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Sharma Y, Bhardwaj R, Kaur A, Singh G, Kulkarni S, Bhatia A, Bala K. Nano-gel formulation of polyphenolic fraction of tobacco stem for wound healing and its inhibitory efficacies against the receptors of chronic wound development. J Biomol Struct Dyn 2024:1-15. [PMID: 38433407 DOI: 10.1080/07391102.2024.2317986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Current investigation deals with the gel formulation of purified polyphenol loaded nanoparticles for enhanced wound healing. Polyphenols purified using column chromatography an were characterized using HPLC in fractions. Silver nanoparticles were characterization using SEM, AFM, TEM, DLS. Cytotoxic effect was checked on L929 (Mouse fibroblast cells). Bioactive loaded nanoparticles were formulated in gel and subjected for physical characterization. Excision wound wistar rat models were established to measure the wound contraction measurement, histopathological studies, and biochemical assays. Docking and Simulation studies were performed to check the binding and stability with receptors progressing the chronic wound. From the column chromatography, B fraction has shown the presence of maximum polyphenolic content and as well as the polyphenol compounds such as quercetin, rutin and tannic acid as confirmed by the HPLC. Synthesize B fraction-AgNP were found to be below 100 nm in size and spherical in shape as per the characterization. No cytotoxic effect was observed on L929 cells treated with B fraction and its nanoparticles. Formulated B fraction-AgNP gel has revealed the better stability and earlier wound contraction, i.e. before the completion of 14 days of topical treatment. Histopathology studies and collagen content has confirmed the re-epithelization in skin wounds. MD simulation revealed the stability with PI3K and AKT. This can be concluded that tobacco stem polyphenol loaded nanoparticles has potent wound healing activity that can be utilized as nano-drug delivery system for suppression of chronic wound development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yash Sharma
- Therapeutics and Molecular Diagnostic Lab, Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Rohit Bhardwaj
- Department of Pharmaceutical Science, Gurukul Kangri Vishwavidyalaya, Haridwar, Uttarakhand, India
| | - Amritpal Kaur
- Therapeutics and Molecular Diagnostic Lab, Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Gagandeep Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Delhi, India
- Section of Microbiology, Central Ayurveda Research Institute Jhansi, CCRAS, Ministry of Ayush, New Delhi, India
| | | | - Amit Bhatia
- Department of Pharmaceutical Science and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, Punjab, India
| | - Kumud Bala
- Therapeutics and Molecular Diagnostic Lab, Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
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2
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [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: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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3
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Lu H, Xie T, Wu Q, Hu Z, Luo Y, Luo F. Alpha-Glucosidase Inhibitory Peptides: Sources, Preparations, Identifications, and Action Mechanisms. Nutrients 2023; 15:4267. [PMID: 37836551 PMCID: PMC10574726 DOI: 10.3390/nu15194267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
With the change in people's lifestyle, diabetes has emerged as a chronic disease that poses a serious threat to human health, alongside tumor, cardiovascular, and cerebrovascular diseases. α-glucosidase inhibitors, which are oral drugs, have proven effective in preventing and managing this disease. Studies have suggested that bioactive peptides could serve as a potential source of α-glucosidase inhibitors. These peptides possess certain hypoglycemic activity and can effectively regulate postprandial blood glucose levels by inhibiting α-glucosidase activity, thus intervening and regulating diabetes. This paper provides a systematic summary of the sources, isolation, purification, bioavailability, and possible mechanisms of α-glucosidase inhibitory peptides. The sources of the α-glucosidase inhibitory peptides were introduced with emphasis on animals, plants, and microorganisms. This paper also points out the problems in the research process of α-glucosidase inhibitory peptide, with a view to providing certain theoretical support for the further study of this peptide.
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Affiliation(s)
- Han Lu
- Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, Central South University of Forestry and Technology, Changsha 410004, China; (H.L.); (T.X.); (Q.W.); (Z.H.)
| | - Tiantian Xie
- Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, Central South University of Forestry and Technology, Changsha 410004, China; (H.L.); (T.X.); (Q.W.); (Z.H.)
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha 410004, China
| | - Qi Wu
- Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, Central South University of Forestry and Technology, Changsha 410004, China; (H.L.); (T.X.); (Q.W.); (Z.H.)
| | - Zuomin Hu
- Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, Central South University of Forestry and Technology, Changsha 410004, China; (H.L.); (T.X.); (Q.W.); (Z.H.)
| | - Yi Luo
- Department of Gastroenterology, Xiangya School of Medicine, Central South University, Changsha 410008, China;
| | - Feijun Luo
- Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, Central South University of Forestry and Technology, Changsha 410004, China; (H.L.); (T.X.); (Q.W.); (Z.H.)
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha 410004, China
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4
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Shaikh N, Linthoi RK, Swamy KV, Karthikeyan M, Vyas R. Comprehensive molecular docking and dynamic simulations for drug repurposing of clinical drugs against multiple cancer kinase targets. J Biomol Struct Dyn 2023; 41:7735-7743. [PMID: 36134605 DOI: 10.1080/07391102.2022.2124453] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Drug repurposing is a method to identify novel therapeutic agents from the existing drugs and clinical compounds. In the present comprehensive work, molecular docking, virtual screening and dynamics simulations were carried out for ten cancer types viz breast, colon, central nervous system, leukaemia, melanoma, ovarian, prostate, renal and lung (non-small and small cell) against validated eighteen kinase targets. The study aims to understand the action of chemotherapy drugs mechanism through binding interactions against selected targets via comparative docking simulations with the state-art molecular modelling suits such as MOE, Cresset-Flare, AutoDock Vina, GOLD and GLIDE. Chemotherapeutic drugs (n = 112) were shortlisted from standard drug databases with appropriate chemoinformatic filters. Based on docking studies it was revealed that leucovorin, nilotinib, ellence, thalomid and carfilzomib drugs possessed potential against other cancer targets. A library was built to enumerate novel molecules based on the scaffold and functional groups extracted from known drugs and clinical compounds. Twenty novel molecules were prioritised further based on drug-like attributes. These were cross docked against 1MQ4 Aurora-A Protein Kinase for prostate cancer and 4UYA Mitogen-activated protein kinase for renal cancer. All docking programs yielded similar results but interestingly AutoDock Vina yielded the lowest RMSD with the native ligand. To further validate the final docking results at atomistic level, molecular dynamics simulations were performed to ascertain the stability of the protein-ligand complex. The study enables repurposing of drugs and lead identification by employing a host of structure and ligand based virtual screening tools and techniques.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nilofer Shaikh
- MIT School of Bioengineering Sciences & Research, MIT Art, Design and Technology University, Pune, Maharashtra, India
| | - R K Linthoi
- CEPD CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - K V Swamy
- MIT School of Bioengineering Sciences & Research, MIT Art, Design and Technology University, Pune, Maharashtra, India
| | | | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT Art, Design and Technology University, Pune, Maharashtra, India
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5
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Ahmed Khan D, Shahid A, Sherif AE, Aati HY, Abdullah M, Mehmood K, Hussain M, Basit A, Ahmad Ghalloo B, ur Rehman Khan K. A detailed biochemical characterization, toxicological assessment and molecular docking studies of Launaea fragilis: An important medicinal xero-halophyte. Saudi Pharm J 2023; 31:1047-1060. [PMID: 37250362 PMCID: PMC10212792 DOI: 10.1016/j.jsps.2023.04.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023] Open
Abstract
Launaea fragilis (Asso) Pau (Family: Asteraceae) is a wild medicinal plant that has been used in the folklore as a potential treatment for numerous ailments such as skin diseases, diarrhea, infected wounds, inflammation, child fever and hepatic pain. This study explored the chemical constitution, in-vivo toxicity, antimicrobial, antioxidant, and enzyme inhibition potential of ethanolic extract of L. fragilis (EELF). Additionally, in-silico docking studies of predominant compounds were performed against in-vitro tested enzymes. Similarly, in-silico ADMET properties of the compounds were performed to determine their pharmacokinetics, physicochemical properties, and toxicity profiles. The EELF was found rich in TFC (73.45 ± 0.25 mg QE/g) and TPC (109.02 ± 0.23 mg GAE/g). GC-MS profiling of EELF indicated the presence of a total of 47 compounds mainly fatty acids and essential oil. EELF showed no toxicity or growth retardation in chicks up to 300 mg/kg with no effect on the biochemistry and hematology of the chicks. EELF gave promising antioxidant activity through the CUPRAC method with an IC50 value of 13.14 ± 0.18 µg/ml. The highest inhibition activity against tyrosinase followed by acetylcholinesterase and α-Glucosidase was detected. Similarly, the antimicrobial study revealed the extract with good antibacterial and antiviral activity. A good docking score was observed in the in silico computational study of the predominant compounds. The findings revealed L. fragilis as a biocompatible, potent therapeutic alternative and suggest isolation and further in vivo pharmacological studies.
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Affiliation(s)
- Duraiz Ahmed Khan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur 63100, Punjab, Pakistan
| | - Afia Shahid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur 63100, Punjab, Pakistan
| | - Asmaa E. Sherif
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdul Aziz University, Alkharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Hanan Y. Aati
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Muhammad Abdullah
- Cholistan Institute of Desert Studies, The Islamia University of Bahawalpur 63100, Punjab, Pakistan
| | - Khalid Mehmood
- Department of Clinical Medicine and Surgery, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur 63100, Punjab, Pakistan
| | - Musaddique Hussain
- Department of Pharmacology, Faculty of Pharmacy, The Islamia University of Bahawalpur 63100, Punjab, Pakistan
| | - Abdul Basit
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai 90112, Songkhla, Thailand
- Drug Delivery System Excellence Center, Prince of Songkla University, Hat Yai 90112, Songkhla, Thailand
| | - Bilal Ahmad Ghalloo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur 63100, Punjab, Pakistan
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota 55454, MN, USA
| | - Kashif ur Rehman Khan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur 63100, Punjab, Pakistan
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6
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Elnaggar MS, Elissawy AM, Youssef FS, Kicsák M, Kurtán T, Singab ANB, Kalscheuer R. Austalide derivative from marine-derived Aspergillus sp. and evaluation of its cytotoxic and ADME/TOPKAT properties. RSC Adv 2023; 13:16480-16487. [PMID: 37274397 PMCID: PMC10233426 DOI: 10.1039/d3ra02632a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023] Open
Abstract
In-depth chemical investigation of an ethyl acetate extract of Aspergillus sp. isolated from the soft coral Sinularia species resulted in the isolation of one new meroterpenoid, austalide Z (1), one known austalide W (2), six known prenylated indole diketopiperazine alkaloids (3-8), and phthalic acid and its ethyl derivative (9-10). The structures were established by means of 1D and 2D NMR (one- and two-dimensional nuclear magnetic resonance) experiments supported by UV analysis and ESI-MS (electrospray ionization mass spectrometry). In vitro cytotoxic evaluation was performed against the Caco-2 cancer cell line using the MTT assay, which showed that the examined compounds had weak to moderate activities, with the new meroterpenoid austalide Z (1) displaying an IC50 value of 51.6 μg mL-1. ADME/TOPKAT (absorption, distribution, metabolism, excretion, and toxicity) predication performed in silico showed that most of the isolated compounds possessed reasonable pharmacokinetic, pharmacodynamic, and toxicity properties. Thus, it can be concluded that Aspergillus sp. could act as a source of drug leads for cancer prevention with promising pharmacokinetic and pharmacodynamic properties and thus could be incorporated in pharmaceutical dosage forms.
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Affiliation(s)
- Mohamed S Elnaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-Universität Düsseldorf 40225 Germany
| | - Ahmed M Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Center of Drug Discovery Research and Development, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Fadia S Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Máté Kicsák
- Department of Organic Chemistry, University of Debrecen Debrecen 4032 Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen Debrecen 4032 Hungary
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia 11566 Cairo Egypt
- Center of Drug Discovery Research and Development, Ain Shams University Abbassia 11566 Cairo Egypt
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-Universität Düsseldorf 40225 Germany
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7
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Nguyen VB, Wang SL, Phan TQ, Pham THT, Huang HT, Liaw CC, Nguyen AD. Screening and Elucidation of Chemical Structures of Novel Mammalian α-Glucosidase Inhibitors Targeting Anti-Diabetes Drug from Herbals Used by E De Ethnic Tribe in Vietnam. Pharmaceuticals (Basel) 2023; 16:ph16050756. [PMID: 37242539 DOI: 10.3390/ph16050756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Among ten extracts of indigenous medicinal plants, the MeOH extract of Terminalia triptera Stapf. (TTS) showed the most efficient mammalian α-glucosidase inhibition for the first time. The data of screening bioactive parts used indicated that the TTS trunk bark and leaves extracts demonstrated comparable and higher effects compared to acarbose, a commercial anti-diabetic drug, with half-maximal inhibitory concentration (IC50) values of 181, 331, and 309 µg/mL, respectively. Further bioassay-guided purification led to the isolation of three active compounds from the TTS trunk bark extract and identified as (-)-epicatechin (1), eschweilenol C (2), and gallic acid (3). Of these, compounds 1 and 2 were determined as novel and potent mammalian α-glucosidase inhibitors. The virtual study indicated that these compounds bind to α-glucosidase (Q6P7A9) with acceptable RMSD values (1.16-1.56 Å) and good binding energy (DS values in the range of -11.4 to -12.8 kcal/mol) by interacting with various prominent amino acids to generate five and six linkages, respectively. The data of Lipinski's rule of five and absorption, distribution, metabolism, excretion and toxicity (ADMET)-based pharmacokinetics and pharmacology revealed that these purified compounds possess anti-diabetic drug properties, and the compounds are almost not toxic for human use. Thus, the findings of this work suggested that (-)-epicatechin and eschweilenol C are novel potential mammalian α-glucosidase inhibitor candidates for type 2 diabetes treatment.
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Affiliation(s)
- Van Bon Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam
| | - San-Lang Wang
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan
- Life Science Development Center, Tamkang University, New Taipei City 25137, Taiwan
| | - Tu Quy Phan
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam
| | - Thi Huyen Thoa Pham
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam
| | - Hung-Tse Huang
- Division of Chinese Materia Medica Development, National Research Institute of Chinese Medicine, Taipei 11221, Taiwan
| | - Chia-Ching Liaw
- Division of Chinese Materia Medica Development, National Research Institute of Chinese Medicine, Taipei 11221, Taiwan
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam
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8
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Ahmad S, Mirza MU, Trant JF. Dock-able linear and homodetic di, tri, tetra and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case study. J Pharm Anal 2023; 13:523-534. [PMID: 37275125 PMCID: PMC10104786 DOI: 10.1016/j.jpha.2023.04.008] [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: 01/05/2023] [Revised: 03/07/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Peptide-based therapeutics are increasingly pushing to the forefront of biomedicine with their promise of high specificity and low toxicity. Although noncanonical residues can always be used, employing only the natural 20 residues restricts the chemical space to a finite dimension allowing for comprehensive in silico screening. Towards this goal, the dataset comprising all possible di-, tri-, and tetra-peptide combinations of the canonical residues has been previously reported. However, with increasing computational power, the comprehensive set of pentapeptides is now also feasible for screening as the comprehensive set of cyclic peptides comprising four or five residues. Here, we provide both the complete and prefiltered libraries of all di-, tri-, tetra-, and penta-peptide sequences from 20 canonical amino acids and their homodetic (N-to-C-terminal) cyclic homologues. The FASTA, simplified molecular-input line-entry system (SMILES), and structure-data file (SDF)-three dimension (3D) libraries can be readily used for screening against protein targets. We also provide a simple method and tool for conducting identity-based filtering. Access to this dataset will accelerate small peptide screening workflows and encourage their use in drug discovery campaigns. As a case study, the developed library was screened against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease to identify potential small peptide inhibitors.
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Affiliation(s)
- Sarfraz Ahmad
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, Ontario, Canada
- Binary Star Research Services, LaSalle N9J 3X8, Ontario, Canada
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9
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Bender O, Shoman ME, Ali TFS, Dogan R, Celik I, Mollica A, Hamed MIA, Aly OM, Alamri A, Alanazi J, Ahemad N, Gan SH, Malik JA, Anwar S, Atalay A, Beshr EAM. Discovery of oxindole-based FLT3 inhibitors as a promising therapeutic lead for acute myeloid leukemia carrying the oncogenic ITD mutation. Arch Pharm (Weinheim) 2023; 356:e2200407. [PMID: 36403191 DOI: 10.1002/ardp.202200407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/16/2022] [Accepted: 10/20/2022] [Indexed: 11/21/2022]
Abstract
FMS-like tyrosine kinase 3 (FLT3) mutations occur in approximately 30% of acute myeloid leukemia (AML) patients. In the current study, the oxindole chemotype is employed as a structural motif for the design of new FLT3 inhibitors as potential hits for AML irradiation. Cell-based screening was performed with 18 oxindole derivatives and 5a-c inhibited 68%-73% and 83%-91% of internal tandem duplication (ITD)-mutated MV4-11 cell growth for 48- and 72-h treatments while only 0%-2% and 27%-39% in wild-type THP-1 cells. The most potent compound 5a inhibited MV4-11 cells with IC50 of 4.3 µM at 72 h while it was 8.7 µM in THP-1 cells, thus showing two-fold selective inhibition against the oncogenic ITD mutation. The ability of 5a to modulate cell death was examined. High-throughput protein profiling revealed low levels of the growth factors IGFBP-2 and -4 with the blockage of various apoptotic inhibitors such as Survivin. p21 with cellular stress mechanisms was characterized by increased expression of HSP proteins along with TNF-β. Mechanistically, compounds 5a and 5b inhibited FLT3 kinase with IC50 values of 2.49 and 1.45 µM, respectively. Theoretical docking studies supported the compounds' ability to bind to the FLT3 ATP binding site with the formation of highly stable complexes as evidenced by molecular dynamics simulations. The designed compounds also provide suitable drug candidates with no violation of drug likeability rules.
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Affiliation(s)
- Onur Bender
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Mai E Shoman
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Taha F S Ali
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Rumeysa Dogan
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Adriano Mollica
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Mohammed I A Hamed
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, Fayoum University, Fayoum, Egypt
| | - Omar M Aly
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Abdulwahab Alamri
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail, Saudi Arabia.,Molecular Diagnostics Unit and Personalized Treatment, University of Hail, Hail, Saudi Arabia
| | - Jowaher Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail, Saudi Arabia.,Molecular Diagnostics Unit and Personalized Treatment, University of Hail, Hail, Saudi Arabia
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor DE, Malaysia
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor DE, Malaysia
| | - Jonaid Ahmad Malik
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, India
| | - Sirajudheen Anwar
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail, Saudi Arabia.,Molecular Diagnostics Unit and Personalized Treatment, University of Hail, Hail, Saudi Arabia
| | - Arzu Atalay
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Eman A M Beshr
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, Egypt
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10
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Optimization and Molecular Mechanism of Novel α-Glucosidase Inhibitory Peptides Derived from Camellia Seed Cake through Enzymatic Hydrolysis. Foods 2023; 12:foods12020393. [PMID: 36673484 PMCID: PMC9857891 DOI: 10.3390/foods12020393] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
In recent years, food-derived hypoglycemic peptides have received a lot of attention in the study of active peptides, but their anti-diabetic mechanism of action is not yet clear. In this study, camellia seed cake protein (CSCP) was used to prepare active peptides with α-glucosidase inhibition. The optimization of the preparation of camellia seed cake protein hydrolyzed peptides (CSCPH) was conducted via response surface methodology (RSM) using a protamex with α-glucosidase inhibition as an indicator. The optimal hydrolysis conditions were pH 7.11, 4300 U/g enzyme concentration, 50 °C hydrolysis temperature, and 3.95 h hydrolysis time. Under these conditions, the α-glucosidase inhibition rate of CSCPH was 58.70% (IC50 8.442 ± 0.33 mg/mL). The peptides with high α-glucosidase inhibitory activity were isolated from CSCPH by ultrafiltration and Sephadex G25. Leu-Leu-Val-Leu-Tyr-Tyr-Glu-Tyr (LLVLYYEY) and Leu-Leu-Leu-Leu-Pro-Ser-Tyr-Ser-Glu-Phe (LLLLPSYSEF) were identified and synthesized for the first time by Liquid chromatography electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS) analysis and virtual screening with IC50 values of 0.33 and 1.11 mM, respectively. Lineweaver-Burk analysis and molecular docking demonstrated that LLVLYYEY was a non-competitive inhibitor of α-glucosidase, whereas LLLLPSYSEF inhibited α-glucosidase, which displayed a mixed inhibition mechanism. The study suggests the possibility of using peptides from Camellia seed cake as hypoglycaemic compounds for the prevention and treatment of diabetes.
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Benchikha N, Messaoudi M, Larkem I, Ouakouak H, Rebiai A, Boubekeur S, Ferhat MA, Benarfa A, Begaa S, Benmohamed M, Almasri DM, Hareeri RH, Youssef FS. Evaluation of Possible Antioxidant, Anti-Hyperglycaemic, Anti-Alzheimer and Anti-Inflammatory Effects of Teucrium polium Aerial Parts (Lamiaceae). LIFE (BASEL, SWITZERLAND) 2022; 12:life12101579. [PMID: 36295014 PMCID: PMC9604868 DOI: 10.3390/life12101579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/07/2022]
Abstract
Teucrium polium L. is commonly used in folk medicine to treat hypertension and diabetes and to heal wounds. The present work aimed to evaluate the different biological activities of T. polium hydroalcoholic extract, its total phenol and flavonoid content, and its mineral elements. Results showed that T. polium extract showed significant antioxidant potential in 2-diphenyl-1-picrylhydrazyl (DPPH) assay with IC50 equal to 8.68 μg/mL but with moderate activity in galvinoxyl assay with IC50 of 21.82 μg/mL and mild activity in the β-carotene assay. It also showed a pronounced anti-hyperglycemic activity using α-amylase inhibitory assay (IC50 = 111.68 µg/mL) and exceeds that of acarbose. T. polium showed excellent activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with IC50 values of 28.69 and 4.93 μg/mL, respectively, postulating its promising anti-Alzheimer potential. The plant extract exhibited a strong anti-inflammatory effect with Bovine Serum Albumin (BSA) denaturation inhibitory potential estimated by 97.53% at 2 mg/mL, which was further confirmed by the in vivo carrageen-induced edema model. The extract revealed its richness in flavonoids and phenols, evidenced by its polyphenols content (36.35 ± 0.294 μg GAE/mg) and flavonoids (24.30 ± 0.44 μg QE/mg). It is rich in minerals necessary for human health, such as calcium, potassium, iron, sodium, magnesium, manganese and zinc. Molecular docking performed for previously identified compounds on human α-amylase, 5-lipoxygenase (5-LOX) and acetylcholine esterase confirmed the results. Thus, it can be concluded that T. polium can be a good candidate for alleviating many health-debilitating problems and can be highly beneficial in the pharmaceutical industry and medical research.
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Affiliation(s)
- Naima Benchikha
- Laboratory of Applied Chemistry and Environment (LCAE), Chemistry Department, University of Hamma Lakhdar El-Oued, B.P.789, El-Oued 39000, Algeria
| | - Mohammed Messaoudi
- Laboratory of Applied Chemistry and Environment (LCAE), Chemistry Department, University of Hamma Lakhdar El-Oued, B.P.789, El-Oued 39000, Algeria
- Nuclear Research Centre of Birine, P.O. Box 180, Ain Oussera, Djelfa 17200, Algeria
| | - Imane Larkem
- Laboratory of Diversity of Ecosystems and Dynamics of Agricultural Production Systems in Arid Zones, Department of Agronomy, Faculty of Nature and Life Science, Biskra University, Biskra 07000, Algeria
| | - Hamza Ouakouak
- Laboratory of Applied Chemistry and Environment (LCAE), Chemistry Department, University of Hamma Lakhdar El-Oued, B.P.789, El-Oued 39000, Algeria
| | - Abdelkrim Rebiai
- Laboratory of Applied Chemistry and Environment (LCAE), Chemistry Department, University of Hamma Lakhdar El-Oued, B.P.789, El-Oued 39000, Algeria
| | - Siham Boubekeur
- Research and Development Centre RDC-SAIDAL, 35Benyoucef Khattab Avenue, Mohammadia, El-Harrah, Algiers 16000, Algeria
| | | | - Adel Benarfa
- Centre de Recherche Scientifique Et Technique en Analyses Physico-Chimiques (CRAPC)-PTAPC, P.O. Box 0354, Laghouat 03000, Algeria
| | - Samir Begaa
- Nuclear Research Centre of Birine, P.O. Box 180, Ain Oussera, Djelfa 17200, Algeria
| | - Mokhtar Benmohamed
- Laboratory of Fundamental Sciences, University Amar Télidji of Laghouat, P.O. Box 37G, Road of Ghardaïa, Laghouat 03000, Algeria
| | - Diena M. Almasri
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rawan H. Hareeri
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fadia S. Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbasia, Cairo 11566, Egypt
- Correspondence:
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High throughput virtual screening (HTVS) of peptide library: Technological advancement in ligand discovery. Eur J Med Chem 2022; 243:114766. [PMID: 36122548 DOI: 10.1016/j.ejmech.2022.114766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/21/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022]
Abstract
High-throughput virtual screening (HTVS) is a leading biopharmaceutical technology that employs computational algorithms to uncover biologically active compounds from large-scale collections of chemical compound libraries. In addition, this method often leverages the precedence of screening focused libraries for assessing their binding affinities and improving physicochemical properties. Usually, developing a drug sometimes takes ages, and lessons are learnt from FDA-approved drugs. This screening strategy saves resources and time compared to laboratory testing in certain stages of drug discovery. Yet in-silico investigations remain challenging in some cases of drug discovery. For the last few decades, peptide-based drug discoveries have received remarkable momentum for several advantages over small molecules. Therefore, developing a high-fidelity HTVS platform for chemically versatile peptide libraries is highly desired. This review summarises the modern and frequently appreciated HTVS strategies for peptide libraries from 2011 to 2021. In addition, we focus on the software used for preparing peptide libraries, their screening techniques and shortcomings. An index of various HTVS methods reported here should assist researchers in identifying tools that could be beneficial for their peptide library screening projects.
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Yang R, Zha X, Gao X, Wang K, Cheng B, Yan B. Multi-stage virtual screening of natural products against p38α mitogen-activated protein kinase: predictive modeling by machine learning, docking study and molecular dynamics simulation. Heliyon 2022; 8:e10495. [PMID: 36105464 PMCID: PMC9465123 DOI: 10.1016/j.heliyon.2022.e10495] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/20/2022] [Accepted: 08/25/2022] [Indexed: 11/20/2022] Open
Abstract
p38α is a mitogen-activated protein kinase (MAPK), and the signaling pathways involved are closely related to the inflammation, apoptosis and differentiation of cells, which also makes it an attractive target for drug discovery. With the high efficiency and low cost, virtual screening technology is becoming an indispensable part of drug development. In this study, a novel multi-stage virtual screening method based on machine learning, molecular docking and molecular dynamics simulation was developed to identify p38α MAPK inhibitors from natural products in ZINC database, which improves the prediction accuracy by considering and utilizing both ligand and receptor information compared to any individual approach. Ultimately, we screened out two candidate inhibitors with acceptable ADMET properties (ZINC4260400 and ZINC8300300). Among the generated machine learning models, Random Forest (RF) and Support Vector Machine (SVM) performed better, with the area under the receiver operating characteristic curve (AUC) values of 0.932 and 0.931 on the test set, as well as 0.834 and 0.850 on the external validation set. In addition, the results of molecular docking and ADMET prediction showed that two compounds with appropriate pharmacokinetic properties had binding free energies less than −8.0 kcal/mol for the target protein, and the results of molecular dynamics simulations further confirmed that they were stable during the process of inhibition.
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Koukab S, Rashid N, Ahmad I, Nadeem H, Ismail H. Synthesis, in-Silico studies, and in-Vitro bio-evaluation of new bi-thiacoumarins. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Antimicrobial Alkaloids from Marine-Derived Fungi as Drug Leads versus COVID-19 Infection: A Computational Approach to Explore their Anti-COVID-19 Activity and ADMET Properties. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5403757. [PMID: 35911157 PMCID: PMC9325633 DOI: 10.1155/2022/5403757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/11/2022] [Indexed: 11/28/2022]
Abstract
Therapeutic strategies based upon enzyme inhibition have recently gained higher attention in treating hazardous ailments. Herein, the potential use of seventy-two antimicrobial alkaloids isolated from marine-derived fungi to fight COVID-19 infection via inhibition of SARS-CoV-2 lethal virus was performed using in silico analyses. Molecular modelling was performed to assess their enzyme inhibitory potential on the main protease SARS-CoV-2 MPro, 3-chymotrypsin-like protease SARS-CoV-2 3CLpro, and papain-like protease SARS-CoV-2 PLpro using Discovery Studio 4.5. Validation of the docking experiments was done by determination of RMSD (root mean square deviation) after redocking the superimposition of the cocrystalized ligands. Results showed that gymnastatin Z (72) showed the best fitting score in SARS-CoV-2 MPro and SARS-CoV-2 3CLpr active sites with ∆G equal −34.15 and −34.28 Kcal/mol, respectively. Meanwhile, scalusamide C (62) displayed the highest fitting within SARS-CoV-2 PLpro active sites (∆G = −26.91 Kcal/mol) followed by eutypellazine M (57). ADMET/TOPKAT prediction displayed that eutypellazine M and scalusamide C showed better pharmacokinetic and pharmacodynamic properties. Gymnastatin Z is safer showing better toxicity criteria and higher rat oral LD50 and rat chronic LOAEL (lowest observed adverse effect level). Chemometric analysis using principle component analysis (PCA) based on the binding energies observed for the compounds with respect to the three tested enzymes revealed the clustering of the compounds into different clusters. Eutypellazine M, scalusamide C, and gymnastatin Z appear in one cluster due to their closeness in activity. Thus, these compounds could serve as promising SARS-CoV-2 enzymes inhibitors that could help in alleviation of COVID-19 infection. Further investigations are recommended to confirm the results of molecular modelling.
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Sharma Y, Kaur A, Mishra R, Kulkarni S, Bharadwaj M, Bala K. Antiproliferative efficacy of the antioxidant bioactive compounds of defatted seeds of Azadirachta indica and Momordica charantia against the regulatory function of tumor suppressor gene inducing oral carcinoma. J Biomol Struct Dyn 2022:1-15. [PMID: 35674735 DOI: 10.1080/07391102.2022.2083015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The present study focuses on the antiproliferative activity of polyphenolic flavonoids found in defatted seeds of Azadirachta indica and Momordica charantia with the regulatory function of tumor suppressor genes inducing Oral Squamous Cell Carcinoma. Polyphenolic flavonoid in extracts was characterized using chromatographic analysis and has confirmed the presence of quercetin, rutin and tannic acid in the extracts of A. indica and M. charantia. According to DPPH assay and reducing power assays, free radical scavenging was found to be high in ethanolic extract of defatted seeds. Antiproliferative efficacies of defatted seed extracts against KB cell line (mouth) were studied by MTT assay and revealed that aqueous extract of defatted seeds of M. charantia has exhibited maximum antiproliferative activity against KB cells. Antioxidant activity of defatted seed extracts were observed on treated KB cells by determining enzymatic activity (SOD, Cat, and GST) and nonenzyme content (GSH and MDA Content). Using the AutoDock tool, quercetin, rutin and tannin acid revealed that mutant p53, TWIST related protein, TGF-β and Snail I have the best binging energy results. MD simulation was observed on best docking results between the molecule and identified flavonoid by Desmond V 5.9 package . This leads to the conclusion that bioactive extracts with antiproliferative activity, antioxidant capacity and polyphenols with binding efficacy against tumor suppressor gene regulatory function could be used as a herbal remedy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yash Sharma
- Therapeutics and Molecular Diagnostic Lab, Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Amritpal Kaur
- Therapeutics and Molecular Diagnostic Lab, Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Rupa Mishra
- Amity Institute of Molecular Medicine and Stem cell Research, Amity University, Noida, India
| | | | | | - Kumud Bala
- Therapeutics and Molecular Diagnostic Lab, Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
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Altyar AE, Youssef FS, Kurdi MM, Bifari RJ, Ashour ML. The Role of Cannabis sativa L. as a Source of Cannabinoids against Coronavirus 2 (SARS-CoV-2): An In Silico Study to Evaluate Their Activities and ADMET Properties. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092797. [PMID: 35566148 PMCID: PMC9104455 DOI: 10.3390/molecules27092797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 12/23/2022]
Abstract
Cannabis sativa L. is an annual herbaceous plant that belongs to the family Cannabinaceae. In this study, the potential use of forty-five cannabinoids, previously identified from Cannabis sativa to alleviate COVID-19 infection via prohibition of crucial SARS-CoV-2 proteins using molecular docking, was examined. In silico studies were performed on three vital enzymes that serve as principle therapeutic targets to prevent SARS-CoV-2 replication. These enzymes are the main protease SARS-CoV-2 MPro, papain-like protease SARS-CoV-2 PLpro and angiotensin-converting enzyme 2 (ACE2). Regarding SARS-CoV-2 MPro, cannabichromanon (32) showed the best fitting within its active centers, followed by cannabinolic acid (22) and cannabinol (21), displaying ∆G of -33.63, -23.24, and -21.60 kcal/mol, respectively. Concerning SARS-CoV-2 PLpro, cannabichromanon (32) followed by cannabinolic acid (22) and cannabicyclolic acid (41) revealed the best binding within its active pockets owing to multiple bond formation with ∆G values of -28.36, -22.81, and -19.89 kcal/mol. Furthermore, cannabichromanon (32), cannabinolic acid (22), and cannabinol (21) showed considerable fitting within the active sites of angiotensin-converting enzyme 2 (ACE2) evidenced by their significant ∆G values that were estimated as -41.77, -31.34, and -30.36 kcal/mol, respectively. ADME/TOPKAT (absorption, distribution, metabolism, excretion, and toxicity) evaluation was performed on the tested cannabinoids to further explore their pharmacokinetics, pharmacodynamics, and toxicity properties. The results indicated the considerable pharmacokinetic, pharmacodynamic, and toxicity properties of cannabinol (21), cannabinolic acid (22), cannabichromanon (32), and cannabicyclolic acid (41) that showed best fitting scores within the active sites of the tested enzymes. Multivariate data analysis revealed that cannabichromanon and cannabinolic acid showed a discriminant nature and hence can be incorporated in pharmaceutical dosage forms to alleviate COVID-19 infection.
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Affiliation(s)
- Ahmed E. Altyar
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia;
| | - Fadia S. Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbasia, Cairo 11566, Egypt;
| | - Maram M. Kurdi
- Faculty of Pharmacy, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia; (M.M.K.); (R.J.B.)
| | - Renad J. Bifari
- Faculty of Pharmacy, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia; (M.M.K.); (R.J.B.)
| | - Mohamed L. Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbasia, Cairo 11566, Egypt;
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
- Correspondence:
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Bakherad Z, Bakherad H, Sepehri S, Faramarzi MA, Mahnam K, Mojtabavi S, Mahdavi M. In silico and in vitro studies of thiosemicarbazone-indole hybrid compounds as potent α-glycosidase inhibitors. Comput Biol Chem 2022; 97:107642. [PMID: 35183819 DOI: 10.1016/j.compbiolchem.2022.107642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 12/28/2021] [Accepted: 02/07/2022] [Indexed: 11/03/2022]
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Mamadalieva NZ, Youssef FS, Hussain H, Zengin G, Mollica A, Al Musayeib NM, Ashour ML, Westermann B, Wessjohann LA. Validation of the Antioxidant and Enzyme Inhibitory Potential of Selected Triterpenes Using In Vitro and In Silico Studies, and the Evaluation of Their ADMET Properties. Molecules 2021; 26:molecules26216331. [PMID: 34770739 PMCID: PMC8587851 DOI: 10.3390/molecules26216331] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
The antioxidant and enzyme inhibitory potential of fifteen cycloartane-type triterpenes’ potentials were investigated using different assays. In the phosphomolybdenum method, cycloalpioside D (6) (4.05 mmol TEs/g) showed the highest activity. In 1,1-diphenyl-2-picrylhydrazyl (DPPH*) radical and 2,2′-azino-bis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) cation radical scavenging assays, cycloorbicoside A-7-monoacetate (2) (5.03 mg TE/g) and cycloorbicoside B (10) (10.60 mg TE/g) displayed the highest activities, respectively. Oleanolic acid (14) (51.45 mg TE/g) and 3-O-β-d-xylopyranoside-(23R,24S)-16β,23;16α,24-diepoxycycloart-25(26)-en-3β,7β-diol 7-monoacetate (4) (13.25 mg TE/g) revealed the highest reducing power in cupric ion-reducing activity (CUPRAC) and ferric-reducing antioxidant power (FRAP) assays, respectively. In metal-chelating activity on ferrous ions, compound 2 displayed the highest activity estimated by 41.00 mg EDTAE/g (EDTA equivalents/g). The tested triterpenes showed promising AChE and BChE inhibitory potential with 3-O-β-d-xylopyranoside-(23R,24S)-16β,23;16α,24-diepoxycycloart-25(26)-en-3β,7β-diol 2′,3′,4′,7-tetraacetate (3), exhibiting the highest inhibitory activity as estimated from 5.64 and 5.19 mg GALAE/g (galantamine equivalent/g), respectively. Compound 2 displayed the most potent tyrosinase inhibitory activity (113.24 mg KAE/g (mg kojic acid equivalent/g)). Regarding α-amylase and α-glucosidase inhibition, 3-O-β-d-xylopyranoside-(23R,24S)-16β,23;16α,24-diepoxycycloart-25(26)-en-3β,7β-diol (5) (0.55 mmol ACAE/g) and compound 3 (25.18 mmol ACAE/g) exerted the highest activities, respectively. In silico studies focused on compounds 2, 6, and 7 as inhibitors of tyrosinase revealed that compound 2 displayed a good ranking score (−7.069 kcal/mole) and also that the ΔG free-binding energy was the highest among the three selected compounds. From the ADMET/TOPKAT prediction, it can be concluded that compounds 4 and 5 displayed the best pharmacokinetic and pharmacodynamic behavior, with considerable activity in most of the examined assays.
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Affiliation(s)
- Nilufar Z. Mamadalieva
- Institute of the Chemistry of Plant Substances, Academy Sciences of Uzbekistan, Tashkent 100170, Uzbekistan
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany; (H.H.); (B.W.); (L.A.W.)
- Correspondence:
| | - Fadia S. Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt; (F.S.Y.); (M.L.A.)
| | - Hidayat Hussain
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany; (H.H.); (B.W.); (L.A.W.)
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Konya 42130, Turkey;
| | - Adriano Mollica
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy;
| | - Nawal M. Al Musayeib
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Mohamed L. Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt; (F.S.Y.); (M.L.A.)
| | - Bernhard Westermann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany; (H.H.); (B.W.); (L.A.W.)
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany; (H.H.); (B.W.); (L.A.W.)
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Youssef FS, Ovidi E, Musayeib NMA, Ashour ML. Morphology, Anatomy and Secondary Metabolites Investigations of Premna odorata Blanco and Evaluation of Its Anti-Tuberculosis Activity Using In Vitro and In Silico Studies. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10091953. [PMID: 34579484 PMCID: PMC8467642 DOI: 10.3390/plants10091953] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 06/06/2023]
Abstract
In-depth botanical characterization was performed on Premna odorata Blanco (Lamiaceae) different organs for the first time. The leaves are opposite, hairy and green in color. Flowers possess fragrant aromatic odors and exist in inflorescences of 4-15 cm long corymbose cyme-type. In-depth morphological and anatomical characterization revealed the great resemblance to plants of the genus Premna and of the family Lamiaceae, such as the presence of glandular peltate trichomes and diacytic stomata. Additionally, most examined organs are characterized by non-glandular multicellular covering trichomes, acicular, and rhombic calcium oxalate crystals. P. odorata leaves n-hexane fraction revealed substantial anti-tuberculous potential versus Mycobacterium tuberculosis, showing a minimum inhibition concentration (MIC) of 100 μg/mL. Metabolic profiling of the n-hexane fraction using gas-chromatography coupled to mass spectrometry (GC/MS) analysis revealed 10 major compounds accounting for 93.01%, with trans-phytol constituting the major compound (24.06%). The virtual screening revealed that trans-phytol highly inhibited MTB C171Q receptor as M. tuberculosis KasA (β-ketoacyl synthases) with a high fitting score (∆G = -15.57 kcal/mol) approaching that of isoniazid and exceeding that of thiolactomycin, the co-crystallized ligand. Absorption, distribution, metabolism, excretion and toxicity predictions (ADME/TOPKAT) revealed that trans-phytol shows lower solubility and absorption levels when compared to thiolactomycin and isoniazid. Still, it is safer, causing no mutagenic or carcinogenic effects with higher lethal dose, which causes the death of 50% (LD50). Thus, it can be concluded that P. odorata can act as a source of lead entities to treat tuberculosis.
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Affiliation(s)
- Fadia S. Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbasia, Cairo 11566, Egypt
| | - Elisa Ovidi
- Department for the Innovation in Biological, Agrofood and Forestal Systems, Tuscia University, 01100 Viterbo, Italy;
| | - Nawal M. Al Musayeib
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Mohamed L. Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbasia, Cairo 11566, Egypt
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Li Y, Zhang Y, Wu X, Gao Y, Guo J, Tian Y, Lin Z, Wang X. Discovery of natural 15-LOX small molecule inhibitors from Chinese herbal medicine using virtual Screening, biological evaluation and molecular dynamics studies. Bioorg Chem 2021; 115:105197. [PMID: 34426159 DOI: 10.1016/j.bioorg.2021.105197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 11/19/2022]
Abstract
Chinese herbal medicines (CHM) are frequently used to treat different types of inflammatory diseases and 15-Lipoxygenase (15-LOX) is a critical target enzyme for treating various inflammatory diseases. In this study, natural 15-LOX inhibitors were identified in CHM using an approach of virtual screening combined with the biological assays. First, an in-house Chinese medicine database containing 360 compounds was screened using a virtual screening approach based on pharmacophore and molecular docking to uncover several novel potential 15-LOX inhibitors. Secondly, the inhibitory effect of virtual screening hits against the 15-LOX enzyme was validated in an in vitro enzyme inhibition assay. Then, a tumor necrosis factor-α (TNF-α) release assay was carried out to explore the anti-inflammatory response of the active compounds. Furthermore, molecular dynamics (MD) simulation and binding free energy calculation were applied to analyze the process of inhibitors binding and also compared the mode of binding of the inhibitors by using the Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) method. Finally, licochalcone B and eriodictyol were confirmed as inhibitors of the 15-LOX enzyme with IC50 values of 9.67 and 18.99 μM, respectively. In vitro cell-based assay showed that licochalcone B and eriodictyol inhibited the release of TNF-α factor in RAW264.7 cells stimulated by lipopolysaccharides (LPS) in a dose-dependent manner. Molecular dynamics and binding free energy analysis showed that the two 15-LOX-ligand systems immediately attained equilibrium with almost 1 Å fluctuation, the calculated binding free energies were found around -18.89 and -12.96 kcal/mol for licochalcone B and eriodictyol, respectively. Thr412, Arg415, Val420, Thr429, Ile602 and Trp606 were the main amino acid residues for the inhibition of 15-LOX enzyme activity. The current study confirms that licochalcone B and eriodictyol are 15-LOX inhibitors and can suppress the release of the TNF-α factor in RAW264.7 cells stimulated by LPS, thus providing a basis for the follow-up research and development for 15-LOX inhibitors.
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Affiliation(s)
- Yatong Li
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yuxin Zhang
- Key Laboratory of Ethnomedicine, School of Pharmacy, Ministry of Education, Minzu University of China, Haidian District, Beijing 100081, China
| | - Xia Wu
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yanbin Gao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Junfang Guo
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yulang Tian
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Ziyue Lin
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China.
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Adzhubei AA, Kulkarni A, Tolstova AP, Anashkina AA, Sviridov D, Makarov AA, Bukrinsky MI. Direct interaction between ABCA1 and HIV-1 Nef: Molecular modeling and virtual screening for inhibitors. Comput Struct Biotechnol J 2021; 19:3876-3884. [PMID: 34584633 PMCID: PMC8440812 DOI: 10.1016/j.csbj.2021.06.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022] Open
Abstract
HIV-1 infection impairs cellular cholesterol efflux by downmodulating the cholesterol transporter ABCA1, leading to metabolic co-morbidities like cardio-vascular disease. The main mechanism of this effect is impairment by the HIV-1 protein Nef of the ABCA1 interaction with the endoplasmic reticulum chaperone calnexin, which leads to a block in ABCA1 maturation followed by its degradation. However, ABCA1 is also downmodulated by Nef delivered with the extracellular vesicles, suggesting involvement of a direct Nef:ABCA1 interaction at the plasma membrane. Here, we present an optimized model of the Nef:ABCA1 interaction, which identifies interaction sites and provides an opportunity to perform a virtual screening for potential inhibitors. Interestingly, the predicted sites on Nef involved in the ABCA1 interaction overlap with those involved in the interaction with calnexin. The compounds previously shown to block Nef:calnexin interaction were among the top ranking ligands in docking simulations with ABCA1-interacting sites on Nef, suggesting the possibility that both interactions can be inhibited by the same chemical compounds. This study identifies a series of compounds for potential development as inhibitors of Nef-mediated co-morbidities of HIV infection.
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Affiliation(s)
- Alexei A. Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Amol Kulkarni
- Howard University College of Pharmacy, Washington, District of Columbia, USA
| | - Anna P. Tolstova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Dmitri Sviridov
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Michael I. Bukrinsky
- The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
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Saleem H, Khurshid U, Sarfraz M, Tousif MI, Alamri A, Anwar S, Alamri A, Ahmad I, Abdallah HH, Mahomoodally FM, Ahemad N. A comprehensive phytochemical, biological, toxicological and molecular docking evaluation of Suaeda fruticosa (L.) Forssk.: An edible halophyte medicinal plant. Food Chem Toxicol 2021; 154:112348. [PMID: 34144099 DOI: 10.1016/j.fct.2021.112348] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/07/2021] [Accepted: 06/12/2021] [Indexed: 01/20/2023]
Abstract
Suaeda fruticosa is an edible medicinal halophyte known for its traditional uses. In this study, methanol and dichloromethane extracts of S. fruticosa were explored for phytochemical, biological and toxicological parameters. Total phenolic and flavonoid constituents were determined by using standard aluminum chloride and Folin-Ciocalteu methods, and UHPLC-MS analysis of methanol extract was performed for tentative identification of secondary metabolites. Different standard methods like DPPH, ABTS, FRAP, CUPRAC, total antioxidant capacity (TAC), and metal chelation assays were utilized to find out the antioxidant potential of extracts. Enzyme inhibition studies of extracts against acetylcholinesterase, butyrylcholinesterase, tyrosinase, α-amylase and, α-glucosidase enzymes were also studied. Likewise, the cytotoxicity was also assessed against MCF-7, MDA-MB-231, and DU-145 cell lines. The higher phenolic and flavonoids contents were observed in methanol extracts which can be correlated to its higher radical scavenging potential. Similarly, 11 different secondary metabolites were tentatively identified by UHPLC profiling. Both the extract showed significant inhibition against all the enzymes except for α-glucosidase. Moreover, docking studies were also performed against the tested enzymes. In the case of cytotoxicity, both the samples were found moderately toxic against the tested cell lines. This plant can be explored further for its potential therapeutic and edible uses.
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Affiliation(s)
- Hammad Saleem
- Institute of Pharmaceutical Sciences (IPS), University of Veterinary & Animal Sciences (UVAS), Lahore, Pakistan; School of Pharmacy, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway Selangor Darul Ehsan, Malaysia.
| | - Umair Khurshid
- Bahawalpur College of Pharmacy, Bahawalpur Medical and Dental College, Bahawalpur, Pakistan
| | - Muhammad Sarfraz
- College of Pharmacy, Al Ain University, Al Ain, United Arab Emirates
| | | | - Abdulwahab Alamri
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Hail, Saudi Arabia
| | - Sirajudheen Anwar
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Hail, Saudi Arabia
| | - Abdulhakeem Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, Taif University, P. O. Box 11099, Taif, 21944, Saudi Arabia
| | - Irshad Ahmad
- Department of Pharmacy, The Islamia University of Bahawalpur, Pakistan
| | - Hassan H Abdallah
- Chemistry Department, College of Education, Salahaddin University, Erbil, Iraq
| | - Fawzi M Mahomoodally
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Mauritius
| | - Nafees Ahemad
- School of Pharmacy, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway Selangor Darul Ehsan, Malaysia
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Senizza B, Zhang L, Rocchetti G, Zengin G, Ak G, Yıldıztugay E, Elbasan F, Jugreet S, Mahomoodally MF, Lucini L. Metabolomic profiling and biological properties of six Limonium species: novel perspectives for nutraceutical purposes. Food Funct 2021; 12:3443-3454. [PMID: 33900332 DOI: 10.1039/d0fo02968h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The genus Limonium includes important halophyte plants containing a variety of bioactive compounds of therapeutic interest. In the present work, the untargeted phytochemical profiles of both aerial part and root extracts from six Limonium species namely, L. bellidifolium, L. globuliferum, L. gmelinii, L. lilacinum, L. sinuatum and L. iconicum from Turkey were determined. Furthermore, several biological activities (in vitro antioxidant and enzyme inhibitory effects) were investigated. Overall, significant amounts of total phenolics (43.64-238.18 mg g-1) and flavonoids (1.61-129.69 mg g-1) were recorded. Particularly, the root extracts of L. gmelinii, L. iconicum and L. globuliferum showed the highest total phenolic content (204.13-238.18 mg g-1), whilst the highest total flavonoid content was recorded in the root extracts of L. gmelinii (129.69 mg g-1). Overall, the tested extracts demonstrated potent radical scavenging activities in both DPPH (2,2- diphenyl-1-picrylhydrazyl) and ABTS (3-ethylbenzothiazoline-6-sulphonic acid) (90.10-507.94 mg g-1 and 163.39-1175.34 mg g-1, respectively). However, the highest scavenging potential (p < 0.05) was displayed by the root extracts of L. iconicum. Conversely, the metal chelating ability assay revealed that L. lilacinum root extract showed the highest activity (21.03 mg g-1). Interestingly, all the extracts were found to be active inhibitors of cholinesterases (AChE (acetylcholinesterase): 4.20-5.11 mg GALAE (galantamine equivalent) per g; BChE (butyrylcholinesterase): 3.89-10.75 mg GALAE per g), amylase (0.52-1.09 mmol ACAE (acarbose equivalent) per g) and tyrosinase (119.41-155.67 mg KAE (kojic acid equivalent) per g), unlike for glucosidase (2.31-2.41 mmol ACAE per g). Taken together, these findings demonstrated a diverse chemical profiles and biological of the extracts, to be potentially considered as phytotherapeutic or functional ingredients due to their antioxidant properties and inhibition of key enzymes involved in several diseases.
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Affiliation(s)
- Biancamaria Senizza
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 29122, Piacenza, Italy.
| | - Leilei Zhang
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 29122, Piacenza, Italy.
| | - Gabriele Rocchetti
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 29122, Piacenza, Italy.
| | - Gokhan Zengin
- Physiology and Biochemistry Laboratory, Department of Biology, Science Faculty, Selcuk University, Campus, 42130 Konya, Turkey
| | - Gunes Ak
- Physiology and Biochemistry Laboratory, Department of Biology, Science Faculty, Selcuk University, Campus, 42130 Konya, Turkey
| | - Evren Yıldıztugay
- Department of Biotechnology, Science Faculty, Selcuk University, Campus, 42130 Konya, Turkey
| | - Fevzi Elbasan
- Department of Biotechnology, Science Faculty, Selcuk University, Campus, 42130 Konya, Turkey
| | - Sharmeen Jugreet
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit, Mauritius
| | - Mohamad Fawzi Mahomoodally
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit, Mauritius
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 29122, Piacenza, Italy.
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Mahomoodally MF, Picot-Allain MCN, Zengin G, Llorent-Martínez EJ, Stefanucci A, Ak G, Senkardes I, Tomczyk M, Mollica A. Chemical profiles and biological potential of tuber extracts from Cyclamen coum Mill. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Cardoso FJB, Xavier LP, Santos AV, Pereira HD, Santos LDS, Molfetta FAD. Identification of potential inhibitors of Schistosoma mansoni purine nucleoside phosphorylase from neolignan compounds using molecular modelling approaches. J Biomol Struct Dyn 2021; 40:8248-8260. [PMID: 33830889 DOI: 10.1080/07391102.2021.1910073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Schistosomiasis is a parasitic disease that is part of the neglected tropical diseases (NTDs), which cause significant levels of morbidity and mortality in millions of people throughout the world. The enzyme purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) represents a potential target for discovering new agents, and neolignans stand out as an important class of compounds. In this work, molecular modeling studies and biological assays of a set of neolignans were conducted against the PNP enzymes of the parasite and the human homologue (HssPNP). The results of the molecular docking described that the neolignans showed good complementarity by the active site of SmPNP. Molecular dynamics (MD) studies revealed that both complexes (Sm/HssPNP - neolignan compounds) were stable by analyzing the root mean square deviation (RMSD) values, and the binding free energy values suggest that the selected structures can interact and inhibit the catalytic activity of the SmPNP. Finally, the biological assay indicated that the selected neolignans presented a better molecular profile of inhibition compared to the human enzyme, as these ligands did not have the capacity to inhibit enzymatic activity, indicating that these compounds are promising candidates and that they can be used in future research in chemotherapy for schistosomiasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fábio José Bonfim Cardoso
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Luciana Pereira Xavier
- Laboratório de Biotecnologia de Enzimas e Biotransformação, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Agenor Valadares Santos
- Laboratório de Biotecnologia de Enzimas e Biotransformação, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Humberto D'Muniz Pereira
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos-SP, Brazil
| | - Lourivaldo da Silva Santos
- Laboratório de Síntese e Produtos Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém-PA, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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Xu P, Ghosh S, Gul AR, Bhamore JR, Park JP, Park TJ. Screening of specific binding peptides using phage-display techniques and their biosensing applications. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Zengin G, Mahomoodally MF, Picot-Allain MCN, Sinan KI, Ak G, Etienne OK, Sieniawska E, Maciejewska-Turska M, Świątek Ł, Rajtar B, Polz-Dacewicz M. Chemical composition, biological properties and bioinformatics analysis of two Caesalpina species: A new light in the road from nature to pharmacy shelf. J Pharm Biomed Anal 2021; 198:114018. [PMID: 33730614 DOI: 10.1016/j.jpba.2021.114018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023]
Abstract
Caesalpinia bonduc and C. decapeleta var. japonica have great importance in traditional medicine systems but scientific information's are still lacking for their potentials. To explore their bioactivity, we assessed the antioxidant, enzyme inhibitory abilities of the dichloromethane (DCM), ethyl acetate, methanol, and water extracts prepared from the leaves and bark. The cytotoxicity and anticancer properties of the extracts were also assessed in vitro. The water extract of C. decapeleta leaves possessed highest phenolic content (108.16 mg gallic acid equivalent (GAE)/g extract), while the highest flavonoid content was recorded for the C. bonduc leaf methanolic extract (27.89 mg rutin equivalent (RE)/g extract). In general, C. decapeleta extracts possessed higher radical scavenging potential compared to C. bonduc extracts. C. decapeleta DCM leaves extract (10.20 mg galantamine equivalent (GALAE)/g extract) showed highest inhibition against butyrylcholinesterase. The cytotoxicity of the most potent methanolic and aqueous extracts were assessed against four cell lines. The chemical profiles of both species appeared to be different. C. bonduc was abundant in organic and phenolic acids as well as their esters. Flavonoid glycosides, bonducellin and its derivatives and caesalminaxins were identified. Whereas, C. decalpetala possessed many galloylated compounds. The cytotoxicity of C. bonduc and C. decapetala extracts was tested using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) based assay on VERO (kidney of an adult African Green monkey cells), HeLa (human cervical adenocarcinoma cells), RKO (human colon carcinoma cells), FaDu (human hypopharyngeal squamous carcinoma cells) cell lines. C. bonduc bark water extract exhibited the highest cytotoxicity towards HeLa (50 % cytotoxic concentration (CC50): 28.5 μg/mL) cancer cell line, as compared to normal VERO cells (CC50:35.87 μg/mL). For C. decapetala, the highest cytotoxicity was found for bark methanol extract on the HeLa cells with CC50 of 46.08 μg/mL and selectivity index of 3.33. In the gene ontology analysis, prostate cancer, nuclear factor kappa B (NF-kappa B) signaling, proteoglycans in cancer pathways might support the results of the cytotoxic assays. These results showed that the tested Caesalpinia species, showing potent inhibitory action against butyrylcholinesterase, might represent novel phytotherapeutic avenues for the management of Alzheimer's disease.
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Affiliation(s)
- Gokhan Zengin
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Konya, Turkey.
| | - Mohamad Fawzi Mahomoodally
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit, Mauritius.
| | | | - Kouadio Ibrahime Sinan
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Konya, Turkey
| | - Gunes Ak
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Konya, Turkey
| | - Ouattara Katinan Etienne
- Laboratoire de Botanique, UFR Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Elwira Sieniawska
- Department of Pharmacognosy, Medical University of Lublin, Chodzki 1, Lublin, 20-093, Poland
| | | | - Łukasz Świątek
- Department of Virology with SARS Laboratory, Medical University of Lublin, Chodzki 1, 20-059, Lublin, Poland
| | - Barbara Rajtar
- Department of Virology with SARS Laboratory, Medical University of Lublin, Chodzki 1, 20-059, Lublin, Poland
| | - Małgorzata Polz-Dacewicz
- Department of Virology with SARS Laboratory, Medical University of Lublin, Chodzki 1, 20-059, Lublin, Poland
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Ademosun MT, Omoba OS, Olagunju AI. Antioxidant properties, glycemic indices, and carbohydrate hydrolyzing enzymes activities of formulated ginger-based fruit drinks. J Food Biochem 2021; 45:e13324. [PMID: 32572973 DOI: 10.1111/jfbc.13324] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/11/2020] [Accepted: 05/21/2020] [Indexed: 12/22/2022]
Abstract
The global prevalence of hyperglycemia has been attributed to unhealthy lifestyle and diet. The study assessed the antioxidant properties, glycemic indices, and carbohydrate hydrolyzing enzymes activities of ginger-based fruit drinks. Drinks prepared from blends of ginger (G), pineapple (P), and apple (A) at varied ratios-G50:P40:A10, G50:P30:A20, G50:P20:A30, G50:P10:A40, G100, and a commercial ginger drink (control) were analyzed for phenolic distribution and antioxidant properties using 2,2-diphenyl-1-picrylhydrazyl [DPPH] and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) [ABTS] radical scavenging abilities. The ferric reducing antioxidant property (FRAP), the glycemic indices and carbohydrate hydrolyzing enzymes activities were also investigated. G50:P10:A40 exhibited the highest phenolic distribution, highest DPPH● , ABTS●+ scavenging abilities as well as FRAP. All formulated ginger-based drinks exhibited low glycemic indices, the G50:P10:A40 showed the strongest inhibition against carbohydrate hydrolyzing enzymes. G50:P10:A40 blend may be suitable for the control of hyperglycemia and some degenerative conditions linked with oxidative stress. PRACTICAL APPLICATIONS: Unchecked activities of reactive oxygen species (ROS) are linked to health disorders such as diabetes mellitus, hypertension, cancer, neurodegenerative, and inflammatory diseases. A practical approach to the management of the deleterious effect of ROS is through the consumption of foods rich in nutritional antioxidants. Ginger (Zingiber officinale) is grown globally for its edible rhizome which has varied utilization in culinary and medicinal applications. Drinks produced from blends of ginger, pineapple, and apple were able to scavenge free radicals and able to exhibit hypoglycemic effects by inhibiting carbohydrate hydrolyzing enzymes. The Ginger-based fruit drinks would, therefore, be an effective functional dietary drink in the management and prevention of diabetes mellitus.
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Affiliation(s)
- Mary T Ademosun
- Department of Food Science and Technology, Federal University of Technology, Akure, Nigeria
| | - Olufunmilayo S Omoba
- Department of Food Science and Technology, Federal University of Technology, Akure, Nigeria
| | - Aderonke I Olagunju
- Department of Food Science and Technology, Federal University of Technology, Akure, Nigeria
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30
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Sinan KI, Luz Cádiz-Gurrea MDL, Javier Leyva-Jiménez F, Fernández-Ochoa Á, Segura-Carretero A, Glamocilja J, Sokovic M, Nenadić M, Aktumsek A, Dall'Acqua S, Zengin G. New insights on Phyllanthus reticulatus Poir. leaves and stem bark extracts: UPLC-ESI-TOF-MS profiles, and biopharmaceutical and in silico analysis. NEW J CHEM 2021. [DOI: 10.1039/d1nj03621a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our results could provide a great scientific starting point on the way from the bench to functional applications through the use of P. reticulatus, namely novel nutraceuticals, pharmaceuticals and cosmeceuticals.
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Affiliation(s)
- Kouadio Ibrahime Sinan
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Campus, Konya, Turkey
| | - María de la Luz Cádiz-Gurrea
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Fuentenueva s/n, E-18071 Granada, Spain
- Functional Food Research and Development Center, Health Science Technological Park, Avenida del Conocimiento s/n, E-18100 Granada, Spain
| | - Francisco Javier Leyva-Jiménez
- Functional Food Research and Development Center, Health Science Technological Park, Avenida del Conocimiento s/n, E-18100 Granada, Spain
| | - Álvaro Fernández-Ochoa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
| | - Antonio Segura-Carretero
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Fuentenueva s/n, E-18071 Granada, Spain
- Functional Food Research and Development Center, Health Science Technological Park, Avenida del Conocimiento s/n, E-18100 Granada, Spain
| | - Jasmina Glamocilja
- Laboratory of Mycology, Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marina Sokovic
- Laboratory of Mycology, Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marija Nenadić
- Laboratory of Mycology, Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Abdurrahman Aktumsek
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Campus, Konya, Turkey
| | - Stefano Dall'Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Gokhan Zengin
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Campus, Konya, Turkey
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31
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Mahindrakar KV, Rathod VK. Antidiabetic potential evaluation of aqueous extract of waste Syzygium cumini seed kernel's by in vitro α-amylase and α-glucosidase inhibition. Prep Biochem Biotechnol 2020; 51:589-598. [PMID: 33185507 DOI: 10.1080/10826068.2020.1839908] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Syzygium cumini, owing to higher bioactive constituents, its parts principally kernels are used for the antidiabetic purpose since the olden days. The current manuscript illustrated batch extraction of phenolic compounds from S. cumini using a stirred extractor. The yields 0.61 mg/g, 35.9 mg/g, 79.89 mg GAE/g, and 7.29 mg CE/g of catechin, gallic acid, TPC and TFC, respectively, were obtained in 105 min. at 1:20 SCKP to water, 50 ± 2 °C temperature, 4 pH, at 250 rpm and 106 µm particle size of SCKP. In vitro evaluation of the antioxidant and antidiabetic potential of the obtained aqueous extract was carried out by DPPH, α-amylase, and α-glucosidase inhibitory assays. The IC50 values of SCKP aqueous extract obtained were 12.97, 9.03, and 7.13 µg/mL for DPPH scavenging, inhibition of α-amylase, and α-glucosidase, respectively. The cost required to extract 1 kg of catechin, gallic acid, TPC, and TFC was Rs 6691.6, 113.7, 51.1, and 559.93/-, respectively. Stirred batch extraction technique manifests traditional but simple, ecofriendly, and efficient compared to other traditional techniques. The output of this research bestows support to utilize the SCKP stirred batch extract as a promising source of antioxidant and antidiabetic compounds in ayurvedic formulations.
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Affiliation(s)
- Komal V Mahindrakar
- Department of Chemical Engineering, Mumbai University Institute of Chemical Technology, Mumbai, India
| | - Virendra K Rathod
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
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32
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Sinan KI, Martinović LS, Peršurić Ž, Pavelić SK, Etienne OK, Mahomoodally MF, Sadeer NB, Zengin G. Novel insights into the biopharmaceutical potential, comparative phytochemical analysis and multivariate analysis of different extracts of shea butter tree -Vitellaria paradoxa C. F. Gaertn. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.07.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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33
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A comparative assessment of biological activities of Gundelia dersim Miller and Gundelia glabra Vitek, Yüce & Ergin extracts and their chemical characterization via HPLC-ESI-TOF-MS. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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34
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Synthesis, in vitro and in silico screening of 2-amino-4-aryl-6-(phenylthio) pyridine-3,5-dicarbonitriles as novel α-glucosidase inhibitors. Bioorg Chem 2020; 100:103879. [PMID: 32413625 DOI: 10.1016/j.bioorg.2020.103879] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 12/23/2022]
Abstract
Inhibition of α-glucosidase enzyme is of prime importance for the treatment of diabetes mellitus (DM). Apart of many organic scaffolds, pyridine based compounds have previously been reported for wide range of bioactivities. The current study reports a series of pyridine based synthetic analogues for their α-glucosidase inhibitory potential assessed by in vitro, kinetics and in silico studies. For this purpose, 2-amino-4-aryl-6-(phenylthio)pyridine-3,5-dicarbonitriles 1-28 were synthesized and subjected to in vitro screening. Several analogs, including 1-3, 7, 9, 11-14, and 16 showed many folds increased inhibitory potential in comparison to the standard acarbose (IC50 = 750 ± 10 µM). Interestingly, compound 7 (IC50 = 55.6 ± 0.3 µM) exhibited thirteen-folds greater inhibition strength than the standard acarbose. Kinetic studies on most potent molecule 7 revealed a competitive type inhibitory mechanism. In silico studies have been performed to examine the binding mode of ligand (compound 7) with the active site residues of α-glucosidase enzyme.
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Evaluation of ACE, α-glucosidase, and lipase inhibitory activities of peptides obtained by in vitro digestion of selected species of edible insects. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03495-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe objective of this study was to examine the inhibition of the activity of enzymes associated with development of the metabolic syndrome by peptide fractions received from simulated gastrointestinal digestion and absorption of heat-treated edible insects. The inhibitory activities of insect-derived peptides were determined against key enzymes relevant to the metabolic syndrome such as the angiotensin-converting enzyme (ACE), pancreatic lipase, and α-glucosidase. After the in vitro absorption process, all hydrolysates showed high inhibitory activity; however, the most effective metabolic syndrome-inhibitory peptides were received after separation on Sephadex G10. The best results were found for peptide fractions obtained from Schistocerca gregaria. The highest enzymes inhibitory activities were obtained for peptide fractions from S. gregaria: boiled for ACE (IC50 3.95 µg mL−1), baked for lipase (IC50 9.84 µg mL−1), and raw for α-glucosiadase (IC50 1.89 µg mL−1) S. gregaria, respectively. Twelve sequences of peptides from the edible insects were identified and their chemical synthesis was carried out as well. Among the synthesized peptides, the KVEGDLK, YETGNGIK, AIGVGAIR, IIAPPER, and FDPFPK sequences of peptides exhibited the highest inhibitory activity. Generally, the heat treatment process applied to edible insects has a positive effect on the properties of the peptide fractions studied.
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Maryam A, Khalid RR, Siddiqi AR, Ece A. E-pharmacophore based virtual screening for identification of dual specific PDE5A and PDE3A inhibitors as potential leads against cardiovascular diseases. J Biomol Struct Dyn 2020; 39:2302-2317. [DOI: 10.1080/07391102.2020.1748718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Arooma Maryam
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul, Turkey
| | | | | | - Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul, Turkey
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Tutumlu G, Dogan B, Avsar T, Orhan MD, Calis S, Durdagi S. Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2. Front Chem 2020; 8:167. [PMID: 32328476 PMCID: PMC7160371 DOI: 10.3389/fchem.2020.00167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Antiapoptotic members of B-cell leukemia/lymphoma-2 (BCL-2) family proteins are one of the overexpressed proteins in cancer cells that are oncogenic targets. As such, targeting of BCL-2 family proteins raises hopes for new therapeutic discoveries. Thus, we used multistep screening and filtering approaches that combine structure and ligand-based drug design to identify new, effective BCL-2 inhibitors from a small molecule database (Specs SC), which includes more than 210,000 compounds. This database is first filtered based on binary “cancer-QSAR” model constructed with 886 training and 167 test set compounds and common 26 toxicity quantitative structure-activity relationships (QSAR) models. Predicted non-toxic compounds are considered for target-driven studies. Here, we applied two different approaches to filter and select hit compounds for further in vitro biological assays and human cell line experiments. In the first approach, a molecular docking and filtering approach is used to rank compounds based on their docking scores and only a few top-ranked molecules are selected for further long (100-ns) molecular dynamics (MD) simulations and in vitro tests. While docking algorithms are promising in predicting binding poses, they can be less prone to precisely predict ranking of compounds leading to decrease in the success rate of in silico studies. Hence, in the second approach, top-docking poses of each compound filtered through QSAR studies are subjected to initially short (1 ns) MD simulations and their binding energies are calculated via molecular mechanics generalized Born surface area (MM/GBSA) method. Then, the compounds are ranked based on their average MM/GBSA energy values to select hit molecules for further long MD simulations and in vitro studies. Additionally, we have applied text-mining approaches to identify molecules that contain “indol” phrase as many of the approved drugs contain indole and indol derivatives. Around 2700 compounds are filtered based on “cancer-QSAR” model and are then docked into BCL-2. Short MD simulations are performed for the top-docking poses for each compound in complex with BCL-2. The complexes are again ranked based on their MM/GBSA values to select hit molecules for further long MD simulations and in vitro studies. In total, seven molecules are subjected to biological activity tests in various human cancer cell lines as well as Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) assay. Inhibitory concentrations are evaluated, and biological activities and apoptotic potentials are assessed by cell culture studies. Four molecules are found to be limiting the proliferation capacity of cancer cells while increasing the apoptotic cell fractions.
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Affiliation(s)
- Gurbet Tutumlu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Timucin Avsar
- Department of Medical Biology, Bahcesehir University, School of Medicine, Istanbul, Turkey.,Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
| | - Muge Didem Orhan
- Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
| | - Seyma Calis
- Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Molecular Biology, Genetics and Biotechnology Graduate Program, Istanbul Technical University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.,Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
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Mora L, González-Rogel D, Heres A, Toldrá F. Iberian dry-cured ham as a potential source of α-glucosidase-inhibitory peptides. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.103840] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Comert Onder F, Durdagi S, Sahin K, Ozpolat B, Ay M. Design, Synthesis, and Molecular Modeling Studies of Novel Coumarin Carboxamide Derivatives as eEF-2K Inhibitors. J Chem Inf Model 2020; 60:1766-1778. [PMID: 32027127 DOI: 10.1021/acs.jcim.9b01083] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eukaryotic elongation factor-2 kinase (eEF-2K) is an unusual alpha kinase commonly upregulated in various human cancers, including breast, pancreatic, lung, and brain tumors. We have demonstrated that eEF-2K is relevant to poor prognosis and shorter patient survival in breast and lung cancers and validated it as a molecular target using genetic methods in related in vivo tumor models. Although several eEF-2K inhibitors have been published, none of them have shown to be potent and specific enough for translation into clinical trials. Therefore, development of highly effective novel inhibitors targeting eEF-2K is needed for clinical applications. However, currently, the crystal structure of eEF-2K is not known, limiting the efforts for designing novel inhibitor compounds. Therefore, using homology modeling of eEF-2K, we designed and synthesized novel coumarin-3-carboxamides including compounds A1, A2, and B1-B4 and evaluated their activity by performing in silico analysis and in vitro biological assays in breast cancer cells. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) area results showed that A1 and A2 have interaction energies with eEF-2K better than those of B1-B4 compounds. Our in vitro results indicated that compounds A1 and A2 were highly effective in inhibiting eEF-2K at 1.0 and 2.5 μM concentrations compared to compounds B1-B4, supporting the in silico findings. In conclusion, the results of this study suggest that our homology modeling along with in silico analysis may be effectively used to design inhibitors for eEF-2K. Our newly synthesized compounds A1 and A2 may be used as novel eEF-2K inhibitors with potential therapeutic applications.
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Affiliation(s)
- Ferah Comert Onder
- Department of Chemistry, Faculty of Science and Arts, Natural Products and Drug Research Laboratory, Canakkale Onsekiz Mart University, 17020 Canakkale, Turkey.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory, Bahcesehir University, Kadikoy, 34734 Istanbul, Turkey
| | - Kader Sahin
- Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory, Bahcesehir University, Kadikoy, 34734 Istanbul, Turkey
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Mehmet Ay
- Department of Chemistry, Faculty of Science and Arts, Natural Products and Drug Research Laboratory, Canakkale Onsekiz Mart University, 17020 Canakkale, Turkey
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Targeting Tumors Using Peptides. Molecules 2020; 25:molecules25040808. [PMID: 32069856 PMCID: PMC7070747 DOI: 10.3390/molecules25040808] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
To penetrate solid tumors, low molecular weight (Mw < 10 KDa) compounds have an edge over antibodies: their higher penetration because of their small size. Because of the dense stroma and high interstitial fluid pressure of solid tumors, the penetration of higher Mw compounds is unfavored and being small thus becomes an advantage. This review covers a wide range of peptidic ligands—linear, cyclic, macrocyclic and cyclotidic peptides—to target tumors: We describe the main tools to identify peptides experimentally, such as phage display, and the possible chemical modifications to enhance the properties of the identified peptides. We also review in silico identification of peptides and the most salient non-peptidic ligands in clinical stages. We later focus the attention on the current validated ligands available to target different tumor compartments: blood vessels, extracelullar matrix, and tumor associated macrophages. The clinical advances and failures of these ligands and their therapeutic conjugates will be discussed. We aim to present the reader with the state-of-the-art in targeting tumors, by using low Mw molecules, and the tools to identify new ligands.
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Dipeptidyl Peptidase-4 Is a Target Protein of Epigallocatechin-3-Gallate. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5370759. [PMID: 32104696 PMCID: PMC7036097 DOI: 10.1155/2020/5370759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/13/2019] [Accepted: 01/04/2020] [Indexed: 11/18/2022]
Abstract
Epigallocatechin-3-gallate (EGCG), a major active ingredient in green tea, has various health benefits. It affects glucose metabolism, but the mechanism is not well understood. This study aimed to identify targets of EGCG related to glucose metabolism. The core fragment of EGCG is a flavonoid. The flavonoid scaffold was used as a substructure to find proteins cocrystallized with flavonoids in the Protein Data Bank. The proteins identified were screened in PubMed for known relationships with diabetes. Dipeptidyl peptidase-4 (DPP4; PDB 5J3J) was identified following this approach. By molecular docking, the interactions of EGCG and DPP4 were assessed. To test the stability of the interactions between EGCG and DPP4, molecular dynamics simulation for 100 ns was performed using Desmond software. In vitro, the concentration of EGCG required to inhibit DPP4 activity by 50% (the IC50 value) was 28.42 μM. These data provide a theoretical basis for intervention in glucose metabolism with EGCG.
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Placines C, Castañeda-Loaiza V, João Rodrigues M, G. Pereira C, Stefanucci A, Mollica A, Zengin G, Llorent-Martínez EJ, Castilho PC, Custódio L. Phenolic Profile, Toxicity, Enzyme Inhibition, In Silico Studies, and Antioxidant Properties of Cakile maritima Scop. (Brassicaceae) from Southern Portugal. PLANTS (BASEL, SWITZERLAND) 2020; 9:E142. [PMID: 31979182 PMCID: PMC7076647 DOI: 10.3390/plants9020142] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Abstract
Cakile maritima Scop. (sea rocket) is an edible halophyte plant with several ethnomedicinal uses. This work reports the chemical profile and bioactivities of food grade extracts from sea rocket organs. Toxicity was determined on mammalian cells, and phenolic profiling and the quantitation of the main metabolites were made by high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS). Enzymatic inhibition was determined towards acetyl- and butyrylcholinesterase (AChE, BuChE), α-glucosidase, α-amylase, and tyrosinase. Docking studies were performed to tyrosinase, on the major metabolites, and samples were tested for antioxidant properties. Extracts were not toxic, were constituted mainly by flavonoids, and some compounds (roseoside and oleuropein) are here described for the first time in the species. The aerial organs' ethanol extract had relevant activity towards 2,2-diphenyl-1-picrylhydrazyl [DPPH, half maximal inhibitory concentration (IC50) = 0.59 mg/mL], and ferric-reducing activity power (FRAP, IC50 = 0.99 mg/mL). All samples were more active towards AChE than on BuChE. The ethanol fruits' extract inhibited α-glucosidase [2.19 mmol of equivalent of acarbose (ACAE)/g]. Samples were active against tyrosinase, especially the aerial organs' ethanol extracts [25.9 mg of equivalent of kojic acid (KAE)/g]. Quercetin and kaempferol glycosides fit well into the enzymatic pocket of tyrosinase. Our results suggest sea rocket as a candidate to be further explored as a source of bioactive products.
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Affiliation(s)
- Chloé Placines
- Centre of Marine Sciences, Faculty of Sciences and Technology, University of Algarve, Ed. 7, Campus of Gambelas, 8005-139 Faro, Portugal; (C.P.); (V.C.-L.); (M.J.R.); (C.G.P.)
| | - Viana Castañeda-Loaiza
- Centre of Marine Sciences, Faculty of Sciences and Technology, University of Algarve, Ed. 7, Campus of Gambelas, 8005-139 Faro, Portugal; (C.P.); (V.C.-L.); (M.J.R.); (C.G.P.)
| | - Maria João Rodrigues
- Centre of Marine Sciences, Faculty of Sciences and Technology, University of Algarve, Ed. 7, Campus of Gambelas, 8005-139 Faro, Portugal; (C.P.); (V.C.-L.); (M.J.R.); (C.G.P.)
| | - Catarina G. Pereira
- Centre of Marine Sciences, Faculty of Sciences and Technology, University of Algarve, Ed. 7, Campus of Gambelas, 8005-139 Faro, Portugal; (C.P.); (V.C.-L.); (M.J.R.); (C.G.P.)
| | - Azzurra Stefanucci
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (A.S.); (A.M.)
| | - Adriano Mollica
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (A.S.); (A.M.)
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Campus, 42250 Konya, Turkey;
| | - Eulogio J. Llorent-Martínez
- Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, E-23071 Jaén, Spain;
| | - Paula C. Castilho
- CQM—Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Luísa Custódio
- Centre of Marine Sciences, Faculty of Sciences and Technology, University of Algarve, Ed. 7, Campus of Gambelas, 8005-139 Faro, Portugal; (C.P.); (V.C.-L.); (M.J.R.); (C.G.P.)
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Multi-targeted potential of Pittosporum senacia Putt.: HPLC-ESI-MSn analysis, in silico docking, DNA protection, antimicrobial, enzyme inhibition, anti-cancer and apoptotic activity. Comput Biol Chem 2019; 83:107114. [DOI: 10.1016/j.compbiolchem.2019.107114] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022]
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Discovery of Novel µ-Opioid Receptor Inverse Agonist from a Combinatorial Library of Tetrapeptides through Structure-Based Virtual Screening. Molecules 2019; 24:molecules24213872. [PMID: 31717871 PMCID: PMC6865014 DOI: 10.3390/molecules24213872] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 11/18/2022] Open
Abstract
Morphine, oxycodone, fentanyl, and other µ-opioid receptors (MOR) agonists have been used for decades in antinociceptive therapies. However, these drugs are associated with numerous side effects, such as euphoria, addiction, respiratory depression, and adverse gastrointestinal reactions, thus, circumventing these drawbacks is of extensive importance. With the aim of identifying novel peptide ligands endowed with MOR inhibitory activity, we developed a virtual screening protocol, including receptor-based pharmacophore screening, docking studies, and molecular dynamics simulations, which was used to filter an in-house built virtual library of tetrapeptide ligands. The three top-scored compounds were synthesized and subjected to biological evaluation, revealing the identity of a hit compound (peptide 1) endowed with appreciable MOR inverse agonist effect and selectivity over δ-opioid receptors. These results confirmed the reliability of our computational approach and provided a promising starting point for the development of new potent MOR modulators.
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Avula SK, Khan A, Halim SA, Al-Abri Z, Anwar MU, Al-Rawahi A, Csuk R, Al-Harrasi A. Synthesis of novel (R)-4-fluorophenyl-1H-1,2,3-triazoles: A new class of α-glucosidase inhibitors. Bioorg Chem 2019; 91:103182. [DOI: 10.1016/j.bioorg.2019.103182] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/04/2019] [Accepted: 08/01/2019] [Indexed: 01/19/2023]
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Erdei AI, Borbély A, Magyar A, Szűcs E, Ötvös F, Gombos D, Al-Khrasani M, Stefanucci A, Dimmito MP, Luisi G, Mollica A, Benyhe S. Biochemical and pharmacological investigation of novel nociceptin/OFQ analogues and N/OFQ-RYYRIK hybrid peptides. Peptides 2019; 112:106-113. [PMID: 30513351 DOI: 10.1016/j.peptides.2018.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
Abstract
The endogenous ligand nociceptin (N/OFQ) and a positively charged synthetic peptide RYYRIK are both selective for the nociceptin opioid receptor (NOPr). Despite their structural dissimilarity, N/OFQ and RYYRIK compete for the same binding site of NOP receptor possessing full and partial agonistic character, respectively. In the view of the message-address concept, hybrid peptide constructs were probed for the NOP receptor combining different regions of N/OFQ and RYYRIK related peptide sequences. Nine novel nociceptin- or Ac-RYYRIK-NH2 peptide variants or hybrid peptides were synthesized and characterized. Peptides P2 and P8 contain fragments of native N/OFQ. The other seven analogues (P1, P3-7, P9) are composed of Ac-RYYRIK-NH2 fragments and parts of the original nociceptin sequence. The analogues were characterized in receptor binding assays and G-protein activation experiments on rat brain membranes, as well as by electrically stimulated mouse vas deferens bioassay. In receptor binding assays ligands P2, P4, P6 (Ki 0.37 nM) and P7 showed higher affinity (Ki 0.65 nM, 0.6 nM, 0.37 nM and 0.44 nM, respectively) for NOP receptor than their parent compounds N/OFQ (Ki 2.8 nM) or Ac-RYYRIK-NH2 (Ki 4.2 nM). In [35S]GTPγS binding experiments P2 and P3 behaved as full agonists. The other variants exhibited partial agonist properties characterized by submaximal stimulatory effects. In mouse vas deferens bioassay only P2 showed agonist activity. P4, P5, P6 inhibited the biological activity of N/OFQ more effectively than the NOP receptor selective antagonist JTC-801. In summary, hybrid peptides P4, P5 and P6 proved to be NOP receptor partial agonists even antagonists, while P2 peptide retained the full agonist property.
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Affiliation(s)
- Anna I Erdei
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62., Hungary; Doctoral School of Theoretical Medicine, University of Szeged, Faculty of Medicine, Szeged, Hungary
| | - Adina Borbély
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117, Budapest, Pázmány Péter sétány 1/A, Hungary
| | - Anna Magyar
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, H-1117, Budapest, Pázmány Péter sétány 1/A, Hungary
| | - Edina Szűcs
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62., Hungary; Doctoral School of Theoretical Medicine, University of Szeged, Faculty of Medicine, Szeged, Hungary
| | - Ferenc Ötvös
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62., Hungary
| | - Dávid Gombos
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62., Hungary
| | - Mahmoud Al-Khrasani
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, H-1445 Budapest, Nagyvárad tér 4., Hungary
| | - Azzurra Stefanucci
- Dipartimento di Farmacia, Università̀ degli Studi "G. d'Annunzio" di Chieti-Pescara, Via dei Vestini 31, Chieti, 66100, Italy
| | - Marilisa Pia Dimmito
- Dipartimento di Farmacia, Università̀ degli Studi "G. d'Annunzio" di Chieti-Pescara, Via dei Vestini 31, Chieti, 66100, Italy
| | - Grazia Luisi
- Dipartimento di Farmacia, Università̀ degli Studi "G. d'Annunzio" di Chieti-Pescara, Via dei Vestini 31, Chieti, 66100, Italy
| | - Adriano Mollica
- Dipartimento di Farmacia, Università̀ degli Studi "G. d'Annunzio" di Chieti-Pescara, Via dei Vestini 31, Chieti, 66100, Italy
| | - Sándor Benyhe
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Temesvári krt. 62., Hungary.
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Discovery of arginine-containing tripeptides as a new class of pancreatic lipase inhibitors. Future Med Chem 2019; 11:5-19. [DOI: 10.4155/fmc-2018-0216] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aim: The inhibition of pancreatic lipase (PL) represents one of the most promising strategies in the search for novel antiobesity drugs. We propose here a pioneering course by exploring tripeptide scaffolds in the way to selective PL inhibitors. Methodology/Results: The peptide series exhibited good PL inhibitory properties in vitro, with all the strongest inhibitors sharing a central arginine, shown in silico to be relevant for the active site-directed activity. The compounds were found devoid of inhibitory properties on acetylcholinesterase. Conclusion: Present results disclosed that basic tripeptides are able to interact efficiently with the PL-binding pocket, where they adopt a binding pose suitable for functional-to-inhibition interactions with key amino acids. Main inhibitor MALA4 may be selected as lead for further optimization.
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Stefanucci A, Dimmito MP, Zengin G, Luisi G, Mirzaie S, Novellino E, Mollica A. Discovery of novel amide tripeptides as pancreatic lipase inhibitors by virtual screening. NEW J CHEM 2019. [DOI: 10.1039/c8nj05884a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A virtual screening workflow for the discovery of pancreatic lipase inhibitors.
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Affiliation(s)
- Azzurra Stefanucci
- Dipartimento di Farmacia
- Università di Chieti-Pescara “G. d’Annunzio”
- 66100 Chieti
- Italy
| | - Marilisa Pia Dimmito
- Dipartimento di Farmacia
- Università di Chieti-Pescara “G. d’Annunzio”
- 66100 Chieti
- Italy
| | - Gokhan Zengin
- Department of Biology
- Science Faculty
- Selcuk University
- Konya
- Turkey
| | - Grazia Luisi
- Dipartimento di Farmacia
- Università di Chieti-Pescara “G. d’Annunzio”
- 66100 Chieti
- Italy
| | - Sako Mirzaie
- Department of Biochemistry
- Islamic Azad University
- Sanandaj
- Iran
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli “Federico II”
- 80131 Naples
- Italy
| | - Adriano Mollica
- Dipartimento di Farmacia
- Università di Chieti-Pescara “G. d’Annunzio”
- 66100 Chieti
- Italy
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49
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Luisi G, Stefanucci A, Zengin G, Dimmito MP, Mollica A. Anti-Oxidant and Tyrosinase Inhibitory In Vitro Activity of Amino Acids and Small Peptides: New Hints for the Multifaceted Treatment of Neurologic and Metabolic Disfunctions. Antioxidants (Basel) 2018; 8:antiox8010007. [PMID: 30587771 PMCID: PMC6356958 DOI: 10.3390/antiox8010007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/14/2018] [Accepted: 12/22/2018] [Indexed: 01/08/2023] Open
Abstract
Oxidative damage is among the factors associated with the onset of chronic pathologies, such as neurodegenerative and metabolic diseases. Several classes of anti-oxidant compounds have been suggested as having a protective role against cellular stressors, but, in this perspective, peptides’ world represents a poorly explored source. In the present study, the free radical scavenging properties, the metal ion reducing power, and the metal chelating activity of a series of sulfurated amino acids and tripeptides were determined in vitro through canonical assays (DPPH, ABTS, CUPRAC, FRAP, PM, and EECC) and estimated in comparison with the corresponding activities of synthetic peptide semicarbazones, incorporating the peculiar non-proteinogenic amino acid, tert-leucine (tLeu). The compounds exhibited remarkable anti-oxidant properties. As expected, sulfurated compounds 1–5 were found to be the most efficient radical scavengers and strongest reductants. Nevertheless, tLeu-containing peptides 7 and 8 disclosed notable metal reducing and chelating activities. These unprecedented results indicate that tLeu-featuring di- and tripeptide backbones, bearing the semicarbazone chelating moiety, are compatible with the emergence of an anti-oxidant potential. Additionally, when tested against a panel of enzymes usually targeted for therapeutic purposes in neurodegenerative and metabolic disorders, all samples were found to be good inhibitors of tyrosinase.
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Affiliation(s)
- Grazia Luisi
- Department of Pharmacy, G. d'Annunzio University of Chieti-Pescara, 66100 Chieti, Italy.
| | - Azzurra Stefanucci
- Department of Pharmacy, G. d'Annunzio University of Chieti-Pescara, 66100 Chieti, Italy.
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Konya 42130, Turkey.
| | - Marilisa Pia Dimmito
- Department of Pharmacy, G. d'Annunzio University of Chieti-Pescara, 66100 Chieti, Italy.
| | - Adriano Mollica
- Department of Pharmacy, G. d'Annunzio University of Chieti-Pescara, 66100 Chieti, Italy.
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Faya M, Kalhapure RS, Dhumal D, Agrawal N, Omolo C, Akamanchi KG, Govender T. Antimicrobial cell penetrating peptides with bacterial cell specificity: pharmacophore modelling, quantitative structure activity relationship and molecular dynamics simulation. J Biomol Struct Dyn 2018; 37:2370-2380. [PMID: 30047310 DOI: 10.1080/07391102.2018.1484814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Current research has shown cell-penetrating peptides and antimicrobial peptides (AMPs) as probable vectors for use in drug delivery and as novel antibiotics. It has been reported that the higher the therapeutic index (TI) the higher would be the bacterial cell penetrating ability. To the best of our knowledge, no in-silico study has been performed to determine bacterial cell specificity of the antimicrobial cell penetrating peptides (aCPP's) based on their TI. The aim of this study was to develop a quantitative structure activity relationship (QSAR) model, which can estimate antimicrobial potential and cell-penetrating ability of aCPPs against S. aureus, to confirm the relationship between the TI and aCPPs and to identify specific descriptors responsible for aCPPs penetrating ability. Molecular dynamics (MD) simulation was also performed to confirm the membrane insertion of the most active aCPPs obtained from the QSAR study. The most appropriate pharmacophore was identified to predict the aCPP's activity. The statistical results confirmed the validity of the model. The QSAR model was successful in identifying the optimal aCPP with high activity prediction and provided insights into the structural requirements to correlate their TI to cell penetrating ability. MD simulation of the best aCPP with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer confirmed its interaction with the membrane and the C-terminal residues of the aCPP played a key role in membrane penetration. The strategy of combining QSAR and molecular dynamics, allowed for optimal estimation of ligand-target interaction and confirmed the importance of Trp and Lys in interacting with the POPC bilayer. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mbuso Faya
- a Department of Pharmaceutical Sciences , University of KwaZulu-Natal , Private Bag , Durban , South Africa
| | - Rahul S Kalhapure
- a Department of Pharmaceutical Sciences , University of KwaZulu-Natal , Private Bag , Durban , South Africa
| | - Dinesh Dhumal
- b Department of Pharmaceutical Sciences and Technology , Institute of Chemical Technology , Mumbai , India
| | - Nikhil Agrawal
- a Department of Pharmaceutical Sciences , University of KwaZulu-Natal , Private Bag , Durban , South Africa
| | - Calvin Omolo
- a Department of Pharmaceutical Sciences , University of KwaZulu-Natal , Private Bag , Durban , South Africa
| | - Krishnacharya G Akamanchi
- b Department of Pharmaceutical Sciences and Technology , Institute of Chemical Technology , Mumbai , India
| | - Thirumala Govender
- a Department of Pharmaceutical Sciences , University of KwaZulu-Natal , Private Bag , Durban , South Africa
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