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Moreno-Ceballos A, Caballero NA, Castro ME, Perez-Aguilar JM, Mammino L, Melendez FJ. In Silico Approach: Anti-Tuberculosis Activity of Caespitate in the H37Rv Strain. Curr Issues Mol Biol 2024; 46:6489-6507. [PMID: 39057029 PMCID: PMC11275643 DOI: 10.3390/cimb46070387] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 07/28/2024] Open
Abstract
Tuberculosis is a highly lethal bacterial disease worldwide caused by Mycobacterium tuberculosis (Mtb). Caespitate is a phytochemical isolated from Helichrysum caespititium, a plant used in African traditional medicine that shows anti-tubercular activity, but its mode of action remains unknown. It is suggested that there are four potential targets in Mtb, specifically in the H37Rv strain: InhA, MabA, and UGM, enzymes involved in the formation of Mtb's cell wall, and PanK, which plays a role in cell growth. Two caespitate conformational structures from DFT conformational analysis in the gas phase (GC) and in solution with DMSO (CS) were selected. Molecular docking calculations, MM/GBSA analysis, and ADME parameter evaluations were performed. The docking results suggest that CS is the preferred caespitate conformation when interacting with PanK and UGM. In both cases, the two intramolecular hydrogen bonds characteristic of caespitate's molecular structure were maintained to achieve the most stable complexes. The MM/GBSA study confirmed that PanK/caespitate and UGM/caespitate were the most stable complexes. Caespitate showed favorable pharmacokinetic characteristics, suggesting rapid absorption, permeability, and high bioavailability. Additionally, it is proposed that caespitate may exhibit antibacterial and antimonial activity. This research lays the foundation for the design of anti-tuberculosis drugs from natural sources, especially by identifying potential drug targets in Mtb.
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Affiliation(s)
- Andrea Moreno-Ceballos
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
| | - Norma A. Caballero
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Edif. BIO1, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico
| | - María Eugenia Castro
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Complejo de Ciencias, ICUAP, Edif. IC10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico;
| | - Jose Manuel Perez-Aguilar
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
| | - Liliana Mammino
- School of Mathematical and Natural Science, University of Venda, Thohoyandou 0950, South Africa;
| | - Francisco J. Melendez
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
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Drioiche A, Baammi S, Zibouh K, Al Kamaly O, Alnakhli AM, Remok F, Saidi S, Amaiach R, El Makhoukhi F, Elomri A, Zair T. A Study of the Synergistic Effects of Essential Oils from Origanum compactum and Origanum elongatum with Commercial Antibiotics against Highly Prioritized Multidrug-Resistant Bacteria for the World Health Organization. Metabolites 2024; 14:210. [PMID: 38668338 PMCID: PMC11051742 DOI: 10.3390/metabo14040210] [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: 03/14/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
The irrational use of antibiotics has favored the emergence of resistant bacteria, posing a serious threat to global health. To counteract antibiotic resistance, this research seeks to identify novel antimicrobials derived from essential oils that operate through several mechanisms. It aims to evaluate the quality and composition of essential oils from Origanum compactum and Origanum elongatum; test their antimicrobial activity against various strains; explore their synergies with commercial antibiotics; predict the efficacy, toxicity, and stability of compounds; and understand their molecular interactions through docking and dynamic simulations. The essential oils were extracted via hydrodistillation from the flowering tops of oregano in the Middle Atlas Mountains in Morocco. Gas chromatography combined with mass spectrometry (GC-MS) was used to examine their composition. Nine common antibiotics were chosen and tested alone or in combination with essential oils to discover synergistic effects against clinically important and resistant bacterial strains. A comprehensive in silico study was conducted, involving molecular docking and molecular dynamics simulations (MD). O. elongatum oil includes borneol (8.58%), p-cymene (42.56%), thymol (28.43%), and carvacrol (30.89%), whereas O. compactum oil is mostly composed of γ-terpinene (22.89%), p-cymene (15.84%), thymol (10.21%), and (E)-caryophyllene (3.63%). With O. compactum proving to be the most potent, these essential oils showed antibacterial action against both Gram-positive and Gram-negative bacteria. Certain antibiotics, including ciprofloxacin, ceftriaxone, amoxicillin, and ampicillin, have been shown to elicit synergistic effects. To fight resistant bacteria, the essential oils of O. compactum and O. elongatum, particularly those high in thymol and (E)-caryophyllene, seem promising when combined with antibiotics. These synergistic effects could result from their ability to target the same bacterial proteins or facilitate access to target sites, as suggested by molecular docking simulations. Molecular dynamics simulations validated the stability of the examined protein-ligand complexes, emphasizing the propensity of substances like thymol and (E)-caryophyllene for particular target proteins, opening the door to potentially effective new therapeutic approaches against pathogens resistant to multiple drugs.
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Affiliation(s)
- Aziz Drioiche
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
- Medical Microbiology Laboratory, Mohamed V. Hospital, Meknes 50000, Morocco
| | - Soukayna Baammi
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco;
| | - Khalid Zibouh
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
| | - Omkulthom Al Kamaly
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; (O.A.K.); (A.M.A.)
| | - Anwar M. Alnakhli
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; (O.A.K.); (A.M.A.)
| | - Firdaous Remok
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
| | - Soukaina Saidi
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
| | - Rachid Amaiach
- Laboratory of Materials, Processes, Catalysis and Environment, School of Technology, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco;
| | - Fadoua El Makhoukhi
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
| | - Abdelhakim Elomri
- UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Normandie University, 76000 Rouen, France;
| | - Touriya Zair
- Research Team of Chemistry of Bioactive Molecules and the Environment, Laboratory of Innovative Materials and Biotechnology of Natural Resources, Faculty of Sciences, Moulay Ismail University, B.P. 11201, Zitoune, Meknes 50070, Morocco; (K.Z.); (F.R.); (S.S.); (F.E.M.)
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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: 5] [Impact Index Per Article: 5.0] [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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Aati HY, Anwar M, Al-Qahtani J, Al-Taweel A, Khan KUR, Aati S, Usman F, Ghalloo BA, Asif HM, Shirazi JH, Abbasi A. Phytochemical Profiling, In Vitro Biological Activities, and In-Silico Studies of Ficus vasta Forssk.: An Unexplored Plant. Antibiotics (Basel) 2022; 11:antibiotics11091155. [PMID: 36139935 PMCID: PMC9495161 DOI: 10.3390/antibiotics11091155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 12/31/2022] Open
Abstract
Ficus vasta Forssk. (Moraceae family) is an important medicinal plant that has not been previously investigated for its phytochemical and biological potential. Phytochemical screening, total bioactive content, and GCMS analysis were used to determine its phytoconstituents profile. Antioxidant, antibacterial, antifungal, anti-viral, cytotoxicity, thrombolytic, and enzyme inhibition activities were examined for biological evaluation. The plant extract exhibited the maximum total phenolic (89.47 ± 3.21 mg GAE/g) and total flavonoid contents (129.2 ± 4.14 mg QE/g), which may be related to the higher antioxidant potential of the extract. The extract showed strong α-amylase (IC50 5 ± 0.21 µg/mL) and α-glucosidase inhibition activity (IC50 5 ± 0.32 µg/mL). Significant results were observed in the case of antibacterial, antifungal, and anti-viral activities. The F. vasta extract inhibited the growth of HepG2 cells in a dose-dependent manner. The GCMS analysis of the extract provided the preliminary identification of 28 phytocompounds. In addition, the compounds identified by GCMS were subjected to in silico molecular docking analysis in order to identify any interactions between the compounds and enzymes (α-amylase and α-glucosidase). After that, the best-docked compounds were subjected to ADMET studies which provide information on pharmacokinetics, drug-likeness, physicochemical properties, and toxicity. The present study highlighted that the ethanol extract of F. vasta has antidiabetic, antimicrobial, anti-viral, and anti-cancer potentials that can be further explored for novel drug development.
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Affiliation(s)
- Hanan Y. Aati
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
- Correspondence: (H.Y.A.); (K.-u.-R.K.)
| | - Mariyam Anwar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Jawaher Al-Qahtani
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Areej Al-Taweel
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Kashif-ur-Rehman Khan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Correspondence: (H.Y.A.); (K.-u.-R.K.)
| | - Sultan Aati
- UWA, University of Western Australia, Nedland, WA 6009, Australia
| | - Faisal Usman
- Department of Pharmaceutics, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Bilal Ahmad Ghalloo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Hafiz Muhammad Asif
- Faculty of Medicine and Allied Health Sciences, University College of Conventional Medicine, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Jafir Hussain Shirazi
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Aliza Abbasi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
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Phytochemical Profiling, Antioxidant Activity, and In Silico Analyses of Sterculia villosa and Vernonia patula. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3190496. [PMID: 35707476 PMCID: PMC9192300 DOI: 10.1155/2022/3190496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/09/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022]
Abstract
Our study aims to evaluate the chemical profiles and antioxidant activities of a methanolic extract of Sterculia villosa bark (MESV) and a methanolic extract of the Vernonia patula whole plant (MEVP). The chemical profiling of MESV and MEVP was performed via gas chromatography-mass spectrometry (GC-MS), which identified 52 and 33 chemical compounds, respectively. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay indicated that both MESV and MEVP displayed concentration-dependent scavenging activities, and half-maximal inhibitory concentration (IC50) values for MEVP, MESV, and ascorbic acid were 305.30, 555.44, and 36.32 μg/mL, respectively. The total flavonoid content (TFC) and total phenolic content (TPC) of MESV were 81.44 ± 2.70 mg quercetin equivalents (QE)/g dry extract and 62.58 ± 1.93 mg gallic acid equivalent (GAE)/g dry extract, whereas these values for MEVP were 291.31 ± 6.61 mg QE/g dry extract and 58.99 ± 3.16 mg GAE/g dry extract, respectively. Molecular docking studies were also evaluated, and absorption, distribution, metabolism, and excretion (ADME) and toxicological properties were assessed. Therefore, these two plants, S. villosa and V. patula, showed potential options for further advanced studies into oxidative stress.
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Deciphering the Pharmacological Potentials of Methanol Extract of Sterculia foetida Seeds Using Experimental and Computational Approaches. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3403086. [PMID: 35502174 PMCID: PMC9056218 DOI: 10.1155/2022/3403086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/18/2022] [Accepted: 04/04/2022] [Indexed: 11/22/2022]
Abstract
The edible herb Sterculia foetida L. has potential nutraceutical and medicinal effects. The present study is performed to assess the possible antidiabetic, neuropharmacological, and antidiarrheal activity of the methanolic extract of S. foetida seeds (MESF) through in vitro, in vivo, and in silico approaches. When compared to standard acarbose, the results of the antidiabetic study provided strong proof that the glucose level in the MESF was gradually decreased by inhibiting the function of α-amylase enzymes. The sedative potential of MESF (200 and 400 mg/kg) was determined by employing open field, hole cross, and thiopental sodium-induced sleeping time tests, which revealed significant reductions in locomotor performance and increased sleep duration following MESF treatment. In addition, mice treated with MESF exhibited superior exploration during elevated plus maze and hole board tests. MESF also showed good antidiarrheal activity in castor oil-induced diarrhea and intestinal motility tests. Previously isolated compounds (captan, 1-azuleneethanol, acetate, and tetraconazole) exhibited good binding affinity in docking studies and drug-likeliness properties in absorption, distribution, metabolism, excretion/toxicity (ADME/T), and toxicological studies. Collectively, these results indicate the bioactivity of S. foetida, which represents a potential candidate in the food and pharmaceutical industries.
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Hossen SMM, Hossain MS, Yusuf ATM, Chaudhary P, Emon NU, Janmeda P. Profiling of phytochemical and antioxidant activity of wild mushrooms: Evidence from the in vitro study and phytoconstituent's binding affinity to the human erythrocyte catalase and human glutathione reductase. Food Sci Nutr 2022; 10:88-102. [PMID: 35035912 PMCID: PMC8751451 DOI: 10.1002/fsn3.2650] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/30/2021] [Accepted: 10/18/2021] [Indexed: 12/23/2022] Open
Abstract
This study was undertaken to evaluate the appearance of phytochemicals and antioxidant activity of seven wild mushrooms of the University of Chittagong campus. Phytochemical screening was performed using standard methods, whereas DPPH radical scavenging assay was used to elucidate the antioxidant effect. Besides, in silico studies were implemented using the targets of human erythrocyte catalase 3-amino-1,2,4-triazole, human glutathione reductase, and selected compounds. Again, the absorption, distribution, metabolism, elimination and toxicity (ADME/T) analysis has been determined by using online tools. Both Ganoderma lucidum (Curtis) Karst. and Ganoderma applanatum (Pers.) Pat. showed a significant (p < .001) increase in the percentage of scavenging activity at 400 μg/ml concentration when compared with ascorbic acid. The methanol extract of G. lucidum, G. applanatum, and Rhodofomes cajanderi (P. Karst.) B. K. Cui, M. L. Han & Y. C. Dai showed strong antioxidant activity with an IC50 value. In addition, molecular docking studies of the previously isolated compounds from three selective mushrooms revealed that the targeted compounds along with positive controls were able to interact strongly (range: -3.498 to -8.655) with the enzymes. The study concludes that the G . lucidum, G. applanatum, and R. cajanderi mushrooms can be a strong source in the management of oxidative stress-induced diseases.
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Affiliation(s)
- S. M. Moazzem Hossen
- Department of PharmacyFaculty of Biological ScienceUniversity of ChittagongChittagongBangladesh
| | | | - A. T. M. Yusuf
- Department of PharmacyUniversity of Science and TechnologyChittagongBangladesh
| | - Priya Chaudhary
- Department of Bioscience & BiotechnologyBanasthali VidyapithBanasthaliIndia
| | - Nazim Uddin Emon
- Department of PharmacyFaculty of Science and EngineeringInternational Islamic University ChittagongChittagongBangladesh
| | - Pracheta Janmeda
- Department of Bioscience & BiotechnologyBanasthali VidyapithBanasthaliIndia
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Santini BL, Zacharias M. Rapid Rational Design of Cyclic Peptides Mimicking Protein-Protein Interfaces. Methods Mol Biol 2022; 2405:231-244. [PMID: 35298817 DOI: 10.1007/978-1-0716-1855-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The cPEPmatch approach is a rapid computational methodology for the rational design of cyclic peptides to target desired regions of protein-protein interfaces. The method selects cyclic peptides that structurally match backbone structures of short segments at a protein-protein interface. In a second step, the cyclic peptides act as templates for designed binders by adapting the amino acid side chains to the side chains found in the target complex. A link to access the different tools that comprise the cPEPmatch method and a detailed step-by-step guide is provided. We outline the protocol by following the application to a trypsin protease in complex with the bovine inhibitor protein (BPTI). An extension of our original approach is also presented, where we give a detailed description of the usage of the cPEPmatch methodology focusing on identifying hot regions of protein-protein interfaces prior to the matching. This extension allows one to reduce the amount of evaluated putative cyclic peptides and to specifically design only those that compete with the strongest protein-protein binding regions. It is illustrated by an application to an MHC class I protein complex.
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Affiliation(s)
- Brianda L Santini
- Center for Functional Protein Assemblies, Physics Department T38, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Physics Department T38, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany.
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Moazzem Hossen S, Hossain MS, Akbar S, Tahmida U, Mawa J, Uddin Emon N. Wild mushrooms showed analgesic and cytotoxic properties along with phytoconstituent's binding affinity to COX-1, COX-2 and cytochrome P450 2C9. Heliyon 2021; 7:e07997. [PMID: 34585013 PMCID: PMC8455681 DOI: 10.1016/j.heliyon.2021.e07997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/05/2021] [Accepted: 09/10/2021] [Indexed: 11/09/2022] Open
Abstract
This study was designed to evaluate the cytotoxic and analgesic potential of methanol extracts of five wild mushrooms available in the University of Chittagong, Bangladesh. The acetic acid-induced writhing method was used for the analgesic activity, while cytotoxicity was tested using brine shrimp lethality bioassay. In silico molecular docking and ADME/T study have been employed by using Schrodinger v11.1, BIOVIA Discovery Studio 2020 and online tool (AdmeSAR) respectively. The methanol extracts of Daldinia concentrica, Trametes lactinea, Fomitopsis cajanderi and Daedaleopsis confragosa exhibited a significant (p < 0.001) decrease in the number of writhing when compared to the control group. Except for Lentinus squarrosulus at 200 mg/kg body weight, the remaining mushroom extracts showed equal to or above 50 % inhibition of writhing. Daldinia concentrica showed the lowest LC50 values with 0.63 μg/mL, while Daedaleopsis confragosa showed the highest LC50 values of 2.33 μg/mL, indicating decisive cytotoxic action all mushrooms extracts. Considering the secondary metabolites, daldinan A and fomlactone A were found the most promising myco-compounds in analgesic and cytotoxic molecular docking studies. Besides, all the selected metabolites meet the rule of Lipinski's drug-likeliness. These results concluded that each mushroom extracts except Lentinus squarrosulus possess a potential analgesic. All the mushroom extracts embrace a promising cytotoxic activity that may guide the progress of a new drug.
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Affiliation(s)
- S.M. Moazzem Hossen
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammad Shahadat Hossain
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Sumaiya Akbar
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Umme Tahmida
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Jannatul Mawa
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Nazim Uddin Emon
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Chittagong 4318, Bangladesh
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Oh KK, Adnan M, Cho DH. Network Pharmacology Study on Morus alba L. Leaves: Pivotal Functions of Bioactives on RAS Signaling Pathway and Its Associated Target Proteins against Gout. Int J Mol Sci 2021; 22:9372. [PMID: 34502281 PMCID: PMC8431517 DOI: 10.3390/ijms22179372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/27/2022] Open
Abstract
M. alba L. is a valuable nutraceutical plant rich in potential bioactive compounds with promising anti-gouty arthritis. Here, we have explored bioactives, signaling pathways, and key proteins underlying the anti-gout activity of M. alba L. leaves for the first-time utilizing network pharmacology. Bioactives in M. alba L. leaves were detected through GC-MS (Gas Chromatography-Mass Spectrum) analysis and filtered by Lipinski's rule. Target proteins connected to the filtered compounds and gout were selected from public databases. The overlapping target proteins between bioactives-interacted target proteins and gout-targeted proteins were identified using a Venn diagram. Bioactives-Proteins interactive networking for gout was analyzed to identify potential ligand-target and visualized the rich factor on the R package via the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway on STRING. Finally, a molecular docking test (MDT) between bioactives and target proteins was analyzed via AutoDock Vina. Gene Set Enrichment Analysis (GSEA) demonstrated that mechanisms of M. alba L. leaves against gout were connected to 17 signaling pathways on 26 compounds. AKT1 (AKT Serine/Threonine Kinase 1), γ-Tocopherol, and RAS signaling pathway were selected as a hub target, a key bioactive, and a hub signaling pathway, respectively. Furthermore, three main compounds (γ-Tocopherol, 4-Dehydroxy-N-(4,5-methylenedioxy-2-nitrobenzylidene) tyramine, and Lanosterol acetate) and three key target proteins-AKT1, PRKCA, and PLA2G2A associated with the RAS signaling pathway were noted for their highest affinity on MDT. The identified three key bioactives in M. alba L. leaves might contribute to recovering gouty condition by inactivating the RAS signaling pathway.
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Affiliation(s)
| | | | - Dong Ha Cho
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (K.K.O.); (M.A.)
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Alam S, Rashid MA, Sarker MMR, Emon NU, Arman M, Mohamed IN, Haque MR. Antidiarrheal, antimicrobial and antioxidant potentials of methanol extract of Colocasia gigantea Hook. f. leaves: evidenced from in vivo and in vitro studies along with computer-aided approaches. BMC Complement Med Ther 2021; 21:119. [PMID: 33845836 PMCID: PMC8042880 DOI: 10.1186/s12906-021-03290-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/29/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Colocasia gigantea, locally named as kochu is well-known due to its various healing power. This research is to investigate the antidiarrheal, antimicrobial and antioxidant possibilities of the methanol soluble extract of Colocasia gigantea. METHODS The antidiarrheal investigation was performed by using in vivo castor oil-induced diarrheal method whereas in vitro antimicrobial and antioxidant investigation have been implemented by disc diffusion and DPPH scavenging method respectively. Moreover, in silico studies were followed by molecular docking analysis of several secondary metabolites that were appraised with Schrödinger-Maestro v11.1 and Biovia Discovery Studio. RESULTS The induction of plant extract (200 and 400 mg/kg, b.w, p.o) has minimized the castor oil mediated diarrhea by 16.96% (p < 0.01) and 38.89% (p < 0.001) respectively compared to control group. The methanol extract of C. gigantea showed mild sensitivity against almost all the tested strains but it shows high consistency of phenolic content and yielded 67.68 μg/mL of IC50 value in the DPPH test. In the PASS prediction, selected isolated compounds have demonstrated significant antidiarrheal and antimicrobial activity following the Lipinski drug rules which have ascertained efficacy with the compounds in molecular docking study. CONCLUSION The results of this scientific research reflects that the methanol soluble extract of C. gigantea is safe and may provide possibilities of alleviation of diarrhea along with being a potential wellspring of antioxidant and antimicrobial agents which can be considered as an alternate source for exploration of new medicinal products in near future.
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Affiliation(s)
- Safaet Alam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Mohammad A. Rashid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Md. Moklesur Rahman Sarker
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid road, Dhanmondi, Dhaka, 1207 Bangladesh
| | - Nazim Uddin Emon
- Department of Public Health, School of Science and Technology, Bangladesh Open University, Gazipur, Dhaka, 1705 Bangladesh
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318 Bangladesh
| | - Mohammad Arman
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318 Bangladesh
| | - Isa Naina Mohamed
- Department of Pharmacology, Faculty of Medicine, Universiti Kebangsaan Malaysia (The National University of Malaysia), Cheras, Malaysia
| | - Mohammad Rashedul Haque
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, 1000 Bangladesh
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12
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Chemical Profiles and Pharmacological Properties with in Silico Studies on Elatostema papillosum Wedd. Molecules 2021; 26:molecules26040809. [PMID: 33557235 PMCID: PMC7913918 DOI: 10.3390/molecules26040809] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
The current study attempted, for the first time, to qualitatively and quantitatively determine the phytochemical components of Elatostema papillosum methanol extract and their biological activities. The present study represents an effort to correlate our previously reported biological activities with a computational study, including molecular docking, and ADME/T (absorption, distribution, metabolism, and excretion/toxicity) analyses, to identify the phytochemicals that are potentially responsible for the antioxidant, antidepressant, anxiolytic, analgesic, and anti-inflammatory activities of this plant. In the gas chromatography-mass spectroscopy analysis, a total of 24 compounds were identified, seven of which were documented as being bioactive based on their binding affinities. These seven were subjected to molecular docking studies that were correlated with the pharmacological outcomes. Additionally, the ADME/T properties of these compounds were evaluated to determine their drug-like properties and toxicity levels. The seven selected, isolated compounds displayed favorable binding affinities to potassium channels, human serotonin receptor, cyclooxygenase-1 (COX-1), COX-2, nuclear factor (NF)-κB, and human peroxiredoxin 5 receptor proteins. Phytol acetate, and terpene compounds identified in E. papillosum displayed strong predictive binding affinities towards the human serotonin receptor. Furthermore, 3-trifluoroacetoxypentadecane showed a significant binding affinity for the KcsA potassium channel. Eicosanal showed the highest predicted binding affinity towards the human peroxiredoxin 5 receptor. All of these findings support the observed in vivo antidepressant and anxiolytic effects and the in vitro antioxidant effects observed for this extract. The identified compounds from E. papillosum showed the lowest binding affinities towards COX-1, COX-2, and NF-κB receptors, which indicated the inconsequential impacts of this extract against the activities of these three proteins. Overall, E. papillosum appears to be bioactive and could represent a potential source for the development of alternative medicines; however, further analytical experiments remain necessary.
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13
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González-Muñiz R, Bonache MÁ, Pérez de Vega MJ. Modulating Protein-Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples. Molecules 2021; 26:445. [PMID: 33467010 PMCID: PMC7830901 DOI: 10.3390/molecules26020445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein-protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.
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Affiliation(s)
- Rosario González-Muñiz
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.Á.B.); (M.J.P.d.V.)
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14
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Rudzińska M, Daglioglu C, Savvateeva LV, Kaci FN, Antoine R, Zamyatnin AA. Current Status and Perspectives of Protease Inhibitors and Their Combination with Nanosized Drug Delivery Systems for Targeted Cancer Therapy. DRUG DESIGN DEVELOPMENT AND THERAPY 2021; 15:9-20. [PMID: 33442233 PMCID: PMC7797289 DOI: 10.2147/dddt.s285852] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
In cancer treatments, many natural and synthetic products have been examined; among them, protease inhibitors are promising candidates for anti-cancer agents. Since dysregulated proteolytic activities can contribute to tumor development and metastasis, antagonization of proteases with tailored inhibitors is an encouraging approach. Although adverse effects of early designs of these inhibitors disappeared after the introduction of next-generation agents, most of the proposed inhibitors did not pass the early stages of clinical trials due to their nonspecific toxicity and lack of pharmacological effects. Therefore, new applications that modulate proteases more specifically and serve their programmed way of administration are highly appreciated. In this context, nanosized drug delivery systems have attracted much attention because preliminary studies have demonstrated that the therapeutic capacity of inhibitors has been improved significantly with encapsulated formulation as compared to their free forms. Here, we address this issue and discuss the current application and future clinical prospects of this potential combination towards targeted protease-based cancer therapy.
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Affiliation(s)
- Magdalena Rudzińska
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Cenk Daglioglu
- Biotechnology and Bioengineering Application and Research Center, Integrated Research Centers, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Lyudmila V Savvateeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Fatma Necmiye Kaci
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Yakutiye, Erzurum 25050, Turkey
| | - Rodolphe Antoine
- CNRS, Institut Lumière Matière, Univ Lyon, Université Claude Bernard Lyon 1, Lyon F-69622, France
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Department of Biotechnology, Sirius University of Science and Technology, Sochi 354340, Russia
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15
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Rudra S, Tahamina A, Emon NU, Adnan M, Shakil M, Chowdhury MHU, Barlow JW, Alwahibi MS, Soliman Elshikh M, Faruque MO, Uddin SB. Evaluation of Various Solvent Extracts of Tetrastigma leucostaphylum (Dennst.) Alston Leaves, a Bangladeshi Traditional Medicine Used for the Treatment of Diarrhea. Molecules 2020; 25:molecules25214994. [PMID: 33126608 PMCID: PMC7662597 DOI: 10.3390/molecules25214994] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022] Open
Abstract
Tetrastigma leucostaphylum (TL) is an important ethnic medicine of Bangladesh used to treat diarrhea and dysentery. Hence, current study has been designed to characterize the antidiarrheal (in vivo) and cytotoxic (in vitro) effects of T. leucostaphylum. A crude extract was prepared with methanol (MTL) and further partitioned into n-hexane (NTL), dichloromethane (DTL), and n-butanol (BTL) fractions. Antidiarrheal activity was investigated using castor oil induced diarrhea, enteropooling, and gastrointestinal transit models, while cytotoxicity was evaluated using the brine shrimp lethality bioassay. In antidiarrheal experiments, all doses (100, 200, and 400 mg/kg) of the DTL extract significantly reduced diarrheal stool frequency, volume and weight of intestinal contents, and gastrointestinal motility in mice. Similarly, in the cytotoxicity assay, all extracts exhibited activity, with the DTL extract the most potent (LC50 67.23 μg/mL). GC-MS analysis of the DTL extract identified 10 compounds, which showed good binding affinity toward M3 muscarinic acetylcholine, 5-HT3, Gut inhibitory phosphodiesterase, DNA polymerase III subunit alpha, and UDP-N-acetylglucosamine-1 carboxyvinyltransferase enzyme targets upon molecular docking analysis. Although ADME/T analyses predicted the drug-likeness and likely safety upon consumption of these bioactive compounds, significant toxicity concerns are evident due to the presence of the known phytotoxin, 2,4-di-tert-butylphenol. In summary, T. leucostaphylum showed promising activity, helping to rationalize the ethnomedicinal use and importance of this plant, its safety profile following both acute and chronic exposure warrants further investigation.
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Affiliation(s)
- Sajib Rudra
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh; (S.R.); (A.T.); (M.S.); (M.H.U.C.)
| | - Afroza Tahamina
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh; (S.R.); (A.T.); (M.S.); (M.H.U.C.)
| | - Nazim Uddin Emon
- Department of Public Health, School of Science and Technology, Bangladesh Open University, Gazipur 1705, Dhaka, Bangladesh;
| | - Md. Adnan
- Department of Bio-Health Technology, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea;
| | - Mohammad Shakil
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh; (S.R.); (A.T.); (M.S.); (M.H.U.C.)
| | - Md. Helal Uddin Chowdhury
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh; (S.R.); (A.T.); (M.S.); (M.H.U.C.)
| | - James W. Barlow
- Department of Chemistry, Royal College Surgeons, Dublin D02YN77, Ireland;
| | - Mona S. Alwahibi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.S.A.); (M.S.E.)
| | - Mohamed Soliman Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (M.S.A.); (M.S.E.)
| | - Mohammad Omar Faruque
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh; (S.R.); (A.T.); (M.S.); (M.H.U.C.)
- Correspondence: (M.O.F.); (S.B.U.); Tel.: +88-018-1839-7345 (M.O.F.); +88-017-1106-5377 (S.B.U.)
| | - Shaikh Bokhtear Uddin
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh; (S.R.); (A.T.); (M.S.); (M.H.U.C.)
- Correspondence: (M.O.F.); (S.B.U.); Tel.: +88-018-1839-7345 (M.O.F.); +88-017-1106-5377 (S.B.U.)
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17
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Unveiling Pharmacological Responses and Potential Targets Insights of Identified Bioactive Constituents of Cuscuta reflexa Roxb. Leaves through In Vivo and In Silico Approaches. Pharmaceuticals (Basel) 2020; 13:ph13030050. [PMID: 32245131 PMCID: PMC7151675 DOI: 10.3390/ph13030050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/02/2023] Open
Abstract
Cuscuta reflexa Roxb. is traditionally used by the indigenous communities of Bangladesh to treat different diseases, such as pain, edema, tumor, jaundice, and skin infections. This study tested neuro-pharmacological, anti-nociceptive, and antidiarrheal activities by in vivo and in silico experiments for the metabolites extracted (methanol) from the leaves of Cuscuta reflexa (MECR). During the anxiolytic evaluation analyzed by elevated plus maze and hole board tests, MECR (200 and 400 mg/kg) exhibited a significant dose-dependent reduction of anxiety-like behavior in mice. Similarly, mice treated with MECR demonstrated a dose-dependent decrease in the time of immobility in both forced swimming and tail suspension tests. In addition, anti-nociceptive activity was assessed by the chemical-induced (acetic acid and formalin) pain models. In both cases, 400 mg/kg was found to be most effective and significantly (p < 0.001) inhibited acetic acid stimulated writhing and formalin-induced licking (pain response) in mice. Furthermore, antidiarrheal efficacy determined by the castor-oil induced diarrheal model manifested an evident inhibition of diarrheal stool frequency. In parallel, previously isolated bioactive compounds were documented based on the biological activities and subjected to in silico studies to correlate with the current pharmacological outcomes. The selected isolated compounds (15) displayed favorable binding affinities to potassium channels, human serotonin receptor, COX-1, COX-2, M3 muscarinic acetylcholine receptor, and 5-HT3 receptor proteins. Additionally, the ADME/T and toxicological properties were justified to unveil their drug-like properties and toxicity level. Overall, Cuscuta reflexa is bioactive and could be a potential source for the development of alternative medicine.
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18
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Investigation of antinociceptive, anti-inflammatory and thrombolytic activity of Caesalpinia digyna (Rottl.) leaves by experimental and computational approaches. ADVANCES IN TRADITIONAL MEDICINE 2020. [DOI: 10.1007/s13596-020-00429-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Jing X, Jin K. A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies. Med Res Rev 2019; 40:753-810. [PMID: 31599007 DOI: 10.1002/med.21639] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.
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Affiliation(s)
- Xiaoshu Jing
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kang Jin
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan, Shandong, China
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20
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Investigation of the Biological Activities and Characterization of Bioactive Constituents of Ophiorrhiza rugosa var. prostrata (D.Don) & Mondal Leaves through In Vivo, In Vitro, and In Silico Approaches. Molecules 2019; 24:molecules24071367. [PMID: 30965575 PMCID: PMC6480688 DOI: 10.3390/molecules24071367] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 11/17/2022] Open
Abstract
Ophiorrhiza rugosa var. prostrata is one of the most frequently used ethnomedicinal plants by the indigenous communities of Bangladesh. This study was designed to investigate the antidiarrheal, anti-inflammatory, anthelmintic and antibacterial activities of the ethanol extract of O. rugosa leaves (EEOR). The leaves were extracted with ethanol and subjected to in vivo antidiarrheal screening using the castor oil-induced diarrhea, enteropooling, and gastrointestinal transit models. Anti-inflammatory efficacy was evaluated using the histamine-induced paw edema test. In parallel, in vitro anthelmintic and antibacterial activities were evaluated using the aquatic worm and disc diffusion assays respectively. In all three diarrheal models, EEOR (100, 200 and 400 mg/kg) showed obvious inhibition of diarrheal stool frequency, reduction of the volume and weight of the intestinal contents, and significant inhibition of intestinal motility. Also, EEOR manifested dose-dependent anti-inflammatory activity. Anthelmintic action was deemed significant (P < 0.001) with respect to the onset of paralysis and helminth death. EEOR also resulted in strong zones of inhibition when tested against both Gram-positive and Gram-negative bacteria. GC-MS analysis identified 30 compounds within EEOR, and of these, 13 compounds documented as bioactive showed good binding affinities to M3 muscarinic acetylcholine, 5-HT3, tubulin and GlcN-6-P synthase protein targets in molecular docking experiments. Additionally, ADME/T and PASS analyses revealed their drug-likeness, likely safety upon consumption and possible pharmacological activities. In conclusion, our findings scientifically support the ethnomedicinal use and value of this plant, which may provide a potential source for future development of medicines.
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Wang D, Yang Y, Jiang L, Wang Y, Li J, Andreasen PA, Chen Z, Huang M, Xu P. Suppression of Tumor Growth and Metastases by Targeted Intervention in Urokinase Activity with Cyclic Peptides. J Med Chem 2019; 62:2172-2183. [PMID: 30707839 DOI: 10.1021/acs.jmedchem.8b01908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Urokinase-type plasminogen activator (uPA) is a diagnostic marker for breast and prostate cancers recommended by American Society for Clinical Oncology and German Breast Cancer Society. Inhibition of uPA was proposed as an efficient strategy for cancer treatments. In this study, we report peptide-based uPA inhibitors with high potency and specificity comparable to monoclonal antibodies. We revealed the binding and inhibitory mechanisms by combining crystallography, molecular dynamic simulation, and other biophysical and biochemical approaches. Besides, we showed that our peptides efficiently inhibited the invasion of cancer cells via intervening with the processes of the degradation of extracellular matrices. Furthermore, our peptides significantly suppressed the tumor growth and the cancer metastases in tumor-bearing mice. This study demonstrates that these uPA peptides are highly potent anticancer agents and reveals the mechanistic insights of these uPA inhibitors, which can be useful for developing other serine protease inhibitors.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,University of Chinese Academy of Sciences , No.19 (A) Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Yongshuai Yang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,University of Chinese Academy of Sciences , No.19 (A) Yuquan Road , Shijingshan District, Beijing 100049 , China.,College of Life Science , Fujian Agriculture and Forestry University , Fuzhou , Fujian 350002 , China
| | - Longguang Jiang
- College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Yu Wang
- College of Life Science , Fujian Agriculture and Forestry University , Fuzhou , Fujian 350002 , China
| | - Jinyu Li
- College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics , Aarhus University , Aarhus C 8000 , Denmark
| | - Zhuo Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China
| | - Mingdong Huang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Peng Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China
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Duffy F, Maheshwari N, Buchete NV, Shields D. Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions. Methods Mol Biol 2019; 2001:73-95. [PMID: 31134568 DOI: 10.1007/978-1-4939-9504-2_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by cyclization. Accordingly, to mimic linear peptide interfaces with cyclic peptides, it can be beneficial to screen combinatorial cyclic peptide libraries. Computational methods have been developed to screen CPs, but face a number of challenges. Here, we review methods to develop in silico computational libraries, and the potential for screening naturally occurring libraries of CPs. The simplest and most rapid computational pharmacophore methods that estimate peptide three-dimensional structures to be screened versus targets are relatively easy to implement, and while the constraint on structure imposed by cyclization makes them more effective than the same approaches with linear peptides, there are a large number of limiting assumptions. In contrast, full molecular dynamics simulations of cyclic peptide structures not only are costly to implement, but also require careful attention to interpretation, so that not only is the computation time rate limiting, but the interpretation time is also rate limiting due to the analysis of the typically complex underlying conformational space of CPs. A challenge for the field of computational cyclic peptide screening is to bridge this gap effectively. Natural compound libraries of short cyclic peptides, and short cyclized regions of proteins, encoded in the genomes of many organisms present a potential treasure trove of novel functionality which may be screened via combined computational and experimental screening approaches.
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Affiliation(s)
- Fergal Duffy
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nikunj Maheshwari
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | | | - Denis Shields
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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Ul Hoque MS, Chowdhury MS, Paul A, Barua J, Zannat SS, Hasan MM, Gupta SD, Barua S, Ahmed S, Kabir MSH. In vivo analgesic effect of different extracts of Hopea odorata leaves in mice and in silico molecular docking and ADME/T property analysis of some isolated compounds from this plant. J Basic Clin Physiol Pharmacol 2018; 30:121-130. [PMID: 30085930 DOI: 10.1515/jbcpp-2018-0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/08/2018] [Indexed: 06/08/2023]
Abstract
Background The current study evaluates the analgesic effect of different extracts of Hopea odorata leaves in mice followed by molecular docking and absorption, distribution, metabolism, excretion, and toxicity (ADME/T) analysis of isolated compounds derived from the plant with the COX-1 enzyme. Methods In the present study, the dried leaves of H. odorata were subjected to extraction using methanol, ethanol, and water. In vivo analgesic activity was evaluated by using the acetic acid-induced writhing test and formalin-induced paw licking test, and in silico molecular docking and ADME/T study were performed using Schrödinger Maestro (version 11.1) and online-based tools, respectively, on eight isolated compounds. Results The results showed that the methanolic extract of leaves has highest significant dose-dependent analgesic activity at both 200 and 400 mg/kg followed by ethanolic extract of leaves. Among all the compounds, ampelopsin showed the best docking score of -7.055, ensuring strong binding affinity between the ligand and the receptor, and ADME/T analysis using Web-based tools ensures the compound has not violated Lipinski's rule of five indicating its safety consumption. Conclusions The result confirms the analgesic activity of H. odorata leaves in both in vivo and in silico assays. The data support ampelopsin to be a potent analgesic compound worthy of future clinical trials and its "drug-likeliness".
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Affiliation(s)
- Md Sajjad Ul Hoque
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
- Drug Discovery, GUSTO A Research Group, Chittagong, Bangladesh
| | - Mohammed Sohel Chowdhury
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
- Drug Discovery, GUSTO A Research Group, Chittagong, Bangladesh
| | - Arkajyoti Paul
- Drug Discovery, GUSTO A Research Group, Chittagong, Bangladesh
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Jackie Barua
- Drug Discovery, GUSTO A Research Group, Chittagong, Bangladesh
- Comilla Medical College, Faculty of Medicine, University of Chittagong, Chittagong, Bangladesh
| | - Syeda Sakiatuz Zannat
- Drug Discovery, GUSTO A Research Group, Chittagong, Bangladesh
- Bioinformatics, Department of Physics, Astronomy and Maths, University of Central Lancashire, Lancashire, England
| | - Md Mehedi Hasan
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Shaibal Das Gupta
- Department of Pharmacy, University of Science and Technology Chittagong, Chittagong, Bangladesh
| | - Sagar Barua
- Abdul Malek Ukil Medical College Noakhali, Faculty of Medicine, University of Chittagong, Chittagong, Bangladesh
| | - Sabbir Ahmed
- Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Solna, Sweden
| | - Mohammad Shah Hafez Kabir
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
- Drug Discovery, GUSTO A Research Group, Chittagong, Bangladesh, Phone: +8801671709737
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Xu P, Huang M. Small Peptides as Modulators of Serine Proteases. Curr Med Chem 2018; 27:3686-3705. [PMID: 30332941 DOI: 10.2174/0929867325666181016163630] [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] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023]
Abstract
Serine proteases play critical roles in many physiological and pathological processes, and are proven diagnostic and therapeutic targets in a number of clinical indications. Suppression of the aberrant proteolytic activities of these proteases has been clinically used for the treatments of relevant diseases. Polypeptides with 10-20 residues are of great interests as medicinal modulators of serine proteases, because these peptides demonstrate the characteristics of both small molecule drugs and macromolecular drugs. In this review, we summarized the recent development of peptide-based inhibitors against serine proteases with potent inhibitory and high specificity comparable to monoclonal antibodies. In addition, we also discussed the strategies of enhancing plasma half-life and bioavailability of peptides in vivo, which is the main hurdle that limits the clinical translation of peptide-based drugs. This review advocates new avenue for the development of effective serine protease inhibitors and highlights the prospect of the medicinal use of these inhibitors.
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Affiliation(s)
- Peng Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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Williams TM, Sable R, Singh S, Vicente MGH, Jois S. Peptide ligands for targeting the extracellular domain of EGFR: Comparison between linear and cyclic peptides. Chem Biol Drug Des 2018; 91:605-619. [PMID: 29052959 PMCID: PMC5775921 DOI: 10.1111/cbdd.13125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/27/2017] [Accepted: 10/04/2017] [Indexed: 01/08/2023]
Abstract
Colorectal cancer (CRC) is the third most common solid internal malignancy among cancers. Early detection of cancer is key to increasing the survival rate of colorectal cancer patients. Overexpression of the EGFR protein is associated with CRC. We have designed a series of peptides that are highly specific for the extracellular domain of EGFR, based on our earlier studies on linear peptides. The previously reported linear peptide LARLLT, known to bind to EGFR, was modified with the goals of increasing its stability and its specificity toward EGFR. Peptide modifications, including D-amino acid substitution, cyclization, and chain reversal, were investigated. In addition, to facilitate labeling of the peptide with a fluorescent dye, an additional lysine residue was introduced onto the linear (KLARLLT) and cyclic peptides cyclo(KLARLLT) (Cyclo.L1). The lysine residue was also converted into an azide group in both a linear and reversed cyclic peptide sequences cyclo(K(N3)larllt) (Cyclo.L1.1) to allow for subsequent "click" conjugation. The cyclic peptides showed enhanced binding to EGFR by SPR. NMR and molecular modeling studies suggest that the peptides acquire a β-turn structure in solution. In vitro stability studies in human serum show that the cyclic peptide is more stable than the linear peptide.
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Affiliation(s)
- Tyrslai M. Williams
- Department of Chemistry, Louisiana State University, Baton Rouge LA 70803, USA
| | - Rushikesh Sable
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
| | - Sitanshu Singh
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
| | - M. Graça H. Vicente
- Department of Chemistry, Louisiana State University, Baton Rouge LA 70803, USA
| | - Seetharama Jois
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
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Xu P, Andreasen PA, Huang M. Structural Principles in the Development of Cyclic Peptidic Enzyme Inhibitors. Int J Biol Sci 2017; 13:1222-1233. [PMID: 29104489 PMCID: PMC5666521 DOI: 10.7150/ijbs.21597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/28/2017] [Indexed: 01/23/2023] Open
Abstract
This review summarizes our studies in the development of small cyclic peptides for specifically modulating enzyme activity. Serine proteases share highly similar active sites but perform diverse physiological and pathological functions. From a phage-display peptide library, we isolated two mono-cyclic peptides, upain-1 (CSWRGLENHRMC) and mupain-1 (CPAYSRYLDC), which inhibit the activity of human and murine urokinase-type plasminogen activators (huPA and muPA) with Ki values in the micromolar or sub-micromolar range, respectively. The following affinity maturations significantly enhanced the potencies of the two peptides, 10-fold and >250-fold for upain-1 and mupain-1, respectively. The most potent muPA inhibitor has a potency (Ki = 2 nM) and specificity comparable to mono-clonal antibodies. Furthermore, we also found an unusual feature of mupain-1 that its inhibitory potency can be enhanced by increasing the flexibility, which challenges the traditional viewpoint that higher rigidity leading to higher affinity. Moreover, by changing a few key residues, we converted mupain-1 from a uPA inhibitor to inhibitors of other serine proteases, including plasma kallikrein (PK) and coagulation factor XIa (fXIa). PK and fXIa inhibitors showed Ki values in the low nanomolar range and high specificity. Our studies demonstrate the versatility of small cyclic peptides to engineer inhibitory potency against serine proteases and to provide a new strategy for generating peptide inhibitors of serine proteases.
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Affiliation(s)
- Peng Xu
- State Key Laboratory of Structural Chemistry and Danish-Chinese Centre for Proteases and Cancer, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, P.R. China
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Mingdong Huang
- State Key Laboratory of Structural Chemistry and Danish-Chinese Centre for Proteases and Cancer, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, P.R. China.,College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P.R. China
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