mostly depends on the phenolic groups on anthraquinone ring. The phenolic groups on other substituents help to improve antioxidant activity and also the position of hydroxy group is a decisive factor for antioxidant ability.

Development of amino acid-modified biodegradable lipid nanoparticles for siRNA delivery

The use of siRNA therapeutics to treat cancer is a very promising approach. However, specific delivery of siRNAs to tumors remains a major challenge. The recent success of siRNA delivery to the liver has incentivized the development of biomaterials for siRNA delivery into tumors. Here, we report a new class of amino acid-modified lipids for siRNA delivery to cancer cells. Eight lipids were developed by headgroup modification with histidine and lysine. The lipids were screened in PC3-luciferase stable cells for gene silencing and cellular cytotoxicity study. The best lipid LHHK shows a pKa of 6.08, which is within the optimal pKa range of lipid nanoparticles (LNPs) for siRNA delivery. The LHHK LNP protects siRNA from serum degradation for up to 24 h and shows higher endosomal release and better cellular uptake compared to other lysine-modified lipids in PC3 cells. The LHHK LNP exhibits significant silencing activity of IKKα and IKBKE in prostate cancer and pancreatic cancer, respectively. Moreover, the LHHK LNP encapsulating IKBKE siRNA inhibits cell proliferation of pancreatic cancer cells and suppresses the tumor progression in a pancreatic cancer mouse model. STATEMENT OF SIGNIFICANCE: Lipid nanoparticle (LNP) is a promising platform for siRNA delivery. However, LNP is generally associated with high systemic toxicity. As a result, efficient and biodegradable lipids are highly needed for siRNA-based cancer therapy. Herein, we develop amino acid-modified biodegradable lipids. These lipids show very low cellular toxicity and high transfection efficiency. The best lipid LHHK shows a pKa of 6.08, which is within the optimal pKa range of LNPs for siRNA delivery. The LHHK LNP efficiently silences IKKα and IKBKE in prostate and pancreatic cancer, respectively. Moreover, the LHHK LNP encapsulating IKBKE siRNA inhibits cell proliferation and suppresses tumor growth of pancreatic cancer in vivo. These results suggest that amino acid-modified lipids possess a great potential for siRNA delivery in cancer therapy.

Understanding and Circumventing the Requirement for Native Thioester Substrates for α-Oxoamine Synthase Reactions

Many enzyme classes require thioester electrophiles such as acyl-carrier proteins and acyl-coenzyme A substrates. For in vitro applications, these substrates can render these chemical transformations impractical. To address this challenge, we have investigated the mechanism of coenzyme A in gating catalysis of one α-oxoamine synthase, SxtA AOS. Through investigating the reactivity of SxtA AOS and corresponding enzyme variants against a panel of substrates and coenzyme A mimics, we determined that activity is gated through the binding of the pantetheine arm and a phosphate group that hydrogen bonds to residue Lys154 that is predicted by an AlphaFold2 model to be located in a tunnel leading to the active site. To provide an economical solution for preparative-scale reactions, in situ transthioesterification was used with pantetheine and simple thioester substrate precursors, resulting in productive reactions. These findings outline a strategy for employing ACP- and CoA-dependent enzymes that are inaccessible through other means without the need for cost-prohibitive coenzyme A or carrier protein-activated substrates.

Recent advances in chemical synthesis, biocatalysis, and biological evaluation of diosgenin derivatives - A review

Extracting organic compounds from plants and developing derivatives are essential methods for drug discovery. Diosgenin, extracted from Dioscoreaceae plants, is a type of spirostan steroid with various biological effects, including anti-inflammation, neuro-protection, and apoptosis-induction. Many researchers committed their work to the chemical semi-synthesis of diosgenin derivatives to improve diosgenin's therapeutic bioavailability and expand its range of applications in disease treatment and prevention. Biotransformation, a mild whole-cell biocatalysis method, also made crucial contributions to the structural diversity of diosgenin analogs in recent years. Although the structural modification of diosgenin has made significant progress, it lacks a comprehensive review. Here, we review the chemical modification and biotransformation of diosgenin along with the biological evaluation of diosgenin derivatives to provide a reference for the structural modification strategy and pharmaceutical application of diosgenin derivatives.

Chiral Flavonoids as Antitumor Agents

Flavonoids are a group of natural products with a great structural diversity, widely distributed in plant kingdom. They play an important role in plant growth, development and defense against aggressors. Flavonoids show a huge variety of biological activities such as antioxidant, anti-inflammatory, anti-mutagenic, antimicrobial and antitumor, being able to modulate a large diversity of cellular enzymatic activities. Among natural flavonoids, some classes comprise chiral molecules including flavanones, flavan-3-ols, isoflavanones, and rotenoids, which have one or more stereogenic centers. Interestingly, in some cases, individual compounds of enantiomeric pairs have shown different antitumor activity. In nature, these compounds are mainly biosynthesized as pure enantiomers. Nevertheless, they are often isolated as racemates, being necessary to carry out their chiral separation to perform enantioselectivity studies. Synthetic chiral flavonoids with promising antitumor activity have also been obtained using diverse synthetic approaches. In fact, several new chiral bioactive flavonoids have been synthesized by enantioselective synthesis. Particularly, flavopiridol was the first cyclin-dependent kinase (CDK) inhibitor which entered clinical trials. The chiral pool approaches using amino acid as chiral building blocks have also been reported to achieve small libraries of chrysin derivatives with more potent in vitro growth inhibitory effect than chrysin, reinforcing the importance of the introduction of chiral moieties to improve antitumor activity. In this work, a literature review of natural and synthetic chiral flavonoids with antitumor activity is reported for the first time.