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Wang J, Guo Y, Zhou H, Hua Y, Wan H, Yang J. Investigating the Mechanistic of Danhong Injection in Brain Damage Caused by Cardiac I/R Injury via Bioinformatics, Computer Simulation, and Experimental Validation. ACS OMEGA 2024; 9:18341-18357. [PMID: 38680343 PMCID: PMC11044240 DOI: 10.1021/acsomega.4c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024]
Abstract
OBJECTIVE Cardiac ischemia-reperfusion (I/R) injury has negative effects on the brain and can even lead to the occurrence of ischemic stroke. Clinical evidence shows that Danhong injection (DHI) protects the heart and brain following ischemic events. This study investigated the mechanisms and key active compounds underlying the therapeutic effect of DHI against brain damage induced by cardiac I/R injury. METHODS The gene expression omnibus database provided GSE66360 and GSE22255 data sets. The R programming language was used to identify the common differentially expressed genes (cDEGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed, and protein-protein interaction network was constructed. Active compounds of DHI were collected from the Traditional Chinese Medicine Systems Pharmacology database. Molecular docking and molecular dynamics simulations were performed. The MMPBSA method was used to calculate the binding-free energy. The pkCSM server and DruLiTo software were used for Absorption, Distribution, metabolism, excretion, and toxicity (ADMET) analysis and drug-likeness analysis. Finally, in vitro experiments were conducted to validate the results. RESULTS A total of 27 cDEGs had been identified. The PPI and enrichment results indicated that TNF-α was considered to be the core target. A total of 80 active compounds were retrieved. The molecular docking results indicated that tanshinone I (TSI), tanshinone IIA (TSIIA), and hydroxyl safflower yellow A (HSYA) were selected as core active compounds. Molecular dynamics verification revealed that the conformations were relatively stable without significant fluctuations. MMPBSA analysis revealed that the binding energies of TSI, TSIIA, and HSYA with TNF-α were -36.01, -21.71, and -14.80 kcal/mol, respectively. LEU57 residue of TNF-α has the highest contribution. TSI and TSIIA passed both the ADMET analysis and drug-likeness screening, whereas HSYA did not. Experimental verification confirmed that DHI and TSIIA reduced the expression of TNF-α, NLRP3, and IL-1β in the injured H9C2 and rat brain microvascular endothelial cells. CONCLUSION TNF-α can be considered to be a key target for BD-CI/R. TSIIA in DHI exerts a significant inhibitory effect on the inflammatory damage of BD-CI/R, providing new insights for future drug development.
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Affiliation(s)
- Jinfu Wang
- School
of Basic Medical Sciences, Zhejiang Chinese
Medical University, Hangzhou, Zhejiang 310053, China
| | - Yan Guo
- Hangzhou
TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Huifen Zhou
- School
of Basic Medical Sciences, Zhejiang Chinese
Medical University, Hangzhou, Zhejiang 310053, China
- Key
Laboratory of TCM Encephalopathy of Zhejiang Province, Hangzhou, Zhejiang 310053, China
| | - Yanjie Hua
- College
of Life Science, Zhejiang Chinese Medical
University, Hangzhou, Zhejiang 310053, China
| | - Haitong Wan
- School
of Basic Medical Sciences, Zhejiang Chinese
Medical University, Hangzhou, Zhejiang 310053, China
- Key
Laboratory of TCM Encephalopathy of Zhejiang Province, Hangzhou, Zhejiang 310053, China
| | - Jiehong Yang
- School
of Basic Medical Sciences, Zhejiang Chinese
Medical University, Hangzhou, Zhejiang 310053, China
- Key
Laboratory of TCM Encephalopathy of Zhejiang Province, Hangzhou, Zhejiang 310053, China
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Moin AT, Robin TB, Patil RB, Rani NA, Prome AA, Sakif TI, Hossain M, Chowdhury DUS, Rashid SS, Mollah AKMM, Islam S, Uddin MH, Khalequzzaman M, Islam T, Islam NN. Antifungal plant flavonoids identified in silico with potential to control rice blast disease caused by Magnaporthe oryzae. PLoS One 2024; 19:e0301519. [PMID: 38578751 PMCID: PMC10997076 DOI: 10.1371/journal.pone.0301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Rice blast disease, caused by the fungus Magnaporthe oryzae, poses a severe threat to rice production, particularly in Asia where rice is a staple food. Concerns over fungicide resistance and environmental impact have sparked interest in exploring natural fungicides as potential alternatives. This study aimed to identify highly potent natural fungicides against M. oryzae to combat rice blast disease, using advanced molecular dynamics techniques. Four key proteins (CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PRE-MRNA-SPLICING FACTOR CEF1) involved in M. oryzae's infection process were identified. A list of 30 plant metabolites with documented antifungal properties was compiled for evaluation as potential fungicides. Molecular docking studies revealed that 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin exhibited superior binding affinities compared to reference fungicides (Azoxystrobin and Tricyclazole). High throughput molecular dynamics simulations were performed, analyzing parameters like RMSD, RMSF, Rg, SASA, hydrogen bonds, contact analysis, Gibbs free energy, and cluster analysis. The results revealed stable interactions between the selected metabolites and the target proteins, involving important hydrogen bonds and contacts. The SwissADME server analysis indicated that the metabolites possess fungicide properties, making them effective and safe fungicides with low toxicity to the environment and living beings. Additionally, bioactivity assays confirmed their biological activity as nuclear receptor ligands and enzyme inhibitors. Overall, this study offers valuable insights into potential natural fungicides for combating rice blast disease, with 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin standing out as promising and environmentally friendly alternatives to conventional fungicides. These findings have significant implications for developing crop protection strategies and enhancing global food security, particularly in rice-dependent regions.
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Affiliation(s)
- Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Anindita Ash Prome
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tahsin Islam Sakif
- Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, United States of America
| | - Mohabbat Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Dil Umme Salma Chowdhury
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Shah Samiur Rashid
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chattogram, Bangladesh
| | | | - Saiful Islam
- Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, Bangladesh
| | - Mohammad Helal Uddin
- Department of Applied Chemistry and Chemical Engineering, University of Chittagong, Chittagong, Bangladesh
| | | | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nazneen Naher Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
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Elseginy SA. Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations. J Comput Aided Mol Des 2024; 38:16. [PMID: 38556596 PMCID: PMC10982093 DOI: 10.1007/s10822-024-00553-5] [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: 12/28/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The kinesin spindle protein (Eg5) is a mitotic protein that plays an essential role in the formation of the bipolar spindles during the mitotic phase. Eg5 protein controls the segregation of the chromosomes in mitosis which renders it a vital target for cancer treatment. In this study our approach to identifying novel scaffold for Eg5 inhibitors is based on targeting the novel allosteric pocket (α4/α6/L11). Extensive computational techniques were applied using ligand-based virtual screening and molecular docking by two approaches, MOE and AutoDock, to screen a library of commercial compounds. We identified compound 8-(3-(1H-imidazol-1-ylpropylamino)-3-methyl-7-((naphthalen-3-yl)methyl)-1H-purine-2, 6 (3H,7H)-dione (compound 5) as a novel scaffold for Eg5 inhibitors. This compound inhibited cancer cell Eg5 ATPase at 2.37 ± 0.15 µM. The molecular dynamics simulations revealed that the identified compound formed stable interactions in the allosteric pocket (α4/α6/L11) of the receptor, indicating its potential as a novel Eg5 inhibitor.
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Affiliation(s)
- Samia A Elseginy
- Chemical Industries Research Division, Green Chemistry Department, National Research Centre, Cairo, 12622, Egypt.
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Hossain MS, Rahman MA, Dey PR, Khandocar MP, Ali MY, Snigdha M, Coutinho HDM, Islam MT. Natural Isatin Derivatives Against Black Fungus: In Silico Studies. Curr Microbiol 2024; 81:113. [PMID: 38472456 DOI: 10.1007/s00284-024-03621-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/18/2024] [Indexed: 03/14/2024]
Abstract
During this coronavirus pandemic, when a lot of people are already severely afflicted with SARS-CoV-19, the dispersion of black fungus is making it worse, especially in the Indian subcontinent. Considering this situation, the idea for an in silico study to identify the potential inhibitor against black fungal infection is envisioned and computational analysis has been conducted with isatin derivatives that exhibit considerable antifungal activity. Through this in silico study, several pharmacokinetics properties like absorption, distribution, metabolism, excretion, and toxicity (ADMET) are estimated for various derivatives. Lipinski rules have been used to observe the drug likeliness property, and to study the electronic properties of the molecules, quantum mechanism was analyzed using the density functional theory (DFT). After applying molecular docking of the isatin derivatives with sterol 14-alpha demethylase enzyme of black fungus, a far higher docking affinity score has been observed for the isatin sulfonamide-34 (derivative 1) than the standard fluconazole. Lastly, molecular dynamic (MD) simulation has been performed for 100 ns to examine the stability of the proposed drug complex by estimating Root Mean Square Deviation (RMSD), Radius of gyration (Rg), Solvent accessible surface area (SASA), Root Mean Square Fluctuation (RMSF), as well as hydrogen bond. Listed ligands have precisely satisfied every pharmacokinetics requirement for a qualified drug candidate and they are non-toxic, non-carcinogenic, and have high stability. This natural molecule known as isatin derivative 1 has shown the potential of being a drug for fungal treatment. However, the impact of the chemicals on living cells requires more investigation and research.
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Affiliation(s)
- Md Saddam Hossain
- Department of Biomedical Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Anisur Rahman
- Department of Pharmacy, Islamic University, Kushtia, 7003, Bangladesh
| | - Prithbey Raj Dey
- Department of Industrial and Production Engineering, Dhaka University of Engineering and Technology, Gazipur, 1707, Bangladesh
| | - Md Parvez Khandocar
- Department of Biomedical Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Yeakub Ali
- Department of Biomedical Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Mahajabin Snigdha
- Department of Pharmacy, Islamic University, Kushtia, 7003, Bangladesh
| | | | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
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Siew ZY, Asudas E, Khoo CT, Cho GH, Voon K, Fang CM. Fighting nature with nature: antiviral compounds that target retroviruses. Arch Microbiol 2024; 206:130. [PMID: 38416180 DOI: 10.1007/s00203-024-03846-3] [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: 11/16/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 02/29/2024]
Abstract
The human immunodeficiency virus (HIV) is a type of lentivirus that targets the human immune system and leads to acquired immunodeficiency syndrome (AIDS) at a later stage. Up to 2021, there are millions still living with HIV and many have lost their lives. To date, many anti-HIV compounds have been discovered in living organisms, especially plants and marine sponges. However, no treatment can offer a complete cure, but only suppressing it with a life-long medication, known as combined antiretroviral therapy (cART) or highly active antiretroviral therapy (HAART) which are often associated with various adverse effects. Also, it takes many years for a discovered compound to be approved for clinical use. Thus, by employing advanced technologies such as automation, conducting systematic screening and testing protocols may boost the discovery and development of potent and curative therapeutics for HIV infection/AIDS. In this review, we aim to summarize the antiretroviral therapies/compounds and their associated drawbacks since the discovery of azidothymidine. Additionally, we aim to provide an updated analysis of the most recent discoveries of promising antiretroviral candidates, along with an exploration of the current limitations within antiretroviral research. Finally, we intend to glean insightful perspectives and propose future research directions in this crucial area of study.
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Affiliation(s)
- Zhen Yun Siew
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia.
| | - Elishea Asudas
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Chia Ting Khoo
- School of Biosciences, University of Nottingham Malaysia, 43500, Semenyih, Selangor, Malaysia
| | - Gang Hyeon Cho
- School of Pharmacy, University of Nottingham Malaysia, 43500, Semenyih, Selangor, Malaysia
| | - Kenny Voon
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Chee-Mun Fang
- Division of Biomedical Sciences, School of Pharmacy, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia.
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Khanum A, Bibi Y, Khan I, Mustafa G, Attia KA, Mohammed AA, Yang SH, Qayyum A. Molecular docking of bioactive compounds extracted and purified from selected medicinal plant species against covid-19 proteins and in vitro evaluation. Sci Rep 2024; 14:3736. [PMID: 38355953 PMCID: PMC10866962 DOI: 10.1038/s41598-024-54470-6] [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: 10/17/2023] [Accepted: 02/13/2024] [Indexed: 02/16/2024] Open
Abstract
Bioactive compounds are secondary metabolites of plants. They offer diverse pharmacological properties. Peganum harmala is reported to have pharmaceutical effects like insecticidal, antitumor, curing malaria, anti-spasmodic, vasorelaxant, antihistaminic effect. Rosa brunonii has medicinal importance in its flower and fruits effective against different diseases and juice of leaf is reported to be applied externally to cure wounds and cuts. Dryopteris ramosa aqueous leaf extract is used to treat stomach ulcers and stomachaches. Each of these three medicinal plants have been indicated to have anticancer, antiviral, antioxidant, cytotoxic and antifungal effects but efficacy of their bioactive compounds remained unexplored. Study was aimed to explore In-vitro and In-silico anticancer, antiviral, antioxidant, cytotoxic and antifungal effects of bioactive compounds of above three medicinal plants. DPPH and ABTS assay were applied for assessment of antioxidant properties of compounds. Antibacterial properties of compounds were checked by agar well diffusion method. Brine shrimp lethality assay was performed to check cytotoxic effect of compounds. Molecular docking was conducted to investigate the binding efficacy between isolated compounds and targeted proteins. The compound isomangiferrin and tiliroside presented strong antioxidant potential 78.32% (± 0.213) and 77.77% (± 0.211) respectively in DPPH assay while harmaline showed 80.71% (± 0.072) at 200 µg/mL in ABTS assay. The compound harmine, harmaline and PH-HM 17 exhibited highest zone of inhibition 22 mm, 23 mm, 22 mm respectively against Xanthomonas while Irriflophenone-3-C-β- D-glucopyranoside showed maximum zone of inhibition 34 mm against E. coli. The compound isomangiferrin and vasicine contained strong antibacterial activity 32 mm and 22 mm respectively against S. aureus. The compound mangiferrin, astragalin, tiliroside, quercitin-3-O-rhamnoside showed maximum inhibitory zone 32 mm, 26 mm, 24 mm and 22 mm respectively against Klebsiella pneumoniae. Highest cytotoxic effect was observed by compound tiliroside i.e. 95% with LD50 value 73.59 µg/mL. The compound tiliroside showed the best binding mode of interaction to all targeted proteins presenting maximum hydrophobic interactions and hydrogen bonds. The binding affinity of tiliroside was - 17.9, - 14.9, - 14.6, - 13.8, - 12.8 against different proteins 6VAR, 5C5S, IEA3, 2XV7 and 6LUS respectively. Bioactive compounds are significant natural antioxidants, which could help to prevent the progression of various diseases caused by free radicals. Based on molecular docking we have concluded that phytochemicals can have better anticancer and antiviral potential.
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Affiliation(s)
- Ayesha Khanum
- Department of Biology, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, 46300, Pakistan
| | - Yamin Bibi
- Department of Botany, Rawalpindi Women University, Rawalpindi, 46300, Pakistan.
| | - Ilham Khan
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Ghazala Mustafa
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Arif Ahmed Mohammed
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, 59626, Republic of Korea.
| | - Abdul Qayyum
- Department of Agronomy, The University of Haripur, Haripur, 22620, Pakistan.
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Er-Rajy M, El Fadili M, Faris A, Zarougui S, Elhallaoui M. Design of potential anti-cancer agents as COX-2 inhibitors, using 3D-QSAR modeling, molecular docking, oral bioavailability proprieties, and molecular dynamics simulation. Anticancer Drugs 2024; 35:117-128. [PMID: 38018861 DOI: 10.1097/cad.0000000000001492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Modeling the structural properties of novel morpholine-bearing 1, 5-diaryl-diazole derivatives as potent COX-2 inhibitor, two proposed models based on CoMFA and CoMSIA were evaluated by external and internal validation methods. Partial least squares analysis produced statistically significant models with Q 2 values of 0.668 and 0.652 for CoMFA and CoMSIA, respectively, and also a significant non-validated correlation coefficient R² with values of 0.882 and 0.878 for CoMFA and CoMSIA, respectively. Both models met the requirements of Golbraikh and Tropsha, which means that both models are consistent with all validation techniques. Analysis of the CoMFA and CoMSIA contribution maps and molecular docking revealed that the R1 substituent has a very significant effect on their biological activity. The most active molecules were evaluated for their thermodynamic stability by performing MD simulations for 100 ns; it was revealed that the designed macromolecular ligand complex with 3LN1 protein exhibits a high degree of structural and conformational stability. Based on these results, we predicted newly designed compounds, which have acceptable oral bioavailability properties and would have high synthetic accessibility.
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Affiliation(s)
- Mohammed Er-Rajy
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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8
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Reese TC, Devineni A, Smith T, Lalami I, Ahn JM, Raj GV. Evaluating physiochemical properties of FDA-approved orally administered drugs. Expert Opin Drug Discov 2024; 19:225-238. [PMID: 37921049 DOI: 10.1080/17460441.2023.2275617] [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: 08/10/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
INTRODUCTION Analyses of orally administered FDA-approved drugs from 1990 to 1993 enabled the identification of a set of physiochemical properties known as Lipinski's Rule of Five (Ro5). The original Ro5 and extended versions still remain the reference criteria for drug development programs. Since many bioactive compounds do not conform to the Ro5, we validated the relevance of and adherence to these rulesets in a contemporary cohort of FDA-approved drugs. AREAS COVERED The authors noted that a significant proportion of FDA-approved orally administered parent compounds from 2011 to 2022 deviate from the original Ro5 criteria (~38%) or the Ro5 with extensions (~53%). They then evaluated if a contemporary Ro5 criteria (cRo5) could be devised to better predict oral bioavailability. Furthermore, they discuss many case studies showcasing the need for and benefit of increasing the size of certain compounds and cover several evolving strategies for improving oral bioavailability. EXPERT OPINION Despite many revisions to the Ro5, the authors find that no single proposed physiochemical rule has universal concordance with absolute oral bioavailability. Innovations in drug delivery and formulation have dramatically expanded the range of physicochemical properties and the chemical diversity for oral administration.
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Affiliation(s)
- Tanner C Reese
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
| | - Anvita Devineni
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
| | - Tristan Smith
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Ismail Lalami
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, USA
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, USA
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Masand VH, Al-Hussain S, Alzahrani AY, El-Sayed NNE, Yeo CI, Tan YS, Zaki MEA. Leveraging nitrogen occurrence in approved drugs to identify structural patterns. Expert Opin Drug Discov 2024; 19:111-124. [PMID: 37811790 DOI: 10.1080/17460441.2023.2266990] [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: 07/27/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND The process of drug development and discovery is costly and slow. Although an understanding of molecular design principles and biochemical processes has progressed, it is essential to minimize synthesis-testing cycles. An effective approach is to analyze key heteroatoms, including oxygen and nitrogen. Herein, we present an analysis focusing on the utilization of nitrogen atoms in approved drugs. RESEARCH DESIGN AND METHODS The present work examines the frequency, distribution, prevalence, and diversity of nitrogen atoms in a dataset comprising 2,049 small molecules approved by different regulatory agencies (FDA and others). Various types of nitrogen atoms, such as sp3-, sp2-, sp-hybridized, planar, ring, and non-ring are included in this investigation. RESULTS The results unveil both previously reported and newly discovered patterns of nitrogen atom distribution around the center of mass in the majority of drug molecules. CONCLUSIONS This study has highlighted intriguing trends in the role of nitrogen atoms in drug design and development. The majority of drugs contain 1-3 nitrogen atoms within 5Å from the center of mass (COM) of a molecule, with a higher preference for the ring and planar nitrogen atoms. The results offer invaluable guidance for the multiparameter optimization process, thus significantly contributing toward the conversion of lead compounds into potential drug candidates.
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Affiliation(s)
- Vijay H Masand
- Department of Chemistry, Vidya Bharati Mahavidyalaya, Amravati, India
| | - Sami Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdullah Y Alzahrani
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail Assir, Saudi Arabia
| | - Nahed N E El-Sayed
- National Organization for Drug Control and Research, Egyptian Drug Authority (EDA), Giza, Egypt
| | - Chien Ing Yeo
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - Yee Seng Tan
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
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Ouassaf M, Bourougaa L, Al-Mijalli SH, Abdallah EM, Bhat AR, A. Kawsar SM. Marine-Derived Compounds as Potential Inhibitors of Hsp90 for Anticancer and Antimicrobial Drug Development: A Comprehensive In Silico Study. Molecules 2023; 28:8074. [PMID: 38138564 PMCID: PMC10871121 DOI: 10.3390/molecules28248074] [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: 11/05/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Marine compounds constitute a diverse and invaluable resource for the discovery of bioactive substances with promising applications in the pharmaceutical development of anti-inflammatory and antibacterial agents. In this study, a comprehensive methodology was employed, encompassing pharmacophore modeling, virtual screening, in silico ADMET assessment (encompassing aspects of absorption, distribution, metabolism, excretion, and toxicity), and molecular dynamics simulations. These methods were applied to identify new inhibitors targeting the Hsp90 protein (heat shock protein 90), commencing with a diverse assembly of compounds sourced from marine origins. During the virtual screening phase, an extensive exploration was conducted on a dataset comprising 31,488 compounds sourced from the CMNPD database, characterized by a wide array of molecular structures. The principal objective was the development of structure-based pharmacophore models, a valuable approach when the pool of known ligands is limited. The pharmacophore model DDRRR was successfully constructed within the active sites of the Hsp90 crystal structure. Subsequent docking studies led to the identification of six compounds (CMNPD 22591, 9335, 10015, 360799, 15115, and 20988) demonstrating substantial binding affinities, each with values below -8.3 kcal/mol. In the realm of in silico ADMET predictions, five of these compounds exhibited favorable pharmacokinetic properties. Furthermore, molecular dynamics simulations and total binding energy calculations using MM-PBSA indicated that these marine-derived compounds formed exceptionally stable complexes with the Hsp90 receptor over a 100-nanosecond simulation period. These findings underscore the considerable potential of these novel marine compounds as promising candidates for anticancer and antimicrobial drug development.
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Affiliation(s)
- Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra 707000, Algeria;
| | - Lotfi Bourougaa
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra 707000, Algeria;
| | - Samiah Hamad Al-Mijalli
- Department of Biology, College of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia;
| | - Ajmal R. Bhat
- Department of Chemistry, RTM Nagpur University, Nagpur 440033, India;
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh;
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Yazdani B, Sirous H, Brogi S, Calderone V. Structure-Based High-Throughput Virtual Screening and Molecular Dynamics Simulation for the Discovery of Novel SARS-CoV-2 NSP3 Mac1 Domain Inhibitors. Viruses 2023; 15:2291. [PMID: 38140532 PMCID: PMC10747130 DOI: 10.3390/v15122291] [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: 10/17/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Since the emergence of SARS-CoV-2, many genetic variations within its genome have been identified, but only a few mutations have been found in nonstructural proteins (NSPs). Among this class of viral proteins, NSP3 is a multidomain protein with 16 different domains, and its largest domain is known as the macrodomain or Mac1 domain. In this study, we present a virtual screening campaign in which we computationally evaluated the NCI anticancer library against the NSP3 Mac1 domain, using Molegro Virtual Docker. The top hits with the best MolDock and Re-Rank scores were selected. The physicochemical analysis and drug-like potential of the top hits were analyzed using the SwissADME data server. The binding stability and affinity of the top NSC compounds against the NSP3 Mac1 domain were analyzed using molecular dynamics (MD) simulation, using Desmond software, and their interaction energies were analyzed using the MM/GBSA method. In particular, by applying subsequent computational filters, we identified 10 compounds as possible NSP3 Mac1 domain inhibitors. Among them, after the assessment of binding energies (ΔGbind) on the whole MD trajectories, we identified the four most interesting compounds that acted as strong binders of the NSP3 Mac1 domain (NSC-358078, NSC-287067, NSC-123472, and NSC-142843), and, remarkably, it could be further characterized for developing innovative antivirals against SARS-CoV-2.
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Affiliation(s)
- Behnaz Yazdani
- Bioscience Department, Faculty of Science and Technology (FCT), Universitat de Vic—Universitat Central de Catalunya (Uvic-UCC), 08500 Vic, Spain;
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Simone Brogi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
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12
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Murad H, Rafeeq M. Cheminformatics approach for identification of N-HyMenatPimeMelly as a novel potential ligand against RAS and renal chloride channel. J Biomol Struct Dyn 2023:1-15. [PMID: 37882351 DOI: 10.1080/07391102.2023.2273439] [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: 05/29/2023] [Accepted: 10/14/2023] [Indexed: 10/27/2023]
Abstract
Some angiotensin receptor (AR) blockers interfere with the renal chloride channel (ClC-K), which plays an important role in urine concentration. Identifying ligands targeting this channel, whether activating or blocking, is highly desirable because it could open the way for interventions that modulate their activity. In this study, the Asinex (BioDesign) complete library was screened to identify a compound with favorable physicochemical and pharmacokinetic properties, which have both AR blocking and ClC-Ka-modulating activities to present it as a novel potential oral candidate which could be useful for treatment of salt-sensitive hypertension without major ClC-K affection. A compound, N-{[4-Hydroxy-1-(2-methyl-1,6-naphthyridin-4-yl)-4-piperidinyl]methyl}-N-methyl-L-lysinamide (N-HyMenatPimeMelly) (Chem Spider ID 68416221), was identified as a potent potential oral ligand of the renin-angiotensin system (RAS) and ClC-Ka with docking scores ranging from -10.978 to -7.324 with the four selected proteins (4YAY: AR type 1, 2PFI: Cytoplasmic domain of ClC-Ka, 6JOD: AR type 2 and 6M0J: Angiotensin-converting enzyme 2). The protein-ligand complex was used to perform molecular dynamics (MD) simulation for 100 ns. The QikProp and SwissADME tools' results showed that the compound has ADME/T and drug-likeness properties, which are within the permissible ranges for 95% of known drugs. The density functional theory (DFT) analysis and MD simulation extended the study toward computational validation. Throughout the study, N-HyMenatPimeMelly has shown good interactions and stable performance in MD simulation and DFT analysis. The whole analysis has produced promising results, and N-HyMenatPimeMelly can be treated as a novel potential RAS and ClC-K oral ligand, however, experimental validation is needed before human use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hussam Murad
- Department of Pharmacology, Faculty of Medicine, Rabigh Campus, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Misbahudin Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh Campus, King Abdulaziz University, Jeddah, Saudi Arabia
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13
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Akash S, Aovi FI, Azad MAK, Kumer A, Chakma U, Islam MR, Mukerjee N, Rahman MM, Bayıl I, Rashid S, Sharma R. A drug design strategy based on molecular docking and molecular dynamics simulations applied to development of inhibitor against triple-negative breast cancer by Scutellarein derivatives. PLoS One 2023; 18:e0283271. [PMID: 37824496 PMCID: PMC10569544 DOI: 10.1371/journal.pone.0283271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/07/2023] [Indexed: 10/14/2023] Open
Abstract
Triple-negative breast cancer (TNBC), accounting for 10-15% of all breast malignancies, is more prevalent in women under 40, particularly in those of African descent or carrying the BRCA1 mutation. TNBC is characterized by the absence of estrogen and progesterone receptors (ER, PR) and low or elevated HER2 expression. It represents a particularly aggressive form of breast cancer with limited therapeutic options and a poorer prognosis. In our study, we utilized the protein of TNBC collected from the Protein Data Bank (PDB) with the most stable configuration. We selected Scutellarein, a bioactive molecule renowned for its anti-cancer properties, and used its derivatives to design potential anti-cancer drugs employing computational tools. We applied and modified structural activity relationship methods to these derivatives and evaluated the probability of active (Pa) and inactive (Pi) outcomes using pass prediction scores. Furthermore, we employed in-silico approaches such as the assessment of absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters, and quantum calculations through density functional theory (DFT). Within the DFT calculations, we analyzed Frontier Molecular Orbitals, specifically the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO). We then conducted molecular docking and dynamics against TNBC to ascertain binding affinity and stability. Our findings indicated that Scutellarein derivatives, specifically DM03 with a binding energy of -10.7 kcal/mol and DM04 with -11.0 kcal/mol, exhibited the maximum binding tendency against Human CK2 alpha kinase (PDB ID 7L1X). Molecular dynamic simulations were performed for 100 ns, and stability was assessed using root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) parameters, suggesting significant stability for our chosen compounds. Furthermore, these molecules met the pharmacokinetics requirements for potential therapeutic candidates, displaying non-carcinogenicity, minimal aquatic and non-aquatic toxicity, and greater aqueous solubility. Collectively, our computational data suggest that Scutellarein derivatives may serve as potential therapeutic agents for TNBC. However, further experimental investigations are needed to validate these findings.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Farjana Islam Aovi
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md. A. K. Azad
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Unesco Chakma
- School of Electronic Science and Engineering, Southeast University, Nanjing, China
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Nobendu Mukerjee
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India
- Department of Microbiology, West Bengal State University, West Bengal, Kolkata, India
| | - Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Summya Rashid
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Science, Banaras Hindu University, Varanasi, India
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14
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Akash S, Bayıl I, Mahmood S, Mukerjee N, Mili TA, Dhama K, Rahman MA, Maitra S, Mohany M, Al-Rejaie SS, Ali N, Semwal P, Sharma R. Mechanistic inhibition of gastric cancer-associated bacteria Helicobacter pylori by selected phytocompounds: A new cutting-edge computational approach. Heliyon 2023; 9:e20670. [PMID: 37876433 PMCID: PMC10590806 DOI: 10.1016/j.heliyon.2023.e20670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/09/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
Background Helicobacter pylori (H. pylori) is a persistent bacterial inhabitant in the stomachs of approximately half the global populace. This bacterium is directly linked to chronic gastritis, leading to a heightened risk of duodenal and gastric ulcer diseases, and is the predominant risk factor for gastric cancer - the second most common cause of cancer-related deaths globally. The increasing prevalence of antibiotic resistance necessitates the exploration of innovative treatment alternatives to mitigate the H. pylori menace. Methods Initiating our study, we curated a list of thirty phytochemicals based on previous literature and subjected them to molecular docking studies. Subsequently, eight phytocompounds-Glabridin, Isoliquiritin, Sanguinarine, Liquiritin, Glycyrrhetic acid, Beta-carotin, Diosgenin, and Sarsasapogenin-were meticulously chosen based on superior binding scores. These were further subjected to an extensive computational analysis encompassing ADMET profiling, drug-likeness evaluation, principal component analysis (PCA), and molecular dynamic simulations (MDs) in comparison with the conventional drug, Mitomycin. Results The natural compounds investigated demonstrated superior docking affinities to H. pylori targets compared to the standard Mitomycin. Notably, the phytocompounds Diosgenin and Sarsasapogenin stood out due to their exceptional binding affinities and pharmacokinetic properties, including favorable ADMET profiles. Conclusion Our comprehensive and technologically-advanced approach showcases the potential of identified phytocompounds as pioneering therapeutic agents against H. pylori-induced gastric malignancies. In light of our promising in silico results, we recommend these natural compounds as potential candidates for advancing H. pylori-targeted drug development. Given their potential, we strongly advocate for subsequent in vitro and in vivo studies to validate their therapeutic efficacy against this formidable gastrointestinal bacterium.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, 1216, Ashulia, Dhaka, Bangladesh
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Turkey
| | - Sajjat Mahmood
- Department of Microbiology, Jagannath University, Chittaranjan Avenue in Sadarghat, Dhaka, 1100, Bangladesh
| | - Nobendu Mukerjee
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute Of Medical and Technical Sciences, Chennai, India
- Department of Microbiology, West Bengal State University, West Bengal, Kolkata, 700126, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Tamanna Akter Mili
- Department of Pharmacy, University of Asia Pacific, 74/A Green Rd, Dhaka, 1205, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, 243122, Bareilly, Uttar Pradesh, India
| | | | - Swastika Maitra
- Department of Microbiology, Adamas University, West Bengal, Kolkata, 700126, India
| | - Mohamed Mohany
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh, 1145, Saudi Arabia
| | - Salim S. Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh, 1145, Saudi Arabia
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh, 1145, Saudi Arabia
| | - Prabhakar Semwal
- Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, 248002, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Science, Banaras Hindu University, Varanasi, 221005, India
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15
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Rafeeq MM, Nahhas AF, Binothman N, Habib AH, Aljadani M, Sain ZM, Tuwaijri AA, Alshehri MA, Alzahrani OR. PheroxyPyrabenz and Carbopyrropyridin against major proteins of SARS CoV-2: a comprehensive in-silico molecular docking and dynamics simulation studies. J Biomol Struct Dyn 2023; 41:9121-9133. [PMID: 36318617 DOI: 10.1080/07391102.2022.2140202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The pandemic that started in 2020 left us with so much information about viruses and respiratory diseases, and the cause behind it was severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The world is still recovering, which costs so many economic and other indirect disasters; despite that, no medications are available on the market. Although the WHO approved a few vaccines on an emergency basis, the remarks and the reinfection chances are still under investigation, and a few pharmaceutical companies are also claiming that a few medications can be effective. However, there is no situation in control. SARS CoV-2 mutates and comes in different forms, making the situation unpredictable. In this study, we have screened the complete Asinex's BioDesign library, which contains 170,269 compounds, and shorted the data against the docking score that helps in the identification of 4-[5-(3-Ethoxy-4-hydroxyphenyl)-1-(2-hydroxyethyl)-1H-pyrazol-3-yl]-1, 2-benzenediol (PheroxyPyrabenz) and 1-[(3R,4R)-1-(5-Aminopentanoyl)-4-hydroxy-3-pyrrolidinyl]-1H-pyrrolo[2,3-b]pyridine-4-carboxamide (Carbopyrropyridin) as a significant drug candidate that can work against the multiple proteins of the SARS CoV-2 resulting in seizing the complete biological process of the virus. Further, the study extended to Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and molecular dynamics (MD) simulation of both the compounds with their complexity. The complete workflow of the study has shown satisfactory results, and both drug candidates can potentially stop the hunt for drugs against this virus after its experimental validation. Further, we checked both compounds' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, showing case-proof validatory results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Alaa F Nahhas
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Majidah Aljadani
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Ziaullah M Sain
- Department of Microbiology, Faculty of Medicine, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), Kingdom of Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Kingdom of Saudi Arabia
| | - Othman R Alzahrani
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
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16
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Akash S, Bibi S, Biswas P, Mukerjee N, Khan DA, Hasan MN, Sultana NA, Hosen ME, Jardan YAB, Nafidi HA, Bourhia M. Revolutionizing anti-cancer drug discovery against breast cancer and lung cancer by modification of natural genistein: an advanced computational and drug design approach. Front Oncol 2023; 13:1228865. [PMID: 37817764 PMCID: PMC10561655 DOI: 10.3389/fonc.2023.1228865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/15/2023] [Indexed: 10/12/2023] Open
Abstract
Breast and lung cancer are two of the most lethal forms of cancer, responsible for a disproportionately high number of deaths worldwide. Both doctors and cancer patients express alarm about the rising incidence of the disease globally. Although targeted treatment has achieved enormous advancements, it is not without its drawbacks. Numerous medicines and chemotherapeutic drugs have been authorized by the FDA; nevertheless, they can be quite costly and often fall short of completely curing the condition. Therefore, this investigation has been conducted to identify a potential medication against breast and lung cancer through structural modification of genistein. Genistein is the active compound in Glycyrrhiza glabra (licorice), and it exhibits solid anticancer efficiency against various cancers, including breast cancer, lung cancer, and brain cancer. Hence, the design of its analogs with the interchange of five functional groups-COOH, NH2 and OCH3, Benzene, and NH-CH2-CH2-OH-have been employed to enhance affinities compared to primary genistein. Additionally, advanced computational studies such as PASS prediction, molecular docking, ADMET, and molecular dynamics simulation were conducted. Firstly, the PASS prediction spectrum was analyzed, revealing that the designed genistein analogs exhibit improved antineoplastic activity. In the prediction data, breast and lung cancer were selected as primary targets. Subsequently, other computational investigations were gradually conducted. The mentioned compounds have shown acceptable results for in silico ADME, AMES toxicity, and hepatotoxicity estimations, which are fundamental for their oral medication. It is noteworthy that the initial binding affinity was only -8.7 kcal/mol against the breast cancer targeted protein (PDB ID: 3HB5). However, after the modification of the functional group, when calculating the binding affinities, it becomes apparent that the binding affinities increase gradually, reaching a maximum of -11.0 and -10.0 kcal/mol. Similarly, the initial binding affinity was only -8.0 kcal/mol against lung cancer (PDB ID: 2P85), but after the addition of binding affinity, it reached -9.5 kcal/mol. Finally, a molecular dynamics simulation was conducted to study the molecular models over 100 ns and examine the stability of the docked complexes. The results indicate that the selected complexes remain highly stable throughout the 100-ns molecular dynamics simulation runs, displaying strong correlations with the binding of targeted ligands within the active site of the selected protein. It is important to further investigate and proceed to clinical or wet lab experiments to determine the practical value of the proposed compounds.
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Affiliation(s)
- Shopnil Akash
- Faculty of Allied Health Science, Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Partha Biswas
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, India
| | - Dhrubo Ahmed Khan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Nazmul Hasan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Nazneen Ahmeda Sultana
- Faculty of Allied Health Science, Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Md. Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Hiba-Allah Nafidi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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17
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Gandla K, Islam F, Zehravi M, Karunakaran A, Sharma I, Haque MA, Kumar S, Pratyush K, Dhawale SA, Nainu F, Khan SL, Islam MR, Al-Mugren KS, Siddiqui FA, Emran TB, Khandaker MU. Natural polymers as potential P-glycoprotein inhibitors: Pre-ADMET profile and computational analysis as a proof of concept to fight multidrug resistance in cancer. Heliyon 2023; 9:e19454. [PMID: 37662819 PMCID: PMC10472248 DOI: 10.1016/j.heliyon.2023.e19454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023] Open
Abstract
P-glycoprotein (P-gp) is known as the "multidrug resistance protein" because it contributes to tumor resistance to several different classes of anticancer drugs. The effectiveness of such polymers in treating cancer and delivering drugs has been shown in a wide range of in vitro and in vivo experiments. The primary objective of the present study was to investigate the inhibitory effects of several naturally occurring polymers on P-gp efflux, as it is known that P-gp inhibition can impede the elimination of medications. The objective of our study is to identify polymers that possess the potential to inhibit P-gp, a protein involved in drug resistance, with the aim of enhancing the effectiveness of anticancer drug formulations. The ADMET profile of all the selected polymers (Agarose, Alginate, Carrageenan, Cyclodextrin, Dextran, Hyaluronic acid, and Polysialic acid) has been studied, and binding affinities were investigated through a computational approach using the recently released crystal structure of P-gp with PDB ID: 7O9W. The advanced computational study was also done with the help of molecular dynamics simulation. The aim of the present study is to overcome MDR resulting from the activity of P-gp by using such polymers that can inhibit P-gp when used in formulations. The docking scores of native ligand, Agarose, Alginate, Carrageenan, Chitosan, Cyclodextrin, Dextran, Hyaluronic acid, and Polysialic acid were found to be -10.7, -8.5, -6.6, -8.7, -8.6, -24.5, -6.7, -8.3, and -7.9, respectively. It was observed that, Cyclodextrin possess multiple properties in drug delivery science and here also demonstrated excellent binding affinity. We propose that drug efflux-related MDR may be prevented by the use of Agarose, Carregeenan, Chitosan, Cyclodextrin, Hyaluronic acid, and/or Polysialic acid in the administration of anticancer drugs.
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Affiliation(s)
- Kumaraswamy Gandla
- Department of Pharmaceutical Analysis, Chaitanya (Deemed to be University), Himayath Nagar, Hyderabad 500075, Telangana, India
| | - Fahadul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Mehrukh Zehravi
- Department of Clinical Pharmacy Girls Section, Prince Sattam Bin Abdul Aziz University, Al-Kharj 11942, Saudi Arabia
| | - Anandakumar Karunakaran
- Department of Pharmaceutical Analysis, Vivekanandha Pharmacy College for Women, Beerachipalayam, Sankari West, Sankari, Salem, Tamil Nadu, - 637 303, India
| | - Indu Sharma
- Department of Physics, Career Point University, Hamirpur, Himachal Pradesh 176041, India
| | - M. Akiful Haque
- Department of Pharmaceutical Analysis, School of Pharmacy, Anurag University, Hyderabad, India
| | - Sanjay Kumar
- Department of Pharmacognosy, Laureate Institute of Pharmacy, VPO Kathog, Dehra, Kangra, Himachal Pradesh 176031, India
| | - Kumar Pratyush
- Department of Pharmaceutical Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, 424001, India
| | - Sachin A. Dhawale
- Shreeyash Institute of Pharmaceutical Education and Research Aurangabad, 431 005, Maharashtra, India
| | - Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Sharuk L. Khan
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa 413520, Maharashtra, India
- Department of Pharmaceutical Chemistry, School of Pharmacy, Anurag University, Hyderabad, India
| | - Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Kholoud Saad Al-Mugren
- Department of Physics, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428 Riyadh 11671, Saudi Arabia
| | - Falak A. Siddiqui
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa 413520, Maharashtra, India
- Department of Pharmaceutical Chemistry, School of Pharmacy, Anurag University, Hyderabad, India
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Selangor, Malaysia
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18
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Akash S, Bayıl I, Rahman MA, Mukerjee N, Maitra S, Islam MR, Rajkhowa S, Ghosh A, Al-Hussain SA, Zaki MEA, Jaiswal V, Sah S, Barboza JJ, Sah R. Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation. Front Microbiol 2023; 14:1189786. [PMID: 37455711 PMCID: PMC10338848 DOI: 10.3389/fmicb.2023.1189786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023] Open
Abstract
Mosquitoes are the primary vector for West Nile virus, a flavivirus. The virus's ability to infiltrate and establish itself in increasing numbers of nations has made it a persistent threat to public health worldwide. Despite the widespread occurrence of this potentially fatal disease, no effective treatment options are currently on the market. As a result, there is an immediate need for the research and development of novel pharmaceuticals. To begin, molecular docking was performed on two possible West Nile virus target proteins using a panel of twelve natural chemicals, including Apigenin, Resveratrol, Hesperetin, Fungisterol, Lucidone, Ganoderic acid, Curcumin, Kaempferol, Cholic acid, Chlorogenic acid, Pinocembrin, and Sanguinarine. West Nile virus methyltransferase (PDB ID: 2OY0) binding affinities varied from -7.4 to -8.3 kcal/mol, whereas West Nile virus envelope glycoprotein affinities ranged from -6.2 to -8.1 kcal/mol (PDB ID: 2I69). Second, substances with larger molecular weights are less likely to be unhappy with the Lipinski rule. Hence, additional research was carried out without regard to molecular weight. In addition, compounds 01, 02, 03, 05, 06, 07, 08, 09, 10 and 11 are more soluble in water than compound 04 is. Besides, based on maximum binding affinity, best three compounds (Apigenin, Curcumin, and Ganoderic Acid) has been carried out molecular dynamic simulation (MDs) at 100 ns to determine their stability. The MDs data is also reported that these mentioned molecules are highly stable. Finally, advanced principal component analysis (PCA), dynamics cross-correlation matrices (DCCM) analysis, binding free energy and dynamic cross correlation matrix (DCCM) theoretical study is also included to established mentioned phytochemical as a potential drug candidate. Research has indicated that the aforementioned natural substances may be an effective tool in the battle against the dangerous West Nile virus. This study aims to locate a bioactive natural component that might be used as a pharmaceutical.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Türkiye
| | | | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Swastika Maitra
- Department of Microbiology, Adamas University, Kolkata, West Bengal, India
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Sanchaita Rajkhowa
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Gwahati, Assam, India
| | - Sami A. Al-Hussain
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Vikash Jaiswal
- Department of Cardiovascular Research, Larkin Community Hospital, South Miami, FL, United States
| | - Sanjit Sah
- Global Consortium for Public Health and Research, Datta Meghe Institute of Higher Education and Research, Jawaharlal Nehru Medical College, Wardha, India
- SR Sanjeevani Hospital, Kayanpur, Siraha, Nepal
| | | | - Ranjit Sah
- Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
- Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
- Department of Public Health Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
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19
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Kaur M, Muzzammel Rehman H, Kaur G, Kaur A, Bansal M. Switching of newly synthesized linker-based derivatives of non-steroidal anti-inflammatory drugs toward anti-inflammatory and anticancer activity. Bioorg Chem 2023; 133:106406. [PMID: 36773455 DOI: 10.1016/j.bioorg.2023.106406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023]
Abstract
A new series of linker-based derivatives of non-steroidal anti-inflammatory drugs were designed and synthesized. All the compounds were well characterized with the help of various spectroscopic techniques such as FT-IR, 1H NMR, 13C NMR, and HRMS. The main emphasis of this paper is to understand the switching of the most promising compounds 8 and 10 towards anti-inflammatory and anticancer activity in terms of in-silico and in-vitro studies in detail. During the molecular docking study, compounds 8 and 10 demonstrated the importance of hetero atoms as well as the perfect alignment of a compound in the binding pocket of a target site, which may affect their bioactivity. Here, the presence of 1,3‑dicarbonyl interactions with ASN 351 in compound 8 (not found in compound 10) may be responsible for its better inhibitory activity against the COX-2 target site. On the other hand, a slight increase in the potency of compound 10 towards anticancer activity may be due to the instantaneous participation of the OH group and carbonyl group to give conventional hydrogen bonds towards THR 149 amino acid residue, which was missing in compound 8. Molecular dynamics simulation was also performed for compounds 10 and 8 toward COX-2 and HER-2 protein sites. Further, compounds 8 and 10 were subjected to in-vitro COX-2 inhibition and cytotoxicity assay and the results obtained were in accordance with the in-silico study. Thus, compound 8 become more potent towards COX-2 inhibition with IC50 value of 48.51 µg/ml and compound 10 showed good bioactivity toward cytotoxic activity with IC50 value of 93.03 µg/ml.
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Affiliation(s)
- Mandeep Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala 147002, India
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Gurmeet Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala 147002, India
| | - Amandeep Kaur
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala 147002, India
| | - Manisha Bansal
- Synthetic and Medicinal Chemistry Laboratory, Department of Chemistry, Punjabi University, Patiala 147002, India.
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20
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Lu L, Chen J, Tao W, Wang Z, Liu D, Zhou J, Wu X, Sun H, Li W, Tanabe G, Muraoka O, Zhao B, Wu L, Xie W. Design and Synthesis of Sulfonium Derivatives: A Novel Class of α-Glucosidase Inhibitors with Potent In Vivo Antihyperglycemic Activities. J Med Chem 2023; 66:3484-3498. [PMID: 36812150 DOI: 10.1021/acs.jmedchem.2c01984] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We report the first attempt of double-spot structural modification on a side-chain moiety of sulfonium-type α-glucosidase inhibitors isolated from genus Salacia. A series of sulfonium salts with benzylidene acetal linkage at the C3' and C5' positions were designed and synthesized. In vitro enzyme inhibition evaluation showed that compounds with a strong electron-withdrawing group attached at the ortho position on the phenyl ring present stronger inhibitory activities. Notably, the most potent inhibitor 21b (1.0 mpk) can exhibit excellent hypoglycemic effects in mice, which can still compete with those of acarbose (20.0 mpk). Molecular docking of 21b demonstrated that besides conventional interacting patterns, the newly introduced benzylidene acetal moiety plays an important role in anchoring the whole molecule in a concave pocket of the enzyme. The successful identification of 21b as a lead compound for new drug discovery may provide a means for structure modification and diversification of the distinguished sulfonium-type α-glucosidase inhibitors.
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Affiliation(s)
- Lu Lu
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jingyi Chen
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Wenxiang Tao
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhimei Wang
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Dan Liu
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jiahui Zhou
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xiaoxing Wu
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Haopeng Sun
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Wei Li
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Genzoh Tanabe
- Faculty of Pharmacy Kinki University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Osamu Muraoka
- Faculty of Pharmacy Kinki University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Bo Zhao
- Department of Chemical and Material Science, Nanjing Normal University, Nanjing 210009, P. R. China
| | - Liang Wu
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Weijia Xie
- State Key Laboratory of Natural Medicines (SKLNM) and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
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21
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Yadav MK, Ahmad S, Raza K, Kumar S, Eswaran M, Pasha Km M. Predictive modeling and therapeutic repurposing of natural compounds against the receptor-binding domain of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:1527-1539. [PMID: 34974820 DOI: 10.1080/07391102.2021.2021993] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a member of the Coronaviridae family, causing major destructions to human life directly and indirectly to the economic crisis around the world. Although there is significant reporting on the whole genome sequences and updated data for the different receptors are widely analyzed and screened to find a proper medication. Only a few bioassay experiments were completed against SARS-CoV-2 spike protein. We collected the compounds dataset from the PubChem Bioassay database having 1786 compounds and split it into the ratio of 80-20% for model training and testing purposes, respectively. Initially, we have created 11 models and validated them using a fivefold validation strategy. The hybrid consensus model shows a predictive accuracy of 95.5% for training and 94% for the test dataset. The model was applied to screen a virtual chemical library of Natural products of 2598 compounds. Our consensus model has successfully identified 75 compounds with an accuracy range of 70-100% as active compounds against SARS-CoV-2 RBD protein. The output of ML data (75 compounds) was taken for the molecular docking and dynamics simulation studies. In the complete analysis, the Epirubicin and Daunorubicin have shown the docking score of -9.937 and -9.812, respectively, and performed well in the molecular dynamics simulation studies. Also, Pirarubicin, an analogue of anthracycline, has widely been used due to its lower cardiotoxicity. It shows the docking score of -9.658, which also performed well during the complete analysis. Hence, after the following comprehensive pipeline-based study, these drugs can be further tested in vivo for further human utilization.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manoj Kumar Yadav
- Department of Bioinformatics, SRM University, Sonepat, Haryana, India
| | - Shaban Ahmad
- Department of Bioinformatics, SRM University, Sonepat, Haryana, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Sunil Kumar
- ICAR-Indian Agricultural Statistical Research Institute, New Delhi, India
| | - Murugesh Eswaran
- Plant Molecular Biology Division, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mussuvir Pasha Km
- Department of Studies and Research in chemistry, Vijayanagara Sri Krishnadevaraya University, Ballari, India
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22
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Tong QL, Luo D, Xiang ZN, Zhang YL, He JX, Hu ZF, Xia RF, Wu JL, Fu XN, Li Q, Peng HM, Huang R, Wan LS, Chen JC, Fang JB. Metabolic profiling integrated with pharmacokinetics to reveal the material basis of Xiaokeyinshui extract combination in the treatment of type 2 diabetes in rats. J Pharm Biomed Anal 2023; 225:115224. [PMID: 36603394 DOI: 10.1016/j.jpba.2022.115224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/24/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023]
Abstract
Xiaokeyinshui extract combination (XEC), originating from a traditional Chinese formula Xiaokeyinshui (XKYS) recorded in ancient Bencao, has been reported to exert significant hypoglycemic effects. However, the chemical profiles, metabolic transformation and pharmacokinetic behavior of XEC in vivo were unclear. The research was to investigate the chemical constituents, metabolic profiles and pharmacokinetic behavior of XEC. A UPLC-QE-Orbitrap-HRMS qualification method was developed to identify the chemical constituents in XEC and xenobiotics of XEC in plasma, urine, feces and bile of rats after oral administration. A LC-MS quantification method was established and applied for the pharmacokinetic studies of major active compounds of XEC in normal and T2DM rats and Coptidis Rhizoma extracts (CRE) in T2DM rats. Fifty eight compounds in XEC and a total of 152 xenobiotics were identified in T2DM rats, including 28 prototypes and 124 metabolites. The metabolic pathways were demethylation, demethyleneization, reduction, hydroxylation, hydrolysis and subsequent binding reactions, including glucuronidation, sulfation and methylation. According to the results of chemical constituents and metabolites, 7 ingredients, including berberine, palmatine, coptisine, epiberberine, berberrubine, magnoflorine and aurantio-obtusin were suggested for markers to comparative pharmacokinetics study in normal rats and T2DM rats. Compared with normal rats, the Tmax of berberine, palmatine, coptisine, epiberberine, berberrubine and magnoflorine was significantly longer. The value of Cmax for palmatine, coptisine, epiberberine and berberrubine was significantly decreased in XEC T2DM group. The value of AUC for alkaloids was higher in diabetic rats. After oral CRE, alkaloids including berberine, palmatine, coptisine, epiberberine, berberrubine and magnoflorine could be detected in vivo. Compared with T2DM rats after oral administration of CRE, the value of Tmax and Cmax for berberine, palmatine, coptisine, epiberberine, berberrubine and magnoflorine exhibited significant differences in XEC T2DM group. This research provided an overview of the chemical profiles and metabolic profiling of XEC and elucidated the effect of diabetic state and compatibility on pharmacokinetic behaviors of active components in XEC. This research also can provide the material basis of XEC for subsequent quality control research.
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Affiliation(s)
- Qi-Lin Tong
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Dan Luo
- Shimadzu Enterprise Management (China) Co., Ltd., Wuhan Branch, Wuhan 430030, China.
| | - Zhi-Nan Xiang
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Ya-Li Zhang
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jia-Xin He
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Zhuo-Fan Hu
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Ru-Feng Xia
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jia-Le Wu
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xiao-Na Fu
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Qiang Li
- Shimadzu Enterprise Management (China) Co., Ltd., Wuhan Branch, Wuhan 430030, China.
| | - Hui-Ming Peng
- Department of Anatomy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Rong Huang
- Department of Ophthalmology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, Hubei, China.
| | - Luo-Shen Wan
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jia-Chun Chen
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jin-Bo Fang
- School of Pharmacy, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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23
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Yang F, Tan Y, Wu C, Xin L, Huang Z, Zhou H, Zhou F. dSTORM-Based Single-Cell Protein Quantitative Analysis Can Effectively Evaluate the Degradation Ability of PROTACs. Chembiochem 2023; 24:e202200680. [PMID: 36564338 DOI: 10.1002/cbic.202200680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
As an emerging therapeutic strategy, proteolysis-targeting chimeras (PROTACs) have been proven to be superior to traditional drugs in many aspects. However, due to their unique mechanism of action, existing methods for evaluating the degradation still have many limitations, which seriously restricts the development of PROTACs. In this methodological study, using direct stochastic optical reconstruction microscopy (dSTORM)-based single-cell protein quantitative analysis, we systematically investigated the dynamic degradation characteristics of FLT3 protein during PROTACs treatment. We found that the distribution of FLT3 varies between FLT3-ITD mutation and FLT3-WT cells. PROTACs had an obvious time-course effect on protein degradation and present two distinct phases; this provided a basis for deciding when to evaluate protein degradation. High concentrations of PROTACs were more effective than long-time administration because a higher Dmax was achieved. Two-color dSTORM-based colocalization analysis efficiently detected the proportion of ternary complexes, making it very useful in screening PROTACs. Taken together, our findings show that the dSTORM method is an ideal tool for evaluating PROTACs and will accelerate the development of new PROTACs.
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Affiliation(s)
- Fuwei Yang
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Yuxin Tan
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Cheng Wu
- Key Laboratory of Biomedical Engineering of Hainan Province School, of Biomedical Engineering, Hainan University, Haikou, Hainan, 570100, P. R. China
| | - Lilan Xin
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Zhenli Huang
- Key Laboratory of Biomedical Engineering of Hainan Province School, of Biomedical Engineering, Hainan University, Haikou, Hainan, 570100, P. R. China
| | - Haibing Zhou
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430000, P. R. China
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24
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Identification of a Family of Glycoside Derivatives Biologically Active against Acinetobacter baumannii and Other MDR Bacteria Using a QSPR Model. Pharmaceuticals (Basel) 2023. [DOI: 10.3390/ph16020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
As the rate of discovery of new antibacterial compounds for multidrug-resistant bacteria is declining, there is an urge for the search for molecules that could revert this tendency. Acinetobacter baumannii has emerged as a highly virulent Gram-negative bacterium that has acquired multiple resistance mechanisms against antibiotics and is considered of critical priority. In this work, we developed a quantitative structure-property relationship (QSPR) model with 592 compounds for the identification of structural parameters related to their property as antibacterial agents against A. baumannii. QSPR mathematical validation (R2 = 70.27, RN = −0.008, a(R2) = 0.014, and δK = 0.021) and its prediction ability (Q2LMO = 67.89, Q2EXT = 67.75, a(Q2) = −0.068, δQ = 0.0, rm2¯ = 0.229, and Δrm2 = 0.522) were obtained with different statistical parameters; additional validation was done using three sets of external molecules (R2 = 72.89, 71.64 and 71.56). We used the QSPR model to perform a virtual screening on the BIOFACQUIM natural product database. From this screening, our model showed that molecules 32 to 35 and 54 to 68, isolated from different extracts of plants of the Ipomoea sp., are potential antibacterials against A. baumannii. Furthermore, biological assays showed that molecules 56 and 60 to 64 have a wide antibacterial activity against clinically isolated strains of A. baumannii, as well as other multidrug-resistant bacteria, including Staphylococcus aureus, Escherichia coli, Klebsiella pneumonia, and Pseudomonas aeruginosa. Finally, we propose 60 as a potential lead compound due to its broad-spectrum activity and its structural simplicity. Therefore, our QSPR model can be used as a tool for the investigation and search for new antibacterial compounds against A. baumannii.
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25
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Er-Rajy M, El Fadili M, Mujwar S, Zarougui S, Elhallaoui M. Design of novel anti-cancer drugs targeting TRKs inhibitors based 3D QSAR, molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:11657-11670. [PMID: 36695085 DOI: 10.1080/07391102.2023.2170471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023]
Abstract
Tropomyosin receptor kinase (TRK) enzymes are responsible for different types of tumors caused by neurotrophic tyrosine receptor kinase gene fusion and have been identified as an effective target for anticancer therapy. The study of the mechanism between polo-like kinase (PLKs) and pyrazol inhibitors was performed using 3D-QSAR modeling, molecular docking, and MD simulations in order to design high-activity inhibitors. The HQSAR (Q2 = 0.793, R2 = 0.917, R2ext = 0.961), CoMFA (Q2 = 0.582, R2 = 0.722, R2ext = 0.951), CoMSIA/SE (Q2 = 0.603, R2 = 0.801, R2ext = 0.849), and Topomer CoMFA (Q2 = 0.726, R2 = 0.992, R2ext = 0.717) showed good reliability and predictability. All models have been successfully tested by external validation, so all five established models are reliable. The analysis of the different contour maps of different models gives structural information to improve the inhibitory function. Molecular docking results show that the amino acids Met 592, GLU 590, LEU 657, VAL 524, and PHE 589 are the active sites of the tropomyosin receptor TRKs. The results obtained by MD showed that compound 19i could form a more stable complex protein (PDB id: 5KVT). Based on these results, we developed new compounds and their expected inhibitory activities. The results of physicochemical and ADME-Tox properties showed that the four proposed molecules are orally bioavailable, and they are not toxic in the Ames test. Thus, these results would provide modeling information that could help experimental researchers find TRK type I inhibitors more efficiently.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammed Er-Rajy
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohamed El Fadili
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Sara Zarougui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Menana Elhallaoui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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26
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Tyagi S, Shukla A, Ram H, Panwar A, Kumar R, Tripathi R. In silico investigations of the multi‐targeted antiviral potential of small molecule phytochemicals of
Nelumbo nucifera
Gaertn. seed extracts against SARS‐CoV‐2 for therapeutics of COVID‐19. FOOD FRONTIERS 2023. [DOI: 10.1002/fft2.202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Saya Tyagi
- Department of Bioscience and Biotechnology Banasthali Vidyapith Banasthali Rajasthan India
| | - Anuradha Shukla
- Department of Bioscience and Biotechnology Banasthali Vidyapith Banasthali Rajasthan India
| | - Heera Ram
- Department of Zoology Jai Narain Vyas University Jodhpur Rajasthan India
| | - Anil Panwar
- Department of Bioinformatics and Computational Biology CCS Haryana Agricultural University Hisar Haryana India
| | - Roshan Kumar
- Department of Zoology Magadh University Bodh Gaya Bihar India
| | - Rashmi Tripathi
- Department of Bioscience and Biotechnology Banasthali Vidyapith Banasthali Rajasthan India
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27
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Yang R, Hou E, Cheng W, Yan X, Zhang T, Li S, Yao H, Liu J, Guo Y. Membrane-Targeting Neolignan-Antimicrobial Peptide Mimic Conjugates to Combat Methicillin-Resistant Staphylococcus aureus (MRSA) Infections. J Med Chem 2022; 65:16879-16892. [PMID: 36512751 DOI: 10.1021/acs.jmedchem.2c01674] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) continue to endanger public health. Here, we report the synthesis of neolignan isomagnolone (I) and its isomer II, and the preparation of a series of novel neolignan-antimicrobial peptide (AMP) mimic conjugates. Notably, conjugates III5 and III15 exhibit potent anti-MRSA activity in vitro and in vivo, comparable to that of vancomycin, a current effective treatment for MRSA. Moreover, III5 and III15 display not only fast-killing kinetics and low resistance frequency but also low toxicity as well as effects on bacterial biofilms. Mechanism studies reveal that III5 and III15 exhibit rapid bactericidal effects through binding to the phosphatidylglycerol (PG) and cardiolipin (CL) of the bacterial membrane, thereby disrupting the cell membranes and allowing increased reactive oxygen species (ROS) as well as protein and DNA leakage. The results indicate that these neolignan-AMP mimic conjugates could be promising antimicrobial candidates for combating MRSA infections.
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Affiliation(s)
- Ruige Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Enhua Hou
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Wanqing Cheng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiaoting Yan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Tingting Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shihong Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Hong Yao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Jifeng Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yong Guo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
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28
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Exploring the anti-inflammatory bioactive metabolites of some marine algae through integration of metabolomics, network pharmacology and molecular docking analyses. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Khan MA, Al Mamun Khan MA, Mahfuz AMUB, Sanjana JM, Ahsan A, Gupta DR, Hoque MN, Islam T. Highly potent natural fungicides identified in silico against the cereal killer fungus Magnaporthe oryzae. Sci Rep 2022; 12:20232. [PMID: 36418863 PMCID: PMC9684433 DOI: 10.1038/s41598-022-22217-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Magnaporthe oryzae is one of the most notorious fungal pathogens that causes blast disease in cereals, and results in enormous loss of grain production. Many chemical fungicides are being used to control the pathogen but none of them are fully effective in controlling blast disease. Therefore, there is a demand for the discovery of a new natural biofungicide to manage the blast disease efficiently. A large number of new natural products showed inhibitory activities against M. oryzae in vitro. To find out effective biofungicides, we performed in silico molecular docking analysis of some of the potent natural compounds targeting four enzymes namely, scytalone dehydratase, SDH1 (PDB ID:1STD), trihydroxynaphthalene reductase, 3HNR (PDB ID:1YBV), trehalose-6-phosphate synthase, Tps1 (PDB ID:6JBI) and isocitrate lyase, ICL1 (PDB ID:5E9G) of M. oryzae fungus that regulate melanin biosynthesis and/or appresorium formation. Thirty-nine natural compounds that were previously reported to inhibit the growth of M. oryzae were subjected to rigid and flexible molecular docking against aforementioned enzymes followed by molecular dynamic simulation. The results of virtual screening showed that out of 39, eight compounds showed good binding energy with any one of the target enzymes as compared to reference commercial fungicides, azoxystrobin and strobilurin. Among the compounds, camptothecin, GKK1032A2 and chaetoviridin-A bind with more than one target enzymes of M. oryzae. All of the compounds except tricyclazole showed good bioactivity score. Taken together, our results suggest that all of the eight compounds have the potential to develop new fungicides, and remarkably, camptothecin, GKK1032A2 and chaetoviridin-A could act as multi-site mode of action fungicides against the blast fungus M. oryzae.
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Affiliation(s)
- Md. Arif Khan
- grid.443057.10000 0004 4683 7084Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, 1209 Bangladesh
| | - Md. Abdullah Al Mamun Khan
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - A. M. U. B. Mahfuz
- grid.443057.10000 0004 4683 7084Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, 1209 Bangladesh
| | - Jannatul Maowa Sanjana
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - Asif Ahsan
- grid.411511.10000 0001 2179 3896Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Dipali Rani Gupta
- grid.443108.a0000 0000 8550 5526Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706 Bangladesh
| | - M. Nazmul Hoque
- grid.443108.a0000 0000 8550 5526Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur, 1706 Bangladesh
| | - Tofazzal Islam
- grid.443108.a0000 0000 8550 5526Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706 Bangladesh
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30
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Mitusova K, Peltek OO, Karpov TE, Muslimov AR, Zyuzin MV, Timin AS. Overcoming the blood–brain barrier for the therapy of malignant brain tumor: current status and prospects of drug delivery approaches. J Nanobiotechnology 2022; 20:412. [PMID: 36109754 PMCID: PMC9479308 DOI: 10.1186/s12951-022-01610-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/18/2022] [Indexed: 01/06/2023] Open
Abstract
Besides the broad development of nanotechnological approaches for cancer diagnosis and therapy, currently, there is no significant progress in the treatment of different types of brain tumors. Therapeutic molecules crossing the blood–brain barrier (BBB) and reaching an appropriate targeting ability remain the key challenges. Many invasive and non-invasive methods, and various types of nanocarriers and their hybrids have been widely explored for brain tumor treatment. However, unfortunately, no crucial clinical translations were observed to date. In particular, chemotherapy and surgery remain the main methods for the therapy of brain tumors. Exploring the mechanisms of the BBB penetration in detail and investigating advanced drug delivery platforms are the key factors that could bring us closer to understanding the development of effective therapy against brain tumors. In this review, we discuss the most relevant aspects of the BBB penetration mechanisms, observing both invasive and non-invasive methods of drug delivery. We also review the recent progress in the development of functional drug delivery platforms, from viruses to cell-based vehicles, for brain tumor therapy. The destructive potential of chemotherapeutic drugs delivered to the brain tumor is also considered. This review then summarizes the existing challenges and future prospects in the use of drug delivery platforms for the treatment of brain tumors.
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Zhao Y, Yang H, Wu F, Luo X, Sun Q, Feng W, Ju X, Liu G. Exploration of N-Arylsulfonyl-indole-2-carboxamide Derivatives as Novel Fructose-1,6-bisphosphatase Inhibitors by Molecular Simulation. Int J Mol Sci 2022; 23:ijms231810259. [PMID: 36142164 PMCID: PMC9499002 DOI: 10.3390/ijms231810259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 11/18/2022] Open
Abstract
A series of N-arylsulfonyl-indole-2-carboxamide derivatives have been identified as potent fructose-1,6-bisphosphatase (FBPase) inhibitors (FBPIs) with excellent selectivity for the potential therapy of type II diabetes mellitus. To explore the structure–activity relationships (SARs) and the mechanisms of action of these FBPIs, a systematic computational study was performed in the present study, including three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, pharmacophore modeling, molecular dynamics (MD), and virtual screening. The constructed 3D-QSAR models exhibited good predictive ability with reasonable parameters using comparative molecular field analysis (q2 = 0.709, R2 = 0.979, rpre2 = 0.932) and comparative molecular similarity indices analysis (q2 = 0.716, R2 = 0.978, rpre2 = 0.890). Twelve hit compounds were obtained by virtual screening using the best pharmacophore model in combination with molecular dockings. Three compounds with relatively higher docking scores and better ADME properties were then selected for further studies by docking and MD analyses. The docking results revealed that the amino acid residues Met18, Gly21, Gly26, Leu30, and Thr31 at the binding site were of great importance for the effective bindings of these FBPIs. The MD results indicated that the screened compounds VS01 and VS02 could bind with FBPase stably as its cognate ligand in dynamic conditions. This work identified several potential FBPIs by modeling studies and might provide important insights into developing novel FBPIs.
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Affiliation(s)
- Yilan Zhao
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Honghao Yang
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Fengshou Wu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xiaogang Luo
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
- School of Materials Science and Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Wuhan Institute of Technology, Wuhan 430205, China
| | - Qi Sun
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Wuhan Institute of Technology, Wuhan 430205, China
| | - Weiliang Feng
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
- Correspondence: (W.F.); (G.L.)
| | - Xiulian Ju
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Genyan Liu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Wuhan Institute of Technology, Wuhan 430205, China
- Correspondence: (W.F.); (G.L.)
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Mangrio GR, Maneengam A, Khalid Z, Jafar TH, Chanihoon GQ, Nassani R, Unar A. RP-HPLC Method Development, Validation, and Drug Repurposing of Sofosbuvir Pharmaceutical Dosage Form: A Multidimensional Study. ENVIRONMENTAL RESEARCH 2022; 212:113282. [PMID: 35487258 DOI: 10.1016/j.envres.2022.113282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
A smooth, exceptionally sensitive, correct, and extra reproducible RP-HPLC technique was developed and demonstrated to estimate Sofosbuvir (SOF) in pharmaceutical dosage formulations. This process was carried out by Agilent High-Pressure Liquid Chromatograph 1260 with GI311C Quat. Pump, Phenomenex Luna C-18 (150 mm × 4.6 mm × 5 μm) (USA), and Photodiode Array Detector (PDA) G1315D. The cell section, including acetonitrile and methanol with 80:20 v/v and solution (B) 0.1% phosphoric acid (40:60), was used for the study. However, 10 μL of the sample was injected with a drift flow of 1 mL/min. The separation occurred at a column temperature of 30 °C, and the eluents used PDA set at 260 nm. The retention time of SOF was 5 min. The calibration curve was modified linearly within the range of 0.05-0.15 mg/mL with a correlation coefficient of 0.99 and genuine linear dating among top vicinity and consciousness in the calibration curve. The detection and quantification restrictions were 0.001 and 0.003 mg/mL, respectively. SOF recovery from pharmaceutical components ranged from 98% to 99%. The percentage assay of SOF was 99%. Analytical validation parameters, such as specificity, linearity, precision, accuracy, and selectivity, were studied, and the percentage relative standard deviation (%RSD) was less than 2%. All other key parameters were observed within the desired thresholds. Hence, the proposed RP-HPLC technique was proven effective for developing SOF in bulk and pharmaceutical pill dosage forms. SOF was found to interact with SARS-COV-2 nsp12, and molecular docking results revealed its high affinity and firm binding within the active site groove of nsp12. The key interacting residues include; LYS-72, GLN-75, MET-80 ALA-99, ASN-99, TRP-100, TYR-101 with ASN-99 and TRP-100 forming hydrogen bonds. Molecular Dynamics simulation of SOF and nsp12 complex elucidated that the system was stable throughout 20ns. Therefore, this drug repurposing strategy for SOF can be used for treating COVID-19 infections by performing animal experiments and accurate clinical trials in the future.
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Affiliation(s)
| | - Apichit Maneengam
- Department of Mechanical Engineering Technology, College of Industrial Technology, King Mongkut's University of Technology North Bangkok, Wongsawang, Bangsue, Bangkok, 10800, Thailand
| | - Zunera Khalid
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, PR China
| | | | - Ghulam Qadir Chanihoon
- National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76090, Pakistan
| | - Rayan Nassani
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ahsanullah Unar
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, PR China.
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33
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Identification and Inhibition of the Druggable Allosteric Site of SARS-CoV-2 NSP10/NSP16 Methyltransferase through Computational Approaches. Molecules 2022; 27:molecules27165241. [PMID: 36014480 PMCID: PMC9416396 DOI: 10.3390/molecules27165241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022] Open
Abstract
Since its emergence in early 2019, the respiratory infectious virus, SARS-CoV-2, has ravaged the health of millions of people globally and has affected almost every sphere of life. Many efforts are being made to combat the COVID-19 pandemic’s emerging and recurrent waves caused by its evolving and more infectious variants. As a result, novel and unexpected targets for SARS-CoV-2 have been considered for drug discovery. 2′-O-Methyltransferase (nsp10/nsp16) is a significant and appealing target in the SARS-CoV-2 life cycle because it protects viral RNA from the host degradative enzymes via a cap formation process. In this work, we propose prospective allosteric inhibitors that target the allosteric site, SARS-CoV-2 MTase. Four drug libraries containing ~119,483 compounds were screened against the allosteric site of SARS-CoV-2 MTase identified in our research. The identified best compounds exhibited robust molecular interactions and alloscore-score rankings with the allosteric site of SARS-CoV-2 MTase. Moreover, to further assess the dynamic stability of these compounds (CHEMBL2229121, ZINC000009464451, SPECS AK-91811684151, NCI-ID = 715319), a 100 ns molecular dynamics simulation, along with its holo-form, was performed to provide insights on the dynamic nature of these allosteric inhibitors at the allosteric site of the SARS-CoV-2 MTase. Additionally, investigations of MM-GBSA binding free energies revealed a good perspective for these allosteric inhibitor–enzyme complexes, indicating their robust antagonistic action on SARS-CoV-2 (nsp10/nsp16) methyltransferase. We conclude that these allosteric repressive agents should be further evaluated through investigational assessments in order to combat the proliferation of SARS-CoV-2.
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Alghamdi YS, Mashraqi MM, Alzamami A, Alturki NA, Ahmad S, Alharthi AA, Alshamrani S, Asiri SA. Unveiling the multitargeted potential of N-(4-Aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine (NSL-CG) against SARS CoV-2: a virtual screening and molecular dynamics simulation study. J Biomol Struct Dyn 2022:1-10. [PMID: 35971958 DOI: 10.1080/07391102.2022.2110158] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The coronaviridae family has caused the most destruction among all the viral families in modern sciences. It is one of the recently discovered and added members of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which has caused the global pandemic and significant destruction worldwide. However, scientists worldwide have developed vaccines, which are being given to humans. The mutated strain of the virus has caused various uncertainties about whether the discovered drug and vaccines affect it. Even after the World Health Organization's approval for the vaccines, their effectiveness and protection ratio are still a major concern. At the community level, to this date, there is no medicine available to cure the patients. In this study, we have screened the vast library from Drug Bank and identified N-(4-Aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine (NSL-CG) that can work against two major targets of SARS CoV-2, replication-transcription and RNA dependent polymerase. Further, we have performed the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and molecular dynamics simulation of the compound with both proteins individually, giving us enough evidence that the said drugs can work against the two targets together. Inhibiting the action of any of both proteins may lead to retaining the virus, and having a dual-targeted drug can be an extra precise measure for this process. The NSL-CG is an experimental drug belonging to the peptidomimetics class included in the small group of drugs with a docking score of -9.079 kcal/mol with replication-transcription -7.885 kcal/mol with RNA-dependent polymerase. Hence, through the complete flowed study, the NSL-CG can be further experimentally validated in in-vitro and in-vivo conditions before human utilisation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, AlQuwayiyah, Saudi Arabia
| | - Norah A Alturki
- Clinical Laboratory Science Department, College of Applied Medical Science, King Saud University, Riyadh, Saudi Arabia
| | - Shaban Ahmad
- Agriculture Knowledge Management Unit, ICAR-Indian Agricultural Research Institute, New Dehli, India
| | - Afaf Awwadh Alharthi
- College of applied medical sciences, Department of Clinical laboratory sciences, Taif University, Taif, Saudi Arabia
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Saeed A Asiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
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Kumar P, Ram H, Kala C, Kashyap P, Singh G, Agnihotri C, Singh BP, Kumar A, Panwar A. DPP-4 inhibition mediated antidiabetic potential of phytoconstituents of an aqueous fruit extract of Withania coagulans (Stocks) Dunal: in-silico, in-vitro and in-vivo assessments. J Biomol Struct Dyn 2022:1-23. [PMID: 35930363 DOI: 10.1080/07391102.2022.2103029] [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: 10/16/2022]
Abstract
The DPP-4 inhibition is an interesting target for the development of antidiabetic agents which promotes the longevity of GPL-1(Glucagon-like peptide 1). The current study was intended to assess DPP-4(Dipeptidyl Peptidase-4) inhibition mediated antidiabetic effect of phytocompounds of an aqueous fruit extract of Withania coagulans (Stocks) Dunal by in-vitro, in-silico and in-vivo approaches. The phytoconstituents screening was executed by LCMS (Liquid Chromatography with tandem mass spectrometry). The in-vitro and in-vivo, DPP-4 assays were performed by using available kits. The in-vitro DPP-4 activity was inhibited up to 68.3% by the test extract. Accordingly, in-silico determinations of molecular docking, molecular dynamics and pharmacokinetics were performed between the target enzyme DPP-4 and leading phytocompounds. The molecular dynamics authenticated the molecular docking data by crucial parameters of cytosolic milieu by the potential energy, RSMD (Root Mean Square Deviation), RSMF (Root Mean Square Fluctuation), system density, NVT (Number of particles at fixed volume, ensemble) and NPT (Number of particles at fixed pressure, ensemble). Accordingly, ADMET predictions assessed the druggability profile. Subsequently, the course of the test extract and the sitagliptin (positive control), instigated significant (p ≤ 0.001) ameliorations in HOMA indices and the equal of antioxidants in nicotinamide-streptozotocin induced type 2 diabetic animal model. Compassionately, the histopathology represented increased pancreatic cellular mass which caused in restoration of histoarchitectures. It has been concluded that phytoconstituents in W. coagulans aqueous fruit extract can regulate DPP-4, resulting in improved glucose homeostasis and enhanced endocrinal pancreatic cellular mass.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pramod Kumar
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Heera Ram
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Chandra Kala
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Priya Kashyap
- University School of Biotechnology, GGS Indraprastha University, New Delhi, India
| | - Garima Singh
- Department of Botany, Pachhunga University College (PUC), Aizawl, India
| | - Charu Agnihotri
- Department of Agriculture & Environmental Sciences (AES), National Institute of Food Technology Entrepreneurship & Management (NIFTEM), Sonepat, India
| | - Bhim Pratap Singh
- Department of Agriculture & Environmental Sciences (AES), National Institute of Food Technology Entrepreneurship & Management (NIFTEM), Sonepat, India
| | - Ashok Kumar
- Centre for System Biology and Bioinformatics, Panjab University, Chandigarh, India
| | - Anil Panwar
- Centre for System Biology and Bioinformatics, Panjab University, Chandigarh, India
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36
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Alturki NA, Mashraqi MM, Alzamami A, Alghamdi YS, Alharthi AA, Asiri SA, Ahmad S, Alshamrani S. In-Silico Screening and Molecular Dynamics Simulation of Drug Bank Experimental Compounds against SARS-CoV-2. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144391. [PMID: 35889265 PMCID: PMC9317596 DOI: 10.3390/molecules27144391] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022]
Abstract
For the last few years, the world has been going through a difficult time, and the reason behind this is severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), one of the significant members of the Coronaviridae family. The major research groups have shifted their focus towards finding a vaccine and drugs against SARS-CoV-2 to reduce the infection rate and save the life of human beings. Even the WHO has permitted using certain vaccines for an emergency attempt to cut the infection curve down. However, the virus has a great sense of mutation, and the vaccine's effectiveness remains questionable. No natural medicine is available at the community level to cure the patients for now. In this study, we have screened the vast library of experimental drugs of Drug Bank with Schrodinger's maestro by using three algorithms: high-throughput virtual screening (HTVS), standard precision, and extra precise docking followed by Molecular Mechanics/Generalized Born Surface Area (MMGBSA). We have identified 3-(7-diaminomethyl-naphthalen-2-YL)-propionic acid ethyl ester and Thymidine-5'-thiophosphate as potent inhibitors against the SARS-CoV-2, and both drugs performed impeccably and showed stability during the 100 ns molecular dynamics simulation. Both of the drugs are among the category of small molecules and have an acceptable range of ADME properties. They can be used after their validation in in-vitro and in-vivo conditions.
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Affiliation(s)
- Norah A. Alturki
- Clinical Laboratory Science Department, College of Applied Medical Science, King Saud University, Riyadh 11433, Saudi Arabia;
| | - Mutaib M. Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (M.M.M.); (S.A.A.)
| | - Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, Al Quwayiyah 11961, Saudi Arabia;
| | - Youssef S. Alghamdi
- Department of Biology, Turabah University College, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Afaf A. Alharthi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Saeed A. Asiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (M.M.M.); (S.A.A.)
| | - Shaban Ahmad
- Agriculture Knowledge Management Unit, ICAR-Indian Agricultural Research Institute, New Dehli 110012, India;
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (M.M.M.); (S.A.A.)
- Correspondence:
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37
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Sishtla K, Lambert-Cheatham N, Lee B, Han DH, Park J, Sardar Pasha SPB, Lee S, Kwon S, Muniyandi A, Park B, Odell N, Waller S, Park IY, Lee SJ, Seo SY, Corson TW. Small-molecule inhibitors of ferrochelatase are antiangiogenic agents. Cell Chem Biol 2022; 29:1010-1023.e14. [PMID: 35090600 PMCID: PMC9233146 DOI: 10.1016/j.chembiol.2022.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 11/10/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Activity of the heme synthesis enzyme ferrochelatase (FECH) is implicated in multiple diseases. In particular, it is a mediator of neovascularization in the eye and thus an appealing therapeutic target for preventing blindness. However, no drug-like direct FECH inhibitors are known. Here, we set out to identify small-molecule inhibitors of FECH as potential therapeutic leads using a high-throughput screening approach to identify potent inhibitors of FECH activity. A structure-activity relationship study of a class of triazolopyrimidinone hits yielded drug-like FECH inhibitors. These compounds inhibit FECH in cells, bind the active site in cocrystal structures, and are antiangiogenic in multiple in vitro assays. One of these promising compounds was antiangiogenic in vivo in a mouse model of choroidal neovascularization. This foundational work may be the basis for new therapeutic agents to combat not only ocular neovascularization but also other diseases characterized by FECH activity.
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Affiliation(s)
- Kamakshi Sishtla
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nathan Lambert-Cheatham
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Bit Lee
- College of Pharmacy, Gachon University, Incheon 21936, South Korea
| | - Duk Hee Han
- College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea
| | - Jaehui Park
- College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea
| | - Sheik Pran Babu Sardar Pasha
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sanha Lee
- College of Pharmacy, Gachon University, Incheon 21936, South Korea
| | - Sangil Kwon
- College of Pharmacy, Gachon University, Incheon 21936, South Korea
| | - Anbukkarasi Muniyandi
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Bomina Park
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Noa Odell
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Spelman College, Atlanta, GA 30314, USA
| | - Sydney Waller
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Il Yeong Park
- College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea
| | - Soo Jae Lee
- College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea.
| | - Seung-Yong Seo
- College of Pharmacy, Gachon University, Incheon 21936, South Korea.
| | - Timothy W Corson
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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Ejaz SA, Alsfouk AA, Batiha GES, Aborode AT, Ejaz SR, Umar HI, Aziz M, Saeed A, Mahmood HMK, Fayyaz A. Identification of N-(4-acetyl-4,5-dihydro-5-(7,8,9-substituted-tetrazolo[1,5-a]-quinolin-4-yl)-1,3,4-thiadiazol-2-yl) acetamide derivatives as potential caspase-3 inhibitors via detailed computational investigations. Struct Chem 2022. [DOI: 10.1007/s11224-022-01986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Elsayed RW, Sabry MA, El-Subbagh HI, Bayoumi SM, El-Sayed SM. Thiazole-based SARS-CoV-2 protease (COV M pro ) inhibitors: Design, synthesis, enzyme inhibition, and molecular modeling simulations. Arch Pharm (Weinheim) 2022; 355:e2200121. [PMID: 35607750 PMCID: PMC9348455 DOI: 10.1002/ardp.202200121] [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: 03/10/2022] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 01/08/2023]
Abstract
As an attempt to contribute to the efforts of combating the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) responsible for COVID‐19, new analogs of the repurposed drug nitazoxanide which showed promising inhibitory efficacy on a viral protease enzyme were designed, synthesized and evaluated for their inhibitory activity on the main protease of the SARS‐CoV‐2 virus, using the COV2‐3CL protease inhibition assay. The obtained results showed that the N‐(substituted‐thiazol‐2‐yl)cinnamamide analogs 19, 20, and 21 were the most active compounds with IC50 values of 22.61, 14.7, 21.99 µM, respectively, against the viral protease compared to the reference drugs, nitazoxanide, and lopinavir. Molecular modeling studies showed binding interactions of 19, 20, and 21 with hydrogen bonds to Gln189 and Glu166, arene–arene interaction between the thiazole moiety and His41, and other hydrophobic interactions between the ethene spacer moiety and Asn142. Moreover, an extra arene–arene interaction between substituted benzo[d]thiazole and His41 was observed regarding compounds 19 and 21. Surface mapping and flexible alignment proved the structural similarity between the new drug candidates and nitazoxanide. Compliance of the new compounds to Lipinski's rule of five was investigated and absorption, distribution, metabolism, excretion, and toxicology data were predicted. The newly synthesized compounds are promising template ligands for further development and optimization.
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Affiliation(s)
- Reham W Elsayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mohamed A Sabry
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Hussein I El-Subbagh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Said M Bayoumi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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Infection Dynamics of ATG8 in Leishmania: Balancing Autophagy for Therapeutics. Molecules 2022; 27:molecules27103142. [PMID: 35630618 PMCID: PMC9147918 DOI: 10.3390/molecules27103142] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/10/2022] Open
Abstract
In many regions of the world, Leishmaniasis is a cause of substantial mortality and ailment. Due to impediment in available treatment, development of novel and effective treatments is indispensable. Significance of autophagy has been accentuated in infectious disease as well as in Leishmaniasis, and it is having capability to be manifested as a therapeutic target. By evincing autophagy as a novel therapeutic regime, this study emphasized on the critical role of ATG4.1-ATG8 and ATG5-ATG12 complexes in Leishmania species. The objective here was to identify ATG8 as a potential therapeutic target in Leishmania. R71T, P56E, R18P are the significant mutations which shows detrimental effect on ATG8 while Arg276, Arg73, Cys75 of ATG4.1 and Val88, Pro89, Glu116, Asn117, and Gly120 are interacting residues of ATG8. Along with this, we also bring into spotlight an enticing role of Thiabendazole derivatives that interferes with the survival mechanisms by targeting ATG8. Further, the study claims that thiabendazole can be a potential drug candidate to target autophagy process in the infectious disease Leishmaniasis.
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41
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Saganuwan SA. Biomedical Applications of Polyurethane Hydrogels, Polyurethane Aerogels and Polyurethane-Graphene Nanocomposite Materials. Cent Nerv Syst Agents Med Chem 2022; 22:79-87. [PMID: 35507789 DOI: 10.2174/1871524922666220429115124] [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] [Received: 08/24/2021] [Revised: 01/06/2022] [Accepted: 02/05/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Increasing new emerging ill-healths have posed therapeutic challenges in modern medicine. Hence polyurethane hydrogels that comprise polyol, copolymer and extender could be prepared from diverse chemical compounds with adjuvants such as ascorbic acid, sorbitol among others. Their mechano-physicochemical properties are functions of their biological activities. Therefore there is need to assess their therapeutic potentials. METHODS literature were searched on synthesis and medical uses of polyurethane - hydrogels, polyurethane - aerogels and polyurethane - graphene nanocomposite materials, with a view to identifying their sources, synthesis, mechanical and physiochemical properties, biomedical applications, chirality, and the relevance of Lipinski's rule of five in the synthesis of oral polyurethane nanocomposite materials. RESULTS The prepared hydrogels and aerogels could be used as polymer carriers for intradermal, cutaneous and intranasal drugs. They can be fabricated and used as prosthetics. In addition the strength modulus (tensile stress-tensile strain ratio), biodegradability, biocompatibility and non-toxic effects of the polyurethane hydrogels and aerogels are the highly desirable properties. However, body and environmental temperatures may contribute to their instability, hence there is need to improve on the synthesis of aerogels and hydrogels of polyurethane that can last for many years. Alcoholism, diabetes, pyrogenic diseases, mechanical and physical forces, and physiological variability may also reduce the life span of polyurethane aerogels and hydrogels. CONCLUSION Synthesis of polyurethane hydrogel-aerogel complex that can be used in complex, rare biomedical cases is of paramount importance. These hydrogels and aerogels may be hydrophobic, hydrophilic, aerophobic-aerophilic or amphiphilic and sometimes lipophilic depending on structural components and the intended biomedical uses. Polyurethane graphene nanocomposite materials are used in the treatment of a myriad of diseases including cancer and bacterial infection.
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Affiliation(s)
- Saganuwan Alhaji Saganuwan
- Department Of Veterinary Pharmacology And Toxicology, College Of Veterinary Medicine, Federal University Of Agriculture P.M.B 2373, Makurdi, Benue State, Nigeria
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Ahmad S, Pasha Km M, Raza K, Rafeeq MM, Habib AH, Eswaran M, Yadav MK. Reporting dinaciclib and theodrenaline as a multitargeted inhibitor against SARS-CoV-2: an in-silico study. J Biomol Struct Dyn 2022; 41:4013-4023. [PMID: 35451934 DOI: 10.1080/07391102.2022.2060308] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is one of the rapid spreading coronaviruses that belongs to the Coronaviridae family. The rapidly evolving nature of SARS-CoV-2 results in a variety of variants with a capability of evasion to existing therapeutics and vaccines. So, there is an imperative need to discover potent drugs that can able to disrupt the function of multiple drug targets to tackle the SARS-CoV-2 menace. Here in this study, we took the different targets of SARS-CoV-2 prepared in the Schrodinger maestro. The library of the DrugBank database is screened against the selected crucial targets. Our molecular docking, Molecular Mechanics/Generalized Born Surface Area (MMGBSA), and molecular dynamics simulation studies led to identifying dinaciclib and theodrenaline as potential drugs against multiple drug targets: main protease, NSP15-endoribonuclease and papain-like-protease, of SARS-CoV-2. Dinaciclib with papain-like protease and NSP15-endoribonuclease show the docking score of -7.015 and -8.737, respectively, while the theodrenaline with NSP15-endoribonuclease and main protease produced the docking score of -8.507 and -7.289, respectively. Furthermore, the binding free energy calculations with MM/GBSA and molecular dynamics simulation studies of the complexes confirm the reliability of the drugs. The selected drugs are capable of binding to multiple targets simultaneously, thus withstanding their activity of target disruption in different variants of SARS-CoV-2. Although, the repurposed drugs are showing potent activity, but may need further in-vitro and in-vivo validations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shaban Ahmad
- Department of Bioinformatics, SRM University, Delhi-NCR, Sonepat, Sonepat, Haryana, India.,Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mussuvir Pasha Km
- Department of Studies and Research in Chemistry, Vijayanagara Sri Krishnadevaraya University, Ballari, Karnataka, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, KSA
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, KSA
| | - Murugesh Eswaran
- Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Manoj Kumar Yadav
- Department of Bioinformatics, SRM University, Delhi-NCR, Sonepat, Sonepat, Haryana, India
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Hemi-Babim and Fenoterol as Potential Inhibitors of MPro and Papain-like Protease against SARS-CoV-2: An In-Silico Study. Medicina (B Aires) 2022; 58:medicina58040515. [PMID: 35454354 PMCID: PMC9025073 DOI: 10.3390/medicina58040515] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 11/17/2022] Open
Abstract
The coronaviruses belong to the Coronaviridae family, and one such member, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is causing significant destruction around the world in the form of a global pandemic. Although vaccines have been developed, their effectiveness and level of protection is still a major concern, even after emergency approval from the World Health Organisation (WHO). At the community level, no natural medicine is currently available as a cure. In this study, we screened the vast library from Drug Bank and identified Hemi-Babim and Fenoterol as agents that can work against SARS-CoV-2. Furthermore, we performed molecular dynamics (MD) simulation for both compounds with their respective proteins, providing evidence that the said drugs can work against the MPro and papain-like protease, which are the main drug targets. Inhibiting the action of these targets may lead to retaining the virus. Fenoterol is a beta-2 adrenergic agonist used for the symptomatic treatment of asthma as a bronchodilator and tocolytic. In this study, Hemi-Babim and Fenoterol showed good docking scores of −7.09 and −7.14, respectively, and performed well in molecular dynamics simulation studies. Re-purposing the above medications has huge potential, as their effects are already well-proven and under public utilisation for asthma-related problems. Hence, after the comprehensive pipeline of molecular docking, MMGBSA, and MD simulation studies, these drugs can be tested in-vivo for further human utilisation.
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Inhibitory effects of selected isoquinoline alkaloids against main protease (Mpro) of SARS-CoV-2, in silico study. In Silico Pharmacol 2022; 10:5. [PMID: 35310017 PMCID: PMC8918422 DOI: 10.1007/s40203-022-00122-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 02/22/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat. Despite the production of various vaccines and different treatments, finding natural compounds to control COVID-19 is still a challenging task. Isoquinoline alkaloids are naturally occurring compounds known to have some potential antiviral activity. In this study, ten abundant isoquinoline alkaloids with antiviral activity were selected to analyze the preventive effect on COVID-19. A scrutinized evaluation based on Lipinski’s rule showed that one out of ten compounds was toxic. Based on molecular docking analysis using Autodock software one of the best molecules with maximum negative binding energy was selected for further analysis. The Gromacs simulation analysis revealed that Coptisine has more action against active site Mpro of COVID-19. Overall, to make a rational design of various preventive analogues that inhibit the COVID-19, associated in vitro and in vivo analyses are needed to confirm this claim.
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The Effects of Acyl Chain Length on Antioxidant Efficacy of Mono- and Multi-Acylated Resveratrol: A Comparative Assessment. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031001. [PMID: 35164266 PMCID: PMC8839368 DOI: 10.3390/molecules27031001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/24/2022]
Abstract
Acylated derivatives of the dietary phenolic, resveratrol, were prepared via enzymatic and chemical transesterification modification with selected vinyl fatty acids to expand the potential application of resveratrol and its acylated derivatives in functional supplement, cosmetic/skincare, and pharmaceutical fields. The acylation was implemented using eight vinyl fatty acids with varying chain lengths (C2:0-C18:0). Eight monoesters enzymatically prepared, eight diesters and four triesters, chemically prepared, were isolated and purified and identified via MS (mass spectra) or/and NMR (nuclear magnetic resonance). The lipophilicity of resveratrol and its acylated derivatives was calculated using ALOGPS 2.1. Compared with related acylated products, resveratrol itself rendered higher antioxidant efficacy in all the antioxidant assays, namely DPPH, ABTS, FRAP, and ferrous chelation tests. Within various ester derivatives of resveratrol, short-chain fatty acid mono- and di-substituted resveratrols, especially the resveratrol monoacetate/diacetate, exhibited higher antioxidant efficacy in DPPH and ABTS assays than the rest of resveratrol derivatives, but the medium-chain monoesters of resveratrol, including caproate, caprylate, caprate, and laurate, showed a higher metal ion chelation ability compared to other acylated resveratrols. These results imply that resveratrol derivatives may be used in lipidic media as health-beneficial antioxidants.
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Chavan PA, Jadhav SB. Synthesis, Characterization and Screening of Some Novel 2-Methyl-N'-
[(Z)-Substituted-Phenyl ethylidene] Imidazo [1, 2-a] Pyridine-3-Carbohy
drazide Derivatives as DPP-IV Inhibitors for the Treatment of Type 2 Diabetes
Mellitus. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210901125958] [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
Background:
One of the leading global metabolic diseases marked by insulin resistance and
chronic hyperglycemia is type 2 diabetes mellitus (T2DM). Since the last decade, DPP-4 enzyme inhibition
has proven to be a successful, safe, and well-established therapy for the treatment of T2DM.
Objective:
The present work reports the synthesis, characterization, and screening of some novel 2-
methyl-N'-[(Z)-substituted-phenyl ethylidene] imidazo [1, 2-a] pyridine-3-carbohydrazide derivatives as
DPP-IV inhibitors for the treatment of T2DM.
Methods:
The molecular docking was performed to study these derivatives' binding mode in the enzyme's
allosteric site. All the synthesized compounds were subjected for DPP-IV enzyme assay and in vivo antihyperglycemic
activity in STZ-induced diabetic rats.
Results:
The synthesized derivatives exhibited potent antidiabetic activity as compared to the standard
drug Sitagliptin. Out of sixteen compounds, A1, A4, B4, C2, C3, and D4 have shown promising antidiabetic
activity against the DPP-IV enzyme. The most promising compound, C2, showed a percentage inhibition
of 72.02±0.27 at 50 μM concentration. On the 21st-day, compound C2 showed a significant reduction
in serum blood glucose level, i.e., 156.16±4.87 mg/dL, then diabetic control, which was
280.00±13.29 mg/dL whereas, standard Sitagliptin showed 133.50±11.80 mg/dL. In the in vivo antihyperglycemic
activity, the compounds have exhibited good hypoglycemic potential in fasting blood glucose
in the T2DM animal model. All the docked molecules have exhibited perfect binding affinity towards
the active pocket of the enzyme. The synthesized derivatives were screened through Lipinski's rule
of five for better optimization, and fortunately, none of them violated the rule.
Conclusion:
The above results indicate that compound C2 is a relatively active and selective hit molecule
that can be structurally modified to enhance the DPP-IV inhibitor's potency and overall pharmacological
profile. From the present work, it has been concluded that substituted pyridine-3-carbohydrazide derivatives
possess excellent DPP-IV inhibitory potential and can be better optimized further by generating
more in vivo, in vitro models.
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Affiliation(s)
- Prerana A. Chavan
- Department of Pharmaceutical Chemistry, PES\'s Modern College of Pharmacy, Nigdi, Pune, Maharashtra 411044,
India
| | - Shailaja B. Jadhav
- Department of Pharmaceutical Chemistry, PES\'s Modern College of Pharmacy, Nigdi, Pune, Maharashtra 411044,
India
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Zha J, Li M, Kong R, Lu S, Zhang J. Explaining and Predicting Allostery with Allosteric Database and Modern Analytical Techniques. J Mol Biol 2022; 434:167481. [DOI: 10.1016/j.jmb.2022.167481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 12/17/2022]
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Zheng J, Zhao S, Mao Y, Du Z, Li G, Sang M. Lipid-Activatable Fluorescent Probe for Intraoperative Imaging of Atherosclerotic Plaque Using In Situ Patch. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104471. [PMID: 34837454 DOI: 10.1002/smll.202104471] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/09/2021] [Indexed: 06/13/2023]
Abstract
The surgical removal of lesions is among the most common and effective treatments for atherosclerosis. It is often the only curative treatment option, and the ability to visualize the full extent of atherosclerotic plaque during the operation has major implications for the therapeutic outcome. Fluorescence imaging is a promising approach for the inspection of atherosclerotic plaques during surgery. However, there is no systematic strategy for intraoperative fluorescent imaging in atherosclerosis. In this study, the in situ attachment of a lipid-activatable fluorescent probe (CN-N2)-soaked patch to the outer arterial surface is reported for rapid and precise localization of the atherosclerotic plaque in ApoE-deficient mouse during surgery. Stable imaging of the plaque is conducted within 5 min via rapid recognition of abnormally accumulated lipid droplets (LDs) in foam cells. Furthermore, the plaque/normal ratio (P/N) is significantly enhanced to facilitate surgical delineation of carotid atherosclerotic plaques. Visible fluorescence bioimaging using lipid-activatable probes can accurately delineate plaque sizes down to diameters of <0.5 mm, and the images can be swiftly captured within the stable plaque imaging time window. These findings on intraoperative fluorescent imaging of plaques via the in situ attachment of the CN-N2 patch hold promise for effective clinical applications.
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Affiliation(s)
- Jinrong Zheng
- Xiamen Cardiovascular Hospital, Xiamen University, 2999 Jinshan Road, Huli District, Xiamen, 361006, China
| | - Shanshan Zhao
- Xiamen Cardiovascular Hospital, Xiamen University, 2999 Jinshan Road, Huli District, Xiamen, 361006, China
| | - Yijie Mao
- Xiamen Cardiovascular Hospital, Xiamen University, 2999 Jinshan Road, Huli District, Xiamen, 361006, China
| | - Zhichao Du
- School of Pharmaceutical Sciences, Tsinghua University, 30 Shuangqing Road, Haiding District, Beijing, 100084, China
- Department of Pharmacy, Xilingol League Central Hospital, 9 Nadam Street, Xilinhot, 026000, China
| | - Gang Li
- Xiamen Cardiovascular Hospital, Xiamen University, 2999 Jinshan Road, Huli District, Xiamen, 361006, China
| | - Mangmang Sang
- Xiamen Cardiovascular Hospital, Xiamen University, 2999 Jinshan Road, Huli District, Xiamen, 361006, China
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Darwish SA, El-Kerdawy MM, Elsheakh AR, Abdelrahman RS, Shaldam MA, Abdel-Aziz HA, Hassan GS, Ghaly MA. New tilomisole-based benzimidazothiazole derivatives as anti-inflammatory agents: Synthesis, in vivo, in vitro evaluation, and in silico studies. Bioorg Chem 2022; 120:105644. [PMID: 35121552 DOI: 10.1016/j.bioorg.2022.105644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/30/2021] [Accepted: 01/23/2022] [Indexed: 11/16/2022]
Abstract
New tilomisole-based benzimidazothiazole derivatives were designed and synthesized in this work. Their anti-inflammatory activity was assessed through the in vivo carrageenan rat paw edema model, and the in vitro COX inhibition assay. Compounds 13, 20, 30, 40, 43, and 46 demonstrated values of inhibition of induced edema in the in vivo assay comparable to celecoxib. All the synthesized compounds expressed their activity on COX-2 enzyme more than COX-1, proving their advantageous selectivity. In addition, compounds 13, 16, 20, 25, and 46 displayed lower IC50 values than celecoxib as a reference drug against COX-2 enzyme; having values of 0.09, 13.87, 32.28, 33.01, and 5.18 nM respectively vs 40.00 nM for celecoxib. Particularly, the most active compound (13) with its extreme potency (400 folds more potent than celecoxib) exhibited a notable high selectivity index (SI = 159.5). In silico studies, including ADMET prediction, compliance to Lipinski's rule of five, and molecular docking into the active site of both COX isozymes were conducted for the synthesized compounds. The results suggested that these compounds are good candidates for orally active drugs, and docking revealed higher number of interactions with COX-2 for 13 as the most active compound compared with COX-1 reflecting its advantageous selectivity and explaining its extreme potency.
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Affiliation(s)
- Sara A Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed M El-Kerdawy
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Ahmad R Elsheakh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Rehab S Abdelrahman
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafr El Sheikh 33516, Egypt
| | - Hatem A Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Centre, Dokki 12622, Egypt
| | - Ghada S Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mariam A Ghaly
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
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Hu Z, Crews CM. Recent Developments in PROTAC-Mediated Protein Degradation: From Bench to Clinic. Chembiochem 2022; 23:e202100270. [PMID: 34494353 PMCID: PMC9395155 DOI: 10.1002/cbic.202100270] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/02/2021] [Indexed: 01/21/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs), an emerging paradigm-shifting technology, hijacks the ubiquitin-proteasome system for targeted protein degradation. PROTACs induce ternary complexes between an E3 ligase and POI, and this induced proximity leads to polyUb chain formation on substrates and eventual proteasomal-mediated POI degradation. PROTACs have shown great therapeutic potential by degrading many disease-causing proteins, such as the androgen receptor and BRD4. The PROTAC technology has advanced significantly in the last two decades, with the repertoire of PROTAC targets increased tremendously. Herein, we describe recent developments of PROTAC technology, focusing on mechanistic and kinetic studies, pharmacokinetic study, spatiotemporal control of PROTACs, covalent PROTACs, resistance to PROTACs, and new E3 ligands.
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Affiliation(s)
- Zhenyi Hu
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven CT 06511 (USA)
| | - Craig M. Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven CT 06511 (USA),Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511(USA),Department of Pharmacology, Yale University, 333 Cedar Street New Haven, CT 06511 (USA)
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