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Zari A, Kurdi LAF, Jaber FA, Alghamdi KMS, Zari TA, Bahieldin A, Hakeem KR, Alnahdi HS, Edris S, Ashraf GM. Investigation and drug design for novel molecules from natural products as inhibitors for controlling multiple myeloma disease using in-silico tools. J Biomol Struct Dyn 2024:1-16. [PMID: 38173181 DOI: 10.1080/07391102.2023.2300409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/02/2023] [Indexed: 01/05/2024]
Abstract
Multiple myeloma (MM) is a disease that causes plasma cell growth in the bone marrow and immune globulin buildup in blood and urine. Despite recent advances in MM therapy, many still die due to its high mortality rate. A study using computational simulations analyzed 100 natural ingredients from the SANC database to determine if they inhibited the IgH domain, a known cause of multiple myeloma. Natural component Diospyrin inhibited the IgH enzyme with the best binding energy of -10.3 kcal/mol and three carbon-hydrogen bonds, followed by Parviflorone F complex with a binding energy of -10.1 kcal/mol and two conventional-hydrogen bonds. As a result, the Molecular Dynamic simulation was used to test the stability of the two complexes. During the simulation, the Diospyrin molecule dissociated from the protein at roughly 67.5 ns, whereas the Parviflorone F molecule stayed attached to the protein throughout. The latter was the subject of the investigation. The analysis of the production run data revealed that the Parviflorone F molecule exhibits a variety of conformations within the binding pocket while keeping a relatively constant distance from the protein's center of mass. The analysis of the production run data revealed that the Parviflorone F molecule exhibited a variety of conformations within the binding pocket while keeping a relatively constant distance from the protein's center of mass. The root mean square deviation (RMSD) plots for both the protein and complex showed a stable and steady average value of 4.4 Å for the first 82 nanoseconds of manufacture. As a result, the average value increased to 8.3 Å. Furthermore, the components of the binding free energy, as computed by MM-GBSA, revealed that the mean binding energy of the Parviflorone F molecule was -23.88 kcal/mol. Finally, after analyzing all of the examination data, Parviflorone F was identified as a powerful inhibitor of the IgH domain and hence of the MM disease, which requires further in-vivo conformation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali Zari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Lina A F Kurdi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatima A Jaber
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Khalid M S Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Talal A Zari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Public Health, Daffodil International University, Dhaka, Bangladesh
| | - Hanan S Alnahdi
- Department of Biochemistry, College of Science, University of Jeddah, Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Al Borg Medical Laboratories, Jeddah, Saudi Arabia
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences and Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
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Qiao X, Ye L, Lu J, Pan C, Fei Q, Zhu Y, Li H, Lin H, Ge RS, Wang Y. Curcumin analogues exert potent inhibition on human and rat gonadal 3β-hydroxysteroid dehydrogenases as potential therapeutic agents: structure-activity relationship and in silico docking. J Enzyme Inhib Med Chem 2023; 38:2205052. [PMID: 37184069 DOI: 10.1080/14756366.2023.2205052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Curcuminoids are functional food additives, and the effect on gonadal hormone biosynthesis remains unclear. Gonads contain 3β-hydroxysteroid dehydrogenase isoforms, h3β-HSD2 (humans) and r3β-HSD1 (rats), which catalyse pregnenolone into progesterone. The potency and mechanisms of curcuminoids to inhibit 3β-HSD activity were explored. The inhibitory potency was bisdemethoxycurcumin (IC50, 1.68 µM) >demethoxycurcumin (3.27 µM) > curcumin (13.87 µM) > tetrahydrocurcumin (109.0 µM) > dihydrocurcumin and octahydrocurcumin on KGN cell h3β-HSD2, while that was bisdemethoxycurcumin (1.22 µM) >demethoxycurcumin (2.18 µM) > curcumin (4.12 µM) > tetrahydrocurcumin (102.61 µM) > dihydrocurcumin and octahydrocurcumin on testicular r3β-HSD1. All curcuminoids inhibited progesterone secretion by KGN cells under basal and forskolin-stimulated conditions at >10 µM. Docking analysis showed that curcuminoids bind steroid-active site with mixed or competitive mode. In conclusion, curcuminoids inhibit gonadal 3β-HSD activity and de-methoxylation of curcumin increases inhibitory potency and metabolism of curcumin by saturation of carbon chain losses inhibitory potency.
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Affiliation(s)
- Xinyi Qiao
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lei Ye
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jialin Lu
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chengshuang Pan
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Reproductive Medicine Center, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qianjin Fei
- Reproductive Medicine Center, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yang Zhu
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Key Laboratory of Environment and Male Reproductive Medicine of Wenzhou, Wenzhou, China
| | - Huitao Li
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Key Laboratory of Environment and Male Reproductive Medicine of Wenzhou, Wenzhou, China
| | - Han Lin
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ren-Shan Ge
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Key Laboratory of Environment and Male Reproductive Medicine of Wenzhou, Wenzhou, China
| | - Yiyan Wang
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Key Laboratory of Environment and Male Reproductive Medicine of Wenzhou, Wenzhou, China
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Rmili F, Frikha F, Chamkha M, Sayari A, Fendri A. Structure elucidation of Staphylococcus capitis lipase. Molecular dynamics simulations to investigate the effects of calcium and zinc ions on the structural stability. J Biomol Struct Dyn 2023; 41:10450-10462. [PMID: 36546696 DOI: 10.1080/07391102.2022.2159528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Cold-adapted and organic solvent tolerant lipases have significant potential in a wide range of synthetic reactions in industry. But there are no sufficient studies on how these enzymes interacts with their substrates. Herein, the predicted structure and function of the Staphylococcus capitis lipase (SCL) are studied. Given the high amino acid sequence homology with the Staphylococcus simulans lipase (SSL), 3D structure models of closed and open forms of the S. capitis lipase were built using the structure of SSL as template. The models suggested the presence of a main lid and a second lid that may act with the former as a double door to control the access to the active site. The SCL models also allowed us to identify key residues involved in binding substrates, calcium or zinc ions. By following this model and utilizing molecular dynamics (MD) simulations, the stability of the S. capitis lipase at low temperatures could be explained in the presence and in the absence of calcium and zinc. Due to its thermolability, the SCL is extremely valuable for different biotechnological applications in a wide variety of industries from molecular biology to detergency to food and beverage preparation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatma Rmili
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Engineering National School of Sfax (ENIS), University of Sfax, Sfax, Tunisia
| | - Fakher Frikha
- Laboratory of Molecular and Cellular Screening Processes Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Mohamed Chamkha
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Adel Sayari
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Engineering National School of Sfax (ENIS), University of Sfax, Sfax, Tunisia
| | - Ahmed Fendri
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Engineering National School of Sfax (ENIS), University of Sfax, Sfax, Tunisia
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Wang H, Sang J, Ji Z, Yu Y, Wang S, Zhu Y, Li H, Wang Y, Zhu Q, Ge R. Bisphenol A Analogues Inhibit Human and Rat 11β-Hydroxysteroid Dehydrogenase 1 Depending on Its Lipophilicity. Molecules 2023; 28:4894. [PMID: 37446556 DOI: 10.3390/molecules28134894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023] Open
Abstract
Bisphenol A (BPA) analogues substituted on the benzene ring are widely used in a variety of industrial and consumer materials. However, their effects on the glucocorticoid-metabolizing enzyme 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1) remain unclear. The inhibitory effects of 6 BPA analogues on the inhibition of human and rat 11β-HSD1 were investigated. The potencies of inhibition on human 11β-HSD1 were bisphenol H (IC50, 0.75 µM) > bisphenol G (IC50, 5.06 µM) > diallyl bisphenol A (IC50, 13.36 µM) > dimethyl bisphenol A (IC50, 30.18 µM) > bisphenol A dimethyl ether (IC50, 33.08 µM) > tetramethyl bisphenol A (>100 µM). The inhibitory strength of these chemicals on rat 11β-HSD1 was much weaker than that on the human enzyme, ranging from 74.22 to 205.7 µM. All BPA analogues are mixed/competitive inhibitors of both human and rat enzymes. Molecular docking studies predict that bisphenol H and bisphenol G both bind to the active site of human 11β-HSD1, forming a hydrogen bond with catalytic residue Ser170. The bivariate correlation of IC50 values with LogP (lipophilicity), molecular weight, heavy atoms, and molecular volume revealed a significant inverse regression and the correlation of IC50 values with ΔG (low binding energy) revealed a positive regression. In conclusion, the lipophilicity, molecular weight, heavy atoms, molecular volume, and binding affinity of a BPA analogue determine the inhibitory strength of human and rat 11β-HSD isoforms.
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Affiliation(s)
- Hong Wang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province and Key Laboratory of Male Health and Environment of Wenzhou, Wenzhou 325000, China
| | - Jianmin Sang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Zhongyao Ji
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Yang Yu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Shaowei Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Yang Zhu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Huitao Li
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Yiyan Wang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Qiqi Zhu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Renshan Ge
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province and Key Laboratory of Male Health and Environment of Wenzhou, Wenzhou 325000, China
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Sravanthi B, Himavathi G, Robert AR, Karunakar P, Kiran KS, Maddila S. Design, synthesis, computational molecular docking studies of novel heterocyclics bearing 1,2,4-triazole, 1,3,4-oxadiazole conjugates as potent antibacterial and antitubercular agents. J Biomol Struct Dyn 2023:1-14. [PMID: 37340639 DOI: 10.1080/07391102.2023.2226743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Herein, we report the synthesis, and characterization of a new series of 1,3,4-oxadiazole and 1,2,4-triazole derivatives based on azaindole acetamides and assigned as potential antibacterial and antitubercular substances. The structures of these compounds were established by 1H NMR, 13C NMR, and HRMS spectral analysis. In preliminary antibacterial studies, analogues 6b, 6d, and 6e were found to be most effective against S. aureus with MIC of 12.5, 6.25, and 12.5 μg/mL, whereas 8d displayed excellent activity against S. aureus, B. subtilis, E. coli bacterial strains with zones of inhibition 12.5, 25, and 12.5 μg/mL respectively. Particularly, the prepared scaffolds 8c, 8d, and 8e showed remarkable antifungal activity with MIC value 12.5, 12.5, and 6.25 μg/mL against A. flavus and 6d, 6c producing an increase in the activity against C. Albicans with zones of inhibition 12.5 and 12.5 μg/mL respectively. Also, through the antitubercular studies, we found that compounds 6e and 8b have a strong activity with M. tuberculosis H37Rv with MICs 3.26, and 6.48 μg/mL, respectively. The protein stability, fluctuations of APO-Protein, and protein-ligand complexes were investigated through Molecular Dynamics (MD) simulations studies using Desmond Maestro 11.3, and potential lead molecules were identified. Our findings were further confirmed using molecular docking, revealing that azaindole based ligand 6e, 6f, and 8a has strong hydrophobic Tyr179, Trp183, Ile177, Ile445, and H-bondings interactions Arg151 and Arg454 through molecular dynamics simulation studies, making it potential biological compound. These compounds were further evaluated for their ADMET and physicochemical properties by using SwissADME.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B Sravanthi
- Department of Chemistry, GITAM School of Sciences, GITAM University, Visakhapatnam, India
- Department of Chemistry, Institute of Aeronautical Engineering, Hyderabad, India
| | - G Himavathi
- Department of Chemistry, GITAM School of Sciences, GITAM University, Visakhapatnam, India
| | - A R Robert
- Department of Chemistry, GITAM School of Sciences, GITAM University, Visakhapatnam, India
| | - Prashantha Karunakar
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvarava Technological University), Bangalore, India
| | - K S Kiran
- Department of Physics, Faculty of Engineering and Technology, Jain University, Bangalore, India
| | - S Maddila
- Department of Chemistry, GITAM School of Sciences, GITAM University, Visakhapatnam, India
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
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Almanaa TN, Mubarak A, Sajjad M, Ullah A, Hassan M, Waheed Y, Irfan M, Khan S, Ahmad S. Design and validation of a novel multi-epitopes vaccine against hantavirus. J Biomol Struct Dyn 2023:1-11. [PMID: 37261466 DOI: 10.1080/07391102.2023.2219324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Hantavirus is a member of the order Bunyavirales and an emerging global pathogen. Hantavirus infections have affected millions of people globally based on available epidemiological data and research studies. Hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) are the two main human diseases associated with hantavirus infections. Hence, efforts are required to develop a potent vaccine against the pathogen. The only vaccine that is in use for hantavirus is an inactivated virus vaccine, "Hantavax", but it failed to produce neutralizing antibodies. Vaccine development is of much importance in dealing with the surge of hantavirus globally. In this study, hantavirus five proteins (N protein, G1 and G2, L protein, and non-structural proteins) were used in NetCTL 1.2 program to predict T-cell epitopes. To predict major histocompatibility complex (MHC) binding alleles, an immune epitope database (IEDB) was used. All predicted epitopes were then investigated for different immunoinformatics analyses such as antigenicity and toxicity analyses. The good water-soluble, non-toxic, probable antigenic, and DRB*0101 binder was selected. A multi-epitopes-based vaccine designing was then done where linkers were used to connect the shortlisted epitopes. In addition, an adjuvant molecule was supplementary to the multi-epitopes peptide to improve the vaccine's immunogenic potential. The final vaccine construct's three-dimensional structure was modeled by ab initio method. The vaccine molecule was then evaluated for its binding potential with TLR-3 immune receptor, which is key for its recognition and processing by the host immune system. Docking studies were performed using HADDOCK software. The best-docked complex was selected and visualized for intermolecular binding and interactions using UCSF Chimera 1.16 software. The findings revealed that the designed vaccine might be a potential vaccine against hantavirus and can be used in experimental animal model testings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Sajjad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Muhammad Hassan
- Department of Pharmacy, Bacha Khan University, Charsadda, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
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Zhai Y, Wang S, Zhang B, Tang Y, Wang H, Li J, Hu Z, Wang Y, Li H, Ge RS. The analysis of pesticides and fungicides in the inhibition of human and rat placental 3β-hydroxysteroid dehydrogenase activity: mode of inhibition and mechanism. Toxicol Lett 2023; 379:76-86. [PMID: 36965607 DOI: 10.1016/j.toxlet.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/25/2023] [Accepted: 03/02/2023] [Indexed: 03/27/2023]
Abstract
3β-Hydroxysteroid dehydrogenase/steroid Δ5,4-isomerase 1 (3β-HSD1) plays a critical role in the biosynthesis of progesterone from pregnenolone in the human placenta to maintain normal pregnancy. Whether they inhibit placental 3β-HSD1 and mode of inhibition remains unclear. In this study, we screened 21 pesticides and fungicides in five classes to inhibit human 3β-HSD1 and compared them to rat homolog 3β-HSD4. 3β-HSD activity was measured by catalyzing pregnenolone to progesterone in the presence of NAD+. Of the 21 chemicals, azoles (difenoconazole), thiocarbamates (thiram and ferbam) and organochlorine (hexachlorophene) significantly inhibited human 3β-HSD1 with half maximal inhibitory concentration (IC50) values of 2.77, 0.24, 0.68, and 17.96 μM, respectively. We also found that difenoconazole, ferbam and hexachlorophene are mixed/competitive inhibitors of 3β-HSD1 while thiram is a mixed/noncompetitive inhibitor. Docking analysis showed that difenoconazole and hexachlorophene bound steroid-binding site. Difenoconazole and hexachlorophene except thiram and ferbam also significantly inhibited rat 3β-HSD4 activity with IC50 of 1.12 and 2.28µM, respectively. Thiram and ferbam significantly inhibited human 3β-HSD1 possibly by interfering with cysteine residues, while they had no effects on rat 3β-HSD4. In conclusion, some pesticides potently inhibit placental 3β-HSD, leading to the reduction of progesterone formation.
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Affiliation(s)
- Yingna Zhai
- Department of Anaesthesiology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, 325000, Zhejiang Province, China
| | - Shaowei Wang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Bingru Zhang
- Department of Anaesthesiology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yunbing Tang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Hong Wang
- Department of Anaesthesiology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, 325000, Zhejiang Province, China
| | - Jingjing Li
- Department of Anaesthesiology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, 325000, Zhejiang Province, China
| | - Zhiyan Hu
- Department of Anaesthesiology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yiyan Wang
- Department of Anaesthesiology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Huitao Li
- Department of Anaesthesiology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Ren-Shan Ge
- Department of Anaesthesiology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, 325000, Zhejiang Province, China.
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Goudzal A, El Aissouq A, El Hamdani H, Hadaji EG, Ouammou A, Bouachrine M. 3D-QSAR modeling and molecular docking studies on a series of 2, 4, 5-trisubstituted imidazole derivatives as CK2 inhibitors. J Biomol Struct Dyn 2023; 41:234-248. [PMID: 35068344 DOI: 10.1080/07391102.2021.2014360] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein case in kinase II alpha subunit (CK2) plays an imperative function in treating cancer disease. Herein, we have performed a three-dimensional quantitative structure activity relationship (3D-QSAR), and molecular docking analysis on a novel series of 2, 4, 5-trisubstituted imidazole derivatives in order to design potent kinase II alpha subunit (CK2) inhibitors. The 3D-QSAR methods such as comparative molecular similarity indexes analysis (COMSIA), and the comparative molecular field analysis (COMFA) were investigate using twenty-four molecules of 2, 4, 5-trisubstituted imidazole derivatives as anticancer agent. The best COMFA and COMSIA models exhibit excellent Q2 values of 0.66 and 0.75 and R2 values of 0.98 and 0.99 respectively. To check the validity of the selected COMFA and COMSIA models, a variety of validation tests were utilized: Internal validation analyses, and externally validation beside Y-randomization according to the principles of the Organization for Economic Co-operation and Development (OECD), and the Golbraikh and Tropsha's criteria for the validation of 3D-QSAR models. The proposed models for COMFA and COMSIA analysis have been successful. The developed models, indicating that they were reliable for activity prediction. Based on the preceding results, we designed several new potent molecules. Such outcome can proffer helpful theoretical references for future experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amina Goudzal
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Sidi Mohamed Ben Abdellah University, Faculty of Sciences, Fez, Morocco
| | - Abdellah El Aissouq
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Sidi Mohamed Ben Abdellah University, Faculty of Sciences, Fez, Morocco
| | - Hicham El Hamdani
- MCNS Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - El Ghalia Hadaji
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Sidi Mohamed Ben Abdellah University, Faculty of Sciences, Fez, Morocco
| | - Abdelkrim Ouammou
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Sidi Mohamed Ben Abdellah University, Faculty of Sciences, Fez, Morocco
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Dunga AK, Allaka TR, Kethavarapu Y, Nechipadappu SK, Pothana P, Kuppan C, Kishore PVVN. Design, Synthesis, Molecular Docking, ADMET, and Biological Studies of Some Novel 1,2,3-Triazole Linked Tetrazoles as Anticancer Agents. Curr Org Synth 2023; 20:576-587. [PMID: 35996261 DOI: 10.2174/1570179419666220822125724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/18/2022] [Accepted: 06/24/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND 1,2,3-Triazole-tetrazoles have received substantial attention because of their unique bioisosteric properties and an extraordinarily broad spectrum of biological activity, making them interesting for the drug design, and synthesis of a delightful class of widely investigated heterocyclic compounds. To address major health concerns, it is consequently important to devote ongoing effort to the identification and development of New Chemical Entities (NCEs) as possible anticancer medicines. METHODS We began our initial investigation of the reaction between 5-(azidomethyl)-1H-pyrrolo[ 2,3-b]pyridine and 1-phenyl substituted-5-(prop-2-yn-1-ylthio)-1 H-tetrazole under click chemistry to give the corresponding triazole precursors and screened for their cytotoxicity reported by variations in therapeutic actions of the parent molecule. All of the prepared scaffolds were characterized by proton, carbon resonance spectroscopy, IR, and mass spectral techniques. RESULTS When tested for in vitro antitumor activity the prepared compounds 7e, 7h had a significant anticancer activity against human adenocarcinoma Hs766T cell line with IC50 = 5.33, 4.92 μg/mL and Hs460 cell line with IC50 = 4.82, 6.15 μg/mL respectively. Final scaffolds 7f, 7h, and 7j acquire the highest potential drug binding scores ΔG = -10.42, -8.80, -9.37 Kcal/, with amino acids residues Ala A:11 (2.195 A˚), Asp A:119 (1.991 A˚), Thr A:58 (1.890 A˚), Lys A:16 (1.253 A˚), Asp A:38 (2.013 A˚), Lys A:117 (2.046 A˚) respectively and process Lipinski's rule of five as good agents for oral bioavailability. CONCLUSION The molecular framework for the synthesis of novel Aza indole 1,2,3-triazole scaffolds coupled to tetrazole core was discovered in our study and evaluated for their anticancer activity.
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Affiliation(s)
- Ananda Kumar Dunga
- Chemistry Division, Department of Sciences and Humanities, VFSTR (Deemed to be University), Vadlamudi, Guntur- 522213, India
| | - Tejeswara Rao Allaka
- Centre for Chemical Sciences and Technology, Institute of Science & Technology, Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad, Telangana-500085, India
| | - Yugandhar Kethavarapu
- Aurobindo Pharma Limited, Industrial Development Area, Pydibimavaram, Srikakulam, Andhra Pradesh-532409, India
| | | | - Pradeep Pothana
- Department of Chemistry, Kakatiya University, Hanamkonda, Warangal, Telangana-506009, India
| | - Chandrasekhar Kuppan
- Chemistry Division, Department of Sciences and Humanities, VFSTR (Deemed to be University), Vadlamudi, Guntur- 522213, India
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Dashyan SS, Babaev EV, Paronikyan EG, Ayvazyan AG, Paronikyan RG, Hunanyan LS. Evaluation of Neurotropic Activity and Molecular Docking Study of New Derivatives of pyrano[4″,3″:4',5']pyrido[3',2':4,5]thieno[3,2- d]pyrimidines on the Basis of pyrano[3,4- c]pyridines. Molecules 2022; 27:3380. [PMID: 35684318 DOI: 10.3390/molecules27113380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022]
Abstract
Background: Heterocyclic compounds and their fused analogs, which contain pharmacophore fragments such as pyridine, thiophene and pyrimidine rings, are of great interest due to their broad spectrum of biological activity. Chemical compounds containing two or more pharmacophore groups due to additional interactions with active receptor centers usually enhance biological activity and can even lead to a new type of activity. The search for new effective neurotropic drugs in the series of derivatives of heterocycles containing pharmacophore groups in organic, bioorganic and medical chemistry is a serious problem. Methods: Modern methodology of drugs involves synthesis, physicochemical study, molecular modeling and selection of active compounds through virtual screening and experimental evaluation of the biological activity of new chimeric compounds with pharmacophore fragments. For the synthesis of new compounds, classical organic methods were used and developed. For the evaluation of neurotropic activity of new synthesized compounds, some biological methods were used according to indicators characterizing anticonvulsant, sedative and antianxiety activity as well as side effects. For docking analysis, various soft ware packages and methods were used. Results: As a result of multistep reactions, 11 new, tri- and tetracyclic heterocyclic systems were obtained. The studied compounds exhibit protection against pentylenetetrazole (PTZ) seizures as well as some psychotropic effects. The biological assays evidenced that nine of the eleven studied compounds showed a high anticonvulsant activity by antagonism with pentylenetetrazole. The toxicity of the compounds is low, and they do not induce muscle relaxation in the studied doses. According to the study of psychotropic activity, it was found that the selected compounds have an activating behavior and anxiolytic effects on the “open field” and “elevated plus maze” (EPM) models. The data obtained indicate the anxiolytic (antianxiety) activity of the derivatives of tricyclic thieno[2,3-b]pyridines and tetracyclic pyridothieno[3,2-d]pyrimidin-8-ones, especially pronounced in compounds 3b–f and 4e. The studied compounds increase the latent time of first immobilization on the “forced swimming” (FS) model and exhibit antidepressant effects; compounds 3e and 3f especially exhibit these effects, similarly to diazepam. Docking studies revealed that compounds 3c and 4b bound tightly in the active site of γ-aminobutyric acid type A (GABAA) receptors with a value of the scoring function that estimates free energy of binding (∆G) at −10.0 ± 5 kcal/mol. Compound 4e showed the best affinity ((∆G) at −11.0 ± 0.54 kcal/mol) and seems to be an inhibitor of serotonin (SERT) transporter. Compounds 3c–f and 4e practically bound with the groove of T4L of 5HT_1A and blocked it completely, while the best affinity observed was in compound 3f ((∆G) at −9.3 ± 0.46 kcal/mol). Conclusions: The selected compounds have an anticonvulsant, activating behavior and anxiolytic effects and at the same time exhibit antidepressant effects.
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Mir WR, Bhat BA, Almilaibary A, Asdaq SMB, Mir MA. Evaluation of the In Vitro Antimicrobial Activities of Delphinium roylei: An Insight from Molecular Docking and MD-Simulation Studies. Med Chem 2022; 18:1109-1121. [PMID: 35507782 DOI: 10.2174/1573406418666220429093956] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/22/2022]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The burden of antimicrobial resistance demands a continued search for new antimicrobial drugs. The synthetic drugs which are used clinically have serious side effects. Natural products or compounds derived from natural sources show diversity in structure and play an essential role in drug discovery and development. OBJECTIVE Delphinium roylei is an important medicinal herb of Kashmir Himalaya, India. Traditionally this medicinal plant treats liver infections, skin problems, and chronic lower back pain. The current study evaluates the antimicrobial potential by various in -vitro and in -silico parameters. METHODS Three extracts and 168 bioactive compounds analysed through LC-MS data, with the vast majority of them having therapeutic applications of D. roylei, have been screened for the antimicrobial activity against bacteria (E. coli, M. luteus, K. pneumoniae, Streptococcus pneumonia, Haemophilus influenzae, Neisseria mucosa) and fungi (Candida albicans, Candida glabrata, Candida Paropsilosis) species through molecular docking using autodock Vina, MD simulation and broth microdilution method for minimum inhibitory concentration (MIC) evaluation. RESULTS The extracts, as well as the compounds analyzed through the LC-MS technique of Delphinium roylie showed significant antimicrobial activity. CONCLUSION Our study established that the leaf extracts of Delphinium roylei exhibit antimicrobial activity and thus confirm its importance in traditional medicine.
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Affiliation(s)
- Wajahat Rashid Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Abdullah Almilaibary
- Department of Family and Community Medicine, Albaha University, Albaha-65511, KSA
| | | | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
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Ortega R, Valdés M, Alarcón-Aguilar FJ, Fortis-Barrera Á, Barbosa E, Velazquez C, Calzada F. Antihyperglycemic Effects of Salvia polystachya Cav. and Its Terpenoids: α-Glucosidase and SGLT1 Inhibitors. Plants (Basel) 2022; 11:plants11050575. [PMID: 35270046 PMCID: PMC8912538 DOI: 10.3390/plants11050575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/13/2022] [Accepted: 02/17/2022] [Indexed: 06/02/2023]
Abstract
The antihyperglycemic activity of ethanolic extract from Salvia polystachya (EESpS) and its products was evaluated using in vivo, ex vivo and in silico assays; additionally, an acute toxicity assay was evaluated. EESpS was classified as a nontoxic class 5 drug. EESpS, ethyl acetate fraction (EtOAcFr), secondary-6-fraction (SeFr6), ursolic acid (UA), and oleanolic acid (OA) reduced the hyperglycemia in DM2 mice. α-glucosidase inhibition was evaluated with oral sucrose and starch tolerance tests (OSuTT and OStTT), an intestinal sucrose hydrolysis (ISH) assay and molecular docking studies using acarbose as control. SGLT1 inhibition was evaluated with oral glucose and galactose tolerance tests (OGTT and OGaTT), an intestinal glucose absorption (IGA) assay and molecular docking studies using canagliflozin as the control. During the carbohydrate tolerance tests, all the treatments reduced the postprandial peak, similar to the control drugs. During the ISH, IC50 values of 739.9 and 726.3 µM for UA and OA, respectively, were calculated. During the IGA, IC50 values of 966.6 and 849.3 for UA, OA respectively, were calculated. Finally, during the molecular docking studies, UA and OA showed ∆G values of -6.41 and -5.48 kcal/mol-1, respectively, on α-glucosidase enzymes. During SGLT1, UA and OA showed ∆G values of -10.55 and -9.65, respectively.
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Affiliation(s)
- Rocio Ortega
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Iztapalapa, UAM-I, Mexico City CP 09340, Mexico
- Av. San Rafael Atlixco 186, Leyes de Reforma 1ra Sección, Iztapalapa, Mexico City CP 09340, Mexico
- Unidad de Investigación Médica en Farmacología, UMAE Hospital de Especialidades, 2° Piso CORSE Centro Médico Nacional Siglo XXI, IMSS, Av. Cuauhtémoc 330, Col. Doctores, Mexico City CP 06725, Mexico
| | - Miguel Valdés
- Unidad de Investigación Médica en Farmacología, UMAE Hospital de Especialidades, 2° Piso CORSE Centro Médico Nacional Siglo XXI, IMSS, Av. Cuauhtémoc 330, Col. Doctores, Mexico City CP 06725, Mexico
| | - Francisco J. Alarcón-Aguilar
- Laboratorio de Farmacología, Departamento de Ciencias de la Salud, División de CBS, Universidad Autónoma Metropolitana-Iztapalapa, UAM-I, Av. San Rafael Atlixco 186, Leyes de Reforma 1ra Sección, Mexico City CP 09340, Mexico; (F.J.A.-A.); (Á.F.-B.)
| | - Ángeles Fortis-Barrera
- Laboratorio de Farmacología, Departamento de Ciencias de la Salud, División de CBS, Universidad Autónoma Metropolitana-Iztapalapa, UAM-I, Av. San Rafael Atlixco 186, Leyes de Reforma 1ra Sección, Mexico City CP 09340, Mexico; (F.J.A.-A.); (Á.F.-B.)
| | - Elizabeth Barbosa
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Salvador Díaz Mirón esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Mexico City CP 11340, Mexico;
| | - Claudia Velazquez
- Área Académica de Farmacia, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Km 4.5, Carretera Pachuca-Tulancingo, Unidad Universitaria, Pachuca CP 42076, Mexico;
| | - Fernando Calzada
- Unidad de Investigación Médica en Farmacología, UMAE Hospital de Especialidades, 2° Piso CORSE Centro Médico Nacional Siglo XXI, IMSS, Av. Cuauhtémoc 330, Col. Doctores, Mexico City CP 06725, Mexico
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Rauf A, Raza M, Humayun Khan M, Hemeg HA, Al-Awthan YS, Bahattab O, Bawazeer S, Naz S, Basoglu F, Saleem M, Khan M, Seyyedamirhossein H, Mubarak MS, Erdogan Orhan I. In vitro and in silico studies on clinically important enzymes inhibitory activities of flavonoids isolated from Euphorbia pulcherrima. Ann Med 2022; 54:495-506. [PMID: 35112936 PMCID: PMC8820783 DOI: 10.1080/07853890.2022.2033826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Introduction: The genus Euphorbia is known to contain diterpenoids, and several isolated compounds which exhibited biological activities including significant multidrug resistance reversal effects. This work is focused on the isolation, in vitro and in silico studies of two natural bio-active flavonoids (1 & 2) isolated from Euphorbia pulcherrima bark for the very first time.Methods: The phytochemical investigation resulted in the identification of two flavonoids: 3,5,7-trihydroxy-2-(4-hydroxy-3-methoxyphenyl)-6-methoxy-4H-chromen-4-one (1) and 2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-6-methoxy-4H-chromen-4-one (2), which were isolated for the first time from Euphorbia pulcherrima.Results: The chemical structures of the two isolated compounds were confirmed by 1H NMR, 13C NMR, and ESI-HRMS spectral data. The Bioactivity activity of these compounds was evaluated; results revealed that compounds 1 & 2 exhibit promising urease inhibitory potential with IC50 values of 15.3 ± 2.13 μM and 19.0 ± 2.43 μM, respectively, whereas the positive control thiourea had an IC50 of 21.0 ± 0.23 μM. Similarly, these compounds were also evaluated against the tyrosinase enzyme; results showed that compound 1 displays significant inhibitory activity with an IC50 value of 48.7 ± 2.19 μM, whereas compound 2 exhibited a moderate effect with an IC50 value of 74.8 ± 1.79 μM, when compared with the standard (alpha-kojic acid, IC50 = 47.6 ± 0.67 μM). Additionally, compounds 1 and 2 also exhibited anti-glycation and phosphodiesterase inhibitory activities.Conclusion: Studies dealing with the drug like properties such as in silico screening (docking study) was also carried out to discover the structural features of both compounds 1 and 2. Results indicated that the docking scores of compounds 1 and 2 are in agreement with their IC50 values. Key messagesIsolation and characterization of two bioactive flavonoids (1 and 2) from Euphorbia pulcherrima.In silico and in vitro enzyme inhibition studies were conducted to identify the therapeutic potential of flavonoids 1 and 2.Drug-like properties were calculated to discover important pharmacophoric features.
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Affiliation(s)
- Abdur Rauf
- Department of Chemistry, University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Muslim Raza
- Department of Chemistry, Bacha Khan University Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Humayun Khan
- Institute of Chemical Sciences, University of Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Hassan A Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Yahya S Al-Awthan
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Saudia Arabia.,Department of Biology, Faculty of Science, Ibb University, Ibb, Yemen
| | - Omar Bahattab
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Saudia Arabia
| | - Sami Bawazeer
- Department of Pharmacognosy, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Saima Naz
- Department Biotechnology and Microbiology, Bacha Khan University Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - Faika Basoglu
- European University of Lefke, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Lefke, Northern Cyprus, Mersin, Turkey
| | | | - Majid Khan
- H.E.J. Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
| | | | | | - Ilkay Erdogan Orhan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara, Turkey
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Arif MN. Catechin Derivatives as Inhibitor of COVID-19 Main Protease (Mpro): Molecular Docking Studies Unveil an Opportunity Against CORONA. Comb Chem High Throughput Screen 2022; 25:197-203. [PMID: 33231155 DOI: 10.2174/1871520620666201123101002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND A newly emergent strain of coronavirus (COVID-19) has affected almost the whole of the world's population. Currently, there is no specific vaccine or drug against COVID-19. Xu et al. (2020) built a homolog model of SARS-CoV-2 Mpro based on SARS-CoV Mpro, which is considered as a target to inhibit the replication of CoV. OBJECTIVE The aim of the current study was to find potential inhibitors of COVID-19 Mpro using docking analysis. METHODS Autodockvina was used to carry out Protein-Ligand docking. COVID-19 main protease Mpro was docked with catechin and its different synthetic derivatives. Nelfinavir, an antiretroviral drug belonging to protease inhibitors, was taken as the standard. RESULTS According to the result obtained, it was found that Compound (4) and Compound (1) have more affinity than nelfinavir. CONCLUSION Compounds were found to have a great potential to become COVID-19 main protease Mpro inhibitor. Nevertheless, for their medicinal use, further investigation is necessary.
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Affiliation(s)
- Muhammad Nouman Arif
- Department of Pharmaceutical Chemistry, Riphah Institute of Pharmaceutical Sciences, Riphah International University Islamabad,Pakistan
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Barazorda-Ccahuana HL, Nedyalkova M, Mas F, Madurga S. Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations. Polymers (Basel) 2021; 13:3823. [PMID: 34771379 PMCID: PMC8587287 DOI: 10.3390/polym13213823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
(1) Background: Main Protease (Mpro) is an attractive therapeutic target that acts in the replication and transcription of the SARS-CoV-2 coronavirus. Mpro is rich in residues exposed to protonation/deprotonation changes which could affect its enzymatic function. This work aimed to explore the effect of the protonation/deprotonation states of Mpro at different pHs using computational techniques. (2) Methods: The different distribution charges were obtained in all the evaluated pHs by the Semi-Grand Canonical Monte Carlo (SGCMC) method. A set of Molecular Dynamics (MD) simulations was performed to consider the different protonation/deprotonation during 250 ns, verifying the structural stability of Mpro at different pHs. (3) Results: The present findings demonstrate that active site residues and residues that allow Mpro dimerisation was not affected by pH changes. However, Mpro substrate-binding residues were altered at low pHs, allowing the increased pocket volume. Additionally, the results of the solvent distribution around Sγ, Hγ, Nδ1 and Hδ1 atoms of the catalytic residues Cys145 and His41 showed a low and high-water affinity at acidic pH, respectively. It which could be crucial in the catalytic mechanism of SARS-CoV-2 Mpro at low pHs. Moreover, we analysed the docking interactions of PF-00835231 from Pfizer in the preclinical phase, which shows excellent affinity with the Mpro at different pHs. (4) Conclusion: Overall, these findings indicate that SARS-CoV-2 Mpro is highly stable at acidic pH conditions, and this inhibitor could have a desirable function at this condition.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Miroslava Nedyalkova
- Department of Inorganic Chemistry, University of Sofia “St. Kl. Okhridski”, 1164 Sofia, Bulgaria;
| | - Francesc Mas
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
| | - Sergio Madurga
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
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Beč A, Hok L, Persoons L, Vanstreels E, Daelemans D, Vianello R, Hranjec M. Synthesis, Computational Analysis, and Antiproliferative Activity of Novel Benzimidazole Acrylonitriles as Tubulin Polymerization Inhibitors: Part 2. Pharmaceuticals (Basel) 2021; 14:1052. [PMID: 34681276 DOI: 10.3390/ph14101052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
We used classical linear and microwave-assisted synthesis methods to prepare novel N-substituted, benzimidazole-derived acrylonitriles with antiproliferative activity against several cancer cells in vitro. The most potent systems showed pronounced activity against all tested hematological cancer cell lines, with favorable selectivity towards normal cells. The selection of lead compounds was also tested in vitro for tubulin polymerization inhibition as a possible mechanism of biological action. A combination of docking and molecular dynamics simulations confirmed the suitability of the employed organic skeleton for the design of antitumor drugs and demonstrated that their biological activity relies on binding to the colchicine binding site in tubulin. In addition, it also underlined that higher tubulin affinities are linked with (i) bulkier alkyl and aryl moieties on the benzimidazole nitrogen and (ii) electron-donating substituents on the phenyl group that allow deeper entrance into the hydrophobic pocket within the tubulin’s β-subunit, consisting of Leu255, Leu248, Met259, Ala354, and Ile378 residues.
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Novy V, Carneiro LV, Shin JH, Larsbrink J, Olsson L. Phylogenetic analysis and in-depth characterization of functionally and structurally diverse CE5 cutinases. J Biol Chem 2021; 297:101302. [PMID: 34653507 PMCID: PMC8577158 DOI: 10.1016/j.jbc.2021.101302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/19/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022] Open
Abstract
Cutinases are esterases that release fatty acids from the apoplastic layer in plants. As they accept bulky and hydrophobic substrates, cutinases could be used in many applications, ranging from valorization of bark-rich side streams to plastic recycling. Advancement of these applications, however, requires deeper knowledge of cutinases’ biodiversity and structure–function relationships. Here, we mined over 3000 members from carbohydrate esterase family 5 for putative cutinases and condensed it to 151 genes from known or putative lignocellulose-targeting organisms. The 151 genes were subjected to a phylogenetic analysis, which showed that cutinases with available crystal structures were phylogenetically closely related. We then selected nine phylogenic diverse cutinases for recombinant production and characterized their kinetic activity against para-nitrophenol substrates esterified with consecutively longer alkyl chains (pNP-C2 to C16). Each investigated cutinase had a unique activity fingerprint against the tested pNP substrates. The five enzymes with the highest activity on pNP-C12 and C16, indicative of activity on bulky hydrophobic compounds, were selected for in-depth kinetic and structure–function analysis. All five enzymes showed a decrease in kcat values with increasing substrate chain length, whereas KM values and binding energies (calculated from in silico docking analysis) improved. Two cutinases from Fusarium solani and Cryptococcus sp. exhibited outstandingly low KM values, resulting in high catalytic efficiencies toward pNP-C16. Docking analysis suggested that different clades of the phylogenetic tree may harbor enzymes with different modes of substrate interaction, involving a solvent-exposed catalytic triad, a lipase-like lid, or a clamshell-like active site possibly formed by flexible loops.
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Affiliation(s)
- Vera Novy
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Wallenberg Wood Science Center, Chalmers University of Technology, Gothenburg, Sweden
| | - Leonor Vieira Carneiro
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jae Ho Shin
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Wallenberg Wood Science Center, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Wallenberg Wood Science Center, Chalmers University of Technology, Gothenburg, Sweden.
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Maltsev DV, Spasov AA, Vassiliev PM, Skripka MO, Miroshnikov MV, Kochetkov AN, Eliseeva NV, Lifanova YV, Kuzmenko TA, Divaeva LN, Morkovnik AS. Synthesis and Pharmacological Evaluation of Novel 2,3,4,5-tetrahydro[1,3]diazepino[1,2- a]benzimidazole Derivatives as Promising Anxiolytic and Analgesic Agents. Molecules 2021; 26:6049. [PMID: 34641593 DOI: 10.3390/molecules26196049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
A number of novel 2,3,4,5-tetrahydro[1,3]diazepino[1,2-a]benzimidazole derivatives 2 were obtained by alkylation mainly in the 1H-tautomeric form of 2,3,4,5-tetrahydro[1,3]diazepino[1,2-a]benzimidazole or its 8,9-dimethyl-substituted analog 4-chlorobenzyl bromide, 4-chloroacetic acid fluoroanilide, and 4-tert-butylphenacyl bromide in neutral medium. Compounds 3 were cyclized and synthesized earlier with 11-phenacyl-substituted diazepino[1,2-a]benzimidazoles upon heating in conc. HBr. The chemical structures of the compounds were clarified by using the 1H Nuclear Magnetic Resonance Spectroscopy (1H-NMR) technique. Anxiolytic properties were evaluated using the elevated plus maze (EPM) and open field (OF) tests. The analgesic effect of compounds was estimated with the tail flick (TF) and hot plate (HP) methods. Besides, possible the influence of the test compounds on motor activities of the animals was examined by the Grid, Wire, and Rotarod tests. Compounds 2d and 3b were the most active due to their prominent analgesic and anxiolytic potentials, respectively. The results of the performed in silico analysis showed that the high anxiolytic activity of compound 3b is explained by the combination of a pronounced interaction mainly with the benzodiazepine site of the GABAA receptor with a prominent interaction with both the specific and allosteric sites of the 5-HT2A receptor.
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Hashemi SA, Kyani A, Bathaie SZ. The in silico mechanism of hVKOR interaction with acetaminophen and its metabolite, as well as N-acetyl cysteine: caution on application in COVID-19 patients. J Biomol Struct Dyn 2021; 40:8274-8285. [PMID: 33879035 PMCID: PMC8074654 DOI: 10.1080/07391102.2021.1910570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acetaminophen and N-acetyl cysteine (NAC) are being used as supportive care in patients suffering from coronavirus disease 2019 (COVID-19). The coagulopathy and cerebral hemorrhage have been recently reported in these patients. Prolonged acetaminophen use increases the international normalized ratio (INR) and the risk of bleeding among patients taking anti-coagulants. Inhibition of vitamin K epoxide reductase (VKOR) by acetaminophen and NAC in chronic applications has been reported, however, detailed knowledge of the molecular mechanism and binding sites are not clear. Herein, we built the homology model of human VKOR (hVKOR) using ITASSER server, confirmed, and applied it for docking analysis of its interaction with acetaminophen and its metabolite, N-acetyl-p-benzoquinone imine (NAPQI), and NAC. We also calculated the lipophilicity and predicted the blood-brain-barrier (BBB) permeation of NAPQI by Swiss ADME. Our analysis showed that NAPQI and NAC, but not acetaminophen, bind strongly to the similar sites in hVKOR via both hydrogen and van der Waals bonding; particularly with Cys135. Thus, it interrupted the vitamin K reducing electron transfer pathway. Further, molecular dynamic (MD) simulation study revealed that the interactions of the ligands with hVKOR are stable. In conclusion, our analysis shed a light on the molecular mechanism of acetaminophen-induced coagulopathy previously reported in some clinical cases with chronic acetaminophen use. Furthermore, considering the anti-coagulopathy of NAPQI and NAC but not acetaminophen, the BBB permeation potency of these agents, and the risk of coagulopathy in COVID-19, we suggest a regular prothrombin time (PT) and INR monitoring of these patients taking acetaminophen and/or NAC.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Ali Hashemi
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.,Department of Laboratory Sciences, Chalus Branch, Islamic Azad University, Chalous, Iran
| | - Armita Kyani
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - S Zahra Bathaie
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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20
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Malmir N, Fard NA, Mgwatyu Y, Mekuto L. Cyanide Hydratase Modification Using Computational Design and Docking Analysis for Improved Binding Affinity in Cyanide Detoxification. Molecules 2021; 26:1799. [PMID: 33806828 DOI: 10.3390/molecules26061799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
Cyanide is a hazardous and detrimental chemical that causes the inactivation of the respiration system through the inactivation of cytochrome c oxidase. Because of the limitation in the number of cyanide-degrading enzymes, there is a great demand to design and introduce new enzymes with better functionality. This study developed an integrated method of protein-homology-modelling and ligand-docking protein-design approaches that reconstructs a better active site from cyanide hydratase (CHT) structure. Designing a mutant CHT (mCHT) can improve the CHT performance. A computational design procedure that focuses on mutation for constructing a new model of cyanide hydratase with better activity was used. In fact, this study predicted the three-dimensional (3D) structure of CHT for subsequent analysis. Inducing mutation on CHT of Trichoderma harzianum was performed and molecular docking was used to compare protein interaction with cyanide as a ligand in both CHT and mCHT. By combining multiple designed mutations, a significant improvement in docking for CHT was obtained. The results demonstrate computational capabilities for enhancing and accelerating enzyme activity. The result of sequence alignment and homology modeling show that catalytic triad (Cys-Glu-Lys) was conserved in CHT of Trichoderma harzianum. By inducing mutation in CHT structure, MolDock score enhanced from −18.1752 to −23.8575, thus the nucleophilic attack can occur rapidly by adding Cys in the catalytic cavity and the total charge of protein in pH 6.5 is increased from −6.0004 to −5.0004. Also, molecular dynamic simulation shows a stable protein-ligand complex model. These changes would help in the cyanide degradation process by mCHT.
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21
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Cuesta SA, Mora JR, Márquez EA. In Silico Screening of the DrugBank Database to Search for Possible Drugs against SARS-CoV-2. Molecules 2021; 26:1100. [PMID: 33669720 DOI: 10.3390/molecules26041100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Coronavirus desease 2019 (COVID-19) is responsible for more than 1.80 M deaths worldwide. A Quantitative Structure-Activity Relationships (QSAR) model is developed based on experimental pIC50 values reported for a structurally diverse dataset. A robust model with only five descriptors is found, with values of R2 = 0.897, Q2LOO = 0.854, and Q2ext = 0.876 and complying with all the parameters established in the validation Tropsha’s test. The analysis of the applicability domain (AD) reveals coverage of about 90% for the external test set. Docking and molecular dynamic analysis are performed on the three most relevant biological targets for SARS-CoV-2: main protease, papain-like protease, and RNA-dependent RNA polymerase. A screening of the DrugBank database is executed, predicting the pIC50 value of 6664 drugs, which are IN the AD of the model (coverage = 79%). Fifty-seven possible potent anti-COVID-19 candidates with pIC50 values > 6.6 are identified, and based on a pharmacophore modelling analysis, four compounds of this set can be suggested as potent candidates to be potential inhibitors of SARS-CoV-2. Finally, the biological activity of the compounds was related to the frontier molecular orbitals shapes.
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Cabrera N, Mora JR, Márquez E, Flores-Morales V, Calle L, Cortés E. QSAR and molecular docking modelling of anti-leishmanial activities of organic selenium and tellurium compounds. SAR QSAR Environ Res 2021; 32:29-50. [PMID: 33241943 DOI: 10.1080/1062936x.2020.1848914] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Leishmaniasis affects mainly rural areas and the poorest people in the world. A computational study of the antileishmanial activity of organic selenium and tellurium compounds was performed. The 3D structures of the compounds were optimized at the wb97xd/lanl2dz level and used in the quantitative structure-activity relationship (QSAR) analysis. The antileishmanial activity was measured by L. donovani β carbonic anhydrase inhibition (Ki) and the half-maximal inhibitory concentration (IC50) against L. infantum amastigotes. The dataset was divided into training (75%) and test sets (25%) by using a k-means clustering algorithm. For pKi prediction, model M3 with seven 3D topographic descriptors was characterized by the following statistical parameters: r 2 = 0.879, Q 2 LOO = 0.822, and Q 2 ext = 0.840. For pIC50 prediction, model M12 with six attributes was characterized by the following statistical parameters: r 2 = 0.907, Q 2 LOO = 0.824, and Q 2 ext = 0.795. Both models met all the requirements of Tropsha´s test, which implies predictions of pIC50 and pKi activities with high accuracy. Concomitantly, favourable interactions of the sulphonamide group with the Zn atom in the protein were revealed by the docking analysis.
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Affiliation(s)
- N Cabrera
- Department of Biomedical Engineering, Texas A&M University , College Station, TX, USA
| | - J R Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito , Quito, Ecuador
| | - E Márquez
- Grupo de Investigaciones en Química y Biología, Departamento de Química y Biología, Facultad de Ciencias Exactas, Universidad del Norte , Barranquilla, Colombia
| | - V Flores-Morales
- Laboratorio de Síntesis Asimétrica y Bioenergética (LSAyB), Ingeniería Química (UACQ), Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Universidad Autónoma de Zacatecas , Zacatecas, Mexico
| | - L Calle
- Instituto de Investigación e Innovación en Salud Integral (ISAIN), Facultad de Ciencias Medicas, Universidad Católica Santiago de Guayaquil , Guayaquil, Ecuador
| | - E Cortés
- Grupo de Investigación en Ciencias Naturales y Exactas, Departamento de Ciencias Naturales y Exactas, Universidad de la Costa , Barranquilla, Colombia
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García S, Mercado-Sánchez I, Bahena L, Alcaraz Y, García-Revilla MA, Robles J, Santos-Martínez N, Ordaz-Rosado D, García-Becerra R, Vazquez MA. Design of Fluorescent Coumarin-Hydroxamic Acid Derivatives as Inhibitors of HDACs: Synthesis, Anti-Proliferative Evaluation and Docking Studies. Molecules 2020; 25:molecules25215134. [PMID: 33158250 PMCID: PMC7662212 DOI: 10.3390/molecules25215134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 01/02/2023] Open
Abstract
Coumarin-hydroxamic acid derivatives 7a-k were herein designed with a dual purpose: as antiproliferative agents and fluorescent probes. The compounds were synthesized in moderate yields (30-87%) through a simple methodology, biological evaluation was carried out on prostate (PC3) and breast cancer (BT-474 and MDA-MB-231) cell lines to determine the effects on cell proliferation and gene expression. For compounds 7c, 7e, 7f, 7i and 7j the inhibition of cancer cell proliferation was similar to that found with the reference compound at a comparable concentration (10 μM), in addition, their molecular docking studies performed on histone deacetylases 1, 6 and 8 showed strong binding to the respective active sites. In most cases, antiproliferative activity was accompanied by greater levels of cyclin-dependent kinase inhibitor p21, downregulation of the p53 tumor suppressor gene, and regulation of cyclin D1 gene expression. We conclude that compounds 7c, 7e, 7f, 7i and 7j may be considered as potential anticancer agents, considering their antiproliferative properties, their effect on the regulation of the genes, as well as their capacity to dock to the active sites. The fluorescent properties of compound 7j and 7k suggest that they can provide further insight into the mechanism of action.
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Affiliation(s)
- Santiago García
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
| | - Itzel Mercado-Sánchez
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
| | - Luis Bahena
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
| | - Yolanda Alcaraz
- Departamento de Farmacia, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (Y.A.); (J.R.)
| | - Marco A. García-Revilla
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
| | - Juvencio Robles
- Departamento de Farmacia, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (Y.A.); (J.R.)
| | - Nancy Santos-Martínez
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (N.S.-M.); (D.O.-R.)
| | - David Ordaz-Rosado
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (N.S.-M.); (D.O.-R.)
| | - Rocío García-Becerra
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Miguel A. Vazquez
- Departamento de Química, Universidad de Guanajuato, Guanajuato, Gto. 36050, Mexico; (S.G.); (I.M.-S.); (L.B.); (M.A.G.-R.)
- Correspondence: ; Tel.: +52-473-732-0006 (ext. 1419)
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Jeong GS, Kaipakasseri S, Lee SR, Marraiki N, Batiha GES, Dev S, Palakkathondi A, Kavully FS, Gambacorta N, Nicolotti O, Mathew B, Kim H. Selected 1,3-Benzodioxine-Containing Chalcones as Multipotent Oxidase and Acetylcholinesterase Inhibitors. ChemMedChem 2020; 15:2257-2263. [PMID: 32924264 DOI: 10.1002/cmdc.202000491] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/18/2020] [Indexed: 01/01/2023]
Abstract
Chalcones are considered effective templates for the development of monoamine oxidase (MAO) and cholinesterase (ChE) inhibitors. The present work describes the syntheses of selected 1,3-benzodioxine-containing chalcones (CD3, CD8 and CD10), and their inhibitory activities against MAO-A, MAO-B, acetylcholinesterase (AChE), and butyrylcholinesterase (BChE). Compound CD8 most potently inhibited MAO-B with an IC50 value of 0.026 μM, followed by CD10 and CD3 (1.54 and 1.68 μM, respectively). CD8 potently and non-selectively inhibited MAO-A (IC50 value of 0.023 μM). On the other hand, CD10 and CD8 inhibited AChE with IC50 values of 5.40 and 9.57 μM, respectively. Kinetics and reversibility experiments showed that all synthesized molecules were competitive and reversible inhibitors, and the Ki values of CD8 for MAO-A and MAO-B were 0.018 and 0.0019 μM, respectively. By in vitro and in silico analyses, all compounds were found to have high passive human gastrointestinal absorptions, blood-brain barrier permeabilities, and non-toxicities. Molecular docking simulations revealed that docking affinity of each compound for MAO-B was higher than that for MAO-A. The results indicate that CD8 is a potent non-selective MAO inhibitor, and CD10 is an effective selective MAO-B inhibitor, and both possess AChE inhibitory activity. Therefore, we suggest that CD8 and CD10 be considered potential dual-targeting inhibitors of MAO and AChE for the treatment of various neurodegenerative disorders.
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Affiliation(s)
- Geum Seok Jeong
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Swafvan Kaipakasseri
- Department of Pharmaceutical Chemistry, Al-Shifa College of Pharmacy, Perinthalmanna, India
| | - Sang Ryong Lee
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Najat Marraiki
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, Al-Beheira, Egypt
| | - Sanal Dev
- Department of Pharmaceutical Chemistry, Al-Shifa College of Pharmacy, Perinthalmanna, India
| | - Ashique Palakkathondi
- Department of Pharmaceutical Chemistry, Al-Shifa College of Pharmacy, Perinthalmanna, India
| | - Fathima Sahla Kavully
- Department of Pharmaceutical Chemistry, Al-Shifa College of Pharmacy, Perinthalmanna, India
| | - Nicola Gambacorta
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via E. Orabona, 4, 70125, Bari, Italy
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via E. Orabona, 4, 70125, Bari, Italy
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi-682 041, Kerala, India
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea
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Xia L, Zhang Y, Zhang J, Lin S, Zhang K, Tian H, Dong Y, Xu H. Identification of Novel Thiazolo[5,4- b]Pyridine Derivatives as Potent Phosphoinositide 3-Kinase Inhibitors. Molecules 2020; 25:E4630. [PMID: 33053730 DOI: 10.3390/molecules25204630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 11/25/2022] Open
Abstract
A series of novel 2-pyridyl, 4-morpholinyl substituted thiazolo[5,4-b]pyridine analogues have been designed and synthesized in this paper. These thiazolo[5,4-b]pyridines were efficiently prepared in seven steps from commercially available substances in moderate to good yields. All of these N-heterocyclic compounds were characterized by nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS) analysis and tested for phosphoinositide 3-kinase (PI3K) enzymatic assay. The results indicated that these N-heterocyclic compounds showed potent PI3K inhibitory activity, and the IC50 of a representative compound (19a) could reach to 3.6 nm. The structure−activity relationships (SAR) study showed that sulfonamide functionality was important for PI3Kα inhibitory activity, and 2-chloro-4-florophenyl sulfonamide (19b), or 5-chlorothiophene-2-sulfonamide (19c) showed potent inhibitory activity with a nanomolar IC50 value. The pyridyl attached to thiazolo[5,4-b]pyridine was another key structural unit for PI3Kα inhibitory potency, and replacement by phenyl lead to a significant decrease in activity. Enzymatic Inhibition results showed that compound 19a inhibited PI3Kα, PI3Kγ, or PI3Kδ with a nanomolar IC50 value, but its inhibitory activity on PI3Kβ was approximately 10-fold reduced. Further docking analysis revealed that the N-heterocyclic core of compound 19a was directly involved in the binding to the kinase through the key hydrogen bonds interaction.
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26
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Alsamghan AS, Alwabli AS, Abadi M, Alsaleem SA, Anbari DM, Alomari AS, Alzahrani O, Alam Q, Tarique M. From sequence analysis of DPP-4 to molecular docking based searching of its inhibitors. Bioinformation 2020; 16:444-451. [PMID: 32884207 PMCID: PMC7452749 DOI: 10.6026/97320630016444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/19/2020] [Accepted: 05/07/2020] [Indexed: 11/23/2022] Open
Abstract
Literature data suggests that Dipeptidyl peptidase-4 (DPP-4) is a potential target for type 2 Diabetes Mellitus. Therefore, it is of interest to identify new DPP-4 inhibitors using molecular docking analysis. We document compounds such as STOCK1N-98884, STOCK1N-98881, and STOCK1N-98866 with optimal binding features with DPP-4 from the ligand database at https://www.ibscreen.com/ for further consideration.
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Affiliation(s)
- Awad Saeed Alsamghan
- Department of Family and Community Medicine, College of Medicine, King Khalid University, Abha, KSA-61421
| | - Afaf S Alwabli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| | - Mohammed Abadi
- Department of Family and Community Medicine, College of Medicine, King Khalid University, Abha, KSA-61421
| | - Safar A Alsaleem
- Department of Family and Community Medicine, College of Medicine, King Khalid University, Abha, KSA-61421
| | - Dalia Mohammed Anbari
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| | - Amani Saleh Alomari
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| | - Othman Alzahrani
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
- Genome and Biotechnology Unit, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Tarique
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India
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Faber SC, Giani Tagliabue S, Bonati L, Denison MS. The Cellular and Molecular Determinants of Naphthoquinone-Dependent Activation of the Aryl Hydrocarbon Receptor. Int J Mol Sci 2020; 21:ijms21114111. [PMID: 32526934 PMCID: PMC7312509 DOI: 10.3390/ijms21114111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 12/30/2022] Open
Abstract
1,2-naphthoquinone (1,2-NQ) and 1,4-naphthoquinone (1,4-NQ) are clinically promising biologically active chemicals that have been shown to stimulate the aryl hydrocarbon receptor (AhR) signaling pathway, but whether they are direct or indirect ligands or activate the AhR in a ligand-independent manner is unknown. Given the structural diversity of AhR ligands, multiple mechanisms of AhR activation of gene expression, and species differences in AhR ligand binding and response, we examined the ability of 1,2-NQ and 1,4-NQ to bind to and activate the mouse and human AhRs using a series of in vitro AhR-specific bioassays and in silico modeling techniques. Both NQs induced AhR-dependent gene expression in mouse and human hepatoma cells, but were more potent and efficacious in human cells. 1,2-NQ and 1,4-NQ stimulated AhR transformation and DNA binding in vitro and was inhibited by AhR antagonists. Ligand binding analysis confirmed the ability of 1,2-NQ and 1,4-NQ to competitively bind to the AhR ligand binding cavity and the molecular determinants for interactions were predicted by molecular modeling methods. NQs were shown to bind distinctly differently from that of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and differences were also observed between species. Mutation of amino acid residues (F289, M334, and M342) involved in critical NQ:AhR binding interactions, decreased NQ- and AhR-dependent gene expression, consistent with a role for these residues in binding and activation of the AhR by NQs. These studies provide insights into the molecular mechanism of action of NQs and contribute to the development of emerging NQ-based therapeutics.
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Affiliation(s)
- Samantha C. Faber
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA;
| | - Sara Giani Tagliabue
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, 20126 Milan, Italy; (S.G.T.); (L.B.)
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, 20126 Milan, Italy; (S.G.T.); (L.B.)
| | - Michael S. Denison
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-(530)-752-3879
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Han J, Ji Y, Youn K, Lim G, Lee J, Kim DH, Jun M. Baicalein as a Potential Inhibitor against BACE1 and AChE: Mechanistic Comprehension through In Vitro and Computational Approaches. Nutrients 2019; 11:E2694. [PMID: 31703329 PMCID: PMC6893645 DOI: 10.3390/nu11112694] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022] Open
Abstract
One of the major neurodegenerative features of Alzheimer's disease (AD) is the presence of neurotoxic amyloid plaques composed of amyloid beta peptide (Aβ). β-Secretase (BACE1) and acetylcholinesterase (AChE), which promote Aβ fibril formation, have become attractive therapeutic targets for AD. P-glycoprotein (P-gp), the major efflux pump of the blood-brain barrier (BBB), plays a critical role in limiting therapeutic molecules. In pursuit of discovering a natural anti-AD candidate, the bioactivity, physicochemical, drug-likeness, and molecular docking properties of baicalein, a major compound from Scutellaria baicalensis, was investigated. Baicalein exhibited strong BACE1 and AChE inhibitory properties (IC50 23.71 ± 1.91 µM and 45.95 ± 3.44 µM, respectively) and reacted in non-competitive and competitive manners with substrates, respectively. in Silico docking analysis was in full agreement with the in vitro results, demonstrating that the compound exhibited powerful binding interaction with target enzymes. Particularly, three continuous hydroxyl groups on the A ring demonstrated strong H-bond binding properties. It is also noteworthy that baicalein complied with all requirements of Lipinski's rule of five by its optimal physicochemical properties for both oral bioavailability and blood-brain barrier permeability. Overall, the present study strongly demonstrated the possibility of baicalein having in vivo pharmacological efficacy for specific targets in the prevention and/or treatment of AD.
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Affiliation(s)
- Jin Han
- Department of Food Science and Nutrition, College of Health Sciences, Dong-A University, Busan 49315, Korea; (J.H.); (Y.J.); (K.Y.)
- Center for Silver-Targeted Biomaterials, Brain Busan 21 Plus Program, Graduate School, Dong-A University, Busan 49315, Korea
| | - Yeongseon Ji
- Department of Food Science and Nutrition, College of Health Sciences, Dong-A University, Busan 49315, Korea; (J.H.); (Y.J.); (K.Y.)
- Center for Silver-Targeted Biomaterials, Brain Busan 21 Plus Program, Graduate School, Dong-A University, Busan 49315, Korea
| | - Kumju Youn
- Department of Food Science and Nutrition, College of Health Sciences, Dong-A University, Busan 49315, Korea; (J.H.); (Y.J.); (K.Y.)
| | - GyuTae Lim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (G.L.); (J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Sciences and Technology, Daejeon 34113, Korea
| | - Jinhyuk Lee
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (G.L.); (J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Sciences and Technology, Daejeon 34113, Korea
| | - Dong Hyun Kim
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Korea;
- Institute of Convergence Bio-Health, Dong-A University, Busan 49315, Korea
| | - Mira Jun
- Department of Food Science and Nutrition, College of Health Sciences, Dong-A University, Busan 49315, Korea; (J.H.); (Y.J.); (K.Y.)
- Center for Silver-Targeted Biomaterials, Brain Busan 21 Plus Program, Graduate School, Dong-A University, Busan 49315, Korea
- Institute of Convergence Bio-Health, Dong-A University, Busan 49315, Korea
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Sakle NS, More SA, Dhawale SA, Mokale SN. Targeting Small Molecule Tyrosine Kinases by Polyphenols: New Move Towards Anti-tumor Drug Discovery. Curr Drug Discov Technol 2019; 17:585-615. [PMID: 31393251 DOI: 10.2174/1570163816666190808120843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/10/2019] [Accepted: 07/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cancer is a complex disease involving genetic and epigenetic alteration that allows cells to escape normal homeostasis. Kinases play a crucial role in signaling pathways that regulate cell functions. Deregulation of kinases leads to a variety of pathological changes, activating cancer cell proliferation and metastases. The molecular mechanism of cancer is complex and the dysregulation of tyrosine kinases like Anaplastic Lymphoma Kinase (ALK), Bcr-Abl (Fusion gene found in patient with Chronic Myelogenous Leukemia (CML), JAK (Janus Activated Kinase), Src Family Kinases (SFKs), ALK (Anaplastic lymphoma Kinase), c-MET (Mesenchymal- Epithelial Transition), EGFR (Epidermal Growth Factor receptor), PDGFR (Platelet-Derived Growth Factor Receptor), RET (Rearranged during Transfection) and VEGFR (Vascular Endothelial Growth Factor Receptor) plays major role in the process of carcinogenesis. Recently, kinase inhibitors have overcome many problems of traditional cancer chemotherapy as they effectively separate out normal, non-cancer cells as well as rapidly multiplying cancer cells. METHODS Electronic databases were searched to explore the small molecule tyrosine kinases by polyphenols with the help of docking study (Glide-7.6 program interfaced with Maestro-v11.3 of Schrödinger 2017) to show the binding energies of polyphenols inhibitor with different tyrosine kinases in order to differentiate between the targets. RESULTS From the literature survey, it was observed that the number of polyphenols derived from natural sources alters the expression and signaling cascade of tyrosine kinase in various tumor models. Therefore, the development of polyphenols as a tyrosine kinase inhibitor against targeted proteins is regarded as an upcoming trend for chemoprevention. CONCLUSION In this review, we have discussed the role of polyphenols as chemoreceptive which will help in future for the development and discovery of novel semisynthetic anticancer agents coupled with polyphenols.
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Affiliation(s)
- Nikhil S Sakle
- Dr. Rafiq Zakaria Campus, Y. B. Chavan College of Pharmacy, Aurangabad-431001, Maharashtra, India
| | - Shweta A More
- Dr. Rafiq Zakaria Campus, Y. B. Chavan College of Pharmacy, Aurangabad-431001, Maharashtra, India
| | - Sachin A Dhawale
- Dr. Rafiq Zakaria Campus, Y. B. Chavan College of Pharmacy, Aurangabad-431001, Maharashtra, India
| | - Santosh N Mokale
- Dr. Rafiq Zakaria Campus, Y. B. Chavan College of Pharmacy, Aurangabad-431001, Maharashtra, India
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Palanisamy CP, Ashafa AOT. Screening of Potential Phytocompounds From Euclea crispa (Thunb.) Leaves Targeting Human Epidermal Growth Factor Receptor 2 (HER2) Signaling Pathway. J Pharm Bioallied Sci 2019; 11:155-161. [PMID: 31148892 PMCID: PMC6537645 DOI: 10.4103/jpbs.jpbs_61_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background: Overexpression of human epidermal growth factor receptor 2 (HER2) plays an important role in the development and progression in a variety of cancers and it is a novel therapeutic target for breast cancer and ovarian cancer. Euclea crispa (E. crispa) is a South African medicinal plant in the family Ebenaceae used in the management of different human diseases and disorders. Aims: The aim of this study was to evaluate the potential inhibitors against HER2 from hexane extract of E. crispa leaves. Materials and Methods: Chemical fingerprinting method was used to identify the presence of natural compounds from the extract whereas their inhibitory activities were analyzed by molecular docking analysis against HER2. Absorption, distribution, metabolism, and excretion (ADME) properties also predicted to establish the pharmacokinetics and pharmacodynamics profiles of the selected compounds. Results: The molecular docking analysis expressed that phenyl glucuronide, hydrocortisone acetate, and 6-(4,6-dioxo-1,4,5,6-tetrahydropyrimidin-2-yl-amino)hexanoic acid trifluoroacetate possess good inhibitory activities with good glide score of −6.63, −5.41, and −5.40 and glide energy of −35.03, −42.51, and −31.38 kcal/mol, respectively when compared with standard Food and Drug Administration–approved drug and other compounds. All the screened compounds were within the acceptable and permissible limits of ADME properties. Conclusion: Thus, from this study it can be concluded that, these screened natural compounds from E. crispa leaves may serve as potential inhibitors for HER2 and they might lead to development of new therapeutic agents against cancer and its associated complications.
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Affiliation(s)
- Chella Perumal Palanisamy
- Phytomedicine and Phytopharmacology Research Group, Department of Plant Sciences, University of the Free State, Qwaqwa Campus, Phuthaditjhaba, South Africa
| | - Anofi Omotayo Tom Ashafa
- Phytomedicine and Phytopharmacology Research Group, Department of Plant Sciences, University of the Free State, Qwaqwa Campus, Phuthaditjhaba, South Africa
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Zhang Y, Lu T, Wang Y, Diao C, Zhou Y, Zhao L, Chen H. Selection of a DNA Aptamer against Zearalenone and Docking Analysis for Highly Sensitive Rapid Visual Detection with Label-Free Aptasensor. J Agric Food Chem 2018; 66:12102-12110. [PMID: 30346760 DOI: 10.1021/acs.jafc.8b03963] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Contamination of feed with zearalenone (ZEN) presents a significant risk to animal health. Here, a visible, rapid, and cost-effective aptamer-based method is described for the detection of ZEN. After 8 rounds of SELEX (systematic evolution of ligands by exponential enrichment) with an affinity-based monitor and counter-screening process, the ssDNA aptamer Z100 was obtained, which had high affinity (dissociation constant = 15.2 ± 3.4 nM) and good specificity. Docking analysis of Z100 indicated that noncovalent bonds (π-π interactions, hydrogen bonds, and hydrophobic interactions) helped ZEN to anchor in the binding sites. Finally, a label-free detection method based on gold nanoparticles and Z100 at 0.25 μM was developed for ZEN determination. Excellent linearity was achieved, and the lowest detection limit was 12.5 nM. This rapid and simple method for ZEN analysis has high sensitivity and can be applied for on-site detection of ZEN in animal feeds.
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Affiliation(s)
- Yuanyuan Zhang
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Harbin 150069 , China
| | - Taofeng Lu
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Harbin 150069 , China
| | - Yue Wang
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Harbin 150069 , China
| | - Chenxi Diao
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Harbin 150069 , China
| | - Yan Zhou
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Harbin 150069 , China
| | - Lili Zhao
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Harbin 150069 , China
| | - Hongyan Chen
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute , Chinese Academy of Agricultural Sciences , Harbin 150069 , China
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Balasubramanian N, Varatharaju G, Shanmugaiah V, Balakrishnan K, Thirunarayan MA. Molecular Cloning and Docking of speB Gene Encoding Cysteine Protease With Antibiotic Interaction in Streptococcus pyogenes NBMKU12 From the Clinical Isolates. Front Microbiol 2018; 9:1658. [PMID: 30131773 PMCID: PMC6091236 DOI: 10.3389/fmicb.2018.01658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pyogenes causes a variety of diseases ranging from mild diseases to severe invasive infections which result in significant morbidity and mortality. This study focuses on the antibiotic resistance of S. pyogenes and their interaction with cysteine protease. Around 36 beta-hemolytic isolates were collected from the clinical lab, of which seven isolates (19.4%) were identified as Streptococcus pyogenes. One of the seven isolates was collected from a urinary tract infection, which was identified by antibody agglutination and MALTI-TOF-MS, and it is designated as S. pyogenes NBMKU12. Around 8.3 to 66.6 % of the isolates were found to be resistant to one or more antimicrobial agents, especially, penicillin-G resistance was exhibited by 29.1% of the isolates. In the NBMKU12 isolate, the beta lactem (TEM) gene was detected among the 13 antibiotic genes for which it was tested. Furthermore, when analysis for presence of 13 virulence genes were carried out in NBMKU12 isolate, only speJ and speB were detected. The speB (streptococcal pyrogenic exotoxin B) encoding cysteine protease gene was cloned. This was followed by performing DNA sequencing to understand the putative cysteine protease interaction with antibiotics, inhibitors, and substrate. The speB gene consists of 1197 nucleotides and encodes a protein with multiple domains, including a signal peptide (aa 1-22), an inhibitor region (aa 27-156), and a catalytic cysteine domain (aa 160-367). The signal peptide cleavage site is predicted between Ala22 and Asn23. The putative 398 amino acid residues were found to have a theoretical pI of 8.76 and a molecular mass of 43,204.36 Da. The tested culture supernatants of NBMKU12 isolate exhibited the proteolytic activity against casein, papaya and pineapple used as substrates. The proteolytic activity suggests the expression of speB gene. Molecular docking analysis of cysteine protease showed that erythromycin (bond length 2.41 Å), followed by chloramphenicol (2.51 Å), exhibited a strong interaction; while penicillin-G (3.24 Å) exhibited a weak interaction, and this factor could be considered as a cause for penicillin-G resistance. The present study contributes to a better understanding of speB gene encoding cysteine protease, antibiotic resistance, and their interaction in the isolate, S. pyogenes NBMKU12. The antibiotics and cysteine protease interaction study confirms the resistance or sensitivity of S. pyogenes. Hence, it could be hypothesized that the isolate NBMKU12 is resistant to most of the tested antibiotics, and this resistance might be a cause for mutation.
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Affiliation(s)
- Natesan Balasubramanian
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Govintharaj Varatharaju
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Vellasamy Shanmugaiah
- Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Karuppiah Balakrishnan
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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Liu J, Chen Y, Li JY, Luo C, Li J, Chen KX, Li XW, Guo YW. Function-Oriented Synthesis of Marine Phidianidine Derivatives as Potential PTP1B Inhibitors with Specific Selectivity. Mar Drugs 2018; 16:md16030097. [PMID: 29558377 PMCID: PMC5867641 DOI: 10.3390/md16030097] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 02/07/2023] Open
Abstract
Phidianidines A and B are two novel marine indole alkaloids bearing an uncommon 1,2,4-oxadiazole ring and exhibiting various biological activities. Our previous research showed that the synthesized phidianidine analogs had the potential to inhibit the activity of protein tyrosine phosphatase 1B (PTP1B), a validated target for Type II diabetes, which indicates that these analogs are worth further structural modification. Therefore, in this paper, a series of phidianidine derivatives were designed and rapidly synthesized with a function-oriented synthesis (FOS) strategy. Their inhibitory effects on PTP1B and T-cell protein tyrosine phosphatase (TCPTP) were evaluated, and several compounds displayed significant inhibitory potency and specific selectivity over PTP1B. The structure–activity relationship (SAR) and molecular docking analyses are also described.
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Affiliation(s)
- Jin Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.
- Nano Science and Technology Institute, University of Science and Technology of China, 166 Ren Ai Road, Suzhou 215123, China.
| | - Yu Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.
| | - Jing-Ya Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.
- Open Studio for Druggability Research of Marine Natural Products, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.
- Open Studio for Druggability Research of Marine Natural Products, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China.
| | - Kai-Xian Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.
- Open Studio for Druggability Research of Marine Natural Products, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China.
| | - Xu-Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.
- Open Studio for Druggability Research of Marine Natural Products, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China.
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.
- Open Studio for Druggability Research of Marine Natural Products, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China.
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Ganou CA, Eleftheriou PT, Theodosis-Nobelos P, Fesatidou M, Geronikaki AA, Lialiaris T, Rekka EA. Docking analysis targeted to the whole enzyme: an application to the prediction of inhibition of PTP1B by thiomorpholine and thiazolyl derivatives. SAR QSAR Environ Res 2018; 29:133-149. [PMID: 29347844 DOI: 10.1080/1062936x.2017.1414874] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
PTP1b is a protein tyrosine phosphatase involved in the inactivation of insulin receptor. Since inhibition of PTP1b may prolong the action of the receptor, PTP1b has become a drug target for the treatment of type II diabetes. In the present study, prediction of inhibition using docking analysis targeted specifically to the active or allosteric site was performed on 87 compounds structurally belonging to 10 different groups. Two groups, consisting of 15 thiomorpholine and 10 thiazolyl derivatives exhibiting the best prediction results, were selected for in vitro evaluation. All thiomorpholines showed inhibitory action (with IC50 = 4-45 μΜ, Ki = 2-23 μM), while only three thiazolyl derivatives showed low inhibition (best IC50 = 18 μΜ, Ki = 9 μΜ). However, free binding energy (E) was in accordance with the IC50 values only for some compounds. Docking analysis targeted to the whole enzyme revealed that the compounds exhibiting IC50 values higher than expected could bind to other peripheral sites with lower free energy, Eo, than when bound to the active/allosteric site. A prediction factor, E- (ΣEo × 0.16), which takes into account lower energy binding to peripheral sites, was proposed and was found to correlate well with the IC50 values following an asymmetrical sigmoidal equation with r2 = 0.9692.
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Affiliation(s)
- C A Ganou
- a Department of Medical Laboratory Studies, School of Health and Medical Care , Alexander Technological Educational Institute of Thessaloniki , Thessaloniki , Greece
| | - P Th Eleftheriou
- a Department of Medical Laboratory Studies, School of Health and Medical Care , Alexander Technological Educational Institute of Thessaloniki , Thessaloniki , Greece
| | - P Theodosis-Nobelos
- b Department of Medicinal Chemistry, School of Pharmacy , Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - M Fesatidou
- b Department of Medicinal Chemistry, School of Pharmacy , Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - A A Geronikaki
- b Department of Medicinal Chemistry, School of Pharmacy , Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - T Lialiaris
- c School of Medicine , Democritus University of Thrace , Alexandroupolis , Greece
| | - E A Rekka
- b Department of Medicinal Chemistry, School of Pharmacy , Aristotle University of Thessaloniki , Thessaloniki , Greece
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Kouatly O, Eleftheriou P, Petrou A, Hadjipavlou-Litina D, Geronikaki A. Docking assisted design of novel 4-adamantanyl-2-thiazolylimino-5-arylidene-4-thiazolidinones as potent NSAIDs. SAR QSAR Environ Res 2018; 29:83-101. [PMID: 29299942 DOI: 10.1080/1062936x.2017.1410220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/23/2017] [Indexed: 06/07/2023]
Abstract
Docking analysis was used to predict the effectiveness of adamantanyl insertion in improving cycloxygenase/lipoxygenase (COX/LOX) inhibitory action of previously tested 2-thiazolylimino-5-arylidene-4-thiazolidinones. The crystal structure data of human 5-LOX (3O8Y), ovine COX-1 (1EQH) and mouse COX-2 (3ln1) were used for docking analysis. All docking calculations were carried out using AutoDock 4.2 software. Following prediction results, 11 adamantanyl derivatives were synthesized and evaluated for biological action. Prediction evaluations correlated well with experimental biological results. Comparison of the novel adamantanyl derivatives with the 2-thiazolylimino-5-arylidene-4-thiazolidinones previously tested showed that insertion of the adamantanyl group led to the production of more potent COX-1 inhibitors, as well as LOX inhibitors (increased activity from 200% to 560%). Five compounds out of the 11 exhibited better activity than naproxen; while nine out of 11 showed better activity than NDGA and seven compounds possessed better anti-inflammatory activity than indomethacin.
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Affiliation(s)
- O Kouatly
- a Department of Pharmaceutical Chemistry, School of Pharmacy , Aristotle University of Thessaloniki , Greece
| | - Ph Eleftheriou
- b Department of Medical Laboratories, School of Health and Care Professions , Alexandrion Technological Educational Institute of Thessaloniki , Greece
| | - A Petrou
- a Department of Pharmaceutical Chemistry, School of Pharmacy , Aristotle University of Thessaloniki , Greece
| | - D Hadjipavlou-Litina
- a Department of Pharmaceutical Chemistry, School of Pharmacy , Aristotle University of Thessaloniki , Greece
| | - A Geronikaki
- a Department of Pharmaceutical Chemistry, School of Pharmacy , Aristotle University of Thessaloniki , Greece
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Zhang J, Wang XJ, Liu X, Huan Y, Yang MM, Shen ZF, Jia WQ, Jing Z, Wang SQ, Xu WR, Cheng XC, Wang RL. Design, sythesis and evaluation of a series of 3- or 4-alkoxy substituted phenoxy derivatives as PPARs agonists. Oncotarget 2017; 8:20766-83. [PMID: 28186999 DOI: 10.18632/oncotarget.15198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/25/2017] [Indexed: 11/25/2022] Open
Abstract
Peroxisome proliferators-activated receptors (PPARα, γ and δ) are potentially effective targets for Type 2 diabetes mellitus therapy. The severe effects of known glitazones and the successfully approved agents (saroglitazar and lobeglitazone) motivated us to study novelly potent PPARs drugs with improved safety profile. In this work, we received 15 carboxylic acids based on the combination principle to integrate the polar head of bezafibrate with the hydrophobic tail of pioglitazone. Another 12 tetrazoles based on the bioisosterism principle were obtained accordingly. Furthermore, in vitro PPARs transactivation assays on these 3- or 4-alkoxy substituted phenoxy derivatives afforded six compounds. Interactions and binding stability from the docking analysis and 20 ns molecular dynamic simulations confirmed the representative compounds to be suitable and plausible for PPARs pockets. The above-mentioned results demonstrated that the compounds may be used as reference for further optimization for enhanced PPARs activities and wide safety range.
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Sawaguchi Y, Yamazaki R, Nishiyama Y, Sasai T, Mae M, Abe A, Yaegashi T, Nishiyama H, Matsuzaki T. Rational Design of a Potent Pan-Pim Kinases Inhibitor with a Rhodanine-Benzoimidazole Structure. Anticancer Res 2017; 37:4051-4057. [PMID: 28739687 DOI: 10.21873/anticanres.11790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM The serine/threonine Pim kinases are overexpressed in various types of solid carcinomas and hematological malignancies, and contribute to regulating cell-cycle progression and cell survival. The aim of this study was to discover a novel pan-Pim kinases inhibitor with potent anti-proliferative activities against cancer cell lines. MATERIALS AND METHODS We screened a panel of small molecule compounds for their ability to inhibit Pim-1 kinase activity, and the hit compound was optimized using the docking analysis to Pim-1. We evaluated kinase-inhibition activities of the rationally-designed compound against Pim-1, 2, 3 and another five kinases. Furthermore, in order to characterize the cellular activities, both solid and hematological cancer cell lines treated with the compound were subjected to anti-proliferative assay, western blotting, FACS and apoptosis assays. RESULTS We discovered a pan-Pim kinases inhibitor, compound 1, with a rhodanine-benzylidene structure via Pim-1 inhibitor screening. Using docking analysis of compound 1 and Pim-1, we optimized it and found a potent- and selective-Pim kinases inhibitor, compound 2, with a rhodanine-benzoimidazole structure. Compound 2 inhibited Pim-1, 2, 3 with IC50 values of 16, 13, and 6.4 nM, respectively, and suppressed proliferation of solid and hematological cancer cell lines at submicromolar concentrations. In both types of cell lines, compound 2 inhibited phosphorylation of Pim signaling substrates and cell-cycle progression and induced apoptosis. CONCLUSION We identified a pan-Pim kinases inhibitor, compound 2, with a rhodanine-benzoimidazole structure. Our data suggest that compound 2 can serve as a lead to novel anticancer agents, effective in the treatment of both solid carcinomas and hematological malignancies.
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Affiliation(s)
| | - Ryuta Yamazaki
- Yakult Central Institute, Yakult Honsha Co., Ltd., Tokyo, Japan
| | | | - Toshio Sasai
- Yakult Central Institute, Yakult Honsha Co., Ltd., Tokyo, Japan
| | - Masayuki Mae
- Yakult Central Institute, Yakult Honsha Co., Ltd., Tokyo, Japan
| | - Atsuhiro Abe
- Yakult Central Institute, Yakult Honsha Co., Ltd., Tokyo, Japan
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Rani RP, Anandharaj M, Ravindran AD. Characterization of Bile Salt Hydrolase from Lactobacillus gasseri FR4 and Demonstration of Its Substrate Specificity and Inhibitory Mechanism Using Molecular Docking Analysis. Front Microbiol 2017; 8:1004. [PMID: 28620369 PMCID: PMC5449720 DOI: 10.3389/fmicb.2017.01004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/19/2017] [Indexed: 01/19/2023] Open
Abstract
Probiotic bacteria are beneficial to the health of poultry animals, thus are used as alternative candidates for antibiotics used as growth promoters (AGPs). However, they also reduce the body weight gain due to innate bile salt hydrolase (BSH) activity. Hence, the addition of a suitable BSH inhibitor along with the probiotic feed can decrease the BSH activity. In this study, a BSH gene (981 bp) encoding 326-amino acids was identified from the genome of Lactobacillus gasseri FR4 (LgBSH). The LgBSH-encoding gene was cloned and purified using an Escherichia coli BL21 (DE3) expression system, and its molecular weight (37 kDa) was confirmed by SDS-PAGE and a Western blot analysis. LgBSH exhibited greater hydrolysis toward glyco-conjugated bile salts compared to tauro-conjugated bile salts. LgBSH displayed optimal activity at 52°C at a pH of 5.5, and activity was further increased by several reducing agents (DTT), surfactants (Triton X-100 and Tween 80), and organic solvents (isopropanol, butanol, and acetone). Riboflavin and penicillin V, respectively, inhibited LgBSH activity by 98.31 and 97.84%. A homology model of LgBSH was predicted using EfBSH (4WL3) as a template. Molecular docking analysis revealed that the glycocholic acid had lowest binding energy of -8.46 kcal/mol; on the other hand, inhibitors, i.e., riboflavin and penicillin V, had relatively higher binding energies of -6.25 and -7.38 kcal/mol, respectively. Our results suggest that L. gasseri FR4 along with riboflavin might be a potential alternative to AGPs for poultry animals.
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Affiliation(s)
- Rizwana Parveen Rani
- Department of Biology, The Gandhigram Rural Institute - Deemed UniversityGandhigram, India
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Ge HQ, Wan GS, Wang D, Wu JM, Sun BH, Wu LJ, Gao HY. Two new isoxazolines from the husks of Xanthoceras sorbifolia Bunge. J Asian Nat Prod Res 2016; 18:744-751. [PMID: 27053149 DOI: 10.1080/10286020.2016.1167045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 03/14/2016] [Indexed: 06/05/2023]
Abstract
Two new isoxazoline compounds, 1-oxa-2-azaspiro[4.5]dec-2-ene-8β-ol (1) and 1-oxa-2-azaspiro[4.5]dec-2-ene-8α-ol (2), were isolated from the husks of fruits of Xanthoceras sorbifolia Bunge and their structures were determined by spectroscopic analyses, including X-ray crystallography, HRESI-MS, UV, IR, and 1D and 2D NMR (HSQC, HMBC, NOESY) methods. Neither compound showed significant inhibitory effects on butyrylcholinesterase (BuchE) and acetylcholinesterase (AChE), nor the selected tumor cells growth. Based on an online activity prediction program (PASS ONLINE), the structures with isoxazoline skeletons were found to show potential anti-asthmatic (AM) and anti-anaphylaxis (AP) activities; moreover, compounds 1 and 2 were predicted to possess high affinities for many enzymes involved in AM and AP according to the RCSB Protein Data Bank. High-affinity binding to phosphodiesterase IV (PDE-4), an important inflammatory modulator in asthma, was demonstrated experimentally, beside that, the predicted structures based on compounds 1 and 2 were analyzed for PDE-4 interactions using the molecular docking methodology of Discovery Studio 3.0 (DS 3.0). The predicted structure 2A-6 exhibited much higher affinity and stability of PDE-4 binding than the clinical PDE-4 inhibitor rolipram.
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Affiliation(s)
- Hui-Qi Ge
- a School of Biopharmaceutical and Chemical Engineering , Liaoning Institute of Science and Technology , Benxi 117004 , China
| | - Guo-Sheng Wan
- b Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Da Wang
- b Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Ji-Ming Wu
- b Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Bo-Hang Sun
- b Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Li-Jun Wu
- c Key Laboratory of Cardiovascular Medicine Research of Ministry of Education , Harbin Medicinal University , Harbin 150081 , China
| | - Hui-Yuan Gao
- b Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , China
- c Key Laboratory of Cardiovascular Medicine Research of Ministry of Education , Harbin Medicinal University , Harbin 150081 , China
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Abstract
HIV-1 Protease (HIV-1 PR) enzymes are essential for accurate assembly and maturation of infectious HIV retroviruses. The significant role of HIV-1 protease in viral replication has made it a potential drug target. In the recent past, phytochemical Gallic Acid (GA) derivatives have been screened for protease inhibitor activity. The present work aims to design and evaluate potential GA-based HIV-1 PR phytoinhibitors by docking approach. The ligands were prepared by ChemDraw and docking was performed in HEX software. In this present study, one of the GA analogues (GA4) emerged as a potent drug candidate for HIV-1 PR inhibition, and docking results showed it to be comparable with anti-HIV drugs, darunavir and amprenavir. The GA4 derivative provided a lead for designing more effective HIV-1 PR inhibitors.
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Affiliation(s)
- Anjali Singh
- 1 Department of Biotechnology, Bengal Institute of Technology, Hadia 700150, West Bengal, India
| | - Tapan Kumar Pal
- 2 Department of Biotechnology, Bengal Institute of Technology, Hadia 700150, West Bengal, India
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Eleftheriou P, Petrou A, Geronikaki A, Liaras K, Dirnali S, Anna M. Prediction of enzyme inhibition and mode of inhibitory action based on calculation of distances between hydrogen bond donor/acceptor groups of the molecule and docking analysis: An application on the discovery of novel effective PTP1B inhibitors. SAR QSAR Environ Res 2015; 26:557-576. [PMID: 26294069 DOI: 10.1080/1062936x.2015.1074939] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 07/16/2015] [Indexed: 06/04/2023]
Abstract
PTP1B is a protein tyrosine phosphatase involved in insulin receptor desensitization. PTP1B inhibition prolongs the activated state of the receptor, practically enhancing the effect of insulin. Thus PTP1B has become a drug target for the treatment of type II diabetes. PTP1b is an enzyme with multiple binding sites for competitive and allosteric inhibitors. Prediction of inhibitory action using docking analysis has limited success in case of enzymes with multiple binding sites, since the selection of the right crystal structure depends on the kind of inhibitor. In the present study, a two-step strategy for the prediction of PTP1b inhibitory action was applied to 12 compounds. Based on the study of known inhibitors, we isolated the structural characteristics required for binding to each binding site. As a first step, 3D-structures of the molecules were produced and their structural parameters were measured and used for prediction of the binding site of the compound. These results were used for the selection of the appropriate crystal structure for docking analysis of each compound, and the final prediction was based on the estimated binding energies. This strategy effectively predicted the activity of all compounds. A linear correlation was found between estimated binding energy and inhibition measured in vitro (r = -0.894).
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Affiliation(s)
- P Eleftheriou
- a Department of Medical Laboratory Studies, School of Health and Medical Care , Alexander Technological Educational Institute of Thessaloniki , Greece
| | - A Petrou
- b Department of Medicinal Chemistry, School of Medicine , Aristotle University of Thessaloniki , Greece
| | - A Geronikaki
- b Department of Medicinal Chemistry, School of Medicine , Aristotle University of Thessaloniki , Greece
| | - K Liaras
- b Department of Medicinal Chemistry, School of Medicine , Aristotle University of Thessaloniki , Greece
| | - S Dirnali
- a Department of Medical Laboratory Studies, School of Health and Medical Care , Alexander Technological Educational Institute of Thessaloniki , Greece
| | - M Anna
- a Department of Medical Laboratory Studies, School of Health and Medical Care , Alexander Technological Educational Institute of Thessaloniki , Greece
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Hasan A, Mazumder HH, Khan A, Hossain MU, Chowdhury HK. Molecular Characterization of Legionellosis Drug Target Candidate Enzyme Phosphoglucosamine Mutase from Legionella pneumophila (strain Paris): An In Silico Approach. Genomics Inform 2014; 12:268-75. [PMID: 25705169 PMCID: PMC4330265 DOI: 10.5808/gi.2014.12.4.268] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 10/13/2014] [Accepted: 10/22/2014] [Indexed: 01/17/2023] Open
Abstract
The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire's disease. The increasing development of drug resistance against legionellosis has led to explore new novel drug targets. It has been found that phosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the most probable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugar and nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this, the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means of homology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structure validation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondary structural features were determined through self-optimized prediction method with alignment (SOPMA) and interacting networks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showed that 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in the generously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 for ERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorable binding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensive investigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.
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Affiliation(s)
- Anayet Hasan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh
| | - Habibul Hasan Mazumder
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh
| | - Arif Khan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Mohammad Uzzal Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Homaun Kabir Chowdhury
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna 9208, Bangladesh
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