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Natural Compounds Applications in Drug Discovery and Development

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A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Pharmaceutical Processes".

Deadline for manuscript submissions: closed (30 December 2023) | Viewed by 21542

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Dr. Alina Bora

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Computational Chemistry, “Coriolan Dragulescu” Institute of Chemistry, Romanian Academy, 24 Mihai Viteazu Ave., 300223 Timisoara, Romania
Interests: computational chemistry; drug discovery; molecular simulation; medicinal chemistry
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Dr. Luminita Crisan

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Computational Chemistry, “Coriolan Dragulescu” Institute of Chemistry, Romanian Academy, 24 Mihai Viteazu Ave., 300223 Timisoara, Romania
Interests: computational chemistry; QSAR; drug discovery; molecular simulation; medicinal chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nature is a valuable source for development and design of drug-lead compounds that could significantly impact the treatment of serious diseases, enhancing general health and wellbeing. Herbal systems play a fundamental role in healthcare, as 60% of chemotherapeutic agents are derived from natural sources. The emergence of cutting-edge technologies and methods that improve the drug design process has provided new ways of processing complex natural products, using their structures to develop new and innovative drug candidates with reduced side-effects.

In this Special Issue of Processes, we aim to summarize the current trends in drug discovery and development, while reporting the latest applications of natural products to combat current and future health challenges, as well as strategies and computational approaches that facilitate the design of new and innovative drugs with greater accuracy, low costs, and high efficiency using natural sources.

This Special Issue welcomes original research papers, communications, reviews, etc., reporting the most recent applications of natural compounds in drug discovery and development, employing advanced computational methods and tools, new protocols, targets, the new combinatorial approach, and innovative technologies with a key role in next-generation drug discovery.

Dr. Alina Bora
Dr. Luminita Crisan
Guest Editors

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Processes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

natural products
drug discovery and development
computational methods
drug repurposing
natural products application
global health challenges

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Published Papers (11 papers)

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Editorial

Jump to: Research

3 pages, 934 KiB

Open AccessEditorial

Editorial on the Special Issue “Natural Compounds Applications in Drug Discovery and Development”

by Alina Bora and Luminita Crisan

Processes 2024, 12(6), 1152; https://doi.org/10.3390/pr12061152 - 3 Jun 2024

Viewed by 784

Abstract

Nature is an amazing source of natural bioactive compounds derived from numerous species of plants, marine bacteria, and fungi [...] Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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Research

Jump to: Editorial

26 pages, 32432 KiB

Open AccessArticle

Exploring the Antimelanoma Potential of Betulinic Acid Esters and Their Liposomal Nanoformulations

by Andreea Milan, Marius Mioc, Alexandra Mioc, Narcisa Marangoci, Roxana Racoviceanu, Gabriel Mardale, Mihaela Bălan-Porcărașu, Slavița Rotunjanu, Irina Şoica and Codruța Șoica

Processes 2024, 12(2), 416; https://doi.org/10.3390/pr12020416 - 19 Feb 2024

Cited by 1 | Viewed by 1486

Abstract

Betulinic acid is a naturally occurring pentacyclic triterpene belonging to the lupane-group that exhibits a wide range of pharmacological activities. BA derivatives are continuously being researched due to their improved anticancer efficacy and bioavailability. The current research was conducted in order to determine the antiproliferative potential of three synthesized BA fatty esters using palmitic, stearic and butyric acids and their liposomal nanoformulations. The cytotoxic potential of BA fatty esters (Pal-BA, St-BA, But-BA) and their respective liposomal formulations (Pal-BA-Lip, St-BA-Lip, But-BA-Lip) has been assessed on HaCaT immortalized human keratinocytes and A375 human melanoma cells. Both the esters and their liposomes acted as cytotoxic agents against melanoma cells in a time- and dose-dependent manner. The butyryl ester But-BA outperformed BA in terms of cytotoxicity (IC₅₀ 60.77 μM) while the nanoformulations St-BA-Lip, But-BA-Lip and BA-Lip also displayed IC₅₀ values (60.11, 50.71 and 59.01 μM) lower compared to BA (IC₅₀ 65.9 μM). The morphological evaluation revealed that the A375 cells underwent morphological changes consistent with apoptosis following 48 h treatment with the tested compounds, while the HaCaT cells’ morphology remained unaltered. Both the esters and their liposomal formulations were able to inhibit the migration of the melanoma cells, suggesting a significant antimetastatic effect. The quantitative real-time PCR revealed that all tested samples were able to significantly increase the expression of the pro-apoptotic Bax and inhibit the anti-apoptotic Bcl-2 proteins. This effect was more potent in the case of liposomal nanoformulations versus non-encapsulated compounds, and overall, But-BA and its formulation exhibited the best results in this regard. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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25 pages, 7085 KiB

Open AccessArticle

Novel Betulin-1,2,4-Triazole Derivatives Promote In Vitro Dose-Dependent Anticancer Cytotoxicity

by Alexandra Prodea, Andreea Milan, Marius Mioc, Alexandra Mioc, Camelia Oprean, Roxana Racoviceanu, Roxana Negrea-Ghiulai, Gabriel Mardale, Ștefana Avram, Mihaela Balan-Porcărașu, Slavița Rotunjanu, Cristina Trandafirescu, Irina Şoica and Codruța Șoica

Processes 2024, 12(1), 24; https://doi.org/10.3390/pr12010024 - 21 Dec 2023

Cited by 1 | Viewed by 1359

Abstract

Betulin is a birch bark-derived lupane-type pentacyclic triterpene with a wide spectrum of biological activities. Given their enhanced antiproliferative potential and enhanced pharmacological profile, betulin derivatives are continuously investigated in scientific studies. The objective of the current study was to in vitro assess the antiproliferative properties of novel synthesized 1,2,4-triazole derivatives of diacetyl betulin. The compounds were investigated using three cancer cell lines: A375 (melanoma), MCF-7 (breast cancer), HT-29 (colorectal cancer), and HaCaT (human keratinocytes). Bet-TZ1 had the lowest recorded IC₅₀ values (ranging from 22.41 to 46.92 μM after 48 h of exposure) than its precursor and other tested compounds in every scenario, with the highest cytotoxicity against the A375 cell line. Bet-TZ3 demonstrated comparable cytotoxicity to the previously mentioned compound, with an IC₅₀ of 34.34 μM against A375. Both compounds caused apoptosis in tested cells, by inducing specific nuclear morphological changes and by increasing the expression of caspase 9, indicating significant cytotoxicity, which was consistent with the literature and viability evaluation. Bet-TZ1 and Bet-TZ3 inhibit cancer cell migration, with the former having a stronger effect than the latter. The HET−CAM test indicated that all compounds have no irritative potential, suggesting that they can be used locally. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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22 pages, 14162 KiB

Open AccessFeature PaperArticle

Dipeptidyl Peptidase 4 Inhibitors in Type 2 Diabetes Mellitus Management: Pharmacophore Virtual Screening, Molecular Docking, Pharmacokinetic Evaluations, and Conceptual DFT Analysis

by Daniela Istrate and Luminita Crisan

Processes 2023, 11(11), 3100; https://doi.org/10.3390/pr11113100 - 28 Oct 2023

Cited by 2 | Viewed by 2367

Abstract

Dipeptidyl Peptidase 4 (DPP-4) expressed on the surface of many different cells is a promising target to develop new candidates for Type 2 diabetes mellitus (T2DM) management. In this light, we performed a computer-aided simulation involving 3-D pharmacophore screening, molecular docking, and drug-likeness assessment to identify novel potential DPP-4 inhibitors with an improved physicochemical profile to treat T2DM. In addition, global reactivity descriptors, including HOMO and LUMO energies, HOMO-LUMO gaps, and Fukui indices, were computed to confirm the essential structural features to achieve DPP-4 activity. The gathered outcomes recommend that eight out of 240 million compounds collected from eight pre-built databases (Molport, Chembl30, ChemDiv, ChemSpace, Mcule, Mcule-ultimate, LabNetwork, and ZINC) are drug-like and nontoxic, and may serve as starting points for designing novel, selective, and potent DPP-4 inhibitors. Furthermore, the success of the current workflow to identify DPP-4-potential inhibitors strengthens its potential efficiency to also predict natural compounds as novel adjutants or main therapy for T2DM or discover hit compounds of other targets. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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18 pages, 4940 KiB

Open AccessArticle

Anticancer Activity of Anti-Tubercular Compound(s) Designed on Pyrrolyl Benzohydrazine Scaffolds: A Repurposing Study

by Turki Al Hagbani, Afrasim Moin, Talib Hussain, N. Vishal Gupta, Farhan Alshammari, Syed Mohd Danish Rizvi and Sheshagiri Dixit

Processes 2023, 11(7), 1889; https://doi.org/10.3390/pr11071889 - 23 Jun 2023

Viewed by 2028

Abstract

The present study explored anti-tubercular pyrrole derivatives against cancer targets using different in silico and in vitro approaches. Initially, nineteen anti-tubercular pyrrolyl benzohydrazide derivatives were screened against a potent cancer target PLK1 using an AutoDock Vina approach. Out of the nineteen derivatives, the two most potent derivatives C8 [N′-(4-(1H-pyrrol-1-yl) benzoyl)-3-chlorobenzohydrazide] and C18 [N′-(4-(1H-pyrrol-1-yl) benzoyl)-4-nitrobenzohydrazide], were subjected to molecular simulation analysis for a 100 ns trajectory. Further, these two derivatives were tested against A549, MCF-7, and HepG2 cell lines using an MTT proliferation assay. Apoptotic cell cycle and DAPI assays were also performed for C8 on A549 cell lines. Molecular dynamic analysis revealed that the stability of the C8–PLK1 protein complex during the 100 ns trajectory run was better than that of the C18–PLK1 protein complex. In addition, C8 showed lower IC₅₀ values against the tested cell lines, in comparison to C18. Thus, C8 was selected for cell cycle, apoptosis, and DAPI analysis. Interestingly, C8 resulted in the significant cell cycle arrest of A549 cells at the G2/M phase, and annexin V-FITC/PI showed a significant increase (from 6.27% to 60.52%) in the percentage of apoptotic A549 cells. The present findings suggest that the anti-tubercular compound (C8) could be translated into a potent repurposed candidate against lung cancer. Nevertheless, in vivo assessment is necessary to further confirm the outcome and its clinical translation. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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15 pages, 1857 KiB

Open AccessArticle

Synthesis and Biological Evaluation of α-Tocopherol Derivatives as Potential Anticancer Agents

by Aneta Baj, Lucie Rárová, Artur Ratkiewicz, Miroslav Strnad and Stanislaw Witkowski

Processes 2023, 11(6), 1860; https://doi.org/10.3390/pr11061860 - 20 Jun 2023

Cited by 1 | Viewed by 1847

Abstract

α-Tocopheryl succinate (α-TS) and α-tocopheryloxyacetic acid (α-TEA) are potent inducers of apoptosis in cancer cells and efficient suppressors of tumors in experimental model cancer cell lines. They exhibit selective cytotoxicity against tumor cells and very limited or no toxicity toward nonmalignant cells. In the present work, a series of new α-tocopherol derivatives were synthesized as analogs of α-TS and α-TEA. The cytotoxic activity of obtained compounds was tested using three human cancer cell lines, including chronic lymphoblastic leukemia (CEM), breast adenocarcinoma (MCF7), cervical adenocarcinoma (HeLa), and normal human fibroblasts (BJ). The introduction of an alkyl substituent into the ether-linked acetic acid moiety in α-TEA increased anticancer activity. α-Tocopheryloxy-2-methylpropanoic acid with two additional geminal methyl groups was more active against CEM cells compared to α-TEA and non-toxic to normal cells. In order to acquire a deeper understanding of the biological activity of synthesized compounds, a molecular docking study was also conducted. Our research confirmed that vitamin E derivatives are interesting and valuable compounds in terms of their potential therapeutic use as anticancer agents. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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17 pages, 1291 KiB

Open AccessArticle

STITCH, Physicochemical, ADMET, and In Silico Analysis of Selected Mikania Constituents as Anti-Inflammatory Agents

by Narayanaswamy Radhakrishnan, Vasantha-Srinivasan Prabhakaran, Mohammad Ahmad Wadaan, Almohannad Baabbad, Ramachandran Vinayagam and Sang Gu Kang

Processes 2023, 11(6), 1722; https://doi.org/10.3390/pr11061722 - 5 Jun 2023

Cited by 15 | Viewed by 1848

Abstract

The Mikania genus has been known to possess numerous pharmacological activities. In the present study, we aimed to evaluate the interaction of 26 selected constituents of Mikania species with (i) cyclooxygenase 2 (COX 2), (ii) human neutrophil elastase (HNE), (iii) lipoxygenase (LOX), matrix metalloproteinase ((iv) MMP 2 and (v) MMP 9), and (vi) microsomal prostaglandin E synthase 2 (mPGES 2) inhibitors using an in silico approach. The 26 selected constituents of Mikania species, namely mikamicranolide, kaurenoic acid, stigmasterol, grandifloric acid, kaurenol, spathulenol, caryophyllene oxide, syringaldehyde, dihydrocoumarin, o-coumaric acid, taraxerol, melilotoside, patuletin, methyl-3,5-di-O-caffeoyl quinate, 3,3′,5-trihydroxy-4′,6,7-trimethoxyflavone, psoralen, curcumene, herniarin, 2,6-dimethoxy quinone, bicyclogermacrene, α-bisabolol, γ-elemene, provincialin, dehydrocostus lactone, mikanin-3-O-sulfate, and nepetin, were assessed based on the docking action with COX 2, HNE, LOX, MMP 2, MMP 9, and mPGES 2 using Discovery Studio (in the case of LOX, the Autodock method was utilized). Moreover, STITCH (Search Tool for Interacting Chemicals), physicochemical, drug-likeness, and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses were conducted utilizing the STITCH web server, the Mol-inspiration web server, and Discovery Studio, respectively. In the present study, STITCH analysis revealed only six ligands (dihydrocoumarin, patuletin, kaurenol, psoralen, curcumene, and nepetin) that showed interactions with human proteins. Physicochemical analysis showed that seventeen ligands complied well with Lipinski’s rule. ADMET analysis showed eleven ligands to possess hepatotoxic effects. Significantly, the binding free energy estimation displayed that the ligand methyl-3, 5-di-O-caffeoyl quinate revealed the highest binding energy for all the target enzymes, excluding LOX, suggesting that this may have efficacy as a non-steroidal anti-inflammatory drug (NSAID). The current study presents a better understanding of how Mikania is used as a traditional medicinal plant. Specifically, the 26 ligands of the Mikania plant are potential inhibitor against COX 2, HNE, LOX, MMP 2, MMP 9, and mPGES 2 for treatments for acute and/or chronic inflammatory diseases. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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20 pages, 9239 KiB

Open AccessArticle

Computational and In Vitro Assessment of a Natural Triterpenoid Compound Gedunin against Breast Cancer via Caspase 3 and Janus Kinase/STAT Modulation

by Talib Hussain, Muteb Alanazi, Jowaher Alanazi, Tareq Nafea Alharby, Aziz Unnisa, Amir Mahgoub Awadelkareem, AbdElmoneim O. Elkhalifa, Mohammad M. Algahtani, SMA Shahid and Syed Mohd Danish Rizvi

Processes 2023, 11(5), 1452; https://doi.org/10.3390/pr11051452 - 11 May 2023

Viewed by 1594

Abstract

Breast cancer is the most prevalent type of malignancy among females as per the report of the World Health Organization. There are several established chemotherapeutic regimes for the clinical management of different solid cancers; however, the after-effects of these therapeutics serve as a significant limiting factor. The natural triterpenoid compound, gedunin is one of the principal phytoconstituent found in Azadirachta indica. In this study, we have investigated the anticancer potential of gedunin against human breast cancer MDA-MB-231 and MCF-7 cells. Based on computational studies, gedunin exhibited significantly higher binding affinity of −7.1 and −6.2 Kcal/mol towards Janus kinase (JAK) and STAT proteins, respectively. Further, the anticancer potential of gedunin against human breast cancer was studied using hormone-independent and -dependent MCF-7 and MDA-MB-231 cell lines, respectively. The results indicated that gedunin inhibited the growth and multiplication of both MCF-7 and MDA-MB-231 cells. The nuclear fragmentation and ROS were qualitatively enhanced in the treated MCF-7 and MDA-MB-231 cells in comparison to untreated cells. The caspase-3 level was significantly enhanced with a concomitant decline in JAK1 and STAT3 mRNA expression. Based on these results, gedunin might be considered as a potential therapeutic lead against hormone-dependent and -independent breast cancer MCF-7 and MDA-MB-231 cells, respectively. However, further detailed mechanistic studies are warranted to conclusively establish the anti-breast cancer effects. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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11 pages, 2707 KiB

Open AccessArticle

Anti-Inflammatory and Anti-Diabetic Activity of Ferruginan, a Natural Compound from Olea ferruginea

by Abdur Rauf, Umer Rashid, Zafar Ali Shah, Gauhar Rehman, Kashif Bashir, Johar Jamil, Iftikhar, Abdur Rahman, Abdulrahman Alsahammari, Metab Alharbi, Abdulmajeed Al-Shahrani and Giovanni Ribaudo

Processes 2023, 11(2), 545; https://doi.org/10.3390/pr11020545 - 10 Feb 2023

Cited by 5 | Viewed by 2068

Abstract

Inflammation is a complex response of the human organism and relates to the onset of various disorders including diabetes. The current research work aimed at investigating the anti-inflammatory and anti-diabetic effects of ferruginan, a compound isolated from Olea ferruginea. Its in vitro anti-inflammatory activity was determined by using the heat-induced hemolysis assay, while the anti-diabetic effect of the compound was studied by the yeast cell glucose uptake assay. Ferruginan exhibited a maximum of 71.82% inhibition of inflammation and also increased the uptake of glucose by yeast cells by up to 74.96% at the highest tested concentration (100 µM). Moreover, ferruginan inhibited α-amylase dose-dependently, by up to 75.45% at the same concentration. These results indicated that ferruginan possesses promising anti-inflammatory and anti-diabetic properties in vitro, even if at high concentrations. To provide preliminary hypotheses on the potentially multi-target mechanisms underlying such effects, docking analyses were performed on α-amylase and on various molecular targets involved in inflammation such as 5′-adenosine monophosphate-activated protein kinase (AMPK, PDB ID 3AQV), cyclooxygenase (COX-1, PDB ID 1EQG, and COX-2, 1CX2), and tumor necrosis factor alpha (TNF-α, PDB ID 2AZ5). The docking studies suggested that the compound may act on α-amylase, COX-2, and AMPK. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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18 pages, 3692 KiB

Open AccessArticle

Novel Semisynthetic Betulinic Acid−Triazole Hybrids with In Vitro Antiproliferative Potential

by Gabriela Nistor, Alexandra Mioc, Marius Mioc, Mihaela Balan-Porcarasu, Roxana Ghiulai, Roxana Racoviceanu, Ștefana Avram, Alexandra Prodea, Alexandra Semenescu, Andreea Milan, Cristina Dehelean and Codruța Șoica

Processes 2023, 11(1), 101; https://doi.org/10.3390/pr11010101 - 29 Dec 2022

Cited by 5 | Viewed by 1885

Abstract

Betulinic acid, BA, is a lupane derivative that has caught the interest of researchers due to the wide variety of pharmacological properties it exhibits towards tumor cells. Because of their prospective increased anti−proliferative efficacy and improved pharmacological profile, BA derivatives continue to be described in the scientific literature. The current work was conducted in order to determine the antiproliferative activity, under an in vitro environment of the newly developed 1,2,4−triazole derivatives of BA. The compounds and their reaction intermediates were tested on three cancer cell lines, namely RPMI−7951 human malignant melanoma, HT−29 colorectal adenocarcinoma, A549 lung carcinoma, and healthy cell line (HaCaT human keratinocytes). BA−triazole derivatives 4a and 4b revealed lower IC₅₀ values in almost all cases when compared to their precursors, exhibiting the highest cytotoxicity against the RPMI−7951 cell line (IC₅₀: 18.8 μM for 4a and 20.7 μM for 4b). Further biological assessment of these compounds executed on the most affected cell line revealed a mitochondrial level induced apoptotic mechanism where both compounds inhibited mitochondrial respiration in RPMI−7951 cells. Furthermore, the triazole−BA derivatives caused a significant decrease of the anti−apoptotic Bcl−2 gene expression, while increasing the pro−apoptotic BAX gene’s expression. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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17 pages, 1054 KiB

Open AccessArticle

Red Clover and the Importance of Extraction Processes—Ways in Which Extraction Techniques and Parameters Affect Trifolium pratense L. Extracts’ Phytochemical Profile and Biological Activities

by Octavia Gligor, Simona Clichici, Remus Moldovan, Dana Muntean, Ana-Maria Vlase, George Cosmin Nadăș, Cristiana Ștefania Novac, Gabriela Adriana Filip, Laurian Vlase and Gianina Crișan

Processes 2022, 10(12), 2581; https://doi.org/10.3390/pr10122581 - 3 Dec 2022

Cited by 8 | Viewed by 2702

Abstract

The purpose of this study was to gain an insight into the manner in which several extraction processes (both classical as well as innovative) affected bioactive compound yield, and subsequently to assess several of their biological activities. Red clover extracts were obtained using maceration, Soxhlet extraction, turbo-extraction, ultrasound-assisted extraction, and a combination of the last two. The resulting extracts were analyzed for total phenolic and flavonoid content. The extracts presenting the best results were subjected to a phytochemical assessment by way of HPLC-MS analysis. After a final sorting based on the phytochemical profiles of the extracts, the samples were assessed for their antimicrobial activity, anti-inflammatory activity, and oxidative stress reduction potential, using animal inflammation models. The Soxhlet extraction yielded the most satisfactory results both qualitatively and quantitatively. The ultrasound-assisted extraction offered comparable yields. The extracts showed a high potential against gram-negative bacteria and induced a modest antioxidant effect on the experimental inflammation model in Wistar rats. Full article

(This article belongs to the Special Issue Natural Compounds Applications in Drug Discovery and Development)

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