Natural Product-based Compounds Research Articles

Nature's Toolbox for Alzheimer's Disease: A Review on the Potential of Natural Products as Alzheimer's Disease Drugs

Numerous clinical trials involving natural products have been conducted to observe cognitive performances and biomarkers in Alzheimer's Disease (AD) patients. However, to date, no natural-based drugs have been approved by the FDA as treatments for AD. In this review, natural product-based compounds that were tested in clinical trials from 2011 to 2023, registered at www.clinicaltrials.gov were reviewed. Thirteen compounds, encompassing 7 different mechanisms of action were covered. Several observations were deduced, which are: i) several compounds showed cognitive improvement, but these improvements may not extend to AD, ii) compounds that are endogenous to the human body showed better outcomes, and iii) Docosahexaenoic acid (DHA) and cerebrolysin had the most potential as AD drugs among the 13 compounds. Based on the current findings, natural products may be more suitable as a supplement than AD drugs in most cases. However, the studies covered here were conducted in a relatively short amount of time, where compounds acting on AD pathways may take time to show any effect. Given the diverse pathways that these natural products are involved in, they may potentially produce synergistic effects that would be beneficial in treating AD. Additionally, natural products benefit from both physicochemical properties being in more favorable ranges and active transport playing a more significant role than it does for synthetic compounds.

Structure-based virtual screening and molecular docking approaches to identify potential inhibitors against KIF2C to combat glioma

Glioma, a kind of malignant brain tumor, is extremely lethal. Kinesin family member 2C (KIF2C) was found to have an aberrant expression in several cancer types, including lung cancer and glioma. KIF2C may therefore be a useful therapeutic target for the treatment of glioma. In the current study, new drug candidates that may function as KIF2C enzyme inhibitors were discovered. MTi OpenScreen was used to carry out the structure-based virtual screening of an inbuilt drug library containing 150,000 compounds. These compounds belong to different classes, such as natural product-based compounds (NP-lib), purchasable approved drugs (Drugs-lib), and food constituents compound collection (FOOD-lib). Based on their binding affinities, a total of 84 compounds were further pushed to calculate ADMET properties. The compounds (16) meeting the ADMET cutoff ranges were then further docked to the receptor to find their plausible binding modes using the Glide tool’s standard precision (SP) technique. The docking results were examined using the Glide gscore, and the best binding compounds (Rimacalib and Sarizotan) were chosen to test their stability with KIF2C protein through molecular dynamics (MD) simulation. Similarly, Principal Component Analysis and cross-correlation matrix were also examined. The MM/GBSA binding free energies showed a considerable energy contribution in the binding of hits with the KIF2C. Collectively, these findings strongly suggest the potential of the lead compounds to inhibit the biological function of KIF2C, emphasizing the need for further investigation in this area. Communicated by Ramaswamy H. Sarma

Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches.

3CLpro is a viable target for developing antiviral therapies against the coronavirus. With the urgent need to find new possible inhibitors, a structure-based virtual screening approach was developed. This study recognized 75 pharmacologically bioactive compounds from our in-house library of 1052 natural product-based compounds that satisfied drug-likeness criteria and exhibited good bioavailability and membrane permeability. Among these compounds, three promising sulfonamide chalcones were identified by combined theoretical and experimental approaches, with SWC423 being the most suitable representative compound due to its competitive inhibition and low cytotoxicity in Vero E6 cells (EC50 = 0.89 ± 0.32 μM; CC50 = 25.54 ± 1.38 μM; SI = 28.70). The binding and stability of SWC423 in the 3CLpro active site were investigated through all-atom molecular dynamics simulation and fragment molecular orbital calculation, indicating its potential as a 3CLpro inhibitor for further SARS-CoV-2 therapeutic research. These findings suggested that inhibiting 3CLpro with a sulfonamide chalcone such as SWC423 may pave the effective way for developing COVID-19 treatments.

Discovery of a chalcone derivative as an anti-fibrotic agent targeting transforming growth factor-β1 signaling: Potential therapy of renal fibrosis

As a final common pathway of renal injuries, renal fibrosis leads to chronic kidney disease (CKD). Currently, there is no safe and effective therapy to prevent the progression of renal fibrosis to CKD. Inhibition of transforming growth factor-β1 (TGF-β1) pathway is proposed as one of the most promising approaches for anti-renal fibrosis therapies. This study aimed to identify novel anti-fibrotic agents using the TGF-β1-induced fibrosis in renal proximal tubule epithelial cells (RPTEC) and characterize their mechanism of action as well as in vivo efficacy. By screening 362 natural product-based compounds for their ability to reduce collagen accumulation assessed by picro-sirius red (PSR) staining in RPTEC cells, a chalcone derivative AD-021 was identified as an anti-fibrotic agent with IC50 of 14.93 μM. AD-021 suppressed TGF-β1-induced collagen production, expression of pro-fibrotic proteins (fibronectin and α-smooth muscle actin (αSMA)), and Smad-dependent and Smad-independent signaling pathways via suppression of TGF-β receptor II (TGFβRII) phosphorylation in RPTEC cells. Furthermore, TGF-β1-induced mitochondrial fission in RPTEC cells was ameliorated by AD-021 via mechanisms involving inhibition of Drp1 phosphorylation. In a mouse model of unilateral ureteral obstruction (UUO)-induced renal fibrosis, AD-021 reduced plasma TGF-β1, ameliorated renal fibrosis and improved renal function. Collectively, AD-021 represents a novel class of natural product-based anti-fibrotic agent that has therapeutic potential in the prevention of fibrosis-associated renal disorders including CKD.

In vitro screening of natural product-based compounds for leishmanicidal activity.

Leishmaniasis is one of the major parasitic diseases, caused by obligate intracellular protozoa Leishmania, having high mortality as well as morbidity rate. As there is no human licensed vaccine available against leishmaniasis, chemotherapy remains the major way of combating this disease. Many disadvantages are known to be associated with the current drug regime including severe side effects and toxicity, long duration and expensive treatment, and the emergence of resistance. An alternative approach is being utilized to search for active molecules using natural sources, rather than relying on synthetic drugs. Many plant-derived secondary metabolites like phenolic compounds, steroids, quinones, etc. are being extensively investigated for their anti-leishmanial potential. One such group of complex phenolic compounds are diarylheptanoids. These compounds have been shown to exhibit anti-inflammatory, anti-parasitic, anti-fungal, and other pharmacological activities. In the present study, a set of sixteen tetrahydropyran derivatives including three natural products were obtained in lyophilized form. These compounds with trans-2,6-disubstituted tetrahydropyrans, Diospongin A, Diospongin B (isolated from Dioscorea spongiosa) and Centrolobine (Centrolobium sclerophyllum) as parent compounds were synthesized by the reaction of 1-phenyl-1-triemthylsiloxyethylene with six-membered cyclic hemiacetals in the presence of iodine as a catalyst. All the sixteen synthesized tetrahydropyran derivatives were used for toxicity analysis against L. donovani promastigotes, amastigotes and THP-1-derived human macrophages. IC50 values and selectivity index were calculated for all the compounds. Out of these sixteen, five compounds showed the best effect in vitro in terms of both leishmanicidal activity and non-toxicity to human macrophages.

An Overview of the Curcumin-Based and Allicin Bioactive Compounds as potential treatment to SARS-CoV-2 with structural bioinformatics tools

The recent outbreak of SARS-CoV-2 across the globe and the absence of a specific cure against the disease lead the scientific community to investigate some alternative indigenous treatments. SARS-CoV-2 is the virus responsible for the coronavirus ailment 2019 (COVID-19). This virus has 4 auxiliary proteins namely the S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins. The main proteases and RNA dependent RNA polymerase are also essential structures by which the virus replicates and survives. Each of these proteins are structures of the virus that are potential targets for drugs which are leads in the drug discovery process of any drug for the virus. Currently available treatments are not specific to the disease and therefore carry unwanted adverse effects that can be highly dangerous and sometimes fatal. Many of these treatments are supplementary in nature or based on repurposed drugs from other viral outbreaks. Alternatives of conventional drugs are required to control the spread and severity of the disease. Allicin, curcumin and their derivatives have been researched for their antiviral property and shown to have good binding affinity towards SARS-CoV-2 structures essential in their survival, especially the main proteases and RNA dependent RNA polymerases. The structural bioinformatics tools have elicited methods to predict the bioactivity of the natural product-based compounds. Apart from the beneficial medication that they offer, natural products carry along other advantages for the current pandemic situation in terms of supply, logistics, and affordability.

Identification of novel natural MurD ligase inhibitors as potential antimicrobial agents targeting Acinetobacter baumannii: In silico screening and biological evaluation

The increased multidrug resistance in Acinetobacter baumannii (A. baumannii) to the present-day known antibiotics has stimulated academic and industrial efforts globally for the development of novel antibacterial agents. Natural compounds as potential drug leads are gaining significant attention due to their less toxic and more tolerant nature. In the current study, the natural product-based compounds were explored as probable inhibitors of UDP-N-acetylmuramoyl-L-alanine:D-glutamate (MurD) ligase from A.baumannii (AbMurD) to provide a new class of drug leads. The prepared natural library of 3,16,714 compounds from ZINC database was screened into the active site of AbMurD using in silico high-throughput virtual screening which resulted in 100 compounds having high binding affinities. Further screening through flexible molecular docking yielded four potential compounds selected on the basis of estimated binding affinity (ΔG) and favorable protein-ligand interactions. MD simulation of these four compounds under physiological conditions and free binding energy calculations using MM/PBSA (molecular mechanics with Poisson- Boltzmann and surface area solvation) approach revealed three compounds ZINC08879777, ZINC30726863, and ZINC95486217 as potential binders of AbMurD. The calculated physicochemical and ADME properties of these compounds revealed that they can be exploited and modified to improve their binding affinity with the enzyme. Two compounds were purchased and tested against bacterial cell cultures of A. baumannii, Salmonella Typhi, and Staphylococcus aureus to determine their broad-spectrum antibacterial activity. The results suggest that the identified compounds can be exploited as potential herbal leads to target both Gram-positive and Gram-negative pathogens. Communicated by Ramaswamy H. Sarma

Natural products as inhibitors of COVID-19 main protease–A virtual screening by molecular docking

Background: The novel coronavirus (2019-nCoV) causes a severe respiratory illness unknown to a human before. Its alarmingly quick transmission to many countries across the world has resulted in a global health emergency. Therefore, an imminent need for drugs to combat this disease has been increased. Worldwide collaborative efforts from scientists are underway to determine a therapy to treat COVID-19 infections and reduce mortality rates. Since herbal medicines and purified natural products have been reported to have antiviral activity against Coronaviruses (CoVs), this in silico evaluation was performed for identifying potential natural compounds with promising inhibitory activities against COVID-19. Methods: In this study, a High Throughput Virtual Screening (HTVS) protocol was used as a fast method for discovering novel drug candidates as potential COVID-19 main protease (Mpro) inhibitors. Over 180,000 natural product-based compounds were obtained from the ZINC database and virtually screened against the COVID-19 Mpro. In this study, the Glide docking program was applied for high throughput virtual screening. Also, Extra precision (XP) has been used following the induced-fit docking (IFD) approach. The ADME properties of all compounds were analyzed and a final selection was made based on the Lipinski rule of five. Also, molecular dynamics (MD) simulations were conducted for a virtual complex of the best scoring compound with COVID-19 protease. Results: Nineteen compounds were introduced as new potential inhibitors. Compound ZINC08765174 (1-[3-(1H-indol-3-yl) propanoyl]-N-(4-phenylbutan-2-yl)piperidine-3-carboxamide showed a strong binding affinity (-11.5 kcal/mol) to the COVID-19 Mpro comparing to peramivir (-9.8 kcal/mol) as a positive control. Conclusions: Based on these findings, nineteen compounds were proposed as possible new COVID-19 inhibitors, of which ZINC08765174 had a high affinity to Mpro. Furthermore, the promising ADME properties of the selected compounds emphasize their potential as attractive candidates for the treatments of COVID-19.

Strategies towards expansion of chemical space of natural product-based compounds to enable drug discovery

Natural products (NPs) are an excellent source of biologically active molecules that provide many biologically biased features that enable innovative designing of synthetic compounds. NPs are characterized by high content of sp3 -hybridized carbon atoms; oxygen; spiro, bridged, and linked systems; and stereogenic centers, with high structural diversity. To date, several approaches have been implemented for mapping and navigating into the chemical space of NPs to explore the different aspects of chemical space. The approaches providing novel opportunities to synthesize NP-inspired compound libraries involve NP-based fragments and ring distortion strategies. These methodologies allow access to areas of chemical space that are less explored, and consequently help to overcome the limitations in the use of NPs in drug discovery, such as lack of accessibility and synthetic intractability. In this review, we describe how NPs have recently been used as a platform for the development of diverse compounds with high structural and stereochemical complexity. In addition, we show developed strategies aiming to reengineer NPs toward the expansion of NP-based chemical space by fragment-based approaches and chemical degradation to yield novel compounds to enable drug discovery.

Activities of wogonin analogs and other flavones against Flavobacterium columnare.

In our on-going pursuit to discover natural products and natural product-based compounds to control the bacterial species Flavobacterium columnare, which causes columnaris disease in channel catfish (Ictalurus punctatus), we synthesized flavone and chalcone analogs, and evaluated these compounds, along with flavonoids from natural sources, for their antibacterial activities against two isolates of F. columnare (ALM-00-173 and BioMed) using a rapid bioassay. The flavonoids chrysin (1a), 5,7-dihydroxy-4'-methoxyflavone (11), isorhamnetin (26), luteolin (27), and biochanin A (29), and chalcone derivative 8b showed strong antibacterial activities against F. columnare ALM-00-173 based on minimum inhibition concentration (MIC) results. Flavonoids 1a, 8, 11, 13 (5,4'-dihydroxy-7-methoxyflavone), 26, and 29 exhibited strong antibacterial activities against F. columnare BioMed based upon MIC results. The 24-h 50% inhibition concentration (IC50 ) results revealed that 27 and 29 were the most active compounds against F. columnare ALM-00-173 (IC50 of 7.5 and 8.5 mg/l, resp.), while 26 and 29 were the most toxic compound against F. columnare BioMed (IC50 of 9.2 and 3.5 mg/l, resp.). These IC50 results were lower than those obtained for wogonin against F. columnare ALM-00-173 and F. columnare BioMed (28.4 and 5.4 mg/l, resp.). However, based on MIC results, none of the compounds evaluated in this study were as active as wogonin (MIC 0.3 mg/l for each F. columnare isolate). Further modification of the wogonin structure to enhance antibacterial is of interest.

Zebrafish: predictive model for targeted cancer therapeutics from nature.

Targeted therapy, the treatment of cancer based on an underlying genetic alteration, is rapidly gaining favor as the preferred therapeutic approach. To date, although natural products represent a rich resource of bio-diverse drug candidates, only a few have been identified to be effective as targeted cancer therapies largely due to the incompatibilities to current high-throughput screening methods. In this article, we review the utility of a zebrafish developmental screen for bioactive natural product-based compounds that target signaling pathways that are intimately shared with those in humans. Any bioactive compound perturbing signaling pathways identified from phenotypic developmental defects in zebrafish embryos provide an opportunity for developing targeted therapies for human cancers. This model provides a promising tool in the search for targeted cancer therapeutics from natural products.

Evaluation of insecticidal activity of camptothecin analogs against Brontispa longissima

Continuing our search for natural product-based compounds for the control of Brontispa longissima Larvae, 31 camptothecin analogs were first tested for their insecticidal activity against the fifth-instar larvae of B. longissima in vivo. Among them, compounds 6–8, 11, 26, 28, and 29 showed more promising and pronounced insecticidal activity than toosendanin, a commercial insecticide derived from Melia azedarach. The different insecticidal activity ranges of compounds 1–31 indicated that variation of chemical structures in the camptothecin skeleton markedly affected the activity profiles of this compound class, and some important SAR information has been revealed from it. The quantitative structure–activity relationship (QSAR) model was applied to provide insight into the camptothecin analogs’ structural properties that are responsible for their activities. The results obtained from SAR analysis showed good correlation with the QSAR studies, which allowed for the rational design of more potent camptothecin analogs in the development of potential new insecticides.

Antifeedant Activity of Spin-Labeled Derivatives of Deoxypodophyllotoxin against Brontispa longissima Larvae

To continue our search for natural product-based compounds for the control of Brontispa longissima larvae, eight spin-labeled podophyllotoxin derivatives (4a-h) and the intermediates 2 and 3 were tested for their insect antifeedant activity against third-instar larvae of B. longissima. Among all the tested compounds, 4a, 4c, 2 and 3 showed pronounced antifeedant activities with AFC50 values of 0.16, 0.31, 0.15 and 0.28 mg/mL, respectively. The different antifeedant activity ranges of these compounds indicated that variation of the structures of L-amino acids in these compounds markedly affected the activity profiles of this compound class, and some important SAR information has been revealed from it.

Synthesis and insect antifeedant activity of stilbene derivatives against Brontispa longissima Larvae

Continuing our search for natural product-based compounds for the control of B. longissima Larvae, 25 stilbene analogs were synthesized and evaluated for insect antifeedant activity against third-instar larvae of B. longissima for the first time. Among all the tested compounds, especially compounds 3a, 3c, and 6 showed pronounced antifeedant activities with AFC50 values of 0.218, 0.327, and 0.226 mg/mL, respectively. The different antifeedant activity ranges of these compounds indicated that variation of chemical structures in the stilbene skeleton markedly affected the activity profiles of this compound class, and some important SAR information has been revealed from it. In addition, to understand the structural requirements for antifeedant activities of the 25 synthesized stilbene analogs, a comparative molecular field analysis (CoMFA) model, which yielded the leave-one-out (LOO) cross-validated correlation coefficient (q2) of 0.533 and a non-cross-validated correlation coefficient (r2) of 0.929, was constructed. Together, these preliminary results may be useful in guiding further modification of stilbenes in the development of potential new antifeedants.

Activity of Lycorine Analogues against the Fish Bacterial Pathogen Flavobacterium columnare

In a continuing effort to discover natural products and natural product-based compounds for the control of columnaris disease in channel catfish (Ictalurus punctatus), 17 lycorine analogues were synthesized, including new benzoyl analogues 6-16, and evaluated for antibacterial activity against two isolates (ALM-00-173 and BioMed) of Flavobacterium columnare using a rapid bioassay. Two of the lycorine analogues had greater antibacterial activity than 1-O-acetyllycorine, an analogue of lycorine evaluated previously that is highly active against both isolates. Carbamate analogue 18 (1S,2S,3a(1)S,12bS)-2,3a(1),4,5,7,12b-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridin-1,2-diylbis(o-tolylcarbamate) had the strongest antibacterial activity toward both F. columnare isolates ALM-00-173 and BioMed, with 24-h IC(50) values of 3.0 ± 1.3 and 3.9 ± 2.2 mg/L, respectively, and a MIC of 5.5 ± 0 mg/L for both isolates. Compound 18 appears to be the most promising lycorine analogue for future efficacy studies to determine its potential for use as an alternative to the currently used compounds to control columnaris disease in channel catfish.

Algicidal Activity of Stilbene Analogues

Continuing our search for natural product and natural product-based compounds for the control of off-flavor in catfish, 29 stilbene analogues were synthesized and evaluated for algicidal activity against the 2-methylisoborneol (MIB)-producing cyanobacterium Oscillatoria perornata. The cis and trans isomers of 4-(3,5-dimethoxystyryl)aniline showed moderate and selective algicidal activity toward O. perornata with the lowest observed inhibitory concentration and lowest complete inhibition concentrations of 10 muM. This is the first report on selective stilbene algicidal activity toward a MIB-producing cyanobacteria species.

Natural Product-Based Phenolic and Nonphenolic Antimicrobial Food Preservatives and 1,2,3,4-Tetrahydroxybenzene as a Highly Effective Representative: A Review of Patent Literature 2000-2005

Conventional chemical preservatives used in prevention of food spoilage caused by microorganisms have shown adverse effects and found to be of low effectiveness. This challenging situation stimulated research to find alternatives. As a result, numerous natural product-based compounds have been patented for use as antimicrobial food preservatives. These compounds comprise phenolic and non-phenolic ones. The phenolic agents include mainly those composed of a single aromatic ring and flavonoid-derived molecules. The phenolic compounds display multifunctional activities, while the nonphenolic do not. Polyhydroxybenzene derivatives exhibit high potential as effective antimicrobial or as antioxidants agents. Among the later category is 1,2,3,4-tetrahydroxybenzene (THB). THB has been recently patented as a highly effective antimicrobial and antioxidant agent. It showed significant and broad-spectrum antimicrobial activity versus a wide range of gram-positive, gram-negative bacteria, yeasts, and fungi, including pathogenic and non-pathogenic organisms. Its effectiveness as an antioxidant is equal or superior to commonly used antioxidants such as butylated hydroxyanisole (BHA) and butylated hydroxytoluene (BHT). Production of 1,2,3,4-tetrahydroxybenzene was accomplished efficiently by adopting a bioengineered synthesis, that is recently disclosed. In addition, there is also a patented simple chemical method.

Cyclooxygenase Inhibitory Natural Products: Current Status

Non-steroidal anti-inflammatory drugs (NSAIDs) are of huge therapeutic benefit in the treatment of rheumatoid arthritis and various types of inflammatory conditions. The target for these drugs is cyclooxygenase (COX), a rate-limiting enzyme involved in the conversion of arachidonic acid into inflammatory prostaglandins. COX-2 selective inhibitors are believed to have the same anti-inflammatory, anti-pyretic and analgesic activities as that of nonselective inhibitor NSAIDs with little or none of the gastrointestinal side effects. Thus, in the last 6-7 years several selective COX-2 inhibitors including coxibs were discovered and introduced into clinic. Recent reports evidence that selective COX-2 inhibitor such as rofecoxib, can lead to thrombotic cardiovascular events through inhibition of prostacyclin formation in the infracted heart. This has resulted in withdrawal of rofecoxib from the clinic in September 2004. Moreover, the COX-2/COX-1 selectivity ratio is vital in the design of COX-2 inhibitory drugs, as it is clear from rofecoxib, which is more than 50-fold COX-2 selective. After looking at all above mentioned facts, natural product-based compounds seem better as these compounds are generally supposed to be devoid of severe side effects. The literature indicates that natural product-based compounds are mainly COX-1 selective. Through minor semi-synthetic changes in the structures, their selectivity towards COX-2 can be increased. The present review article addresses natural product COX inhibitors of plant and marine origin, reported during last ten years and their advantages, possible leads for further development and current status. In addition we describe our experience in the characterization, design and synthesis of potential natural COX inhibitors.