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Shah SK, Chaple DD, Masand VH, Jawarkar RD, Chaudhari S, Abiramasundari A, Zaki MEA, Al-Hussain SA. Multi-Target In-Silico modeling strategies to discover novel angiotensin converting enzyme and neprilysin dual inhibitors. Sci Rep 2024; 14:15991. [PMID: 38987327 PMCID: PMC11237057 DOI: 10.1038/s41598-024-66230-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Cardiovascular diseases, including heart failure, stroke, and hypertension, affect 608 million people worldwide and cause 32% of deaths. Combination therapy is required in 60% of patients, involving concurrent Renin-Angiotensin-Aldosterone-System (RAAS) and Neprilysin inhibition. This study introduces a novel multi-target in-silico modeling technique (mt-QSAR) to evaluate the inhibitory potential against Neprilysin and Angiotensin-converting enzymes. Using both linear (GA-LDA) and non-linear (RF) algorithms, mt-QSAR classification models were developed using 983 chemicals to predict inhibitory effects on Neprilysin and Angiotensin-converting enzymes. The Box-Jenkins method, feature selection method, and machine learning algorithms were employed to obtain the most predictive model with ~ 90% overall accuracy. Additionally, the study employed virtual screening of designed scaffolds (Chalcone and its analogues, 1,3-Thiazole, 1,3,4-Thiadiazole) applying developed mt-QSAR models and molecular docking. The identified virtual hits underwent successive filtration steps, incorporating assessments of drug-likeness, ADMET profiles, and synthetic accessibility tools. Finally, Molecular dynamic simulations were then used to identify and rank the most favourable compounds. The data acquired from this study may provide crucial direction for the identification of new multi-targeted cardiovascular inhibitors.
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Affiliation(s)
- Sapan K Shah
- Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Hingna Road, Nagpur, 440016, Maharashtra, India.
| | - Dinesh D Chaple
- Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Hingna Road, Nagpur, 440016, Maharashtra, India
| | - Vijay H Masand
- Department of Chemistry, Vidya Bharati Mahavidyalaya, Amravati, 444602, Maharashtra, India
| | - Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr. Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, 444603, India
| | - Somdatta Chaudhari
- Department of Pharmaceutical Chemistry, Modern College of Pharmacy, Nigdi, Pune, India
| | | | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, 11623, Saudi Arabia.
| | - Sami A Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, 11623, Saudi Arabia
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Norouzi H, Sohrabi M, Yousefi M, Boustie J. Tridepsides as potential bioactives: a review on their chemistry and the global distribution of their lichenic and non-lichenic natural sources. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1088966. [PMID: 37746133 PMCID: PMC10512237 DOI: 10.3389/ffunb.2023.1088966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/24/2023] [Indexed: 09/26/2023]
Abstract
Tridepsides, as fully oxidized polyketides, have been known to exist in lichens for more than a century. Recent studies have showed that these possible defensive lichenochemicals possess various biological activities. Also, a candidate biosynthetic gene cluster was recently reported for gyrophoric acid (GA), an important tridepside. The present study focused on biosynthesis, natural sources, biological activities, and bioanalytical methods of tridepside molecules. Our survey shows that, so far, lichenic tridepsides have been reported from 37 families, 111 genera, and 526 species of lichen. Because many of their species contain tridepsides, the families Parmeliaceae, Lobariaceae, and Peltigeraceae can be considered critical lichenic sources of tridepsides. Furthermore, several species of Hypotrachyna in Parmeliaceae family showed lichenic tridepsides, suggesting that this genus is a viable source of tridepsides. This research also explored tridepsides from non-lichenic sources, such as non-lichenized fungi, lichenicolous fungi, endophytes, parasites, and liverworts, which offer substantial potential as biotechnological sources to produce tridepsides, which are produced in small amounts in lichen thalli. Two lichenic tridepsides have also been detected in non-lichenic sources: GA and tenuiorin (TE). Additionally, no significant correlation was found between tridepside biosynthesis and geographical distribution patterns for several potentially tridepside-producing lichens. We further showed that GA is the most studied tridepside with various reported biological activities, including anticancer, wound healing, photoprotection, anti-aging, antioxidant, cardiovascular effect, DNA interaction, anti-diabetes, anti-Alzheimer's, anti-bacterial, and antifungal. Last but not least, this study provides an overview of some bioanalytical methods used to analyze tridepsides over the past few years.
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Affiliation(s)
- Hooman Norouzi
- Department of Horticultural Sciences, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Mohammad Sohrabi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Masoud Yousefi
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Joel Boustie
- Univ Rennes, Centre National de la Recherche Scientifique (CNRS), ISCR (Institut des Sciences Chimiques de Rennes) - Mixed Research Unit (MRU) 6226, Rennes, France
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Lichen Depsides and Tridepsides: Progress in Pharmacological Approaches. J Fungi (Basel) 2023; 9:jof9010116. [PMID: 36675938 PMCID: PMC9866793 DOI: 10.3390/jof9010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Depsides and tridepsides are secondary metabolites found in lichens. In the last 10 years, there has been a growing interest in the pharmacological activity of these compounds. This review aims to discuss the research findings related to the biological effects and mechanisms of action of lichen depsides and tridepsides. The most studied compound is atranorin, followed by gyrophoric acid, diffractaic acid, and lecanoric acid. Antioxidant, cytotoxic, and antimicrobial activities are among the most investigated activities, mainly in in vitro studies, with occasional in silico and in vivo studies. Clinical trials have not been conducted using depsides and tridepsides. Therefore, future research should focus on conducting more in vivo work and clinical trials, as well as on evaluating the other activities. Moreover, despite the significant increase in research work on the pharmacology of depsides and tridepsides, there are many of these compounds which have yet to be investigated (e.g., hiascic acid, lassalic acid, ovoic acid, crustinic acid, and hypothamnolic acid).
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Lin Y, Zhang Y, Wang D, Yang B, Shen YQ. Computer especially AI-assisted drug virtual screening and design in traditional Chinese medicine. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 107:154481. [PMID: 36215788 DOI: 10.1016/j.phymed.2022.154481] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/14/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Traditional Chinese medicine (TCM), as a significant part of the global pharmaceutical science, the abundant molecular compounds it contains is a valuable potential source of designing and screening new drugs. However, due to the un-estimated quantity of the natural molecular compounds and diversity of the related problems drug discovery such as precise screening of molecular compounds or the evaluation of efficacy, physicochemical properties and pharmacokinetics, it is arduous for researchers to design or screen applicable compounds through old methods. With the rapid development of computer technology recently, especially artificial intelligence (AI), its innovation in the field of virtual screening contributes to an increasing efficiency and accuracy in the process of discovering new drugs. PURPOSE This study systematically reviewed the application of computational approaches and artificial intelligence in drug virtual filtering and devising of TCM and presented the potential perspective of computer-aided TCM development. STUDY DESIGN We made a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Then screening the most typical articles for our research. METHODS The systematic review was performed by following the PRISMA guidelines. The databases PubMed, EMBASE, Web of Science, CNKI were used to search for publications that focused on computer-aided drug virtual screening and design in TCM. RESULT Totally, 42 corresponding articles were included in literature reviewing. Aforementioned studies were of great significance to the treatment and cost control of many challenging diseases such as COVID-19, diabetes, Alzheimer's Disease (AD), etc. Computational approaches and AI were widely used in virtual screening in the process of TCM advancing, which include structure-based virtual screening (SBVS) and ligand-based virtual screening (LBVS). Besides, computational technologies were also extensively applied in absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction of candidate drugs and new drug design in crucial course of drug discovery. CONCLUSIONS The applications of computer and AI play an important role in the drug virtual screening and design in the field of TCM, with huge application prospects.
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Affiliation(s)
- Yumeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - You Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dongyang Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bowen Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Mohammadi M, Bagheri L, Badreldin A, Fatehi P, Pakzad L, Suntres Z, van Wijnen AJ. Biological Effects of Gyrophoric Acid and Other Lichen Derived Metabolites, on Cell Proliferation, Apoptosis and Cell Signaling pathways. Chem Biol Interact 2022; 351:109768. [PMID: 34864007 PMCID: PMC8808380 DOI: 10.1016/j.cbi.2021.109768] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 09/23/2021] [Accepted: 11/29/2021] [Indexed: 01/07/2023]
Abstract
Secondary metabolites from fungi, algae and lichens have remarkable biological activities as antibiotics, fungicides, antiviral drugs, and cancer therapeutics. This review focuses on the lichen-derived metabolite gyrophoric acid and other select secondary metabolites (e.g., usnic acid, salazinic acid, physodic acid, vulpinic acid ceratinalone, flavicansone, ramalin, physciosporin, tumidulin, atranorin, parmosidone) that modulate a number of cellular pathways relevant to several biomedical diseases and disorders, including cancer, diabetes and cardiovascular disease. We discuss the chemical structure and biochemical activities of gyrophoric acid and other compounds relative to the molecular mechanisms and cellular processes that these metabolites target in a distinct human and rodent cell types. The therapeutic promise of gyrophoric acid and similar lichen derived metabolites is associated with the chemical versatility of these compounds as polyaromatic depsides with functional carboxyl and hydroxyl side-groups that may permit selective interactions with distinct enzymatic active sites. Gyrophoric acid has been examined in a series of studies as an effective anticancer drug because it impinges on topoisomerase 1 activity, as well as causes cell cycle arrest, comprises cell survival, and promotes apoptosis. Because gyrophoric acid has cytostatic properties, its biological roles and possible medicinal utility may extend beyond effects on cancer cells and be relevant to any process that is controlled by cell growth and differentiation.
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Affiliation(s)
- Mahshid Mohammadi
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA; Biorefining Research Institute (BRI), Lakehead University, Thunder Bay, Canada.
| | - Leila Bagheri
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA.
| | - Amr Badreldin
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA.
| | - Pedram Fatehi
- Biorefining Research Institute (BRI), Lakehead University, Thunder Bay, Canada.
| | - Leila Pakzad
- Biorefining Research Institute (BRI), Lakehead University, Thunder Bay, Canada.
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