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Shah SK, Chaple DD, Masand VH, Jawarkar RD, Chaudhari S, Abiramasundari A, Zaki MEA, Al-Hussain SA. Multi-Target In-Silico modeling strategies to discover novel angiotensin converting enzyme and neprilysin dual inhibitors. Sci Rep 2024; 14:15991. [PMID: 38987327 PMCID: PMC11237057 DOI: 10.1038/s41598-024-66230-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Cardiovascular diseases, including heart failure, stroke, and hypertension, affect 608 million people worldwide and cause 32% of deaths. Combination therapy is required in 60% of patients, involving concurrent Renin-Angiotensin-Aldosterone-System (RAAS) and Neprilysin inhibition. This study introduces a novel multi-target in-silico modeling technique (mt-QSAR) to evaluate the inhibitory potential against Neprilysin and Angiotensin-converting enzymes. Using both linear (GA-LDA) and non-linear (RF) algorithms, mt-QSAR classification models were developed using 983 chemicals to predict inhibitory effects on Neprilysin and Angiotensin-converting enzymes. The Box-Jenkins method, feature selection method, and machine learning algorithms were employed to obtain the most predictive model with ~ 90% overall accuracy. Additionally, the study employed virtual screening of designed scaffolds (Chalcone and its analogues, 1,3-Thiazole, 1,3,4-Thiadiazole) applying developed mt-QSAR models and molecular docking. The identified virtual hits underwent successive filtration steps, incorporating assessments of drug-likeness, ADMET profiles, and synthetic accessibility tools. Finally, Molecular dynamic simulations were then used to identify and rank the most favourable compounds. The data acquired from this study may provide crucial direction for the identification of new multi-targeted cardiovascular inhibitors.
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Affiliation(s)
- Sapan K Shah
- Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Hingna Road, Nagpur, 440016, Maharashtra, India.
| | - Dinesh D Chaple
- Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Hingna Road, Nagpur, 440016, Maharashtra, India
| | - Vijay H Masand
- Department of Chemistry, Vidya Bharati Mahavidyalaya, Amravati, 444602, Maharashtra, India
| | - Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr. Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, 444603, India
| | - Somdatta Chaudhari
- Department of Pharmaceutical Chemistry, Modern College of Pharmacy, Nigdi, Pune, India
| | | | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, 11623, Saudi Arabia.
| | - Sami A Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, 11623, Saudi Arabia
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2
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Kadsanit N, Worsawat P, Sakonsinsiri C, McElroy CR, Macquarrie D, Noppawan P, Hunt AJ. Sustainable methods for the carboxymethylation and methylation of ursolic acid with dimethyl carbonate under mild and acidic conditions. RSC Adv 2024; 14:16921-16934. [PMID: 38799212 PMCID: PMC11124730 DOI: 10.1039/d4ra02122c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Ursolic acid is a triterpene plant extract that exhibits significant potential as an anti-cancer, anti-tumour, and anti-inflammatory agent. Its direct use in the pharmaceutical industry is hampered by poor uptake of ursolic acid in the human body coupled with rapid metabolism causing a decrease in bioactivity. Modification of ursolic acid can overcome such issues, however, use of toxic reagents, unsustainable synthetic routes and poor reaction metrics have limited its potential. Herein, we demonstrate the first reported carboxymethylation and/or methylation of ursolic acid with dimethyl carbonate (DMC) as a green solvent and sustainable reagent under acidic conditions. The reaction of DMC with ursolic acid, in the presence of PTSA, ZnCl2, or H2SO4-SiO2 yielded the carboxymethylation product 3β-[[methoxy]carbonyl]oxyurs-12-en-28-oic acid, the methylation product 3β-methoxyurs-12-en-28-oic acid and the dehydration product urs-2,12-dien-28-oic acid. PTSA demonstrated high conversion and selectivity towards the previously unreported carboxymethylation of ursolic acid, while the application of formic acid in the system led to formylation of ursolic acid (3β-formylurs-12-en-28-oic acid) in quantitative yields via esterification, with DMC acting solely as a solvent. Meanwhile, the methylation product of ursolic acid, 3β-methoxyurs-12-en-28-oic acid, was successfully synthesised with FeCl3, demonstrating exceptional conversion and selectivity, >99% and 99%, respectively. Confirmed with the use of qualitative and quantitative green metrics, this result represents a significant improvement in conversion, selectivity, safety, and sustainability over previously reported methods of ursolic acid modification. It was demonstrated that these methods could be applied to other triterpenoids, including corosolic acid. The study also explored the potential pharmaceutical applications of ursolic acid, corosolic acid, and their derivatives, particularly in anti-inflammatory, anti-cancer, and anti-tumour treatments, using molecular ADMET and docking methods. The methods developed in this work have led to the synthesis of novel molecules, thus creating opportunities for the future investigation of biological activity and the modification of a wide range of triterpenoids applying acidic DMC systems to deliver novel active pharmaceutical intermediates.
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Affiliation(s)
- Nuttapong Kadsanit
- Materials Chemistry Research Center (MCRC), Department of Chemistry and Centre of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Pattamabhorn Worsawat
- Materials Chemistry Research Center (MCRC), Department of Chemistry and Centre of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University Khon Kaen 40002 Thailand
| | - Con R McElroy
- School of Chemistry, University of Lincoln Brayford Pool Campus Lincoln LN6 7TS UK
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Duncan Macquarrie
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Pakin Noppawan
- Department of Chemistry, Faculty of Science, Mahasarakham University Maha Sarakham 44150 Thailand
| | - Andrew J Hunt
- Materials Chemistry Research Center (MCRC), Department of Chemistry and Centre of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
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3
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Sonker P, Tamang R, Mehata AK, Nidhar M, Sharma VP, Kumar V, Muthu MS, Koch B, Tewari AK. PTSA-induced synthesis, in silico and nano study of novel ethylquinolin-thiazolo-triazole in cervical cancer. Future Med Chem 2024; 16:751-767. [PMID: 38596902 PMCID: PMC11221538 DOI: 10.4155/fmc-2023-0344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/23/2024] [Indexed: 04/11/2024] Open
Abstract
Aim: p-Toluenesulfonic acid-(PTSA) and grinding-induced novel synthesis of ethylquinolin-thiazolo-triazole derivatives was performed using green chemistry. Materials & methods: Development of a nanoconjugate drug-delivery system of ethylquinolin-thiazolo-triazole was carried out with D-α-tocopheryl polyethylene glycol succinate (TPGS) and the formulation was further characterized by transmission electron microscopy, atomic force microscopy, dynamic light scattering and in vitro drug release assay. The effect of 3a nanoparticles was assessed against a cervical cancer cell line (HeLa) through the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, and the effect on apoptosis was determined. Results & discussion: The 3a nanoparticles triggered the apoptotic mode of cell death after increasing the intracellular reactive oxygen level by enhancing cellular uptake of micelles. Furthermore, in silico studies revealed higher absorption, distribution, metabolism, elimination and toxicity properties and bioavailability of the enzyme tyrosine protein kinase. Conclusion: The 3a nanoparticles enhanced the therapeutic potential and have higher potential for targeted drug delivery against cervical cancer.
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Affiliation(s)
- Priyanka Sonker
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Rupen Tamang
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Abhishesh K Mehata
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Manisha Nidhar
- Amrita school of pharmacy, Amrita Vishwa Vidhyapeetham, AIMS, Health Science Campus, Kochi, 682041, India
| | - Vishal P Sharma
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Vipin Kumar
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Madaswamy S Muthu
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Biplob Koch
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ashish K Tewari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
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4
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Sharma P, Joshi T, Joshi T, Mathpal S, Maiti P, Nand M, Chandra S, Tamta S. In silico screening of natural compounds to inhibit interaction of human ACE2 receptor and spike protein of SARS-CoV-2 for the prevention of COVID-19. J Biomol Struct Dyn 2023; 41:646-658. [PMID: 34854365 DOI: 10.1080/07391102.2021.2010599] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A computational investigation was carried out to find out potential phytochemicals that could inhibit the binding of human angiotensin-converting enzyme-2 (ACE2) receptors to spike protein of SARS-CoV-2 which is an essential step to gain entry inside human cells and onset of viral infection known as Coronavirus disease (COVID-19). A library of phytochemicals was screened by virtual screening against ACE2 receptors resulting in twenty phytochemicals out of 686 which had binding energy (-11.8 to -6.9 kcal/mol). Drug-likeness gave five hits, but ADMET analysis yielded 4 nontoxic hit phytochemicals. Molecular dynamics simulation of four-hit compounds resulted in acceptable stability and good dynamics behavior. These phytochemicals are Hinokinin, Gmelanone, Isocolumbin, and Tinocordioside, from Vitis vinifera, Gmelina arborea, and Tinospora cordifolia. The above-mentioned phytochemicals may be promising ACE2 inhibitors and can prevent infection of SARS-CoV-2 by inhibiting the entry of the virus into host cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Sharma
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Tanuja Joshi
- Department of Botany, S.S.J Campus, Kumaun University, Almora, Uttarakhand, India
| | - Tushar Joshi
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Bhimtal, Uttarakhand, India
| | - Shalini Mathpal
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Bhimtal, Uttarakhand, India
| | - Priyanka Maiti
- Center for Environmental Assessment and Climate Change, G.B. Pant National Institute of Himalayan Environment, Kosi, Katarmal, Almora
| | - Mahesh Nand
- ENVIS Center on Himalayn Ecology, G.B. Pant National Institute of Himalayan Environment, Kosi, Katarmal, Almora
| | - Subhash Chandra
- Department of Botany, S.S.J Campus, Kumaun University, Almora, Uttarakhand, India.,Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Sushma Tamta
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, India
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5
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Pundir H, Joshi T, Pant M, Bhat S, Pandey J, Chandra S, Tamta S. Identification of SARS-CoV-2 RNA dependent RNA polymerase inhibitors using pharmacophore modelling, molecular docking and molecular dynamics simulation approaches. J Biomol Struct Dyn 2022; 40:13366-13377. [PMID: 34637693 DOI: 10.1080/07391102.2021.1987329] [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: 01/18/2023]
Abstract
The RNA-dependent RNA polymerase (RdRp) is one of the crucial enzymes in severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) catalysing the replication of RNA, therefore acts as a potential target for antiviral drug design. The fixation of a ligand in the active site of RdRp may alter the SARS-CoV-2 life cycle. Present work aimed at identifying novel inhibitors of the SARS-CoV-2 RdRp enzyme by performing pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation (MDS). Initially, the pharmacophore model of SARS-CoV-2 RdRp was constructed and the resulting model was used to screen compounds from ChEMBL, ZINC and PubChem databases. During the investigation, 180 compounds were screened using the above model and subjected to molecular docking with RdRp. Two compounds viz. ChEMBL1276156 and PubChem135548348 showed a strong binding affinity with RdRp than its standard inhibitor, Remdesivir. Toxicity prediction of these two compounds reveals their non-toxic nature. These compounds were further subjected to MDS for 100 ns to check their stability after binding with RdRp. The MDS of RdRp-ChEMBL1276156 and RdRp-PubChem135548348 complexes show enhanced stability in comparison to the RdRp-Remdesivir complex. The average interaction energy calculated after 100 ns of MDS was -146.56 and -172.68 KJ mol-1 for RdRp-CHEMBL1276156 complex and RdRp-PubChem135548348 complex, respectively, while -59.90 KJ mol-1 for RdRp-Remdesivir complex. The current investigation reveals that these two compounds are potent inhibitors of SARS-CoV-2 RdRp and they could be tested in the experimental condition to evaluate their efficacy against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hemlata Pundir
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Manish Pant
- Department of Post-Harvest Process and Food Engineering, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Sunaullah Bhat
- Insect Biosystematics & Insect-Pest Management Laboratory, Department of Zoology, Kumaun University-SSJ Campus, Almora, Uttarakhand, India
| | - Jyoti Pandey
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Sushma Tamta
- Department of Botany, D.S.B Campus, Kumaun University, Nainital, Uttarakhand, India
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6
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Chandel S, Singh R, Gautam A, Ravichandiran V. Screening of Azadirachta indica phytoconstituents as GSK-3β inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study. J Biomol Struct Dyn 2022; 40:12827-12840. [PMID: 34569452 DOI: 10.1080/07391102.2021.1977705] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycogen synthase kinase-3 (GSK-3), a constitutively active serine/threonine kinase, primary regulator of various cellular activities varying from glycogen metabolism to cell proliferation and regulation. GSK-3β is associated with the pathogenesis of numerous human diseases, including cancer, metabolic disorder, and Alzheimer's disease. In this study, Azadirachta indica compounds were selected and further screened on the BOILED-Egg model. The compounds showing good GIT absorption were docked with the crystal structure of GSK-3β. The compounds with high docking score were submitted for the molecular dynamic simulation (MDS) and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA). Based upon the MDS and MM-PBSA study, gedunin showed the highest binding energy throughout the MDS process. Gedunin was isolated from the Azadirachta indica, and its efficacy on GSK-3β inhibition was studied in the human neuroblastoma (SH-SY5Y) cells. Gedunin induced apoptosis and anti-proliferative activity by arresting G2/M phase, as evident by cell-cycle analysis. From immunoblot study, gedunin significantly enhanced the expression of an inhibitory form of GSK-3β (p-GSK-3β Ser9) in concentration-dependent manner. Our findings demonstrate that gedunin may act as an effective GSK-3β inhibitor suggesting that this compound may be used for the management of neuroblastoma. Further preclinical and clinical investigation is desirable.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivani Chandel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
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7
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Sharma P, Joshi T, Mathpal S, Chandra S, Tamta S. In silico identification of antidiabetic target for phytochemicals of A. marmelos and mechanistic insights by molecular dynamics simulations. J Biomol Struct Dyn 2022; 40:10543-10560. [PMID: 34225570 DOI: 10.1080/07391102.2021.1944910] [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: 12/25/2022]
Abstract
The leaves and fruits of Aegle marmelos (L.) have antidiabetic activity. However, the mode of action and molecules having antidiabetic activity are not known. Hence, we conducted molecular docking of phytochemicals with various molecular antidiabetic targets to find the same. Docking prioritized Dipeptidyl peptidase-4 (DPP-4) as the main target for phytochemicals of Aegle marmelos. DPP-4 inactivates intestinal peptides, glucagon-like peptide-1 (GLP-1), and Gastric inhibitory polypeptide (GIP). GLP-1 and GIP stimulate a decline in blood glucose levels, but DPP-4 inhibits their functions resulting high level of glucose. Hence inhibiting the activity of DPP-4 is a well-known strategy to treat Type 2 diabetes. Therefore, to find a mechanism that may be involved to act as a natural inhibitor of DPP-4, we screened five phytochemicals out of seventy-three based on Virtual Screening, ADMET Drug-likeness analysis, and PAINS filtering. Further, all five phytochemicals, i.e. Aegeline, Citral, Marmesinin, Auraptene, β-Bisabolene, and reference compound subjected MDS for analyzing the stability of docked complexes to assess the fluctuation and conformational changes during protein-ligand interaction. The values of RMSD, RG, RMSF, SASA, and Gibbs energy revealed the good stability of these phytochemicals in the active site pocket of DPP-4 in comparison to reference. Additionally, we have done the pharmacophore analysis, which revealed many common pharmacophore features between screened phytochemicals of A. marmelos and reference molecule. Our results show that these phytochemicals are potential antidiabetic candidates and can be further modified and evaluated to develop more effective antidiabetic drugs against DPP-4 to treat Type 2 Diabetes. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Sharma
- Department of Botany, D.S.B. Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Tushar Joshi
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Shalini Mathpal
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, S.S.J Campus, Almora, Kumaun University, Nainital, Uttarakhand, India.,Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Sushma Tamta
- Department of Botany, D.S.B. Campus, Kumaun University, Nainital, Uttarakhand, India
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8
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Mathpal S, Sharma P, Joshi T, Joshi T, Pande V, Chandra S. Screening of potential bio-molecules from Moringa olifera against SARS-CoV-2 main protease using computational approaches. J Biomol Struct Dyn 2022; 40:9885-9896. [PMID: 34151733 DOI: 10.1080/07391102.2021.1936183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
COVID-19 caused by SARS-CoV-2 is responsible for the deaths of millions of people worldwide. It is having devastating effects on the people of all countries. In this regard, the phytochemicals of medicinal plants could be explored to prevent this disease. M. oleifera is a miracle plant with antibacterial, antiviral, and antioxidant properties because of its high content of flavonoids, glucosides and glucosinolates. Therefore, we constructed a library of 294 phytochemicals of M. oleifera and filtered it through the FAF-Drugs4. Further, molecular docking studies of filtered phytochemicals were performed with Mpro enzyme to investigate the binding interactions. Drug likeness properties, ADMET prediction were analyzed to determine the therapeutic aspect of these compounds. Based on the binding energy score of the top 4 compounds, the results indicate that Vicenin-2 has the highest binding affinity (-8.6 kcal mol-1) as compared to the reference molecule (-8.4 kcal mol-1). ADMET result reveals that all top four compounds have minimal toxic effects and good absorption. Further, 500 ns molecular dynamics simulation of the top four compounds showed that Kaempferol-3-O-rutinoside and Vitexin have good stability with Mpro. These two compounds were then subjected for MMPBSA (last 50 ns) calculation to analyze the protein-ligand stability and dynamic behavior. Kaempferol-3-O-rutinoside and Vitexin showed very good binding free energy i.e. -40.136 kJ mol-1 and -26.784 kJ mol-1, respectively. Promising outcomes from MD simulations evidence the worth of these compounds for future drug development to combat coronavirus disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shalini Mathpal
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India
| | - Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Tanuja Joshi
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India.,Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India.,Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India.,Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India.,Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India
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9
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Xiao L. A Review: Meridianins and Meridianins Derivatives. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248714. [PMID: 36557848 PMCID: PMC9781522 DOI: 10.3390/molecules27248714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Meridianins are a family of indole alkaloids derived from Antarctic tunicates with extensive pharmacological activities. A series of meridianin derivatives had been synthesized by drug researchers. This article reviews the extraction and purification methods, biological activities and pharmacological applications, pharmacokinetic characters and chemical synthesis of meridianins and their derivatives. And prospects on discovering new bioactivities of meridianins and optimizing their structure for the improvement of the ADMET properties are provided.
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Affiliation(s)
- Linxia Xiao
- School of Pharmacology, Jiangsu Vocational College of Medicine, Yancheng 224005, China
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10
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Exploring the phytoconstituents targeting TNF-α as potential lead compounds to treat inflammatory diseases: an in-silico approach. DIGITAL CHINESE MEDICINE 2022. [DOI: 10.1016/j.dcmed.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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11
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Fonseca SA, Cunha AL, Lima FCA, Silva MSCE, Silva KWL, Araújo MV, Moreira MSA, Bento ES, Sabino AR, Rocha TJM, Ferreira RCS, Costa JGD, Santos AF, Santana AEG. Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire. BRAZ J BIOL 2022; 82:e256261. [PMID: 35894349 DOI: 10.1590/1519-6984.256261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/29/2022] [Indexed: 11/22/2022] Open
Abstract
Interest in antiviral plant species has grown exponentially and some have been reported to have anti-HIV properties. This research aims to perform the bio-guided phytochemical fractionation by antiretroviral activity of Lafoensia pacari stem barks. This in vitro experimental study involved the preparation of plant material, obtention of ethanolic extract, fractionation, purification, identification and quantification of fractions, acid-base extraction, nuclear magnetic resonance, HIV-1 RT inhibition test and molecular docking studies. From the bio-guided fractionation by the antiretroviral activity there was a higher activity in the acetanolic subfractions, highlighting the acetate subfraction - neutrals with 60.98% of RT inhibition and ellagic acid with 88.61% of RT inhibition and absence of cytotoxicity. The macrophage lineage cytotoxicity assay showed that the chloroform fraction was more toxic than the acetate fraction. The analysis of the J-resolved spectrum in the aromatic region showed a singlet at 7.48 and 6.93 ppm which was identified as ellagic acid and gallic acid, respectively. The 5TIQ enzyme obtained better affinity parameter with the ellagic acid ligand, which was confirmed by the HSQC-1H-13C spectra. Gallic acid was also favorable to form interaction with the 5TIQ enzyme, being confirmed through the HSQC-1H-13C spectrum. From the PreADMET evaluation it was found that ellagic acid is a promising molecule for its RT inhibition activity and pharmacokinetic and toxicity parameters.
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Affiliation(s)
- S A Fonseca
- Universidade Federal de Alagoas, Instituto de Química e Biotecnologia, Maceió, AL, Brasil
| | - A L Cunha
- Universidade Federal de Alagoas, Instituto de Química e Biotecnologia, Maceió, AL, Brasil
| | - F C A Lima
- Universidade Estadual do Piauí - UESPI, Departamento de Química, Curso de Licenciatura Plena em Química, Laboratório de Quântica Computacional & Planejamento de Fármaco, Teresina, PI, Brasil
| | - M S Cruz E Silva
- Universidade Estadual do Piauí - UESPI, Departamento de Química, Curso de Licenciatura Plena em Química, Laboratório de Quântica Computacional & Planejamento de Fármaco, Teresina, PI, Brasil
| | - K W L Silva
- Centro Universitário Cesmac, Maceió, AL, Brasil
| | - M V Araújo
- Universidade Federal de Alagoas, Instituto de Ciências Biológicas, Maceió, AL, Brasil
| | - M S A Moreira
- Universidade Federal de Alagoas, Instituto de Ciências Biológicas, Maceió, AL, Brasil
| | - E S Bento
- Universidade Federal de Alagoas, Instituto de Química e Biotecnologia, Maceió, AL, Brasil
| | - A R Sabino
- Universidade Federal de Alagoas, Instituto de Química e Biotecnologia, Maceió, AL, Brasil
| | - T J M Rocha
- Centro Universitário Cesmac, Maceió, AL, Brasil.,Universidade Estadual de Ciências da Saúde de Alagoas, Núcleo de Ciências Biológicas, Maceió, AL, Brasil
| | - R C S Ferreira
- Universidade Federal de Alagoas, Laboratório de Farmacologia Antiviral e Celular, Maceió, AL, Brasil
| | - J G da Costa
- Embrapa Tabuleiros Costeiros (UEP-Rio Largo), Rio Largo, AL, Brasil
| | - A F Santos
- Centro Universitário Cesmac, Maceió, AL, Brasil.,Universidade Estadual de Alagoas, Arapiraca, AL, Brasil
| | - A E G Santana
- Universidade Federal de Alagoas, Centro de Ciências Agrárias, Rio Largo, AL, Brasil
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12
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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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Panda M, Purohit P, Meher BR. Structure-based virtual screening, ADMET profiling, and molecular dynamics simulation studies on HIV-1 protease for identification of active phytocompounds as potential anti-HIV agents. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2060968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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Folarin BT, Abdallah M, Oluseyi TO, Harrad S, Olayinka KO. Concentrations and Toxic Implications of Dioxin-Like Polychlorinated Biphenyls in Soil Samples from Electrical Power Stations in Lagos, Nigeria. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:800-809. [PMID: 34918382 DOI: 10.1002/etc.5277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/09/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Dioxin-like polychlorinated biphenyls (dl-PCBs) are ubiquitous chemicals which mediate toxicity in a way similar to polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans. In silico modeling was used to predict the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of eight dioxin-like PCBs in soil samples of 12 power stations in Lagos, Nigeria. Concentrations of Σdl-PCB8 in soil samples ranged from 490 to 61,000 pg g-1 , with mean concentrations of 17,000 pg g-1 . The corresponding toxic equivalent (TEQ) concentrations of Ʃdl-PCB8 ranged from 0.01 to 450 pg TEQ g-1 , with a mean value of 42 pg TEQ g-1 . Mean TEQ concentrations for Ʃdl-PCB8 in soil samples from all but one of the sites exceeded the Canadian guideline value of 4 pg TEQ g-1 and the US and German guideline values of 5-10 pg TEQ g-1 . However, the TEQ concentrations obtained were all below the US action level of 1000 pg TEQ g-1 . The ADMET predictions revealed that all studied dl-PCBs are inhibitors of three major isoforms (1A2, 2C9, and 2C19) of cytochrome P450 enzyme. Acute oral toxicity (median lethal dose) predictions revealed that all target dl-PCBs were class III compounds. Hepatotoxicity and carcinogenicity were positive, signifying that the studied compounds all have a tendency to elicit these effects. Occupational daily TEQ exposure via soil ingestion was estimated for an average adult worker weighing 70 kg. The maximum exposure obtained was 0.14 pg TEQ kg-1 body weight day-1 , which is half of the European Food Safety Authority (EFSA) tolerable daily intake (TDI) for dioxin-like compounds. This raises concern over the possible exceedance of the EFSA TDI for these workers if other dietary and nondietary exposure pathways and dioxin-like compounds are considered. Environ Toxicol Chem 2022;41:800-809. © 2021 SETAC.
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Affiliation(s)
- Bilikis T Folarin
- Department of Chemistry, University of Lagos, Lagos, Nigeria
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Chemistry, College of Natural and Applied Sciences, Chrisland University, Abeokuta, Nigeria
| | - Mohamed Abdallah
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Stuart Harrad
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
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15
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Shaslinah N, Sangavi P, Sangeetha R, Gowthamkumar S, Sindhu V, Langeswaran K. Screening and identification of potential inhibitor for visceral leishmaniasis (VL) through computational analysis. J Genet Eng Biotechnol 2022; 20:35. [PMID: 35195803 PMCID: PMC8866605 DOI: 10.1186/s43141-022-00318-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022]
Abstract
Aim The aim of this investigation is to detect potential inhibitor for visceral leishmaniasis through computational analysis. Background Leishmaniasis is categorized as a vector born pathogenic infection prevalent in tropical, subtropical, and in Mediterranean zones spread by intra-macrophage protozoa. The clinical syndrome of leishmaniasis is divided into the following type’s namely cutaneous leishmaniasis, mucocutaneous leishmaniasis, visceral leishmaniasis, and dermal leishmaniasis. Trypanothione synthetase is a key enzyme involving in glutathione biosynthesis as well as hydrolysis. Trypanothione is one of the promising drug targets for parasites. Parasites are inimitable with concern to their dependence on trypanothione to regulate intracellular thiol-redox balance in fighting against oxidative stress and biochemical anxiety. However, trypanothione synthetase was presumed as the target therapeutic alternate in VL therapy. Objective The important objective of this current investigation is to identify or analyze the potential inhibitor for V. leishmaniasis through computational approaches which include virtual screening, molecular docking, ADME prediction, and molecular dynamic simulation. Methods An investigation was performed to develop a 3D protein structure, using computational screening among associated similar structured proteins from popular compound database banks such as Specs, Maybridge, and Enamine, to detect novel staging with a series of validation for emerging innovative drugs molecules. Modeled protein ligand complex was further analyzed to know the binding ability of the complex. Molecular dynamics were performed to ascertain its stability at 50 ns. Results Trypanothione synthetase overall ability in the outcome of series of analysis. Among three database compounds screened, the compound from the Specs database exhibited the better protein-ligand docking scores and fulfilled the drug-like properties through ADMET analysis, and the docked complexes had better stability throughout the simulation. Besides, the other two database leads fulfilled the pharmacological properties, and the complexes were stable in the simulation. Conclusion By analyzing the various compounds from different databases, we concluded that the Specs database compound exhibits potential activity against the target protein and is considered a promising inhibitor for trypanothione synthetase.
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Affiliation(s)
- N Shaslinah
- Cancer Informatics Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - P Sangavi
- Cancer Informatics Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - R Sangeetha
- Department of Physics, Mannar Thirumalai Naicker College, Pasumalai, Madurai, Tamil Nadu, India
| | - S Gowthamkumar
- Faculty of Allied Health Sciences, Chettinad Hospital & Research Institute, Chettiand Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - V Sindhu
- Faculty of Allied Health Sciences, Chettinad Hospital & Research Institute, Chettiand Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - K Langeswaran
- Cancer Informatics Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India.
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16
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de Sá ÉRA, Souza JL, Costa RKM, Barros RO, de Lima CEB, Lima FDCA, Ramos RM. Computational investigation of the alkaloids of Pilocarpus microphyllus species as phytopharmaceuticals for the inhibition of sterol 14α-demethylase protease of Trypanosoma cruzi. J Biomol Struct Dyn 2022; 41:2555-2573. [PMID: 35132947 DOI: 10.1080/07391102.2022.2035819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Trypanosoma cruzi is a protozoan transmitted by the insect Triatoma infestans, popularly known as kissing bug. This protozoan causes the Chagas disease, a Neglected Tropical Disease. This study aimed to investigate, through DFT method and B3LYP hybrid functional, the physicochemical, pharmacokinetic, and pharmacodynamic properties of the alkaloids present in the leaves of the species Pilocarpus microphyllus (jaborandi) as a potential inhibitory activity on the protease sterol 14α-demethylase of T. cruzi associated with the techniques of molecular docking, molecular dynamics, MM-PBSA and ADMET predictions. The molecules of isopilosine, epiisopiloturine, epiisopilosine, and pilosine showed up the lowest binding energies by molecular docking, good human intestinal absorption, low penetration in the blood-brain barrier, antiprotozoal and anticarcinogenic activities in ADMET studies. It has been observed a better binding affinity of the sterol 14α-demethylase protease with isopilosine in molecular dynamics and MM-PBSA studies, which indicates it as a potential drug candidate for Chagas disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ézio R. A. de Sá
- Federal Institute of Education, Science and Technology of Piauí, IFPI, Picos, Piauí, Brazil
- Graduate Program in Chemistry, Federal University of Piauí, PPGQ/UFPI, Teresina, Piauí, Brazil
- Research Laboratory of the Computational Quantum Chemistry and Drug Planning Group, Chemistry Department, State University of Piauí, GQQC&PF/UESPI, Teresina, Piauí, Brazil
- Research Laboratory in Information Systems, Information Department, Environment, Health and Food Production, Federal Institute of Education, Science and Technology of Piauí, LaPeSI/IFPI, Teresina, Piauí, Brazil
| | - Janilson L. Souza
- Federal Institute of Education, Science and Technology of Maranhão, IFMA, Bacabal, Maranhão, Brazil
| | - Rayla K. M. Costa
- Research Laboratory of the Computational Quantum Chemistry and Drug Planning Group, Chemistry Department, State University of Piauí, GQQC&PF/UESPI, Teresina, Piauí, Brazil
| | - Rômulo O. Barros
- Research Laboratory in Information Systems, Information Department, Environment, Health and Food Production, Federal Institute of Education, Science and Technology of Piauí, LaPeSI/IFPI, Teresina, Piauí, Brazil
| | - Carlos E. B. de Lima
- University Hospital, Federal University of Piauí, Discipline of Cardiology, Department of General Practice - Cardiology and Health Sciences Center, DCG/CCS/UFPI, Teresina, Piauí, Brazil
| | - Francisco das C. A. Lima
- Research Laboratory of the Computational Quantum Chemistry and Drug Planning Group, Chemistry Department, State University of Piauí, GQQC&PF/UESPI, Teresina, Piauí, Brazil
| | - Ricardo M. Ramos
- Research Laboratory in Information Systems, Information Department, Environment, Health and Food Production, Federal Institute of Education, Science and Technology of Piauí, LaPeSI/IFPI, Teresina, Piauí, Brazil
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17
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Ajiboye BO. Molecular interaction of bioactive compounds from Senecio biafrae leaf with α-amylase and α-glucosidase receptors. CLINICAL PHYTOSCIENCE 2022. [DOI: 10.1186/s40816-021-00335-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Diabetes mellitus is one of the silent killer diseases affecting millions of people globally and some of the key enzymes in managing this disease are α-amylase and α-glucosidase This study was designed to investigate the possible molecular interactions between various bioactive compounds of Senecio biafrae leaf on α-amylase and α-glucosidase (enzymes) receptors an important target protein in Type 2 diabetes mellitus.
Methods
This study involved the investigation of the of gallic acid, chlorogenic, caffeic acid, rutin, quercetin, and kaempferol (ligands) for Lipinski’s rule of five using Molinspiration, ADMET profiles using admetSAR server and molecular docking of 3D structures of the six bioactive compounds and metformin against α-amylase and α-glucosidase were carried out using AutoDockVina.
Results
The results revealed that caffeic acid, quercetin, and kaempferol obey Lipinski’s rule of five. All the ligands demonstrated high gastrointestinal tract absorption except rutin and chlorogenic acid, only one can serve as a P-glycoprotein substrate and three of the ligands used can act as cytochrome P450 inhibitors isoforms. All the ligands had a high binding affinity than metformin (the standard drug used).
Conclusion
In can be concluded that some of the bioactive compounds (especially caffeic acid) in Senecio biafrae leaf have antidiabetic activity, which they may serve as a potential antidiabetic drug in the management of diabetes mellitus than metformin.
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Mustafa G, Mahrosh HS, Zafar M, Attique SA, Arif R. Exploring the antihyperglycemic potential of tetrapeptides devised from AdMc1 via different receptor proteins inhibition using in silico approaches. Int J Immunopathol Pharmacol 2022; 36:3946320221103120. [PMID: 35574607 PMCID: PMC9112693 DOI: 10.1177/03946320221103120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Introduction: Diabetes mellitus is a heterogenous group of chronic metabolic disorders that results due to deficiency in insulin secretion and signalling. Multiple factors held responsible for onset of diabetes due to defects in glucose metabolism and cellular signalling mechanism. Over the past few years, many plant derived bioactive compounds have been recorded with increased efficacy and fewer side-effects against variety of diseases. Methods: In the current study, molecular docking and molecular dynamics simulation approaches were employed to evaluate the tetrapeptides devised from AdMc1 protein of Momordica charantia. Due to unavailability of appropriate template for modelling of 3D structure of AdMc1 protein, I-TASSER server was employed for prediction of good quality tertiary structure. Predicted model was refined by GalaxyRefine Web and evaluated by Verify 3D, ERRAT and Ramachandran plot analysis. Next, a ready-to-dock library of fifty tetrapeptides as potent inhibitors was prepared and docked against aldose reductase (AR), protein tyrosine phosphatase 1B (PTP1B), α-glucosidase, α-amylase and glycogen synthase kinase 3-beta as receptor proteins. Molecular dynamics (MD) simulation was performed on Schrodinger’s Desmond Module to check stability of the best docking complex. Results: Top five ligands were selected against each receptor protein based on their binding pattern and docking scores. Among selected ligands (i.e. VEID, TVEV, AYAY, EEIA, ITTV, TTIT, LPSM, RGIE, TTVE and EIAR) followed all parameters in drug scanning and ADMET screening tests. The MD simulations confirmed that the best selected peptide (i.e. VEID) docked with AR and PTP1B was structurally stable. Conclusion: In the light of overall results of all analyses employed in this study, the selected ligands could be further processed as potential hypoglycaemic drug candidates.
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Affiliation(s)
- Ghulam Mustafa
- Department of Biochemistry, 72594Government College University, Faisalabad, Pakistan
| | - Hafiza S Mahrosh
- Department of Biochemistry, 66724University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muddassar Zafar
- Department of Biochemistry and Biotechnology, 128417University of Gujrat, Hafiz Hayat Campus, Gujrat, Pakistan
| | - Syed A Attique
- School of Interdisciplinary Engineering & Science (SINES), National University of Sciences & Technology (NUST), Islamabad, Pakistan
| | - Rawaba Arif
- Department of Biochemistry, University of Jhang, Jhang, Pakistan
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Investigation of glutathione as a natural antioxidant and multitarget inhibitor for Alzheimer’s disease: Insights from molecular simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Simultaneous quantification and ADME prediction of AD-1 and its eight metabolites in rat feces, and screening of PARP-1 inhibitors through molecular docking. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Rahman MM, Junaid M, Hosen SMZ, Mostafa M, Liu L, Benkendorff K. Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition. Molecules 2021; 26:molecules26216538. [PMID: 34770946 PMCID: PMC8587571 DOI: 10.3390/molecules26216538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammation plays an important role in different chronic diseases. Brominated indoles derived from the Australian marine mollusk Dicathais orbita (D. orbita) are of interest for their anti-inflammatory properties. This study evaluates the binding mechanism and potentiality of several brominated indoles (tyrindoxyl sulfate, tyrindoleninone, 6-bromoisatin, and 6,6′-dibromoindirubin) against inflammatory mediators cyclooxygenases-1/2 (COX-1/2) using molecular docking, followed by molecular dynamics simulation, along with physicochemical, drug-likeness, pharmacokinetic (pk), and toxicokinetic (tk) properties. Molecular docking identified that these indole compounds are anchored, with the main amino acid residues, positioned in the binding pocket of the COX-1/2, required for selective inhibition. Moreover, the molecular dynamics simulation based on root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), and root mean square fluctuation (RMSF) analyses showed that these natural brominated molecules transit rapidly to a progressive constant configuration during binding with COX-1/2 and seem to accomplish a consistent dynamic behavior by maintaining conformational stability and compactness. The results were comparable to the Food and Drug Administration (FDA)-approved selective COX inhibitor, aspirin. Furthermore, the free energy of binding for the compounds assessed by molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) confirmed the binding capacity of indoles towards COX-1/2, with suitable binding energy values except for the polar precursor tyrindoxyl sulfate (with COX-1). The physicochemical and drug-likeness analysis showed zero violations of Lipinski’s rule, and the compounds are predicted to have excellent pharmacokinetic profiles. These indoles are projected to be non-mutagenic and free from hepatotoxicity, with no inhibition of human ether-a-go–go gene (hERG) I inhibitors, and the oral acute toxicity LD50 in rats is predicted to be similar or lower than aspirin. Overall, this work has identified a plausible mechanism for selective COX inhibition by natural marine indoles as potential therapeutic candidates for the mitigation of inflammation.
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Affiliation(s)
- Md. Mominur Rahman
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Md. Junaid
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - S. M. Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
- Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for AppliedMedical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mohammad Mostafa
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - Lei Liu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
- Correspondence:
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22
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Azad I, Khan T, Maurya AK, Irfan Azad M, Mishra N, Alanazi AM. Identification of Severe Acute Respiratory Syndrome Coronavirus-2 inhibitors through in silico structure-based virtual screening and molecular interaction studies. J Mol Recognit 2021; 34:e2918. [PMID: 34132436 PMCID: PMC8420533 DOI: 10.1002/jmr.2918] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023]
Abstract
The novel coronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) or COVID-19 has caused a worldwide pandemic. The fatal virus has affected the health of human beings as well as the socio-economic situation all over the world. To date, no concrete medicinal solution has been proposed to combat the viral infection, calling for an urgent, strategic, and cost-effective drug development approach that may be achievable by applying targeted computational and virtual screening protocols. Immunity is the body's natural defense against disease-causing pathogens, which can be boosted by consuming plant-based or natural food products. Active constituents derived from natural sources also scavenge the free radicals and have anti-inflammatory activities. Herbs and spices have been used for various medicinal purposes. In this study, 2,96 365 natural and synthetic derivatives (ligands) belonging to 102 classes of compounds were obtained from PubChem and assessed on Lipinski's parameters for their potential bioavailability. Out of all the derivatives, 3254 obeyed Lipinski's rule and were virtually screened. The 115 top derivatives were docked against SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-HKV1 main proteases (Mpro s) as receptors using AutoDock Vina, AutoDock, and iGEMDOCK 2.1. The lowest binding energy was exhibited by ligands 2 and 6 against all the four Mpro s. The molecular dynamic simulation was also performed with ligand 6 using the GROMACS package. Good bioactivity scores, absorption, distribution, metabolism, excretion, and toxicity profile and drug-like pharmacokinetic parameters were also obtained. Hydroxychloroquine was used as the control drug.
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Affiliation(s)
- Iqbal Azad
- Department of ChemistryIntegral UniversityLucknowIndia
| | - Tahmeena Khan
- Department of ChemistryIntegral UniversityLucknowIndia
| | - Akhilesh Kumar Maurya
- Department of Applied SciencesIndian Institute of Information Technology AllahabadPrayagrajIndia
| | | | - Nidhi Mishra
- Department of Applied SciencesIndian Institute of Information Technology AllahabadPrayagrajIndia
| | - Amer M. Alanazi
- Department of Pharmaceutical ChemistryCollege of Pharmacy, King Saud UniversityRiyadhSaudi Arabia
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Yende SR, Shah SK, Arora SK, Moharir KS, Lohiya GK. In silico prediction of phytoconstituents from Ehretia laevis targeting TNF-α in arthritis. DIGITAL CHINESE MEDICINE 2021. [DOI: 10.1016/j.dcmed.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Synthesis, In Silico Study, and Anti-Cancer Activity of Thiosemicarbazone Derivatives. Biomedicines 2021; 9:biomedicines9101375. [PMID: 34680491 PMCID: PMC8533299 DOI: 10.3390/biomedicines9101375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022] Open
Abstract
Thiosemicarbazones are known for their biological and pharmacological activities. In this study, we have synthesized and characterized 3-Methoxybenzaldehyde thiosemicarbazone (3-MBTSc) and 4-Nitrobenzaldehyde thiosemicarbazone (4-NBTSc) using IR, 1HNMR and 13C NMR. The compound’s in vitro anticancer activities against different cell lines were evaluated. Molecular docking, Insilco ADMET, and drug-likeness prediction were also done. The test compounds showed a comparative IC50 and growth inhibition with the standard drug Doxorubicin. The IC50 ranges from 2.82 µg/mL to 14.25 µg/mL in 3-MBTSc and 2.80 µg/mL to 7.59 µg/mL in 4-NBTSc treated cells. The MTT assay result revealed, 3-MBTSc inhibits 50.42 and 50.31 percent of cell growth in B16-F0 and EAC cell lines, respectively. The gene expression showed that tumor suppressor genes such as PTEN and BRCA1 are significantly upregulated in 7.42 and 5.33 folds, and oncogenes, PKC, and RAS are downregulated −7.96 and −7.64 folds, respectively in treated cells. The molecular docking performed on the four targeted proteins (PARP, VEGFR-1, TGF-β1, and BRAFV600E) indicated that both 4-NBTSc and 3-MBTSc potentially bind to TGF-β1 with the best binding energy of −42.34 Kcal/mol and −32.13 Kcal/mol, respectively. In addition, the test compound possesses desirable ADMET and drug-likeness properties. Overall, both 3-MBTSc and 4-NBTSc have the potential to be multitargeting drug candidates for further study. Moreover, 3-MBTSc showed better activity than 4-NBTSc.
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Mamun AA, Akter F, Khan M, Ahmed SS, Uddin MG, Tasfia NT, Efaz FM, Ali MA, Sultana MUC, Halim MA. Identification of potent inhibitors against transmembrane serine protease 2 for developing therapeutics against SARS-CoV-2. J Biomol Struct Dyn 2021; 40:13049-13061. [PMID: 34590967 PMCID: PMC8500310 DOI: 10.1080/07391102.2021.1980109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 09/08/2021] [Indexed: 12/27/2022]
Abstract
In viral binding and entry, the Spike(S) protein of SARS-CoV-2 uses transmembrane serine protease 2 (TMPRSS2) for priming to cleavage themselves. In this study, we have screened 'drug-like' 7476 ligands and found that over thirty ligands can effectively inhibit the TMPRSS-2 better than the control ligand. Finally, the three best drug agents L1, L2, and L6 were selected according to their average binding affinities and fitting score. These ligands interact with Asp435, Cys437, Ser436, Trp461, and Cys465 amino acid residues. The three best candidates and a reported drug Nafamostat mesylate (NAM) were selected to run 250 ns molecular dynamics (MD) simulations. Various properties of ligand-protein interactions obtained from MD simulation such as bonds, angle, dihedral, planarity, coulomb, and van der Waals (VdW) were used for principal component analysis (PCA) calculation. PCA discloses the evidence of the structural similarities to the corresponding complexes of L1, L2, and L6 with the complex of TMPRSS2(TM) and Nafamostat mesylate (TM-NAM). Moreover, Quantitative structure-activity relationship (QSAR) pattern recognition was generated using PCA for the investigation of structural similarities among the selected ligands. Multiple Linear Regression (MLR) model was built to predict the binding energy compared to the binding energy obtained from molecular docking. The MLR regression model reveals an accuracy of 80% for the prediction of the binding energy of ligands. ADMET analysis demonstrates that these drug agents are appeared to be safer inhibitors. These three ligands can be used as potential inhibitors against the TMPRSS2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdulla Al Mamun
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, P. R. China
| | - Farjana Akter
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Maksud Khan
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Sayeda Samina Ahmed
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md. Giash Uddin
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
- Department of Pharmacy, University of Chittagong, Chittagong, Bangladesh
| | - Nabila Tabassum Tasfia
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Faiyaz Md. Efaz
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mossammad Umme Chand Sultana
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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Zhu Y, Zhao J, Luo L, Gao Y, Bao H, Li P, Zhang H. Research progress of indole compounds with potential antidiabetic activity. Eur J Med Chem 2021; 223:113665. [PMID: 34192642 DOI: 10.1016/j.ejmech.2021.113665] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 01/07/2023]
Abstract
New types of antidiabetic agents are continually needed with diabetes becoming the epidemic in the world. Indole alkaloids play an important role in natural products owing to their variable structures and versatile biological activities like anticonvulsant, anti-inflammatory, antidiabetic, antimicrobial, and anticancer activities, which are a promising source of novel antidiabetic drugs discovery. The synthesized indole derivatives possess similar properties to natural indole alkaloids. In the last two decades, more and more indole derivatives have been designed and synthesized for searching their bioactivities. This present review describes comprehensive structures of indole compounds with the potential antidiabetic activity including natural indole alkaloids and the synthetic indole derivatives based on the structure classification, summarizes their approaches isolated from natural sources or by synthetic methods, and discusses the antidiabetic effects and the mechanisms of action. Furthermore, this review also provides briefly synthetic procedures of some important indole derivatives.
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Affiliation(s)
- Yuqian Zhu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jinran Zhao
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Longbiao Luo
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yang Gao
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - He Bao
- Department of Pharmacy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Pengfei Li
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Hailong Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China.
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Schepetkin IA, Plotnikov MB, Khlebnikov AI, Plotnikova TM, Quinn MT. Oximes: Novel Therapeutics with Anticancer and Anti-Inflammatory Potential. Biomolecules 2021; 11:biom11060777. [PMID: 34067242 PMCID: PMC8224626 DOI: 10.3390/biom11060777] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Oximes have been studied for decades because of their significant roles as acetylcholinesterase reactivators. Over the last twenty years, a large number of oximes have been reported with useful pharmaceutical properties, including compounds with antibacterial, anticancer, anti-arthritis, and anti-stroke activities. Many oximes are kinase inhibitors and have been shown to inhibit over 40 different kinases, including AMP-activated protein kinase (AMPK), phosphatidylinositol 3-kinase (PI3K), cyclin-dependent kinase (CDK), serine/threonine kinases glycogen synthase kinase 3 α/β (GSK-3α/β), Aurora A, B-Raf, Chk1, death-associated protein-kinase-related 2 (DRAK2), phosphorylase kinase (PhK), serum and glucocorticoid-regulated kinase (SGK), Janus tyrosine kinase (JAK), and multiple receptor and non-receptor tyrosine kinases. Some oximes are inhibitors of lipoxygenase 5, human neutrophil elastase, and proteinase 3. The oxime group contains two H-bond acceptors (nitrogen and oxygen atoms) and one H-bond donor (OH group), versus only one H-bond acceptor present in carbonyl groups. This feature, together with the high polarity of oxime groups, may lead to a significantly different mode of interaction with receptor binding sites compared to corresponding carbonyl compounds, despite small changes in the total size and shape of the compound. In addition, oximes can generate nitric oxide. This review is focused on oximes as kinase inhibitors with anticancer and anti-inflammatory activities. Oximes with non-kinase targets or mechanisms of anti-inflammatory activity are also discussed.
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Affiliation(s)
- Igor A. Schepetkin
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA;
| | - Mark B. Plotnikov
- Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, 634028 Tomsk, Russia;
| | - Andrei I. Khlebnikov
- Kizhner Research Center, National Research Tomsk Polytechnic University, 634050 Tomsk, Russia;
- Scientific Research Institute of Biological Medicine, Altai State University, 656049 Barnaul, Russia
| | - Tatiana M. Plotnikova
- Department of Pharmacology, Siberian State Medical University, 634050 Tomsk, Russia;
| | - Mark T. Quinn
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA;
- Correspondence: ; Tel.: +1-406-994-4707; Fax: +1-406-994-4303
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Fisli H, Hennig A, Chelaghmia ML, Abdaoui M. The relationship between solvatochromic properties and in silico ADME parameters of new chloroethylnitrosourea derivatives with potential anticancer activity and their β-Cyclodextrin complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119579. [PMID: 33611219 DOI: 10.1016/j.saa.2021.119579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
In view of the anticancer effect of nitrosoureas a set of four new N-(2-chloroethyl)-N-nitrosourea (CENU) derivatives was synthesized. An in silico absorption, distribution, metabolism, excretion and toxicity (ADME/Tox) prediction study revealed that the CENU derivatives satisfied all the required criteria for oral administration and introduced them as remarkable anticancer candidates in the central nervous system (CNS). A comparative solvatochromic study including the Kamlet-Taft, Catalán and Laurence models indicated that the solvatochromic behavior of the CENUs depended on both, unspecific and specific solvent-solute interactions. In detail, the solvatochromic effect of the solvent polarity on the absorption and emission maxima was significant for all CENUs, whereas the solvatochromic effect of the solvent's ability to donate or accept hydrogen bonds on the absorption and emission maxima was critically dependent on the electron density of the N'-aryl group. From the solvatochromic comparison method, excellent correlations (r ≥ 0.890) were obtained between the ADME parameters and the solvatochromic regression coefficients obtained by the Catalán model. As potential stabilizers, inclusion complexes of the investigated CENU derivatives with β-cyclodextrin (β-CD) were also explored. The spectrofluorimetric host-guest experiments included double-reciprocal Benesi-Hildebrand plots as well as the molar ratio and continuous variation plots (Job's plots), which established a 1:1 β-CD to CENU binding stoichiometry and relatively high affinities of β-CD for CENU derivatives.
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Affiliation(s)
- Hassina Fisli
- Laboratory of Applied Chemistry, Université 8 Mai 1945 Guelma, Algeria.
| | - Andreas Hennig
- Institute of Chemistry of New Materials, Universität Osnabrück, Germany
| | | | - Mohamed Abdaoui
- Laboratory of Applied Chemistry, Université 8 Mai 1945 Guelma, Algeria
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Chen XY, Chen XH, Li L, Su CP, Zhang YL, Jiang YY, Guo SZ, Liu B. Deciphering the effective combinatorial components from Si-Miao-Yong-An decoction regarding the intervention on myocardial hypertrophy. JOURNAL OF ETHNOPHARMACOLOGY 2021; 271:113833. [PMID: 33465437 DOI: 10.1016/j.jep.2021.113833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Si-Miao-Yong-An decoction (SMYAD), a classical traditional Chinese medicine (TCM) formula, has been used to treat various cardiovascular diseases in clinics. AIM OF THE STUDY The aim of this study is to investigate the effective combinatorial components from SMYAD and its mechanism regarding the intervention on myocardial hypertrophy. MATERIALS AND METHODS SMYAD constituents absorbed in rat plasma and heart were identified using UHPLC Q-Exactive-Orbitrap MS/MS. The identified constituents in SMYAD were further analyzed using ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction and molecular docking. The effective constituents were identified using isoproterenol (ISO)-induced H9c2 cardiomyocyte hypertrophy, and neochlorogenic acid (NCA), chlorogenic acid (CA), cryptochlorogenic acid (CCA), isochlorogenic acid C (ICAC), angoroside C (AGDC), isochlorogenic acid A (ICAA), sweroside (SRD), and harpagide (HPD) in SMYAD extract were quantified by HPLC for compatibility. Finally, anti-hypertrophic activities of candidate effective combinatorial components, which were prepared according to the determined molar concentration ratio of effective constituents using reference substance solution, were analyzed using immunofluorescence staining and Quantitative real-time PCR. The expression levels of PI3Kα, p-ERK, p-Akt, Akt, p-mTOR, mTOR and HIF-1α were measured using Western blot. RESULTS 32 prototypes of SMYAD were identified from plasma and heart tissue of rat. Combining with ADMET prediction, 31 dominant constituents were focused. Based on HIF-1 pathway identified in preliminary result, 17 targets were focused, which were used to dock with 31 constituents. 27 constituents were therefore hit as the potential effective constituents of SMYAD in inhibiting myocardial hypertrophy. Bioactivity evaluation showed that NCA, CA, CCA, ICAC, AGDC, ICAA, SRD, and HPD significantly inhibited the increase of H9c2 cell surface area induced by ISO. Except for ICAA and AGDC, the remaining 6 effective constituents, showing a certain inhibitory effect on ISO-induced ANP mRNA overexpression at high and low concentrations, participated in compatibility based on the molar concentration ratio determined by HPLC. Effective combinatorial components composed of the 6 effective constituents (effective combinatorial components ABC) showed significant inhibitory effect on the increase of cell surface area, and the overexpression of ANP and β-MHC mRNA in H9c2 cells induced by ISO. Moreover, effective combinatorial components ABC significantly inhibited the protein overexpressions of p-Akt, p-mTOR and HIF-1α. Based on the results, we put forward the strategy of "Focusing constituents" and "Focusing targets" for the effective constituents research of TCM formula. CONCLUSION Effective combinatorial components ABC composed of NCA, CA, CCA, ICAC, SRD and HPD from SMYAD inhibited ISO-induced cardiomyocyte hypertrophy and down-regulated expression of ANP and β-MHC mRNA through the inactivation of Akt/mTOR/HIF-1α pathway.
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MESH Headings
- Animals
- Atrial Natriuretic Factor/genetics
- Cardiomegaly/drug therapy
- Cardiomegaly/metabolism
- Cell Line
- Drugs, Chinese Herbal/chemistry
- Drugs, Chinese Herbal/metabolism
- Drugs, Chinese Herbal/pharmacology
- Drugs, Chinese Herbal/therapeutic use
- Extracellular Signal-Regulated MAP Kinases/metabolism
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Isoproterenol/toxicity
- Male
- Medicine, Chinese Traditional
- Molecular Docking Simulation
- Myocytes, Cardiac/drug effects
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Myosin Heavy Chains/genetics
- Phosphatidylinositol 3-Kinase/metabolism
- Phytochemicals/analysis
- Phytochemicals/pharmacology
- Phytochemicals/therapeutic use
- Plasma/chemistry
- Proto-Oncogene Proteins c-akt/metabolism
- Rats, Sprague-Dawley
- TOR Serine-Threonine Kinases/metabolism
- Rats
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Affiliation(s)
- Xiang-Yang Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, Beijing, PR China
| | - Xiao-He Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, Beijing, PR China
| | - Lin Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, Beijing, PR China
| | - Cong-Ping Su
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, Beijing, PR China
| | - Yan-Ling Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, Beijing, PR China
| | - Yan-Yan Jiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, Beijing, PR China
| | - Shu-Zhen Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, Beijing, PR China.
| | - Bin Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, Beijing, PR China.
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Chowrasia D, Jafri A, Azad I, Rais J, Sharma N, Khan F, Kumar A, Kumar S, Arshad M. In vitro and in silico growth inhibitory, anti-ovarian & anti-lung carcinoma effects of 1,5 diarylpenta-1,4-dien-3-one as synthetically modified curcumin analogue. J Biomol Struct Dyn 2021; 40:8569-8586. [PMID: 33955334 DOI: 10.1080/07391102.2021.1914166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The synthesized 1,5 diarylpenta-1,4-dien-3-one derivatives (compounds 1-6) as synthetic curcumin analogues were tested for their potential anticancer activity against human ovarian and lung adenocarcinoma cells. The absorption, distribution, metabolism, excretion, and toxicity (ADMET/pharmacokinetic) parameters of all the compounds were predicted by admetSAR software. The pharmacokinetics, pharmacodynamics and bioactivity scores properties based on Lipinski rule and Ghose filter, calculated with the help of Molinspiration and ChemDraw. Molecular docking evaluation of all the compounds was also performed by using AutoDock Vina and iGEMDOCK against three most common human anticancer targets; epidermal growth factor receptor (EGFR), heat shock protein (Hsp 90-α), and vascular endothelial growth factor receptor-2 (VEGFR2). The obtained results were compared with the reference compound 7 and drugs 8-10 (7: GO-035; 8: Quinazolin; 9: Naquotinib and 10: Ribofuranuronamide). Finding indicates, all the compounds were potentially interacting with VEGFR2 through the average -9.1 binding energy (BE) with closer contact <5.0 Å deep in the active site of the ligand-receptor complex. All the compounds showed excellent oral bioavailability, bioactivity score, and none of the compounds are virtually found to be toxic. Compounds 1-6 were also successfully characterized by the physical properties as well as spectroscopic techniques (FT-IR and 1H-NMR). In vitro anti-proliferative activity was tested via MTT method against human ovarian carcinoma (PA-1) and human lung adenocarcinoma (A549) cells and further screened for apoptotic parameters such as nuclear fragmentation and ROS generation. Compound 4 exhibits good dose-dependent anti-proliferative activity (IC50 73 and 79.7 µM) against human ovarian carcinoma and human lung adenocarcinoma, respectively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deepak Chowrasia
- University Institute of Pharmacy, CSJM University, Kanpur, India
| | - Asif Jafri
- Department of Zoology, Molecular Endocrinology Lab, University of Lucknow, Lucknow, India.,Department of Zoology, Molecular and Human Genetics Lab, University of Lucknow, Lucknow, India
| | - Iqbal Azad
- Department of Chemistry, Medicine and Computational Chemistry, Integral University, Lucknow, India
| | - Juhi Rais
- Department of Zoology, Molecular Endocrinology Lab, University of Lucknow, Lucknow, India
| | - Nisha Sharma
- University Institute of Pharmacy, CSJM University, Kanpur, India
| | - Fahad Khan
- Department of Biotechnology, Noida Institute of Engineering and Technology, Greater Noida, India
| | - Ajay Kumar
- University Institute of Pharmacy, CSJM University, Kanpur, India
| | - Sudhir Kumar
- Department of Zoology, Molecular and Human Genetics Lab, University of Lucknow, Lucknow, India
| | - Md Arshad
- Department of Zoology, Molecular Endocrinology Lab, University of Lucknow, Lucknow, India.,Department of Zoology, Aligarh Muslim University, Aligarh, India
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Wadhwa P, Jain P, Jadhav HR. Glycogen Synthase Kinase 3 (GSK3): Its Role and Inhibitors. Curr Top Med Chem 2021; 20:1522-1534. [PMID: 32416693 DOI: 10.2174/1568026620666200516153136] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 12/23/2022]
Abstract
Glycogen Synthase Kinase 3 (GSK3) is one of the Serine/Threonine protein kinases, which has gained a lot of attention for its role in a variety of pathways. It has two isoforms, GSK3α and GSK3β. However, GSK3β is highly expressed in different areas of the brain and has been implicated in Alzheimer's disease as it is involved in tau phosphorylation. Due to its high specificity concerning substrate recognition, GSK3 has been considered as an important target. In the last decade, several GSK3 inhibitors have been reported and two molecules are in clinical trials. This review collates the information published in the last decade about the role of GSK3 in Alzheimer's disease and progress in the development of its inhibitors. Using this collated information, medicinal chemists can strategize and design novel GSK3 inhibitors that could be useful in the treatment of Alzheimer's disease.
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Affiliation(s)
- Pankaj Wadhwa
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani- 333031, Rajasthan, India
| | - Priti Jain
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani- 333031, Rajasthan, India
| | - Hemant R Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani- 333031, Rajasthan, India
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Cruz-Vicente P, Passarinha LA, Silvestre S, Gallardo E. Recent Developments in New Therapeutic Agents against Alzheimer and Parkinson Diseases: In-Silico Approaches. Molecules 2021; 26:2193. [PMID: 33920326 PMCID: PMC8069930 DOI: 10.3390/molecules26082193] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
Neurodegenerative diseases (ND), including Alzheimer's (AD) and Parkinson's Disease (PD), are becoming increasingly more common and are recognized as a social problem in modern societies. These disorders are characterized by a progressive neurodegeneration and are considered one of the main causes of disability and mortality worldwide. Currently, there is no existing cure for AD nor PD and the clinically used drugs aim only at symptomatic relief, and are not capable of stopping neurodegeneration. Over the last years, several drug candidates reached clinical trials phases, but they were suspended, mainly because of the unsatisfactory pharmacological benefits. Recently, the number of compounds developed using in silico approaches has been increasing at a promising rate, mainly evaluating the affinity for several macromolecular targets and applying filters to exclude compounds with potentially unfavorable pharmacokinetics. Thus, in this review, an overview of the current therapeutics in use for these two ND, the main targets in drug development, and the primary studies published in the last five years that used in silico approaches to design novel drug candidates for AD and PD treatment will be presented. In addition, future perspectives for the treatment of these ND will also be briefly discussed.
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Affiliation(s)
- Pedro Cruz-Vicente
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Sciences and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Luís A. Passarinha
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Sciences and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
| | - Samuel Silvestre
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Eugenia Gallardo
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
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Ukwenya VO, Adelakun SA, Elekofehinti OO. Exploring the antidiabetic potential of compounds isolated from Anacardium occidentale using computational aproach: ligand-based virtual screening. In Silico Pharmacol 2021; 9:25. [PMID: 33868895 DOI: 10.1007/s40203-021-00084-z] [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: 06/29/2020] [Accepted: 03/12/2021] [Indexed: 10/21/2022] Open
Abstract
Diabetes mellitus is becoming an important public health challenge worldwide and especially in developing nations. About 8.8 percent of the world adult population has been reported to have diabetes. Glutamine-fructose-6-phosphate amidotransferase 1 (GFAT1) catalyses the first committed step in the pathway for biosynthesis of hexosamines in mammals, and its inhibition has been thought to prevent hyperglycaemia. Dipeptidyl peptidase-4 (DPP-4), on the other hand, degrades hormone glucagon-like peptide-1 (GLP-1), an enzyme that plays a major role in the enhancement of glucose-dependent insulin secretion, making these two proteins candidate targets for diabetes. To find potential inhibitors of DPP-4 and GFAT1 from Anacardium occidentale using a computational approach, glide XP (extra precision) docking, Induced Fit Docking (IFD), Binding free energy of the compounds were determined against prepared crystal structure of DPP-4 and GFAT1 using the Maestro molecular interface of Schrödinger suites. The Lipinski's rule of five (RO5) and ADME properties of the compounds were assessed. Predictive models for both protein targets were built using AutoQSAR. This study identified 8 hit compounds. Most of these compounds passed the RO5 and were within the recommended range for defined ADME parameters. In addition, the predicted pIC50 for the hit compounds were promising. The results obtained from the present study can be used to design an antidiabetic drug. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00084-z.
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Affiliation(s)
- Victor Okoliko Ukwenya
- Department of Human Anatomy, School of Health and Health Technology, Federal University of Technology, Akure, Nigeria
| | - Sunday Aderemi Adelakun
- Department of Human Anatomy, School of Health and Health Technology, Federal University of Technology, Akure, Nigeria
| | - Olusola Olalekan Elekofehinti
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, School of Sciences, Federal University of Technology, Akure, Nigeria
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Viana Nunes AM, das Chagas Pereira de Andrade F, Filgueiras LA, de Carvalho Maia OA, Cunha RLOR, Rodezno SVA, Maia Filho ALM, de Amorim Carvalho FA, Braz DC, Mendes AN. preADMET analysis and clinical aspects of dogs treated with the Organotellurium compound RF07: A possible control for canine visceral leishmaniasis? ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2020; 80:103470. [PMID: 32814174 DOI: 10.1016/j.etap.2020.103470] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/07/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Tellurium compounds have been described as potential leishmanicides, bearing promising leishmanicidal and antimalarial effects. Therefore, the present study investigated the pharmacological potential of the organotellurane compound RF07 through preADMET parameters, such as absorption, distribution, metabolism and excretion. After studying the pharmacokinetic properties of RF07, studies were carried out on dogs naturally infected with visceral leishmaniasis after the administration of RF07, in order to assess pathophysiological parameters. Thus, dogs were divided into 4 groups with administration of daily intraperitoneal injections for 3 weeks (containing RF07 or placebo). During the trial, hematological parameters, renal and hepatic toxicity were evaluated. Serum urea, creatinine, alkaline phosphatase, transaminases (GOT and GPT), as well as hemogram results, were evaluated before the first administration and during the second and third weeks after the start of the treatment. In dogs with VL, RF07 improved liver damage, regulated GPT levels and significantly decreased leukocyte count, promoting its regularization. These phenomena occurred at the end of the third week of treatment. The administration of RF07 promoted a significant decrease in the average levels of GOT and GPT after the third week of treatment and did not significantly alter the hematological parameters. The application of RF07 in the treatment of visceral leishmaniasis suggests that it is an alternative to the disease, since the reversal of clinical signs in dogs with VL requires the use of 0.6 mg/kg.
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Affiliation(s)
| | | | - Lívia Alves Filgueiras
- Departament of Biophysics and Physiology, Federal University of Piauí, Teresina, Piauí, Brazil
| | | | - Rodrigo L O R Cunha
- Laboratory of Chemical Biology, Center for Natural Sciences and Humanities, Federal University of ABC (UFABC), Santo André, São Paulo, Brazil
| | - Sindy V A Rodezno
- Laboratory of Chemical Biology, Center for Natural Sciences and Humanities, Federal University of ABC (UFABC), Santo André, São Paulo, Brazil
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35
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Khamouli S, Belaidi S, Ouassaf M, Lanez T, Belaaouad S, Chtita S. Multi-combined 3D-QSAR, docking molecular and ADMET prediction of 5-azaindazole derivatives as LRRK2 tyrosine kinase inhibitors. J Biomol Struct Dyn 2020; 40:1285-1298. [DOI: 10.1080/07391102.2020.1824815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Saida Khamouli
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Salah Belaidi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Touhami Lanez
- VTRS Laboratory, Faculty of Sciences and Technology, University of El Oued, El Oued, Algeria
| | - Said Belaaouad
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Sidi Othman, Casablanca, Morocco
| | - Samir Chtita
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Sidi Othman, Casablanca, Morocco
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Wu F, Zhou Y, Li L, Shen X, Chen G, Wang X, Liang X, Tan M, Huang Z. Computational Approaches in Preclinical Studies on Drug Discovery and Development. Front Chem 2020; 8:726. [PMID: 33062633 PMCID: PMC7517894 DOI: 10.3389/fchem.2020.00726] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Because undesirable pharmacokinetics and toxicity are significant reasons for the failure of drug development in the costly late stage, it has been widely recognized that drug ADMET properties should be considered as early as possible to reduce failure rates in the clinical phase of drug discovery. Concurrently, drug recalls have become increasingly common in recent years, prompting pharmaceutical companies to increase attention toward the safety evaluation of preclinical drugs. In vitro and in vivo drug evaluation techniques are currently more mature in preclinical applications, but these technologies are costly. In recent years, with the rapid development of computer science, in silico technology has been widely used to evaluate the relevant properties of drugs in the preclinical stage and has produced many software programs and in silico models, further promoting the study of ADMET in vitro. In this review, we first introduce the two ADMET prediction categories (molecular modeling and data modeling). Then, we perform a systematic classification and description of the databases and software commonly used for ADMET prediction. We focus on some widely studied ADMT properties as well as PBPK simulation, and we list some applications that are related to the prediction categories and web tools. Finally, we discuss challenges and limitations in the preclinical area and propose some suggestions and prospects for the future.
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Affiliation(s)
- Fengxu Wu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China
| | - Yuquan Zhou
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Langhui Li
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xianhuan Shen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Ganying Chen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Xiaoqing Wang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xianyang Liang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Mengyuan Tan
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
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Wu C, Luo J, Wu M, Meng F, Cai Z, Chen Y, Sun T. Design, Synthesis and Biological Evaluation of Anti-tuberculosis Agents based on Bedaquiline Structure. Med Chem 2020; 16:703-714. [DOI: 10.2174/1573406415666190613094433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/07/2019] [Accepted: 05/18/2019] [Indexed: 11/22/2022]
Abstract
Background:
Bedaquiline is a novel anti-tuberculosis drug that inhibits Mycobacterial
ATP synthase. However, studies have found that bedaquiline has serious side effects due to high
lipophilicity. Recently, the complete structure of ATP synthase was first reported in the Journal of
Science.
Objective:
The study aimed to design, synthesise and carry out biological evaluation of antituberculosis
agents based on the structure of bedaquiline.
Methods:
The mode of action of bedaquiline and ATP synthase was determined by molecular
docking, and a series of low lipophilic bedaquiline derivatives were synthesized. The inhibitory
activities of bedaquiline derivatives towards Mycobacterium phlei 1180 and Mycobacterium tuberculosis
H37Rv were evaluated in vitro. A docking study was carried out to elucidate the structureactivity
relationship of the obtained compounds. The predicted ADMET properties of the synthesized
compounds were also analyzed.
Results:
The compounds 5c3, 6a1, and 6d3 showed good inhibitory activities (MIC=15.62
ug.mL-1). At the same time, the compounds 5c3, 6a1, and 6d3 also showed good drug-like properties
through molecular docking and ADMET properties prediction.
Conclusion:
The results of in vitro anti-tuberculosis activity assays, docking studies and ADMET
predictions indicate that the synthesized compounds have potential antifungal activity, with compounds
6a1 being further optimized and developed as lead compounds.
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Affiliation(s)
- Chengjun Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
| | - Jinghan Luo
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
| | - Mengtong Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
| | - Fanzhen Meng
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
| | - Zhiqiang Cai
- College of Petrochemical Engineering, Shenyang University of Technology, Liaoyang 111003, China
| | - Yu Chen
- College of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tiemin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
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Joshi T, Joshi T, Pundir H, Sharma P, Mathpal S, Chandra S. Predictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease. J Biomol Struct Dyn 2020; 39:6728-6746. [PMID: 32752947 PMCID: PMC7484589 DOI: 10.1080/07391102.2020.1802341] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The whole world is facing a great challenging time due to Coronavirus disease (COVID-19) caused by SARS-CoV-2. Globally, more than 14.6 M people have been diagnosed and more than 595 K deaths are reported. Currently, no effective vaccine or drugs are available to combat COVID-19. Therefore, the whole world is looking for new drug candidates that can treat the COVID-19. In this study, we conducted a virtual screening of natural compounds using a deep-learning method. A deep-learning algorithm was used for the predictive modeling of a CHEMBL3927 dataset of inhibitors of Main protease (Mpro). Several predictive models were developed and evaluated based on R2, MAE MSE, RMSE, and Loss. The best model with R2=0.83, MAE = 1.06, MSE = 1.5, RMSE = 1.2, and loss = 1.5 was deployed on the Selleck database containing 1611 natural compounds for virtual screening. The model predicted 500 hits showing the value score between 6.9 and 3.8. The screened compounds were further enriched by molecular docking resulting in 39 compounds based on comparison with the reference (X77). Out of them, only four compounds were found to be drug-like and three were non-toxic. The complexes of compounds and Mpro were finally subjected to Molecular dynamic (MD) simulation for 100 ns. The MMPBSA result showed that two compounds Palmatine and Sauchinone formed very stable complex with Mpro and had free energy of −71.47 kJ mol−1 and −71.68 kJ mol−1 respectively as compared to X77 (−69.58 kJ mol−1). From this study, we can suggest that the identified natural compounds may be considered for therapeutic development against the SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Kumaun University, S.S.J Campus, Almora, India
| | - Tushar Joshi
- Department of Biotechnology, Kumaun University Uttarakhand, Bhimtal Campus, Bhimtal, India
| | - Hemlata Pundir
- Department of Botany, Kumaun University, D.S.B Campus, Nainital, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, D.S.B Campus, Nainital, India
| | - Shalini Mathpal
- Department of Biotechnology, Kumaun University Uttarakhand, Bhimtal Campus, Bhimtal, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Kumaun University, S.S.J Campus, Almora, India
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Sharma P, Joshi T, Joshi T, Chandra S, Tamta S. Molecular dynamics simulation for screening phytochemicals as α-amylase inhibitors from medicinal plants. J Biomol Struct Dyn 2020; 39:6524-6538. [PMID: 32748738 DOI: 10.1080/07391102.2020.1801507] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Diabetes mellitus (DM) is a complicated metabolic disorder with several enzymes, including α-amylase and α-glycosidase. The α-amylase is responsible for postprandial glucose levels; therefore, inhibiting its activity is helpful in diabetes management. Hence, to find natural inhibitors of α-amylase, we have prepared a 257 phytochemical library from selected medicinal plants with antidiabetic activity and conducted a virtual screening and molecular dynamics study. Seventy-nine phytochemicals were screened out of 257 phytochemicals based on binding energy, ranged from -10.1 kcal mol-1 to -7.6 kcal mol-1. The binding energies of screened compounds were lower or equal to the reference molecule (-7.6 kcal mol-1). The binding affinity of six screened phytochemicals was re-scored by X-SCORE. These phytochemicals were subjected to ADMET and Drug-likeness analysis. After screening docking and drug-likeness analysis, six phytochemicals viz., Shahidine, Epicatechin, Quercetin, Isocolumbin, Ellagic acid, Luteolin and a reference molecule (Acarbose) were subjected to Molecular dynamics (MD) simulation to analyze the stability of the docked protein-ligand complex. The values of root mean square deviation, RMSF, RG, SASA, H-Bond, the interaction energy of all protein-ligand complexes were calculated after 30 ns of MD simulation. The results of screened complexes revealed good stability as compared to reference Acarbose. Pharmacophore features of the screened phytochemicals and α-amylase inhibitors showed many common pharmacophore features. Based on finding the screened phytochemicals, e.g. Shahidine, Epicatechin, Quercetin, Isocolumbin, Ellagic acid, and Luteolin, may be used as a potential inhibitors against α-amylase. These phytochemicals could be optimized and synthesized to develop potential drugs to manage and treat diabetes, targeting α-amylase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Sharma
- Department of Botany, D.S.B. Campus, Kumaun University, Nainital, India
| | - Tushar Joshi
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India
| | - Tanuja Joshi
- Department of Botany, S.S.J Campus, Almora, Kumaun University, Nainital, India
| | - Subhash Chandra
- Department of Botany, S.S.J Campus, Almora, Kumaun University, Nainital, India
| | - Sushma Tamta
- Department of Botany, D.S.B. Campus, Kumaun University, Nainital, India
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40
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Discovery of potent and highly selective covalent inhibitors of Bruton’s tyrosine kinase bearing triazine scaffold. Eur J Med Chem 2020; 199:112339. [DOI: 10.1016/j.ejmech.2020.112339] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 11/20/2022]
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41
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Molecular docking and ADMET-based mining of terpenoids against targets of type-II diabetes. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s13721-020-00229-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Phenanthridine derivatives as promising new anticancer agents: synthesis, biological evaluation and binding studies. Future Med Chem 2020; 12:709-739. [PMID: 32208986 DOI: 10.4155/fmc-2019-0016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Phenanthridines are an essential class of nitrogenous heterocycles with extensive applications in medicinal chemistry. The development of efficient and eco-friendly methods for the preparation of chirally pure dihydropyrrolo[1,2-f]phenanthridines (5a-h), and their in vitro evaluation and modeling studies as potential anticancer, antioxidant and DNA cleavage agents is reported. Methodology & results: Compounds 5a-h were prepared through a facile one-pot synthesis and characterized by infrared, high resolution mass spectrometry, 1H and 13C nuclear magnetic resonance. The molecules were subjected to virtual screening and docking analysis against selected human molecular targets. Compound 5g displayed good binding properties as well as significant anticancer and DNA cleavage activity. Conclusion: Compound 5g has been identified as a potential lead candidate for further testing against additional cancer cell lines and animal models in future.
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43
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Joshi T, Joshi T, Sharma P, Chandra S, Pande V. Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting peptide deformylase. J Biomol Struct Dyn 2020; 39:823-840. [PMID: 31965918 DOI: 10.1080/07391102.2020.1719200] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Xanthomonas oryzae pv. Oryzae (Xoo) causes bacterial leaf blight (BLB) of rice which results in a huge loss in production. Many chemicals are used to control BLB disease. However, these chemicals are toxic to the environments, animals and human beings. Thus, there is a demand to discover potential and safe natural pesticides to manage BLB disease successfully. Therefore, we screened a library of phytochemicals of different plants having antibacterial activity by targeting Peptide Deformylase (PDF) of Xoo using in silico techniques. A library of 318 phytochemicals was prepared and subjected to rigid and flexible molecular docking against PDF followed by molecular dynamics simulation and free energy analysis of protein-ligand complexes. The results of virtual screening showed that 14 compounds from different plants have good binding energy as compare to reference molecule (3 R)-2,3-dihydro[1,3] thiazolo [3,2 a]benzimidazol-3-ol) (-7.7 kcal mol-1). Out of 14 hit compounds, eight compounds that were selected based on binding energy were analyzed by Molecular dynamic (MD) simulation. Analysis of MD simulation revealed that eight compounds namely; Bisdemethoxycurcumin, Rosmarinic acid, Piperanine, Dihydropiperlonguminine, Piperdardine, Dihydrocurcumin and Lonhumosides B achieved good stability during the 80 ns MD simulation at 300 K in term of the RMSD. Further, we calculated RMSF, RG, SASA, and interaction energy after 40 ns due to showing the stability of complexes. From our results, we conclude that these natural compounds could inhibit Xoo by targeting PDF receptor and can be used as potential bactericidal candidates against BLB disease of rice against Xoo and other bacteria. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India.,Department of Botany, Kumaun University, Almora, Uttarakhand, India
| | - Tanuja Joshi
- Department of Botany, Kumaun University, Almora, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, Almora, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
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44
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Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9214538] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AutoDock and Vina are two of the most widely used protein–ligand docking programs. The fact that these programs are free and available under an open source license, also makes them a very popular first choice for many users and a common starting point for many virtual screening campaigns, particularly in academia. Here, we evaluated the performance of AutoDock and Vina against an unbiased dataset containing 102 protein targets, 22,432 active compounds and 1,380,513 decoy molecules. In general, the results showed that the overall performance of Vina and AutoDock was comparable in discriminating between actives and decoys. However, the results varied significantly with the type of target. AutoDock was better in discriminating ligands and decoys in more hydrophobic, poorly polar and poorly charged pockets, while Vina tended to give better results for polar and charged binding pockets. For the type of ligand, the tendency was the same for both Vina and AutoDock. Bigger and more flexible ligands still presented a bigger challenge for these docking programs. A set of guidelines was formulated, based on the strengths and weaknesses of both docking program and their limits of validation.
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45
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Joshi T, Sharma P, Joshi T, Chandra S. In silico screening of anti-inflammatory compounds from Lichen by targeting cyclooxygenase-2. J Biomol Struct Dyn 2019; 38:3544-3562. [PMID: 31524074 DOI: 10.1080/07391102.2019.1664328] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Non-steroidal anti-inflammatory drugs (NSAID) targeting cyclooxygenase-2 are clinically effective. However, they lack anti-thrombotic activity resulting in incidences of adverse effects like myocardial infarction, gastrointestinal and abdominal discomfort which necessitate for discovering new drug candidates with improved therapeutic effects and tolerability. Various recent researches have suggested that many lichens offer a vast reservoir for anti-inflammatory drug candidates which are natural as well as safe for human consumption. Drug discovery is a very complex and time-consuming process; however, in silico techniques can make this process simple and economic. Hence to find out natural anti-inflammatory compounds, we have carried out the virtual screening of 412 lichen compounds by molecular docking with human Cox-2 enzyme and validated the docking score by X-Score followed by ADMET and Drug-likeness analysis. The resulting 6 top-scored compounds were subjected to Molecular dynamics simulation (MDS) to analyze the stability of docked protein-ligand complex, to assess the fluctuation and conformational changes during protein-ligand interaction. The values of RMSD, Rg, and interaction energy after 30 ns of MDS revealed the good stability of these Lichen compounds in the active site pocket of Cox-2 in compare to reference, JMS. Additionally, we have done the pharmacophore analysis which found many common pharmacophore features between Lichen compounds and well known anti-inflammatory compounds. Our result shows that these lichen compounds are potential anti-inflammatory candidates and could be further modified and evaluated to develop more effective anti-inflammatory drugs with fewer side effects for the treatment of inflammatory diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tanuja Joshi
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, D.S.B. Campus, Nainital, Uttarakhand, India
| | - Tushar Joshi
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India.,Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India
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Zhao W, Xue S, Yu Z, Ding L, Li J, Liu J. Novel ACE inhibitors derived from soybean proteins using in silico and in vitro studies. J Food Biochem 2019; 43:e12975. [PMID: 31489673 DOI: 10.1111/jfbc.12975] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022]
Abstract
The widespread application of soybean-derived peptides is currently limited due to the challenges in the identification of peptides. In the present work, in silico and in vitro analysis were applied to identify ACE inhibitory tri-peptides from soybean protein. The soybean protein was cleaved by PeptideCutter. Then, unknown tri-peptides were selected to solubility estimation and ADME prediction. Subsequently, Discovery Studio was applied to evaluate the interaction mechanism between ACE and tri-peptides. Finally, in vitro activity of theoretical ACE inhibitory tri-peptides was verified by RP-HPLC method. As a result, DMG was selected as a potent ACE inhibitory peptide. Cell experiment showed that DMG had no cytotoxic effects on HEK-293 cells. And molecular docking results indicated that DMG contacted well with ACE's active sites (Gln281, His353, Ala354, Glu384, Lys511, His513, and Tyr520). Furthermore, DMG could exert potent activity against ACE, with IC50 value of 3.95 ± 0.11 mM. PRACTICAL APPLICATIONS: Present research showed soybean is a potential protein resource to obtain ACE inhibitory peptides. Simultaneously, virtual screening method is a feasible way to substitute for classical method in emerging nutritional fields. What's more, present study provides a theoretical basis for industrial research on foodstuff for ACE inhibitory peptides without side effects.
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Affiliation(s)
- Wenzhu Zhao
- College of Food Science and Engineering, Bohai University, Jinzhou, P.R. China
| | - Siyu Xue
- College of Food Science and Engineering, Bohai University, Jinzhou, P.R. China
| | - Zhipeng Yu
- College of Food Science and Engineering, Bohai University, Jinzhou, P.R. China
| | - Long Ding
- Lab of Nutrition and Functional Food, Jilin University, Changchun, P.R. China
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University, Jinzhou, P.R. China
| | - Jingbo Liu
- Lab of Nutrition and Functional Food, Jilin University, Changchun, P.R. China
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47
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Appiah-Kubi P, Olotu FA, Soliman MES. Probing Binding Landscapes and Molecular Recognition Mechanisms of Atypical Antipsychotic Drugs towards the Selective Targeting of D 2 Dopamine Receptor. Mol Inform 2019; 38:e1900044. [PMID: 31433121 DOI: 10.1002/minf.201900044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/22/2019] [Indexed: 11/09/2022]
Abstract
Dopamine receptors constitute a unique class of G-protein coupled receptors that mediate the activities of dopamine, a neurotransmitter implicated in diverse neurological diseases when dysregulated. Over the years, antipsychotic drugs have been primarily directed towards D2 dopamine receptor (DRD2) while associable adverse effects have been centred on non-selective targeting. The recent crystal structure of DRD2 in complex with atypical antipsychotic could further aid the structure-based design of highly DRD2-selective antipsychotics. Therefore, in this study, we comprehensively investigate the molecular recognition and differential binding landscapes of class-I and II DRD2 atypical antipsychotics, using membrane-bilayer molecular dynamics simulation and binding free energy techniques. Findings revealed that selected class-I antipsychotics exhibited binding dynamics and poses dissimilar to the class-II types with different interactive mechanisms at the binding cavity of DRD2. More interestingly, the class-II drugs established a highly coordinated binding at the DRD2 active site with a pertinent and recurrent involvement of Asp114 via strong hydrogen interactions. Furthermore, while these compounds exert distinct effects on DRD2 structure, findings revealed that the class-II types favourably engaged the deep hydrophobic pocket of DRD2 compared to the class-I drugs. We speculate that these findings will be fundamental to the discovery of highly selective DRD2 antipsychotics.
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Affiliation(s)
- Patrick Appiah-Kubi
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Fisayo Andrew Olotu
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
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Nazifi SMR, Sadeghi-aliabadi H, Fassihi A, Aliomrani M, Saghaie L. Synthesis and antiproliferative evaluation of some iron chelators as polyamine transporter targeting agents. CAN J CHEM 2019. [DOI: 10.1139/cjc-2019-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series of kojic acid derivatives based on monoamines, diamines, and triamines have been synthesized in good yield and purity. A spermidine (spd) rescue experiment was applied against MCF-7 cells to evaluate the polyamine transporter selectivity, and in vitro antiproliferative effects were determined against Hela and DU-145 cell lines. Overall, 5b showed the best selectivity for the polyamine transporter and antiproliferative effects. Therefore, the in-silico metabolism profile and ADMET properties of the title compounds were calculated by the PreADMET server. Additionally, physicochemical properties of ligands were predicted by using the Molinspiration online property calculation server.
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Affiliation(s)
- Seyed Mohamad Reza Nazifi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461 Isfahan, Iran
| | - Hojjat Sadeghi-aliabadi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461 Isfahan, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461 Isfahan, Iran
| | - Mehdi Aliomrani
- Department of Toxicology and Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences and Health Services, Isfahan, Iran
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461 Isfahan, Iran
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Shukla R, Munjal NS, Singh TR. Identification of novel small molecules against GSK3β for Alzheimer's disease using chemoinformatics approach. J Mol Graph Model 2019; 91:91-104. [PMID: 31202091 DOI: 10.1016/j.jmgm.2019.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease is a rapidly increasing neurodegenerative disease. It is a multifactorial disease and also a global threat. Several enzymes are implicated in the disease in which Glycogen Synthase Kinase 3 beta is a key enzyme to increase the disease progression by the hyperphosphorylation of the tau protein. We have used an integrative chemoinformatics and pharmacokinetics approach for the identification of novel small molecules. We have retrieved a subset from the ZINC database (n = 5,36,709) and screened against GSK3β in four steps. From here top 298 potent compounds were selected and employed for their pharmacokinetics analysis. We had seen that 29 compounds showed the key characteristics to be a novel drug candidate therefore, all these compounds were employed for redocking studies using Autodock Vina and Autodock. This analysis revealed that four compounds were showing good binding affinity. All these four compounds were employed for MDS analysis of 100 ns From here using a bunch of MD analyses we have found that out of four compounds GSK3β-ZINC21011059 and GSK3β-ZINC21011066 act as a stable protein-ligand complex. Therefore we proposed ZINC21011059 and ZINC21011066 can serve as a novel compounds against GSK3β and predicted scaffold can be used for further optimization towards the improvement of isoform selectivity, and warranting further investigations towards their in vitro and in vivo validation of the bioactivity.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, H.P, 173234, India
| | - Nupur S Munjal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, H.P, 173234, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, H.P, 173234, India.
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50
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Liu L, Li X, Cheng Y, Wang L, Yang H, Li J, He S, shuangjie Wu, Yin Q, Xiang H. Optimization of novel benzofuro[3,2-b]pyridin-2(1H)-one derivatives as dual inhibitors of BTK and PI3Kδ. Eur J Med Chem 2019; 164:304-316. [DOI: 10.1016/j.ejmech.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/08/2018] [Accepted: 12/22/2018] [Indexed: 11/30/2022]
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