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Zhao YH, Song XY, Sun XX, He RS, Yang WZ, Jiang MM, He J, Zhang LH, Wu HH. Constituents from Dendrobium aphyllum: Bibenzyls, furfurals, phenanthrenes, and phenylpropanoids and their antioxidant and anti-inflammatory potentials. Fitoterapia 2024:106122. [PMID: 38992474 DOI: 10.1016/j.fitote.2024.106122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Chemical investigation on the aqueous extract of Dendrobium aphyllum led to the isolation of thirty-one constituents with structures identified by analysis of the extensive spectroscopic data (1D/2D NMR, MS, UV, and ECD), including previously undescribed two bibenzyls, one furfural, and one phenolic acid, namely trigonopol D (1), trigonopol C (2), dendrofunan A (10), and 6-(4-hydroxy-3-methoxyphenyl)-3,6-dioxohexyl acetate (30), respectively, as well as twenty-seven known ones. Among them, there were one new natural product (11), seven compounds (6-7, 9, 12, 20, 28, 31) described from the genus Dendrobium for the first time, and fifteen compounds (8, 13-17, 19, 21-27, 29) isolated from D. aphyllum for the first time. Further, the antioxidant and anti-inflammatory potentials of fifteen compounds (4-5, 8, 11-12, 14-19, 22, 24, 26, and 29) with significant scavenging capacities against DPPH and hydroxyl radicals, and virtual docking activities inhibiting COX-2 and 5-LOX, respectively. Our study may draw the attention of medicinal plant taxonomists and supply potential quality markers for discrimination of D. aphyllum from other species in Dendrobium genus.
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Affiliation(s)
- Yu-Heng Zhao
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China
| | - Xiao-Yan Song
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China
| | - Xiao-Xue Sun
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China
| | - Ru-Shang He
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China
| | - Wen-Zhi Yang
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China
| | - Miao-Miao Jiang
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China
| | - Jun He
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China
| | - Li-Hua Zhang
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China.
| | - Hong-Hua Wu
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China; Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin 301617, People's Republic of China.
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Luo K, Yu X, Wang J, Liu J, Li X, Pan M, Huang D, Mai K, Zhang W. Ascorbic acid biosynthesis in Pacific abalone Haliotis discus hannai Ino and L-gulonolactone oxidase gene loss as an independent event. Int J Biol Macromol 2024; 268:131733. [PMID: 38649080 DOI: 10.1016/j.ijbiomac.2024.131733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Up to now, it has been believed that invertebrates are unable to synthesize ascorbic acid (AA) in vivo. However, in the present study, the full-length CDs (Coding sequence) of L-gulonolactone oxidase (GLO) from Pacific abalone (Haliotis discus hannai Ino) were obtained through molecular cloning. The Pacific abalone GLO contained a FAD-binding domain in the N-termination, and ALO domain and conserved HWAK motif in the C-termination. The GLO gene possesses 12 exons and 11 introns. The Pacific abalone GLO was expressed in various tissues, including the kidney, digestive gland, gill, intestine, muscle and mantle. The GLO activity assay revealed that GLO activity was only detected in the kidney of Pacific abalone. After a 100-day feeding trial, dietary AA levels did not significantly affect the survival, weight gain, daily increment in shell length, and feed conversion ratio of Pacific abalone. The expression of GLO in the kidney was downregulated by dietary AA. These results implied that the ability to synthesize AA in abalone had not been lost. From the evolutionary perspective, the loss of GLO occurred independently as an independent event by matching with the genomes of various species. The positive selection analysis revealed that the GLO gene underwent purifying selective pressure during its evolution. In conclusion, the present study provided direct evidence to prove that the GLO activity and the ability to synthesize AA exist in abalone. The AA synthesis ability in vertebrates might have originated from invertebrates dating back 930.31 million years.
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Affiliation(s)
- Kai Luo
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China; Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, PR China
| | - Xiaojun Yu
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China
| | - Jia Wang
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China
| | - Jiahuan Liu
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China
| | - Xinxin Li
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China
| | - Mingzhu Pan
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China
| | - Dong Huang
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China
| | - Kangsen Mai
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China
| | - Wenbing Zhang
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs); Key Laboratory of Mariculture (Ministry of Education); Ocean University of China, Qingdao 266003, PR China.
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3
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Eum DY, Jeong M, Park SY, Kim J, Jin Y, Jo J, Shim JW, Lee SR, Park SJ, Heo K, Yun H, Choi YJ. AM-18002, a derivative of natural anmindenol A, enhances radiosensitivity in mouse breast cancer cells. PLoS One 2024; 19:e0296989. [PMID: 38625901 PMCID: PMC11020960 DOI: 10.1371/journal.pone.0296989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/25/2023] [Indexed: 04/18/2024] Open
Abstract
Natural anmindenol A isolated from the marine-derived bacteria Streptomyces sp. caused potent inhibition of inducible nitric oxide synthase without any significant cytotoxicity. This compound consists of a structurally unique 3,10-dialkylbenzofulvene skeleton. We previously synthesized and screened the novel derivatives of anmindenol A and identified AM-18002, an anmindenol A derivative, as a promising anticancer agent. The combination of AM-18002 and ionizing radiation (IR) improved anticancer effects, which were exerted by promoting apoptosis and inhibiting the proliferation of FM3A mouse breast cancer cells. AM-18002 increased the production of reactive oxygen species (ROS) and was more effective in inducing DNA damage. AM-18002 treatment was found to inhibit the expansion of myeloid-derived suppressor cells (MDSC), cancer cell migration and invasion, and STAT3 phosphorylation. The AM-18002 and IR combination synergistically induced cancer cell death, and AM-18002 acted as a potent anticancer agent by increasing ROS generation and blocking MDSC-mediated STAT3 activation in breast cancer cells.
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Affiliation(s)
- Da-Young Eum
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan, Republic of Korea
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Myeonggyo Jeong
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
- Research Institute for Drug Development, Pusan National University, Busan, Republic of Korea
| | - Soon-Yong Park
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan, Republic of Korea
| | - Jisu Kim
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Yunho Jin
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan, Republic of Korea
| | - Jeyun Jo
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Jae-Woong Shim
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan, Republic of Korea
| | - Seoung Rak Lee
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
- Research Institute for Drug Development, Pusan National University, Busan, Republic of Korea
| | - Seong-Joon Park
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan, Republic of Korea
| | - Kyu Heo
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan, Republic of Korea
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
- Research Institute for Drug Development, Pusan National University, Busan, Republic of Korea
| | - Yoo-Jin Choi
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan, Republic of Korea
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Akash S, Aovi FI, Azad MAK, Kumer A, Chakma U, Islam MR, Mukerjee N, Rahman MM, Bayıl I, Rashid S, Sharma R. A drug design strategy based on molecular docking and molecular dynamics simulations applied to development of inhibitor against triple-negative breast cancer by Scutellarein derivatives. PLoS One 2023; 18:e0283271. [PMID: 37824496 PMCID: PMC10569544 DOI: 10.1371/journal.pone.0283271] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/07/2023] [Indexed: 10/14/2023] Open
Abstract
Triple-negative breast cancer (TNBC), accounting for 10-15% of all breast malignancies, is more prevalent in women under 40, particularly in those of African descent or carrying the BRCA1 mutation. TNBC is characterized by the absence of estrogen and progesterone receptors (ER, PR) and low or elevated HER2 expression. It represents a particularly aggressive form of breast cancer with limited therapeutic options and a poorer prognosis. In our study, we utilized the protein of TNBC collected from the Protein Data Bank (PDB) with the most stable configuration. We selected Scutellarein, a bioactive molecule renowned for its anti-cancer properties, and used its derivatives to design potential anti-cancer drugs employing computational tools. We applied and modified structural activity relationship methods to these derivatives and evaluated the probability of active (Pa) and inactive (Pi) outcomes using pass prediction scores. Furthermore, we employed in-silico approaches such as the assessment of absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters, and quantum calculations through density functional theory (DFT). Within the DFT calculations, we analyzed Frontier Molecular Orbitals, specifically the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO). We then conducted molecular docking and dynamics against TNBC to ascertain binding affinity and stability. Our findings indicated that Scutellarein derivatives, specifically DM03 with a binding energy of -10.7 kcal/mol and DM04 with -11.0 kcal/mol, exhibited the maximum binding tendency against Human CK2 alpha kinase (PDB ID 7L1X). Molecular dynamic simulations were performed for 100 ns, and stability was assessed using root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) parameters, suggesting significant stability for our chosen compounds. Furthermore, these molecules met the pharmacokinetics requirements for potential therapeutic candidates, displaying non-carcinogenicity, minimal aquatic and non-aquatic toxicity, and greater aqueous solubility. Collectively, our computational data suggest that Scutellarein derivatives may serve as potential therapeutic agents for TNBC. However, further experimental investigations are needed to validate these findings.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Farjana Islam Aovi
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md. A. K. Azad
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Unesco Chakma
- School of Electronic Science and Engineering, Southeast University, Nanjing, China
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Nobendu Mukerjee
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India
- Department of Microbiology, West Bengal State University, West Bengal, Kolkata, India
| | - Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Summya Rashid
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Science, Banaras Hindu University, Varanasi, India
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5
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Wulan FF, Wahyuningsih TD, Astuti E, Prasetyo N. Towards targeting EGFR and COX-2 inhibitors: comprehensive computational studies on the role of chlorine group in novel thienyl-pyrazoline derivative. J Biomol Struct Dyn 2023:1-16. [PMID: 37643080 DOI: 10.1080/07391102.2023.2252915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
To enhance the effectiveness of chemotherapy and overcome resistance, scientists must develop novel drugs or scaffolds that have a combined effect, such as the inhibition of EGFR and COX-2. This research employed virtual screening techniques, such as docking, and dynamics simulation, to predict chlorinated thienyl-pyrazoline derivatives that inhibit these proteins. The study proposed eleven (11) ligands with binding energies ranging from -7.8 kcal/mol to -8.7 kcal/mol for EGFR and -6.4 kcal/mol to -8.4 kcal/mol for COX-2. Ligands P1 and P11 exhibited the highest binding affinity for both proteins. The results of RMSD, RMSF, RoG, SASA the number of hydrogen bonds, and BAR free binding energy demonstrated the good stability of ligands P1 and P11 when binding to both proteins over 180 ns simulations. In addition, the absorption, distribution, metabolism, excretion, and toxicity properties of the selected ligands were assessed to predict their toxicity and drug likeliness. Based on the results, these compounds can be proposed for further synthesis and in vitro studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fia Fathiana Wulan
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tutik Dwi Wahyuningsih
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endang Astuti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Niko Prasetyo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
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6
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Fonseca Hernández D, Mojica L, Berhow MA, Brownstein K, Lugo Cervantes E, Gonzalez de Mejia E. Black and pinto beans (Phaseolus vulgaris L.) unique mexican varieties exhibit antioxidant and anti-inflammatory potential. Food Res Int 2023; 169:112816. [PMID: 37254392 DOI: 10.1016/j.foodres.2023.112816] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/14/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Oxidative stress and inflammation play a key role in diverse pathological conditions such as cancer and metabolic disorders. The objective of this study was to determine the antioxidant and anti-inflammatory potentials of crude extract (CE) and phenolic-enriched extract (PHE) obtained from the seed coats (SCs) of black bean (BB) and pinto bean (PB) varieties. Delphinidin-3-O-glucoside (46 mg/g SC), malvidin-3-O-glucoside (29.9 mg/g SC), and petunidin-3-O-glucoside (7.5 mg/g SC) were found in major concentrations in the PHE-BB. Pelargonidin (0.53 mg/g SC) was only identified in the PHE-PB. PHE from both varieties showed antioxidant and radical scavenging capacities, with strong correlations associated with total phenolic content (TPC). Polyphenolics, including catechin, myricetin, kaempferol, quercetin, and isorhamnetin glucosides, were identified in the extracts. In terms of the anti-inflammatory potentials, PHE-PB had an IC50 of 10.5 µg dry extract/mL (µg DE/mL) for cyclooxygenase-2 (COX-2) inhibition. The inhibition values for cyclooxygenase-1 (COX-1) ranged from 118.1 to 162.7 µg DE/mL. Regarding inducible nitric oxide synthase (iNOS) inhibition, PHE-BB had an IC50 of 62.6 µg DE/mL. As determined via in silico analysis, pelargonidin showed binding affinities of -7.8 and -8.5 kcal/mol for COX-1 and iNOS, respectively, and catechin had a value of -8.3 kcal/mol for COX-2. Phenolic-enriched extracts from seed coats of black and pinto beans showed good antioxidant and anti-inflammatory potential that warrants in vitro and in vivo studies.
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Affiliation(s)
- David Fonseca Hernández
- Tecnología Alimentaria, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
| | - Luis Mojica
- Tecnología Alimentaria, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico.
| | - Mark A Berhow
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Function Food Research, 1815 N University, Peoria, IL 61604, USA
| | | | - Eugenia Lugo Cervantes
- Tecnología Alimentaria, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico
| | - Elvira Gonzalez de Mejia
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
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7
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Chahal S, Rani P, Kiran, Sindhu J, Joshi G, Ganesan A, Kalyaanamoorthy S, Mayank, Kumar P, Singh R, Negi A. Design and Development of COX-II Inhibitors: Current Scenario and Future Perspective. ACS OMEGA 2023; 8:17446-17498. [PMID: 37251190 PMCID: PMC10210234 DOI: 10.1021/acsomega.3c00692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/21/2023] [Indexed: 09/29/2023]
Abstract
Innate inflammation beyond a threshold is a significant problem involved in cardiovascular diseases, cancer, and many other chronic conditions. Cyclooxygenase (COX) enzymes are key inflammatory markers as they catalyze prostaglandins production and are crucial for inflammation processes. While COX-I is constitutively expressed and is generally involved in "housekeeping" roles, the expression of the COX-II isoform is induced by the stimulation of different inflammatory cytokines and also promotes the further generation of pro-inflammatory cytokines and chemokines, which affect the prognosis of various diseases. Hence, COX-II is considered an important therapeutic target for drug development against inflammation-related illnesses. Several selective COX-II inhibitors with safe gastric safety profiles features that do not cause gastrointestinal complications associated with classic anti-inflammatory drugs have been developed. Nevertheless, there is mounting evidence of cardiovascular side effects from COX-II inhibitors that resulted in the withdrawal of market-approved anti-COX-II drugs. This necessitates the development of COX-II inhibitors that not only exhibit inhibit potency but also are free of side effects. Probing the scaffold diversity of known inhibitors is vital to achieving this goal. A systematic review and discussion on the scaffold diversity of COX inhibitors are still limited. To address this gap, herein we present an overview of chemical structures and inhibitory activity of different scaffolds of known COX-II inhibitors. The insights from this article could be helpful in seeding the development of next-generation COX-II inhibitors.
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Affiliation(s)
- Sandhya Chahal
- Department
of Chemistry, COBS&H, CCS Haryana Agricultural
University, Hisar 125004, India
| | - Payal Rani
- Department
of Chemistry, COBS&H, CCS Haryana Agricultural
University, Hisar 125004, India
| | - Kiran
- Department
of Chemistry, COBS&H, CCS Haryana Agricultural
University, Hisar 125004, India
| | - Jayant Sindhu
- Department
of Chemistry, COBS&H, CCS Haryana Agricultural
University, Hisar 125004, India
| | - Gaurav Joshi
- Department
of Pharmaceutical Sciences, Hemvati Nandan
Bahuguna Garhwal (A Central) University, Chauras Campus, Tehri Garhwal, Uttarakhand 249161, India
- Adjunct
Faculty at Department of Biotechnology, Graphic Era (Deemed to be) University, 566/6, Bell Road, Clement Town, Dehradun, Uttarakhand 248002, India
| | - Aravindhan Ganesan
- ArGan’sLab,
School of Pharmacy, University of Waterloo, Waterloo, Ontario N2G 1C5, Canada
| | | | - Mayank
- University
College of Pharmacy, Guru Kashi University, Talwandi Sabo, Punjab 151302, India
| | - Parvin Kumar
- Department
of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Rajvir Singh
- Department
of Chemistry, COBS&H, CCS Haryana Agricultural
University, Hisar 125004, India
| | - Arvind Negi
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo 02150, Finland
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8
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Li SM, Chou JY, Tsai SE, Tseng CC, Chung CY, Zeng WZ, Hu YP, Uramaru N, Huang GJ, Wong FF. Synthesis and anti-inflammatory activity evaluation of NO-releasing furoxan/1,2,4-triazole hybrid derivatives. Eur J Med Chem 2023; 257:115496. [PMID: 37224762 DOI: 10.1016/j.ejmech.2023.115496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/07/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023]
Abstract
An efficient synthesis method was developed for furoxan/1,2,4-triazole hybrids 5a-k from methyl 5-(halomethyl)-1-aryl-1H-1,2,4-triazole-3-carboxylates 1 through two-steps reaction including hydrolyzation and esterification. All of the furoxan/1,2,4-triazole hybrid derivatives were characterized by spectroscopy. On the other hand, the influence of newly synthesized multi-substituted 1,2,4-triazoles on the exogenous NO release ability, in vitro and in vivo anti-inflammatory activity, and in silico predictions were experimentally evaluated. Based on the exogenous NO release ability study and SAR studies of in vitro anti-inflammatory activity, all of compounds 5a-k exhibited slightly NO release ability and potential anti-inflammatory activity on LPS-induced RAW264.7 cells (IC50 = 5.74-15.3 μM) compared to Celecoxib (IC50 = 16.5 μM) and Indomethacin (IC50 = 56.8 μM). Furthermore, compounds 5a-k were also subjected to in vitro COX-1/COX-2 inhibition assays. Particularly, compound 5f exhibited extraordinary COX-2 inhibition (IC50 = 0.0455 μM) and selectivity (SI = 209). In addition, compound 5f was also examined in vivo pro-inflammatory cytokine productions and gastric safety and possessed the better inhibition of cytokine and safety compared with Indomethacin at the same concentration. Through the molecular modeling and in silico physicochemical and pharmacokinetic properties prediction, compound 5f was stabilized in COX-2 active binding site and possessed the fundamental strong H-bond interaction with Arg499 to form the significant physicochemical and pharmacological properties as a candidate drug. Following the in vitro, in vivo, and in silico study results, compound 5f demonstrated to be a potential anti-inflammatory agent and had comparable effects with Celecoxib.
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Affiliation(s)
- Sin-Min Li
- Institute of Translation Medicine and New Drug Development, China Medical University, Taichung, 40402, Taiwan
| | - Jia-Yu Chou
- Master Program for Pharmaceutical Manufacture, China Medical University, Taichung, 40402, Taiwan
| | - Shuo-En Tsai
- Ph.D. Program for Biotech Pharmaceutical Industry, China Medical University, Taichung, 40402, Taiwan
| | - Ching-Chun Tseng
- Ph.D. Program for Biotech Pharmaceutical Industry, China Medical University, Taichung, 40402, Taiwan
| | - Cheng-Yen Chung
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, 40402, Taiwan
| | - Wei-Zheng Zeng
- Department of Nutrition, China Medical University, Taichung, 406040, Taiwan
| | - Yu-Pei Hu
- Department of Biological Science and Technology, China Medical University, Taichung, 406040, Taiwan
| | - Naoto Uramaru
- Department of Environmental Science, Nihon Pharmaceutical University, Komuro Inamachi Kita-adachi-gun, Saitama-ken, 10281, Japan
| | - Guan-Jhong Huang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, 40402, Taiwan; Department of Food Nutrition and Healthy Biotechnology, Asia University, Taichung, 413, Taiwan
| | - Fung-Fuh Wong
- Ph.D. Program for Biotech Pharmaceutical Industry, China Medical University, Taichung, 40402, Taiwan; School of Pharmacy, China Medical University, Taichung, 40402, Taiwan.
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Sardari E, Ebadi A, Razzaghi-Asl N. In silico repurposing of CNS drugs for multiple sclerosis. Mult Scler Relat Disord 2023; 73:104622. [PMID: 36958175 DOI: 10.1016/j.msard.2023.104622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 02/10/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune neurodegenerative disease affecting numerous people worldwide. While the relapsing subtypes of MS are to some extent treatable, the disease remains incurable leading to progressive disability. Limited efficacy of current small molecule drugs necessitates development of efficient and safe MS medications. Accordingly, drug repurposing is an invaluable strategy that recognizes new targets for known drugs especially in the field of poorly addressed therapeutic areas. Drug discovery largely depends on the identification of potential binding molecules to the intended biomolecular target(s). In this regard, current study was devoted to in silico repurposing of 263 small molecule CNS drugs to achieve superior binders to some MS-related targets. On the basis of molecular docking scores, thioxanthene and benzisothiazole-based antipsychotics could be identified as potential binders to sphingosine-1-phosphate lyase (S1PL) and cyclophilin D (CypD). Tightest interaction modes were observed for zuclopenthixol-S1PL (ΔGb -7.96 kcal/mol) and lurasidone-CypD (ΔGb -8.84 kcal/mol) complexes. Molecular dynamics (MD) simulations proved the appropriate and stable accommodation of top-ranked drugs inside enzyme binding sites during 100 ns. Hydroxyethyl piperazine of zuclopenthixol and benzisothiazole of lurasidone flipped inside the binding pocket to interact with adjacent polar and apolar residues. Solvent accessible surface area (SASA) fluctuations confirmed the results of binding trajectory analysis and showed that non-polar hydrophobic interactions played significant roles in acquired stabilities. Our results on lurasidone binding pattern were interestingly in accordance with previous reports on X-ray structures of other norbornane maleimide derivatives as CypD inhibitors. According to this, Asn144, Phe102 and Phe155 served as important residues in providing stable binding pose of lurasidone through both exo and endo conformations. Although experimental results are necessary to be achieved, the outcomes of this study proposed the potentiality of some thioxanthene and benzisothiazole-based antipsychotics for binding to S1PL and CypD, respectively, as MS-related targets.
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Affiliation(s)
- Elham Sardari
- Student Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Ahmad Ebadi
- Department of Medicinal Chemistry, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Nima Razzaghi-Asl
- Department of Medicinal Chemistry School of Pharmacy, Ardabil University of Medical Sciences, Ardabil PO code: 5618953141, Iran.
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10
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Ibrahim JM, A S, Nair AS, Oommen OV, Sudhakaran PR. In silico screening and epitope mapping of leptospiral outer membrane protein-Lsa46. J Biomol Struct Dyn 2023; 41:26-44. [PMID: 34821205 DOI: 10.1080/07391102.2021.2003247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Leptospirosis is one of the neglected diseases caused by the spirochete, Leptospira interrogans. Leptospiral surface adhesion (Lsa) proteins are surface exposed outer membrane proteins present in the pathogen. It acts as laminin and plasminogen binding proteins which enable them to infect host cells. The major target for the development of vaccine in the current era focuses on surface exposed outer membrane proteins, as they can induce strong and fast immune response in hosts. Therefore, the present study mapped the potential epitopes of the Leptospiral outer membrane proteins, mainly the surface adhesion proteins. Protein sequence analysis of Lsa proteins was done by in silico methods. The primary protein sequence analysis revealed Lsa46 as a suitable target which can be a potent Leptospiral vaccine candidate. Its structure was modelled by threading based method in I-TASSER server and validated by Ramachandran plot. The predicted epitope's interactions with human IgG, IgM(Fab) and T-cell receptor TCR(αβ) were performed by molecular docking studies using Biovia Discovery studio 2018. One of the predicted B-cell epitopes and the IgG showed desirable binding interactions, while four of the predicted B-cell epitopes and T-cell epitopes showed desirable binding interactions with IgM and TCR respectively. The molecular dynamic simulation studies carried out with the molecular docked complexes gave minimized energies indicating stable interactions. The structural analysis of the entire simulated complex showed a stable nature except for one of the Epitope-IgM complex. Further the binding free energy calculation of eight receptor-ligand complex predicted them energetically stable. The results of the study help in elucidating the structural and functional characterization of Lsa46 for epitope-based vaccine design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Junaida M Ibrahim
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Shanitha A
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Achuthsankar S Nair
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Oommen V Oommen
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Perumana R Sudhakaran
- Department of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
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11
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Rezvani S, Ebadi A, Razzaghi-Asl N. In silico identification of potential Hsp90 inhibitors via ensemble docking, DFT and molecular dynamics simulations. J Biomol Struct Dyn 2022; 40:10665-10676. [PMID: 34286666 DOI: 10.1080/07391102.2021.1947383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The molecular chaperone heat shock protein 90 (Hsp90) has emerged as one of the most exciting targets for anticancer drug development and Hsp90 inhibitors are potentially useful chemotherapeutic agents in cancer. Within the current study, Hsp90 inhibitors that entered different phases of clinical trials were subjected to Zinc15 structure query to find similar compounds (≥ 78%). Obtained small molecules (1-29) with defined similarity cut-off were docked into ensemble of Hsp90-α NTDs. Docked complexes were ranked on the basis of binding modes and Gibbs free energies as Hsp90 binders (cut-off point; ΔGb ≤ -12 kcal/mol). Top-ranked compounds were subjected to energy decomposition analysis per residue of binding pocket via density functional theory (DFT) calculations in B3LYP level of theory. Subsequent MD simulations of the top-ranked complexes were performed for 100 ns to explore the stable binding modes during a reasonable period in explicit water. Results of molecular docking and intermolecular binding analysis indicated that H-bond, hydrophobic and salt bridge interactions were determinant forces in complex formation. Compounds 19 and 20 were well accommodated in binding pocket of Hsp90 via relatively varied conformations. It was revealed that Asn51 and Phe138 were key residues that interacted stably to 19 and 20. Although primary mechanism of action for proposed molecules are unknown and yet to be explored, results of the present study revealed key structural features for future structure-guided optimization toward potent inhibitors of Hsp90-α NTD. HighlightsHsp90 inhibitors that entered different phases of clinical trials were subjected to Zinc15 based structure query to afford potential enzyme inhibitors 19 and 20.Quantum chemical calculations confirmed docking results and verified pivotal role of a conserved residues (Asn51, Leu103, Phe138 and Tyr139) in making effective hydrogen bonds.MD simulations of top-ranked docked derivatives revealed the achievement of stable binding modes with less conformational variation of 20 than 19 in the active site of Hsp90-α NTD.H-bond, hydrophobic contacts and salt bridge interactions were determinant forces in binding interactions of in silico hits.Resorcinol and isoxazole were important structural motifs of in silico hits in binding to the active site of Hsp90-α NTD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saba Rezvani
- Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Ahmad Ebadi
- Department of Medicinal Chemistry, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Nima Razzaghi-Asl
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
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12
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Yang YS, Man RJ, Xu JF, Wang CY, Wang X, Li DD, Zhu HL. Discovery of novel 1,3-diaryl pyrazolyl ester derivatives as COX-2 inhibitory candidates with anti-tumor effect. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Zhang M, Zhou S, Obaid NH, Altimari US, Adel Mohammed M, Kareem Obaid Aldulaim A, Salaam Abood E, Kotb H, Enayati A, Khori V, Mirzaei H, Salehi A, Soltani A, Sani Sarjadi M, Lutfor Rahman M. Chromenone-based GSK-3β inhibitors as potential therapeutic targets for cardiovascular diseases: in silico study, molecular dynamics, and ADMET profiles. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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14
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Shah M, Bibi S, Kamal Z, Al-Sabahi JN, Alam T, Ullah O, Murad W, Rehman NU, Al-Harrasi A. Bridging the Chemical Profile and Biomedical Effects of Scutellaria edelbergii Essential Oils. Antioxidants (Basel) 2022; 11:antiox11091723. [PMID: 36139797 PMCID: PMC9496006 DOI: 10.3390/antiox11091723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
The present study explored chemical constituents of Scutellaria edelbergii essential oils (SEEO) for the first time, extracted through hydro-distillation, and screened them against the microbes and free radicals scavenging effect, pain-relieving, and anti-inflammatory potential employing standard techniques. The SEEO ingredients were noticed via Gas Chromatography-Mass-Spectrometry (GC-MS) analysis and presented fifty-two bioactive compounds contributed (89.52%) with dominant volatile constituent; 3-oxomanoyl oxide (10.09%), 24-norursa-3,12-diene (8.05%), and methyl 7-abieten-18-oate (7.02%). The MTT assay via 96 well-plate and agar-well diffusion techniques against various microbes was determined for minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), IC50, and zone of inhibitions (ZOIs). The SEEO indicated considerable antimicrobial significance against tested bacterial strains viz. Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterococcus faecalis and the fungal strains Fusarium oxysporum and Candida albicans. The free radicals scavenging potential was noticed to be significant in 1,1-Diphenyl-2-picryl-hydrazyl (DPPH) as compared to 2,2′-azino-bis-3-ethylbenzotiazolin-6-sulfonic acid (ABTS) assays with IC50 = 125.0 ± 0.19 µg/mL and IC50 = 153.0 ± 0.31 µg/mL correspondingly; similarly, the antioxidant standard in the DPPH assay was found efficient as compared to ABTS assay. The SEEO also offered an appreciable analgesic significance and presented 54.71% in comparison with standard aspirin, 64.49% reduction in writhes, and an anti-inflammatory potential of 64.13%, as compared to the standard diclofenac sodium inhibition of 71.72%. The SEEO contain bioactive volatile ingredients with antimicrobial, free radical scavenging, pain, and inflammation relieving potentials. Computational analysis validated the anti-inflammatory potential of selected hit “methyl 7-abieten-18-oate” as a COX-2 enzyme inhibitor. Docking results were very good in terms of docked score (−7.8704 kcal/mol) and binding interactions with the functional residues; furthermore, MD simulation for 100 ns has presented a correlation with docking results with minor fluctuations. In silico, ADMET characteristics supported that methyl 7-abieten-18-oate could be recommended for further investigations in clinical tests and could prove its medicinal status as an anti-inflammatory drug.
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Affiliation(s)
- Muddaser Shah
- Department of Botany, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mauz, P.O. Box 33, Nizwa 616, Oman
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad 44000, Pakistan
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
| | - Zul Kamal
- Department of Pharmacy, Shaheed Benazir Bhutto University, Upper Dir 18000, Pakistan
| | - Jamal Nasser Al-Sabahi
- Central Instrument Laboratory, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat 123, Oman
| | - Tanveer Alam
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mauz, P.O. Box 33, Nizwa 616, Oman
| | - Obaid Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mauz, P.O. Box 33, Nizwa 616, Oman
- Department of Chemistry, University of Chakdara, Chakdara 18800, Pakistan
| | - Waheed Murad
- Department of Botany, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
- Correspondence: (W.M.); (N.U.R.); (A.A.-H.)
| | - Najeeb Ur Rehman
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mauz, P.O. Box 33, Nizwa 616, Oman
- Correspondence: (W.M.); (N.U.R.); (A.A.-H.)
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mauz, P.O. Box 33, Nizwa 616, Oman
- Correspondence: (W.M.); (N.U.R.); (A.A.-H.)
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15
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Screening of Potential Breast Cancer Inhibitors through Molecular Docking and Molecular Dynamics Simulation. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3338549. [PMID: 35800218 PMCID: PMC9256436 DOI: 10.1155/2022/3338549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
Abstract
Cyclooxygenase-2 (COX-2) is a key enzyme involved in overexpression in several human cancerous diseases including breast cancer. By performing efficient virtual screening in a series of active molecules or compounds from the Maybridge, NCI (National Cancer Institute), and Enamine databases, potential identification of COX-2 inhibitors could lead to new prognostic strategies in the treatment of breast cancer. Based on a 50% structural similitude, compounds were chosen as the inductive model of COX-2 inhibitions from these databases. Selected compounds were filtered and tested with Lipinski’s rule of five followed by absorption, distribution, metabolism, and excretion (ADME) properties. Subsequently, molecular docking was performed to achieve accuracy in screening and also to find an interactive mechanism between hit compounds with their respective binding sites. Simultaneously, molecular simulations of top-scored compounds were selected and coded such as Maybridge_55417, NCI_30552, and Enamine_62410. Chosen compounds were analyzed and interpreted with COX-2 affinity. Results endorsed that hydrophobic affinity and optimum hydrogen bonds were the forces driven in the interactive mechanism of in silico hits compounds with COX-2 and can be used as efficient alternative therapeutic agents targeting deleterious breast cancer. With these in silico findings, compounds identified may prevent the action of the COX-2 enzyme and thereby diminish the incidence of breast cancer.
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16
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Li S, Wang L, Meng J, Zhao Q, Zhang L, Liu H. De Novo design of potential inhibitors against SARS-CoV-2 Mpro. Comput Biol Med 2022; 147:105728. [PMID: 35763931 PMCID: PMC9197785 DOI: 10.1016/j.compbiomed.2022.105728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/31/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022]
Abstract
The impact of the ravages of COVID-19 on people's lives is obvious, and the development of novel potential inhibitors against SARS-CoV-2 main protease (Mpro), which has been validated as a potential target for drug design, is urgently needed. This study developed a model named MproI-GEN, which can be used for the de novo design of potential Mpro inhibitors (MproIs) based on deep learning. The model was mainly composed of long-short term memory modules, and the last layer was re-trained with transfer learning. The validity (0.9248), novelty (0.9668), and uniqueness (0.0652) of the designed potential MproI library (PMproIL) were evaluated, and the results showed that MproI-GEN could be used to design structurally novel and reasonable molecules. Additionally, PMproIL was filtered based on machine learning models and molecular docking. After filtering, the potential MproIs were verified with molecular dynamics simulations to evaluate the binding stability levels of these MproIs and SARS-CoV-2 Mpro, thereby illustrating the inhibitory effects of the potential MproIs against Mpro. Two potential MproIs were proposed in this study. This study provides not only new possibilities for the development of COVID-19 drugs but also a complete pipeline for the discovery of novel lead compounds.
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Affiliation(s)
- Shimeng Li
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Lianxin Wang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Jinhui Meng
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China.
| | - Li Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China; Shenyang Key Laboratory of Computer Simulating and Information Processing of Bio-macromolecules, Shenyang, 110036, China.
| | - Hongsheng Liu
- Shenyang Key Laboratory of Computer Simulating and Information Processing of Bio-macromolecules, Shenyang, 110036, China; Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Province, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China; School of Pharmaceutical Sciences, Liaoning University, Shenyang, 110036, China.
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17
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Swargiary A, Mahmud S, Saleh MA. Screening of phytochemicals as potent inhibitor of 3-chymotrypsin and papain-like proteases of SARS-CoV2: an in silico approach to combat COVID-19. J Biomol Struct Dyn 2022; 40:2067-2081. [PMID: 33089730 PMCID: PMC7594184 DOI: 10.1080/07391102.2020.1835729] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/05/2020] [Indexed: 01/30/2023]
Abstract
COVID-19 and its causative organism SARS-CoV2 that emerged from Wuhan city, China have paralyzed the world. With no clinically approved drugs, the global health system is struggling to find an effective treatment measure. At this crucial juncture, screening of plant-derived compounds may be an effective strategy to combat COVID-19. The present study investigated the binding affinity of phytocompounds with 3-Chymotrypsin-like (3CLpro) and Papain-like proteases (PLpro) of SARS-CoV2 using in-silico techniques. A total of 32 anti-protease phytocompounds were investigated for the binding affinity to the proteins. Docking was performed in Autodock Vina. Pharmacophore descriptors of best ligands were studied using LigandScout. Molecular dynamics (MD) simulation of apo-protein and ligand-bound complexes was carried out in YASARA software. The druglikeness properties of phytocompounds were studied using ADMETlab. Out of 32 phytochemicals, amentoflavone and gallocatechin gallate showed the best binding affinity to 3CLpro (-9.4 kcal/mol) and PLpro (-8.8 kcal/mol). Phytochemicals such as savinin, theaflavin-3,3-digallate, and kazinol-A also showed strong affinity. MD simulation revealed ligand-induced conformational changes in the protein with decreased surface area and higher stability. The RMSD/F of proteins and ligands showed stability of the protein suggesting the effective binding of the ligand in both the proteins. Both amentoflavone and gallocatechin gallate possess promising druglikeness property. The present study thus suggests that Amentoflavone and Gallocatechin gallate may be potential inhibitors of 3CLpro and PLpro proteins and effective drug candidates for SARS-CoV2. However, the findings of in silico study need to be supported by in vivo studies to establish the exact mode of action.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ananta Swargiary
- Department of Zoology, Bodoland University, Kokrajhar, Assam, India
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Bioinformatics Division, Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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Bakherad Z, Bakherad H, Sepehri S, Faramarzi MA, Mahnam K, Mojtabavi S, Mahdavi M. In silico and in vitro studies of thiosemicarbazone-indole hybrid compounds as potent α-glycosidase inhibitors. Comput Biol Chem 2022; 97:107642. [PMID: 35183819 DOI: 10.1016/j.compbiolchem.2022.107642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 12/28/2021] [Accepted: 02/07/2022] [Indexed: 11/03/2022]
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19
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Patel CN, Goswami D, Jaiswal DG, Jani SP, Parmar RM, Rawal RM, Pandya HA. Excavating phytochemicals from plants possessing antiviral activities for identifying SARS-CoV hemagglutinin-esterase inhibitors by diligent computational workflow. J Biomol Struct Dyn 2022; 41:2382-2397. [PMID: 35098887 DOI: 10.1080/07391102.2022.2033642] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coronaviruses (CoVs) belong to a group of RNA viruses that cause diseases in vertebrates including. Newer and deadlier than SARS CoV-2 are sought to appear in future for which the scientific community must be prepared with the strategies for their control. Spike protein (S-protein) of all the CoVs require angiotensin-converting enzyme2 (ACE2), while CoVs also require hemagglutinin-acetylesterase (HE) glycoprotein receptor to simultaneously interact with O-acetylated sialic acids on host cells, both these interactions enable viral particle to enter host cell leading to its infection. Target inhibition of viral S-protein and HE glycoprotein receptor can lead to a development of therapy against the SARS CoV-2. The proposition is to recognize molecules from the bundle of phytochemicals of medicinal plants known to possess antiviral potentials as a lead that could interact and mask the active site of, HE glycoprotein which would ideally bind to O-acetylated sialic acids on human host cells. Such molecules can be addressed as 'HE glycoprotein blockers'. A library of 110 phytochemicals from Withania somnifera, Asparagus racemosus, Zinziber officinalis, Allium sativum, Curcuma longa and Adhatoda vasica was constructed and was used under present study. In silico analysis was employed with plant-derived phytochemicals. The molecular docking, molecular dynamics simulations over the scale of 1000 ns (1 μs) and ADMET prediction revealed that the Withania somnifera (ashwagandha) and Asparagus racemosus (shatavari) plants possessed various steroidal saponins and alkaloids which could potentially inhibit the COVID-19 virus and even other CoVs targeted HE glycoprotein receptor.
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Affiliation(s)
- Chirag N Patel
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Dharmesh G Jaiswal
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Siddhi P Jani
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Robin M Parmar
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh M Rawal
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Himanshu A Pandya
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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20
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de Menezes RPB, Viana JDO, Muratov E, Scotti L, Scotti MT. Computer-Assisted Discovery of Alkaloids with Schistosomicidal Activity. Curr Issues Mol Biol 2022; 44:383-408. [PMID: 35723407 PMCID: PMC8929062 DOI: 10.3390/cimb44010028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/08/2022] [Accepted: 01/09/2022] [Indexed: 11/28/2022] Open
Abstract
Schistosomiasis is a chronic parasitic disease caused by trematodes of the genus Schistosoma; it is commonly caused by Schistosoma mansoni, which is transmitted by Bioamphalaria snails. Studies show that more than 200 million people are infected and that more than 90% of them live in Africa. Treatment with praziquantel has the best cost–benefit result on the market. However, hypersensitivity, allergy, and drug resistance are frequently presented after administration. From this perspective, ligand-based and structure-based virtual screening (VS) techniques were combined to select potentially active alkaloids against S. mansoni from an internal dataset (SistematX). A set of molecules with known activity against S. mansoni was selected from the ChEMBL database to create two different models with accuracy greater than 84%, enabling ligand-based VS of the alkaloid bank. Subsequently, structure-based VS was performed through molecular docking using four targets of the parasite. Finally, five consensus hits (i.e., five alkaloids with schistosomicidal potential), were selected. In addition, in silico evaluations of the metabolism, toxicity, and drug-like profile of these five selected alkaloids were carried out. Two of them, namely, 11,12-methylethylenedioxypropoxy and methyl-3-oxo-12-methoxy-n(1)-decarbomethoxy-14,15-didehydrochanofruticosinate, had plausible toxicity, metabolomics, and toxicity profiles. These two alkaloids could serve as starting points for the development of new schistosomicidal compounds based on natural products.
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Affiliation(s)
- Renata Priscila Barros de Menezes
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil; (R.P.B.d.M.); (J.d.O.V.); (L.S.)
| | - Jéssika de Oliveira Viana
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil; (R.P.B.d.M.); (J.d.O.V.); (L.S.)
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Luciana Scotti
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil; (R.P.B.d.M.); (J.d.O.V.); (L.S.)
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil; (R.P.B.d.M.); (J.d.O.V.); (L.S.)
- Correspondence: ; Tel.: +55-83-998690415
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21
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Roney M, Huq AKMM, Rullah K, Hamid HA, Imran S, Islam MA, Mohd Aluwi MFF. Virtual Screening-Based Identification of Potent DENV-3 RdRp Protease Inhibitors via In-House Usnic Acid Derivative Database. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Dengue virus (DENV) is the causative agent of dengue fever, dengue hemorrhagic disease and dengue shock syndrome (DSS), transmitted predominantly in tropical and subtropical regions by Aedes aegypti. It infects millions of people and causes thousands of deaths each year, but there is no antiviral drug against DENV. Usnic acid lately piqued the interest of researchers for extraordinary biological characteristics, including antiviral activity. Based on high larvicidal activities against Aedes aegypti, this study aims to search usnic acid derivatives as novel anti-DENV agents through a combination of ligand-based and pharmacophore-based virtual screening. One hundred and sixteen (116) usnic acid derivatives were obtained from a database of 428 in-house usnic acid derivatives through pharmacophore filtering steps. Subsequent docking simulation on DENV-3 NS-5 RdRp afforded 41 compounds with a strong binding affinity towards the enzyme. The pharmacokinetics and drug likeness prediction resulted in seven hit compounds, which eventually undergo cytochrome P450 enzyme screening to obtain the lead compound, labelled as 362. In addition, molecular dynamic (MD) simulation of lead compound 362 was performed to verify the stability of the docked complex and the binding posture acquired in docking experiments. Overall, the lead compounds have shown a high fit value of pharmacophore, strong binding affinity towards RdRp enzyme, good pharmacokinetics, and drug likeness properties. The discovery of a new usnic acid derivative as a novel anti-DENV agent targeting RdRp could lead to further drug development and optimization to treat dengue.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - AKM Moyeenul Huq
- Department of Pharmacy, School of Medicine, University of Asia Pacific, 74/A, Green Road, Dhaka 1205, Bangladesh
| | - Kamal Rullah
- Kulliyyah of Pharmacy, International Islamic University Malaysia (IIUM), Jalan Sultan Ahmad Shah, 25200 Kuantan, Pahang, Malaysia
| | - Hazrulrizawati Abd Hamid
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Syahrul Imran
- Atta-ur-Rahman Institute for Natural Product Discovery, UiTM Selangor, Kampus Puncak Alam, 42300 Bandar Puncak Alam, Malaysia
| | - Md. Alimul Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University Mymensingh 2202, Bangladesh
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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22
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Razzaghi-Asl N, Hashemi N. Identification of potential antileishmanial agents via structure-based molecular simulations. J Mol Graph Model 2021; 110:108039. [PMID: 34736055 DOI: 10.1016/j.jmgm.2021.108039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/26/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Leishmaniasis is a parasitic disease with frequent annual incidence. An important issue in chemotherapy is the emergence of resistance, toxicity and lack of cost-effectiveness within current drugs. Therefore, it is of utmost importance to design effective drugs against disease. Current contribution was devoted to the in-silico analysis of binding a few flavonoids/alkaloids to relevant leishmanial targets. Docking scores were used to prioritize acquired affinities and top ranked binders were subjected to subsequent 100-ns MD simulation in explicit water. Binding trajectories revealed the tightest interaction modes for two flavonoid molecules (acerosin and nevadensin) in the uracil DNA glycolase (UDG) active site. Acerosin showed less conformational changes whereas, nevadensin interacted stably during longer simulation time. Conserved interactions of Gln205 and His331 to acerosin indicated their dominant biological role in complex stability. No conserved residues were perceived for nevadensin interactions and a completely new and stable binding conformation could be retrieved after 12 ns simulation. Moreover; acerosin was subjected to DFT analysis for pairwise decomposition evaluations of interacted residues. Although primary mechanisms of action are yet to be discovered, UDG may be a promising target for developing antileishmanial flavonoids.
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Affiliation(s)
- Nima Razzaghi-Asl
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, 5618953141, Iran.
| | - Niloufar Hashemi
- Student Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
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23
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Ahmed S, Mahtarin R, Ahmed SS, Akter S, Islam MS, Mamun AA, Islam R, Hossain MN, Ali MA, Sultana MUC, Parves MDR, Ullah MO, Halim MA. Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2. J Biomol Struct Dyn 2021; 39:6290-6305. [PMID: 32720571 PMCID: PMC7441766 DOI: 10.1080/07391102.2020.1796804] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 virus outbreak poses a major threat to humans worldwide due to its highly contagious nature. In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. The RNA-dependent RNA polymerase is a vital enzyme of coronavirus replication/transcription complex whereas the main protease acts on the proteolysis of replicase polyproteins. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. To explore the dynamic nature of the interaction, 100 ns molecular dynamics (MD) simulation is performed on the selected protein-drug complexes and apo-protein. Binding free energy of the selected drugs is performed by MM/PBSA. Besides docking and dynamics, partial least square (PLS) regression method is applied for the quantitative structure activity relationship to generate and predict the binding energy for drugs. PLS regression satisfactorily predicts the binding energy of the effective antiviral drugs compared to binding energy achieved from molecular docking with a precision of 85%. This study highly recommends researchers to screen these potential drugs in vitro and in vivo against SARS-CoV-2 for further validation of utility.
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Affiliation(s)
- Sinthyia Ahmed
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Rumana Mahtarin
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Sayeda Samina Ahmed
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shaila Akter
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md. Shamiul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Abdulla Al Mamun
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Rajib Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Nayeem Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mossammad U. C. Sultana
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - MD. Rimon Parves
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - M. Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas - Fort Smith, Fort Smith, Arkansas, USA
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24
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Yadav AK, Singh TR. Novel inhibitors design through structural investigations and simulation studies for human PKMTs (SMYD2) involved in cancer. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1957882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Arvind Kumar Yadav
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
- Centre of Excellence in Healthcare Technologies and Informatics (CHETI), Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Solan, India
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25
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Dutta M, Tareq AM, Rakib A, Mahmud S, Sami SA, Mallick J, Islam MN, Majumder M, Uddin MZ, Alsubaie A, Almalki ASA, Khandaker MU, Bradley D, Rana MS, Emran TB. Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations. BIOLOGY 2021; 10:789. [PMID: 34440024 PMCID: PMC8389631 DOI: 10.3390/biology10080789] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/05/2021] [Accepted: 08/15/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus's severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography-mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics-generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (-5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (-5.39 kcal/mol), and lorazepam, 2TMS derivative (-5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand-Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.
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Affiliation(s)
- Mycal Dutta
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (A.M.T.); (M.N.I.)
| | - Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.)
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.)
| | - Jewel Mallick
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Mohammad Nazmul Islam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (A.M.T.); (M.N.I.)
| | - Mohuya Majumder
- Drug Discovery, GUSTO A Research Group, Chittagong 4203, Bangladesh;
| | - Md. Zia Uddin
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Abdullah Alsubaie
- Department of Physics, College of Khurma, Taif University, Taif 21944, Saudi Arabia;
| | | | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (M.U.K.); (D.A.B.)
| | - D.A. Bradley
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (M.U.K.); (D.A.B.)
- Department of Physics, University of Surrey, Guilford GU2 7XH, UK
| | - Md. Sohel Rana
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; (M.D.); (J.M.); (M.Z.U.)
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26
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Sagha M, Mousaei F, Salahi M, Razzaghi-Asl N. Synthesis of new 2-aminothiazolyl/benzothiazolyl-based 3,4-dihydropyrimidinones and evaluation of their effects on adenocarcinoma gastric cell migration. Mol Divers 2021; 26:1039-1051. [PMID: 34050874 DOI: 10.1007/s11030-021-10229-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/27/2021] [Indexed: 11/26/2022]
Abstract
Gastric cancer is one of the malignant tumors of the gastrointestinal tract that, despite its decrease in recent years, is still the fourth most common cancer and the second leading cause of cancer-related death. Various strategies including chemotherapy are used to keep cancer cells from spreading and induce apoptotic death in them. Recent studies have shown that dihydropyrimidinones (DHPMs) are privileged structures in medicinal chemistry due to their pharmacological effects. A number of new 2-aminothiazolyl/benzothiazolyl derivatives of 3,4-DHPMs (3-8) were synthesized and structurally identified, and then their effects on the migration behavior of human AGS cells (gastric cancer cells) were investigated. Molecular docking and molecular dynamics (MD) simulations were applied to explore binding potential and realistic binding model of the assessed derivatives through identification of key amino acid residues within L5/α2/α3 allosteric site of kinesin 5 (Eg5) as a validated microtubule-dependent target for monastrol as a privileged DHPM derivative.
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Affiliation(s)
- Mohsen Sagha
- Research Laboratory for Embryology and Stem Cells, Department of Anatomical Sciences, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Fatemeh Mousaei
- Student Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mahtab Salahi
- Student Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Nima Razzaghi-Asl
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, 5618953141, Ardabil, Iran.
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27
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Rakib A, Nain Z, Sami SA, Mahmud S, Islam A, Ahmed S, Siddiqui ABF, Babu SMOF, Hossain P, Shahriar A, Nainu F, Emran TB, Simal-Gandara J. A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation. Brief Bioinform 2021; 22:1476-1498. [PMID: 33623995 PMCID: PMC7929402 DOI: 10.1093/bib/bbab045] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/17/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a global pandemic by the World Health Organization, and the situation worsens daily, associated with acute increases in case fatality rates. The main protease (Mpro) enzyme produced by SARS-CoV-2 was recently demonstrated to be responsible for not only viral reproduction but also impeding host immune responses. The element selenium (Se) plays a vital role in immune functions, both directly and indirectly. Thus, we hypothesised that Se-containing heterocyclic compounds might curb the activity of SARS-CoV-2 Mpro. We performed a molecular docking analysis and found that several of the selected selenocompounds showed potential binding affinities for SARS-CoV-2 Mpro, especially ethaselen (49), which exhibited a docking score of -6.7 kcal/mol compared with the -6.5 kcal/mol score for GC376 (positive control). Drug-likeness calculations suggested that these compounds are biologically active and possess the characteristics of ideal drug candidates. Based on the binding affinity and drug-likeness results, we selected the 16 most effective selenocompounds as potential anti-COVID-19 drug candidates. We also validated the structural integrity and stability of the drug candidate through molecular dynamics simulation. Using further in vitro and in vivo experiments, we believe that the targeted compound identified in this study (ethaselen) could pave the way for the development of prospective drugs to combat SARS-CoV-2 infections and trigger specific host immune responses.
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Affiliation(s)
- Ahmed Rakib
- Department of Pharmaceutical Sciences, College of Pharmacy, 881 Madison Ave, Memphis, TN 38163, USA
| | - Zulkar Nain
- Department of Biotechnology and Genetic Engineering, Islamic University, Bangladesh
| | - Saad Ahmed Sami
- Department of Biotechnology and Genetic Engineering, Islamic University, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Bangladesh
| | - Ashiqul Islam
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Bangladesh
| | - Shahriar Ahmed
- Department of Pharmacy, University of Chittagong, Bangladesh
| | | | | | - Payar Hossain
- Bachelor of Pharmacy professional degree focused in Pharmacy from University of Chittagong, Bangladesh
| | - Asif Shahriar
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, USA
| | - Firzan Nainu
- Faculty of Pharmacy Universitas Hasanuddin, Indonesia
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28
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Cruz JV, Giuliatti S, Alves LB, Silva RC, Ferreira EFB, Kimani NM, Silva CHTP, Souza JSND, Espejo-Román JM, Santos CBR. Identification of novel potential cyclooxygenase-2 inhibitors using ligand- and structure-based virtual screening approaches. J Biomol Struct Dyn 2021; 40:5386-5408. [PMID: 33427075 DOI: 10.1080/07391102.2020.1871413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cyclooxygenase 2 (COX-2) is a well-established target for the design of anti-inflammatory intermediates. Celecoxib was selected as a template molecule to perform ligand-based virtual screening, i.e. to search for structures with similarity in shape and electrostatic potential, with a gradual increase in accuracy through the combined fitting of several steps using eight commercial databases. The molecules ZINC408709 and ZINC2090319 reproduced values within the limits established in an initial study of absorption and distribution in the body. No alert was fired for possible toxic groups when these molecules were subjected to toxicity prediction. Molecular docking results with these compounds showed a higher binding affinity in comparison to rofecoxib for the COX-2 target. Additionally, ZINC408709 and ZINC2090319 were predicted to be potentially biologically active. In in silico prediction of endocrine disruption potential, it was established that the molecule ZINC2090319 binds strongly to the target related to cardiovascular risk in a desirable way as a non-steroidal antagonist and ZINC408709 binds strongly to the target that is associated with the treatment of inflammatory pathologies and similar to celecoxib. Metabolites generated from these compounds are less likely to have side effects. Simulations were used to evaluate the interaction of compounds with COX-1 and COX-2 during 200 ns. Despite the differences, ZINC408709 molecule showed better stability for COX-2 during molecular dynamics simulation. In the calculations of free energy MM/PBSA, the molecule ZINC408709 ΔGbind value has a higher affinity to celecoxib and rofecoxib COX-2. This demonstrates that the selected substances can be considered as promising COX-2 inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Josiane V Cruz
- Graduate Program in Pharmaceutical Innovation, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil.,Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
| | - Silvana Giuliatti
- Bioinformatics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Levy B Alves
- Bioinformatics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Raí C Silva
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP, Brazil
| | - Elenilze F B Ferreira
- Graduate Program in Pharmaceutical Innovation, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil.,Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil.,Laboratory of Organic Chemistry and Biochemistry, University of the State of Amapá, Macapá, Brazil
| | - Njogu M Kimani
- Department of Physical Sciences, University of Embu, Embu, Kenya
| | - Carlos H T P Silva
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP, Brazil.,Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - João S N de Souza
- Department of Chemistry, Federal University of Piaui, Teresina, Brazil
| | - José M Espejo-Román
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Biosanitary Institute of Granada (Ibs.GRANADA), University of Granada, Granada, Spain
| | - Cleydson B R Santos
- Graduate Program in Pharmaceutical Innovation, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil.,Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
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29
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Muthumanickam S, Indhumathi T, Boomi P, Balajee R, Jeyakanthan J, Anand K, Ravikumar S, Kumar P, Sudha A, Jiang Z. In silico approach of naringin as potent phosphatase and tensin homolog (PTEN) protein agonist against prostate cancer. J Biomol Struct Dyn 2020; 40:1629-1638. [PMID: 33034258 DOI: 10.1080/07391102.2020.1830855] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Prostate cancer (PC) is one of the major impediments affecting men, which leads approximately 31,620 deaths in both developing and developed countries. Although some chemotherapy drugs have been reported for prostate cancer, they are not effective due to the lack of safety, efficacy and low selectivity. Hence, the novel alternative anticancer agents with remarkable effect are highly appreciable. Natural plants contain several bio-active compounds which have been traditionally used for the various medical treatments. Particularly, naringin is a natural bio-active compound commonly found in the citrus fruits, which have shown numerous biological activities. Phosphatase and tensin homolog (PTEN) is a tumor suppressor gene, which activates both lipid phosphates and protein phosphates. The PTEN gene is negative regulator of PI3K/AKT/mTOR pathways, since, this signaling pathway play an essential role in the cell survival, proliferation and migration. In the present in silico investigation, structure based virtual screening, molecular docking, molecular dynamics simulation and Adsorption, Distribution, Metabolism, Excretion (ADME) prediction were employed to determine the binding affinity, stability and drug likeness properties of top ranked screened compounds and naringin, respectively. The results revealed that the complex has good molecular interactions, binding stability (peak between 0.3 and 0.4 nm) and no violations in the Lipinski Rule of 5 in naringin, but the screened compounds violated the drug likeness properties. From the in silico analyses, it is identified that naringin compound might assist in the development of novel therapeutic candidate against prostate cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Pandi Boomi
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | | | - Krishnan Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences and National Health Laboratory Service, University of the Free State, Bloemfontein, South Africa
| | - Sundaram Ravikumar
- Department of Biomedical Science, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ponnuchamy Kumar
- Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Arumugam Sudha
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, Tamil Nadu, India
| | - Zhihui Jiang
- School of life Science, Department of Biotechnology, Anyang Institute of Technology, Henan, China
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30
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Jiménez-Alberto A, Ribas-Aparicio RM, Aparicio-Ozores G, Castelán-Vega JA. Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors. Comput Biol Chem 2020; 88:107325. [PMID: 32623357 PMCID: PMC7316061 DOI: 10.1016/j.compbiolchem.2020.107325] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/30/2020] [Accepted: 06/25/2020] [Indexed: 12/28/2022]
Abstract
The global emergency caused by COVID-19 makes the discovery of drugs capable of inhibiting SARS-CoV-2 a priority, to reduce the mortality and morbidity of this disease. Repurposing approved drugs can provide therapeutic alternatives that promise rapid and ample coverage because they have a documented safety record, as well as infrastructure for large-scale production. The main protease of SARS-CoV-2 (Mpro) is an excellent therapeutic target because it is critical for viral replication; however, Mpro has a highly flexible active site that must be considered when performing computer-assisted drug discovery. In this work, potential inhibitors of the main protease (Mpro) of SARS-Cov-2 were identified through a docking-assisted virtual screening procedure. A total of 4384 drugs, all approved for human use, were screened against three conformers of Mpro. The ligands were further studied through molecular dynamics simulations and binding free energy analysis. A total of nine currently approved molecules are proposed as potential inhibitors of SARS-CoV-2. These molecules can be further tested to speed the development of therapeutics against COVID-19.
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Affiliation(s)
- Alicia Jiménez-Alberto
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico.
| | - Rosa María Ribas-Aparicio
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico.
| | - Gerardo Aparicio-Ozores
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico.
| | - Juan A Castelán-Vega
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico.
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Monteiro AFM, Scotti MT, Speck-Planche A, Barros RPC, Scotti L. In Silico Studies for Bacterystic Evaluation against Staphylococcus aureus of 2-Naphthoic Acid Analogues. Curr Top Med Chem 2020; 20:293-304. [DOI: 10.2174/1568026619666191206111742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/01/2019] [Accepted: 09/10/2019] [Indexed: 01/27/2023]
Abstract
Background:
Staphylococcus aureus is a gram-positive spherical bacterium commonly present in
nasal fossae and in the skin of healthy people; however, in high quantities, it can lead to complications that
compromise health. The pathologies involved include simple infections, such as folliculitis, acne, and delay in
the process of wound healing, as well as serious infections in the CNS, meninges, lung, heart, and other areas.
Aim:
This research aims to propose a series of molecules derived from 2-naphthoic acid as a bioactive in the
fight against S. aureus bacteria through in silico studies using molecular modeling tools.
Methods:
A virtual screening of analogues was done in consideration of the results that showed activity according
to the prediction model performed in the KNIME Analytics Platform 3.6, violations of the Lipinski
rule, absorption rate, cytotoxicity risks, energy of binder-receptor interaction through molecular docking, and
the stability of the best profile ligands in the active site of the proteins used (PDB ID 4DXD and 4WVG).
Results:
Seven of the 48 analogues analyzed showed promising results for bactericidal action against S.
aureus.
Conclusion:
It is possible to conclude that ten of the 48 compounds derived from 2-naphthoic acid presented
activity based on the prediction model generated, of which seven presented no toxicity and up to one violation
to the Lipinski rule.
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Affiliation(s)
| | - Marcus Tullius Scotti
- Federal University of Paraíba, Health Science Center, 50670-910, Joao Pessoa, PB, Brazil
| | - Alejandro Speck-Planche
- Department of Chemistry, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8, b. 2, 119992, Moscow, Russian Federation
| | | | - Luciana Scotti
- Federal University of Paraíba, Health Science Center, 50670-910, Joao Pessoa, PB, Brazil
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Heidarpoor Saremi L, Ebrahimi A, Lagzian M. Identification of new potential cyclooxygenase-2 inhibitors: insight from high throughput virtual screening of 18 million compounds combined with molecular dynamic simulation and quantum mechanics. J Biomol Struct Dyn 2020; 39:1717-1734. [PMID: 32122267 DOI: 10.1080/07391102.2020.1737574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cyclooxygenase isoenzymes (COX-1 and COX-2) have a critical role in inflammation, fever, and pain. In contrary to COX-1, COX-2 is specifically expressed in inflamed tissues. Because of the subtle difference between both enzyme active sites, targeting COX-2 represents an efficient strategy for the development of novel inhibitors against inflammation with fewer side effects. In order to identify potential inhibitors of COX-2, more than 18,000,000 small molecules were retrieved from the ZINC database and virtually screened against it with a gradual increase in the precision through combined multistep docking. The results were sorted according to the rank-by-rank, induced-fit docking, and MM-GBSA evaluation. Subsequently from the final hit list, two top hits along with an approved selective inhibitor (celecoxib) were further investigated by the molecular dynamics (MD) simulations. The results were indicated that ZINC16934653 and ZINC40484701 demonstrate the highest affinity for the COX-2 binding pocket. Both ligands were bound to the important active-site residues, which are necessary for the correct orientation of inhibitors inside the binding cavity. Their binding free energies were comparable to celecoxib. 100 ns MD simulation is revealed that ZINC40484701 is more preferred in comparison with ZINC16934653 and celecoxib. In addition, non-covalent interactions between the compounds and key residues located in 6 Å distance from the COX-2 binding site show similar patterns of bonding by the reduced density gradient and the independent gradient model. Therefore, ZINC40484701 can be a potential candidate for further in vitro and in vivo analysis after lead-optimization efforts.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Leily Heidarpoor Saremi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ali Ebrahimi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Milad Lagzian
- Department of Biology, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
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Trivedi M, Vaidya D, Patel C, Prajapati S, Bhatt J. In silico and in vitro studies to elucidate the role of 1HYN and 1QKI activity in BPA induced toxicity and its amelioration by Gallic acid. CHEMOSPHERE 2020; 241:125076. [PMID: 31683422 DOI: 10.1016/j.chemosphere.2019.125076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/10/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Bisphenol A (BPA) is well known as an artificial environmental endocrine disrupting (ED) chemical. BPA also leads to many deleterious impacts on human blood through the production of reactive oxygen species and by some unknown mechanism. Up to now, very few studies have been conducted to assess the impact of BPA on Red Blood Corpuscle (RBC), Complete Blood Count (CBC), and no study on 1HYN (Erythrocyte Band 3 membrane protein) and 1QKI (Human Glucose 6 Phosphate Dehydrogenase) have been so far carried out. Besides, no study has been conducted to assess the ameliorating impact of the most commonly available antioxidant like Gallic Acid (GA). The present investigation revealed that BPA exposure (50-200 μg ml-1) causes significant increase in percent hemolysis and morphological alteration of RBC, as well as significant reduction in CBC except White Blood Cell (WBC), Platelet, and Red blood density width (RDW). BPA exposure also caused a significant reduction in G6PD activity. In silico docking study revealed that BPA effectively binds with 1HYN and 1QKI protein to alter its activity. Concurrent addition of GA (10-50 μg ml-1) with highest dose of BPA (200 μg ml-1) ameliorates all parameters significantly as compared to BPA (200 μg ml-1) treatment. Ameliorating effect of GA is mainly due to its antioxidant property and interaction with BPA, was confirmed using UV-VIS-NIR Spectrophotometric, molecular dynamic simulation and docking approach by YASARA software.
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Affiliation(s)
- Mrugesh Trivedi
- Molecular Ecology and Toxicology Laboratory, Department of Earth and Environmental Science, KSKV Kachchh University, Bhuj-Kachchh, Gujarat, India.
| | - Druma Vaidya
- Molecular Ecology and Toxicology Laboratory, Department of Earth and Environmental Science, KSKV Kachchh University, Bhuj-Kachchh, Gujarat, India
| | - Chirag Patel
- Department of Bioinformatics, Gujarat University, Ahmedabad, India
| | - Sagar Prajapati
- Molecular Ecology and Toxicology Laboratory, Department of Earth and Environmental Science, KSKV Kachchh University, Bhuj-Kachchh, Gujarat, India
| | - Jyotindra Bhatt
- Department of Chemistry, KSKV Kachchh University, Bhuj-Kachchh, India
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Three-component synthesis of chromeno β-lactam hybrids for inflammation and cancer screening. Eur J Med Chem 2019; 179:389-403. [DOI: 10.1016/j.ejmech.2019.06.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022]
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Barros RPC, Scotti L, Scotti MT. Exploring Secondary Metabolites Database of Apocynaceae, Menispermaceae, and Annonaceae to Select Potential Anti-HCV Compounds. Curr Top Med Chem 2019; 19:900-913. [PMID: 31074368 DOI: 10.2174/1568026619666190510094228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Hepatitis C is a disease that constitutes a serious global health problem, is often asymptomatic and difficult to diagnose and about 60-80% of infected patients develop chronic diseases over time. As there is no vaccine against hepatitis C virus (HCV), developing new cheap treatments is a big challenge. OBJECTIVE The search for new drugs from natural products has been outstanding in recent years. The aim of this study was to combine structure-based and ligand-based virtual screening (VS) techniques to select potentially active molecules against four HCV target proteins from in-house secondary metabolite dataset (SistematX). MATERIALS AND METHODS From the ChEMBL database, we selected four sets of 1199, 355, 290 and 237chemical structures with inhibitory activity against different targets of HCV to create random forest models with an accuracy value higher than 82% for cross-validation and test sets. Afterward, a ligandbased virtual screen of the entire 1848 secondary metabolites database stored in SistematX was performed. In addition, a structure-based virtual screening was also performed for the same set of secondary metabolites using molecular docking. RESULTS Finally, using consensus analyses approach combining ligand-based and structure-based VS, three alkaloids were selected as potential anti-HCV compounds. CONCLUSION The selected structures are a starting point for further studies in order to develop new anti- HCV compounds based on natural products.
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Affiliation(s)
- Renata P C Barros
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, Brazil
| | - Luciana Scotti
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, Brazil
| | - Marcus T Scotti
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, Brazil
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Sillapachaiyaporn C, Chuchawankul S. HIV-1 protease and reverse transcriptase inhibition by tiger milk mushroom ( Lignosus rhinocerus) sclerotium extracts: In vitro and in silico studies. J Tradit Complement Med 2019; 10:396-404. [PMID: 32695657 PMCID: PMC7365780 DOI: 10.1016/j.jtcme.2019.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/22/2022] Open
Abstract
Background and aim Lignosus rhinocerus (LR) is an edible mushroom with a variety of medicinal properties such as neurostimulation, immunomodulation, anti-inflammation, anti-oxidation, anti-proliferation, anti-diabetes and especially antiviral activity. Human immunodeficiency virus type-1 (HIV-1) needs the HIV-1 protease (PR) and reverse transcriptase (RT) for its replication. Therefore, both HIV-1 PR and RT are important targets for antiretroviral drug development. Experimental procedure The crude hexane (LRH), ethanol (LRE) and water (LRW) extracts of LR were in vitro screened for inhibitory activity against HIV-1 PR and RT, then anti-HIV-1 activity on the infected MOLT-4 cells were determined. Chemical constituents of the extracts were identified by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography (LC)-MS. The identified compounds were in silico analysed for drug-likeness property and molecular modelling. Results and conclusion According to our screening assays, LRE and LRW significantly inhibited both enzymes (25–55%), while LRH suppressed only the HIV-1 PR activity (88.97%). At 0.5 mg/ml of LRW showed significant inhibition of HIV-1 induced syncytial formation and p24 production in the infected MOLT-4 cells. Investigation of chemical analysis revealed that major groups of identified constituents found in the extracts were fatty acids, peptides and terpenoids. In silico analysis showed that heliantriol F and 6 alpha-fluoroprogesterone displayed great binding energies with HIV-1 PR and HIV-1 RT, respectively. These findings suggest that LR could be a potential source of compounds to inhibit HIV-1 PR and/or RT activities in vitro. Furthermore, our results provide beneficial data for the development of novel HIV-1 PR and RT inhibitors. The hexane extract of L. rhinocerus strongly inhibited HIV-1 PR activity. The ethanol and water extracts of L. rhinocerus showed HIV-1 PR and RT inhibitions. Chemical constituents of L. rhinocerus could block HIV-1 PR and RT in silico studies.
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Affiliation(s)
- Chanin Sillapachaiyaporn
- Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Siriporn Chuchawankul
- Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand.,Immunomodulation of Natural Products Research Group, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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Ramírez-Marroquín OA, Manzano-Pérez F, López-Torres A, Hernández-López A, Cortés-Pacheco A, Reyes-González MA. First mechanosynthesis of piperlotines A, C, and derivatives through solvent-free Horner-Wadsworth-Emmons reaction. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2018.1550204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | | | | | | | | | - Miguel Angel Reyes-González
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza Nuevo León, Mexico
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Synthesis and in vivo anti- or pro-inflammatory activity of new bisphosphonates and vinylphosphonates. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-018-2328-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Cytotoxic Desulfated Saponin from Holothuria atra Predicted to Have High Binding Affinity to the Oncogenic Kinase PAK1: A Combined In Vitro and In Silico Study. Sci Pharm 2018; 86:scipharm86030032. [DOI: 10.3390/scipharm86030032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 11/16/2022] Open
Abstract
Sea cucumbers have long been utilized in foods and Asiatic folk medicines for their nutritive and health benefits. Herein, three sea cucumber species were investigated and Holothuria atra showed the highest cytotoxicity among these. Next, a desulfated saponin, desulfated echinoside B (DEB), was purified from H. atra through bioassay-guided fractionation. LC-ESI-MS (Liquid chromatography-electrospray ionization mass spectrometry) analysis also showed H. atra to be a rich source of saponins. DEB showed cytotoxicity on cancer cells with IC50 values of 0.5–2.5 µM, and on brine shrimps with an IC50 value of 9.2 µM. In molecular docking studies, DEB was found to bind strongly with the catalytic domain of PAK1 (p21-activated kinase 1) and it showed binding energy of −8.2 kcal/mol compared to binding energy of −7.7 kcal/mol for frondoside A (FRA). Both of them bind to the novel allosteric site close to the ATP-binding cleft. Molecular dynamics (MD) simulation demonstrated that DEB can form a more stable complex with PAK1, remaining inside the allosteric binding pocket and forming the maximum number of hydrogen bonds with the surrounding residues. Moreover, important ligand binding residues were found to be less fluctuating in the DEB-PAK1 complex than in the FRA-PAK1 complex throughout MD simulation. Our experimental and computational studies showed that both DEB and FRA can act as natural allosteric PAK1 inhibitors and DEB appeared to be more promising than FRA.
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