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Saini A, Kumar A, Jangid K, Kumar V, Jaitak V. Identification of terpenoids as dihydropteroate synthase and dihydrofolate reductase inhibitors through structure-based virtual screening and molecular dynamic simulations. J Biomol Struct Dyn 2024; 42:1966-1984. [PMID: 37173829 DOI: 10.1080/07391102.2023.2203249] [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: 10/10/2022] [Accepted: 04/09/2023] [Indexed: 05/15/2023]
Abstract
Bacterial infections are rising, and antimicrobial resistance (AMR) in bacteria has worsened the scenario, requiring extensive research to find alternative therapeutic agents. Terpenoids play an essential role in protecting plants from herbivores and pathogens. The present study was designed to focus on in silico evaluation of terpenoids for their affinity towards two necessary enzymes, i.e. DHFR and DHPS, which are involved in forming 5, 6, 7, 8-tetrahydrofolate, a key component in bacterial DNA synthesis proteins. Additionally, to account for activity against resistant bacteria, their affinity towards the L28R mutant of DHFR was also assessed in the study. The structure-based drug design approach was used to screen the compound library of terpenes for their interaction with active sites of DHFR and DHPS. Further, compounds were screened based on their dock score, pharmacokinetic properties, and binding affinities. A total of five compounds for each target protein were screened, having dock scores better than their respective standard drug molecules. CNP0169378 (-8.4 kcal/mol) and CNP0309455 (-6.5 kcal/mol) have been identified as molecules with a higher affinity toward the targets of DHFR and DHPS, respectively. At the same time, one molecule CNP0298407 (-5.8 kcal/mol for DHPS, -7.6 kcal/mol for DHFR, -6.1 kcal/mol for the L28R variant), has affinity for both proteins (6XG5 and 6XG4). All the molecules have good pharmacokinetic properties. We further validated the docking study by binding free energy calculations using the MM/GBSA approach and molecular dynamics simulations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhishek Saini
- Laboratory of Natural Product Chemistry, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Amit Kumar
- Laboratory of Natural Product Chemistry, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Kailash Jangid
- Department of Chemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Vinod Kumar
- Department of Chemistry, Central University of Punjab, Bathinda, Punjab, India
| | - Vikas Jaitak
- Laboratory of Natural Product Chemistry, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
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Hameed AR, Ali SF, Alsallameh SMS, Muhseen ZT, Almansour NM, ALSuhaymi N, Alsugoor MH, Allemailem KS. Structural Dynamics of P-Rex1 Complexed with Natural Leads Establishes the Protein as an Attractive Target for Therapeutics to Suppress Cancer Metastasis. BIOMED RESEARCH INTERNATIONAL 2023; 2023:3882081. [PMID: 38098889 PMCID: PMC10721353 DOI: 10.1155/2023/3882081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/30/2022] [Accepted: 06/24/2022] [Indexed: 12/17/2023]
Abstract
Phosphatidylinositol 3,4,5-trisphosphate- (PIP3-) dependent Rac exchanger 1 (P-Rex1) functions as Rho guanine nucleotide exchange factor and is activated by synergistic activity of Gβγ and PIP3 of the heterotrimeric G protein. P-Rex1 activates Rac GTPases for regulating cell invasion and migration and promotes metastasis in several human cancers including breast, prostate, and skin cancer. The protein is a promising therapeutic target because of its multifunction roles in human cancers. Herein, the present study attempts to identify selective P-Rex1 natural inhibitors by targeting PIP3-binding pocket using large-size multiple natural molecule libraries. Each library was filtered subsequently in FAF-Drugs4 based on Lipinski's rule of five (RO5), toxicity, and filter pan assay interference compounds (PAINS). The output hits were virtually screened at the PIP3-binding pocket through PyRx AutoDock Vina and cross-checked by GOLD. The best binders at the PIP3-binding pocket were prioritized using a comparative analysis of the docking scores. Top-ranked two compounds with high GOLD fitness score (>80) and lowest AutoDock binding energy (< -12.7 kcal/mol) were complexed and deciphered for molecular dynamics along with control-P-Rex1 complex to validate compound binding conformation and disclosed binding interaction pattern. Both the systems were seen in good equilibrium, and along the simulation time, the compounds are in strong contact with the P-Rex1 PIP3-binding site. Hydrogen bonding analysis towards simulation end identified the formation of 16 and 22 short- and long-distance hydrogen bonds with different percent of occupancy to the PIP3 residues for compound I and compound 2, respectively. Radial distribution function (RDF) analysis of the key hydrogen bonds between the compound and the PIP3 residues demonstrated a strong affinity of the compounds to the mentioned PIP3 pocket. Additionally, MMGB/PBSA energies were performed that confirmed the dominance of Van der Waals energy in complex formation along with favorable contribution from hydrogen bonding. These findings were also cross-validated by a more robust WaterSwap binding energy predictor, and the results are in good agreement with a strong binding affinity of the compounds for the protein. Lastly, the key contribution of residues in interaction with the compounds was understood by binding free energy decomposition and alanine scanning methods. In short, the results of this study suggest that P-Rex1 is a good druggable target to suppress cancer metastasis; therefore, the screened druglike molecules of this study need in vitro and in vivo anti-P-Rex1 validation and may serve as potent leads to fight cancer.
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Affiliation(s)
- Alaa R. Hameed
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad, Iraq
| | - Sama Fakhri Ali
- Department of Anesthesia Techniques, School of Life Sciences, Dijlah University College, Baghdad, Iraq
| | - Sarah M. S. Alsallameh
- Ministry of Higher Education and Scientific Research, Gilgamesh Ahliya University College, College of Health and Medical Techniques, Department of Medical Laboratories Techniques, Baghdad, Iraq
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon 51001, Iraq
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Naif ALSuhaymi
- Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Mecca 21912, Saudi Arabia
| | - Mahdi H. Alsugoor
- Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Mecca 21912, Saudi Arabia
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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Saleh NAM, El-bary RBEDA, Mpingirika EZ, Essa HL, El-Sayed MMH, Sherbetjian MS, Elfandi HF, Wahed MAA, Arafeh R, Amleh A. Evaluating the Potential Anticancer Properties of Salvia triloba in Human-Osteosarcoma U2OS Cell Line and Ovarian Adenocarcinoma SKOV3 Cell Line. APPLIED SCIENCES 2022; 12:11545. [DOI: 10.3390/app122211545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Salvia triloba (S. triloba) is an herb inherently linked to traditional medicine systems in the Eastern Mediterranean region. There is minimal experimental evidence however, regarding the anticancer effects of S. triloba in both osteosarcoma and ovarian cancer. In this study, we investigated the effects of crude (macerated) S. triloba ethanol and acetone leaf extracts on viability, migratory ability, and the expression of genes regulating these activities in U2OS and SKOV3 cells using MTT assay, scratch-wound healing/trans-well migration assay, and RT-qPCR respectively. MTT assay results indicated that the acetone extract significantly reduced both U2OS and SKOV3 cell viability with half-maximal inhibitory concentrations (IC50) of 54.51 ± 1.10 µg/mL and 75.96 ± 1.0237 µg/mL respectively; these concentrations further displayed negligible hemolytic activity. The combination of acetone extract (19 µg/mL) and paclitaxel (0.787 µg/mL) displayed synergy and reduced SKOV3 cell viability by over 90%. Additionally, the trans-well migration assay illustrated that the acetone extract (IC50) inhibited both U2OS and SKOV3 cell migration by more than 50%. Moreover, S. triloba acetone extract significantly downregulated the steady-state mRNA expression of key genes involved in driving select cancer hallmarks. Four fractions were generated from the acetone extract by thin layer chromatography (TLC), and the obtained retention factors (Rf) (ranging from 0.2 to 0.8) suggested a mixture of high and moderately polar compounds whose bioactivities require further investigation. In addition, FTIR measurements of the extract revealed peaks corresponding to OH, aliphatic CH, and ester groups suggesting the presence of phenolic compounds, terpenes, and polysaccharides. Altogether, these results suggest that S. triloba possesses potential therapeutic compounds that inhibit cell proliferation and migration, and modulate several genes involved in osteosarcoma and ovarian carcinoma progression.
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Oyedele AQK, Adelusi TI, Ogunlana AT, Adeyemi RO, Atanda OE, Babalola MO, Ashiru MA, Ayoola IJ, Boyenle ID. Integrated virtual screening and molecular dynamics simulation revealed promising drug candidates of p53-MDM2 interaction. J Mol Model 2022; 28:142. [PMID: 35536362 DOI: 10.1007/s00894-022-05131-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/28/2022] [Indexed: 12/13/2022]
Abstract
In the vast majority of malignancies, the p53 tumor suppressor pathway is compromised. In some cancer cells, high levels of MDM2 polyubiquitinate p53 and mark it for destruction, thereby leading to a corresponding downregulation of the protein. MDM2 interacts with p53 via its hydrophobic pocket, and chemical entities that block the dimerization of the protein-protein complex can restore p53 activity. Thus far, only a few chemical compounds have been reported as potent arsenals against p53-MDM2. The Protein Data Bank has crystallogaphic structures of MDM2 in complex with certain compounds. Herein, we have exploited one of the complexes in the identification of new p53-MDM2 antagonists using a hierarchical virtual screening technique. The initial stage was to compile a targeted library of structurally appropriate compounds related to a known effective inhibitor, Nutlin 2, from the PubChem database. The identified 57 compounds were subjected to virtual screening using molecular docking to discover inhibitors with high binding affinity for MDM2. Consequently, five compounds with higher binding affinity than the standard emerged as the most promising therapeutic candidates. When compared to Nutlin 2, four of the drug candidates (CID_140017825, CID_69844501, CID_22721108, and CID_22720965) demonstrated satisfactory pharmacokinetic and pharmacodynamic profiles. Finally, MD simulation of the dynamic behavior of lead-protein complexes reveals the stability of the complexes after a 100,000 ps simulation period. In particular, when compared to the other three leads, overall computational modeling found CID_140017825 to be the best pharmacological candidate. Following thorough experimental trials, it may emerge as a promising chemical entity for cancer therapy.
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Affiliation(s)
- Abdul-Quddus Kehinde Oyedele
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria.,Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Temitope Isaac Adelusi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Abdeen Tunde Ogunlana
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Rofiat Oluwabusola Adeyemi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria.,Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Opeyemi Emmanuel Atanda
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | | | - Mojeed Ayoola Ashiru
- Department of Chemical Sciences, Biochemistry Unit, College of Natural and Applied Science, Fountain University, Osogbo, Nigeria
| | - Isong Josiah Ayoola
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Ibrahim Damilare Boyenle
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria. .,College of Health Sciences, Crescent University, Abeokuta, Nigeria.
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Alam M, Alam S, Shamsi A, Adnan M, Elasbali AM, Al-Soud WA, Alreshidi M, Hawsawi YM, Tippana A, Pasupuleti VR, Hassan MI. Bax/Bcl-2 Cascade Is Regulated by the EGFR Pathway: Therapeutic Targeting of Non-Small Cell Lung Cancer. Front Oncol 2022; 12:869672. [PMID: 35402265 PMCID: PMC8990771 DOI: 10.3389/fonc.2022.869672] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
Non-small cell lung carcinoma (NSCLC) comprises 80%-85% of lung cancer cases. EGFR is involved in several cancer developments, including NSCLC. The EGFR pathway regulates the Bax/Bcl-2 cascade in NSCLC. Increasing understanding of the molecular mechanisms of fundamental tumor progression has guided the development of numerous antitumor drugs. The development and improvement of rationally planned inhibitors and agents targeting particular cellular and biological pathways in cancer have been signified as a most important paradigm shift in the strategy to treat and manage lung cancer. Newer approaches and novel chemotherapeutic agents are required to accompany present cancer therapies for improving efficiency. Using natural products as a drug with an effective delivery system may benefit therapeutics. Naturally originated compounds such as phytochemicals provide crucial sources for novel agents/drugs and resources for tumor therapy. Applying the small-molecule inhibitors (SMIs)/phytochemicals has led to potent preclinical discoveries in various human tumor preclinical models, including lung cancer. In this review, we summarize recent information on the molecular mechanisms of the Bax/Bcl-2 cascade and EGFR pathway in NSCLC and target them for therapeutic implications. We further described the therapeutic potential of Bax/Bcl-2/EGFR SMIs, mainly those with more potent and selectivity, including gefitinib, EGCG, ABT-737, thymoquinone, quercetin, and venetoclax. In addition, we explained the targeting EGFR pathway and ongoing in vitro and in vivo and clinical investigations in NSCLC. Exploration of such inhibitors facilitates the future treatment and management of NSCLC.
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Affiliation(s)
- Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, India
| | - Shoaib Alam
- Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, India
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Sakaka, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia.,Health Sciences Research Unit, Jouf University, Sakaka, Saudi Arabia
| | - Mousa Alreshidi
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia.,Molecular Diagnostics and Personalized Therapeutics Unit, University of Hail, Hail, Saudi Arabia
| | | | - Anitha Tippana
- Regional Agricultural Research Station, Acharya N. G. Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Visweswara Rao Pasupuleti
- Department of Biomedical Sciences and Therapeutics, Faculty of Medicine & Health Sciences, University Malaysia Sabah, Kota Kinabalu, Malaysia.,Department of Biochemistry, Faculty of Medicine and Health Sciences, Abdurrab University, Pekanbaru, Indonesia.,Centre for International Collaboration and Research, Reva University, Rukmini Knowledge Park, Bangalore, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, India
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Merecz-Sadowska A, Sitarek P, Śliwiński T, Zajdel K, Malinowska K, Zielińska-Bliźniewska H, Kucharska E, Zajdel R. In Vitro and In Silico Studies on Leonotis nepetifolia (L.) R. Br. Root
Extract against Cancer Cells. Curr Pharm Biotechnol 2022; 23:1383-1395. [DOI: 10.2174/1389201023666220304095225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/28/2021] [Accepted: 11/19/2021] [Indexed: 11/22/2022]
Abstract
Background:
Leonotis nepetifolia (L.) R. Br. (Lamiaceae) is a shrub traditionally used
to alleviate inflammatory conditions.
Objective:
The present study aimed at investigating the biological activity of methanolic nontransformed and transformed Rhizobium rhizogenes root extracts from L. nepetifolia against human
melanoma cells.
Methods:
Cytotoxicity and genotoxicity properties, the impact on topoisomerase I activity, and
proapoptotic activity were evaluated by the MTT test, comet assay, topoisomerase I assay, and
fluorescence-activated cell sorting analysis. Moreover, the expressions of p53 were examined by
qPCR and Western blot analysis. Docking studies were conducted to assess the potential interactions of the identified phytochemicals with the p53 binding protein Mdm-2, and computational
analyses exhibited their antioxidant potential.
Results:
Both extracts showed cytotoxic potential against human melanoma cells, but generally the
activity was more potent for transformed roots than untransformed (IC50 760 μg/mL and 980
μg/mL, respectively). A similar effect was revealed during the evaluation of genotoxic and
proapoptotic properties. Moreover, the expression of p53 was also found to be increased after extract treatment. The most dominant identified compounds in both extracts were as follows: (+)-
catechin, p-coumaric acid, m-coumaric acid, and (+)-rosmarinic acid. Docking studies and computational analysis showed that (+)-rosmarinic acid possesses the highest binding affinity to the p53
binding protein, Mdm-2, and exhibits the best antioxidant property from the most commonly identified phytochemicals.
Conclusion:
Our findings revealed the potential of L. nepetifolia transformed root extract as a
source of bioactive compounds with cytotoxic, genotoxic, and proapoptotic activity against human
melanoma cells as well as antioxidant properties.
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Affiliation(s)
| | - Przemysław Sitarek
- Department of Biology and Pharmaceutical
Botany, Medical University of Lodz, Lodz, Poland
| | - Tomasz Śliwiński
- Laboratory of Medical Genetics, Faculty of Biology and Environmental
Protection, University of Lodz, Lodz, Poland
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Karolina Zajdel
- Department of Medical Informatics and Statistics, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Malinowska
- Department of Allergology and
Respiratory Rehabilitation, Medical University of Lodz, Lodz, Poland
| | | | - Ewa Kucharska
- Chair of Gerontology, Geriatrics and Social Work at the
Faculty of Pedagogy, Ignatianum Academy in Cracow, Cracow, Poland
| | - Radosław Zajdel
- Department of Computer Science in Economics, University of Lodz, Lodz, Poland
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Almansour NM. Triple-Negative Breast Cancer: A Brief Review About Epidemiology, Risk Factors, Signaling Pathways, Treatment and Role of Artificial Intelligence. Front Mol Biosci 2022; 9:836417. [PMID: 35145999 PMCID: PMC8824427 DOI: 10.3389/fmolb.2022.836417] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a kind of breast cancer that lacks estrogen, progesterone, and human epidermal growth factor receptor 2. This cancer is responsible for more than 15-20% of all breast cancers and is of particular research interest as it is therapeutically challenging mainly because of its low response to therapeutics and highly invasive nature. The non-availability of specific treatment options for TNBC is usually managed by conventional therapy, which often leads to relapse. The focus of this review is to provide up-to-date information related to TNBC epidemiology, risk factors, metastasis, different signaling pathways, and the pathways that can be blocked, immune suppressive cells of the TNBC microenvironment, current and investigation therapies, prognosis, and the role of artificial intelligence in TNBC diagnosis. The data presented in this paper may be helpful for researchers working in the field to obtain general and particular information to advance the understanding of TNBC and provide suitable disease management in the future.
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Affiliation(s)
- Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
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Nasar MQ, Zohra T, Khalil AT, Ovais M, Ullah I, Ayaz M, Zahoor M, Shinwari ZK. Extraction optimization, Total Phenolic-Flavonoids content, HPLC-DAD finger printing, antimicrobial, antioxidant and cytotoxic potentials of Chinese folklore Ephedra intermedia Schrenk & C. A. Mey. BRAZ J PHARM SCI 2022. [DOI: 10.1590/s2175-97902022e20989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
| | | | | | | | | | | | | | - Zabta Khan Shinwari
- Quaid-i-Azam University, Pakistan; Lady Reading Hospital (MTI), Pakistan; Pakistan Academy of Sciences, Pakistan
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Muhseen ZT, Ali MH, Jaber NR, Mashrea DS, Alfalki AM, Li G. Determination of Novel Anti-Cancer Agents by Targeting OGG1 Enzyme Using Integrated Bioinformatics Methods. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:13290. [PMID: 34948899 PMCID: PMC8706639 DOI: 10.3390/ijerph182413290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022]
Abstract
The 8-oxoguanine DNA glycosylase (OGG1) enzyme is a key DNA glycosylase mediating the excision of 7,8-dihydro-8-oxoguanine (8-oxoG) from DNA molecule to the start base excision repair pathway. The OGG1 glycosylase function depletion has been seen to obstruct pathological conditions such as inflammation, A3 T-cell lymphoblastic acute leukemia growth, and neurodegenerative diseases, thus warranting OGG1 as an attractive anti-cancer enzyme. Herein, we employed several drug libraries intending to screen non-toxic inhibitory molecules against the active pocket of the enzyme that achieved stable binding mode in dynamics. Two anti-cancer compounds ([O-]C1=C(CC2=CC=CC=C2)SC(=[N+]1CC(=O)NC3=NC=C(CC4=CC=CC=C4)S3)S and CCCN(CCC)[S]-(=O)(=O)C1=CC=C(C=C1)C(=O)NNC2=NC3=CC=C(Br)C=C3C(=N2)C4=CC=CC=C4) from Selleckchem.com were identified to occupy the active pocket of OGG1 and bind with greater affinity than Control TH5487. The binding affinity of Top-1 is -11.6 kcal/mol while that of Top-2 is -10.7 kcal/mol in contrast to TH5487 Control (-9 kcal/mol). During molecular dynamic simulations versus time, the said compounds are tightly held by the enzyme with no minor structural deviations reported except flexible loops in particular those present at the N and C-terminal. Both the compounds produced extensive hydrophobic interactions with the enzyme along with stable hydrogen bonding. The docking and molecular dynamics simulations predictions were further validated by molecular mechanics with generalized Born and surface area solvation (MM/GBSA) and Poisson Boltzmann surface area (MM/PBSA), and WaterSwap binding energies that validated strong binding of the compounds to the enzyme. The MM/GBSA binding free energy for Top-1 complex is -28.10 kcal/mol, Top-2 complex is -50.14 kcal/mol) and Control is -46.91 kcal/mol while MM/PBSA value for Top-1, Top-2 and Control is -23.38 kcal/mol, -35.29 kcal/mol and -38.20 kcal/mol, respectively. Computational pharmacokinetics support good druglike candidacy of the compounds with acceptable profile of pharmacokinetics and very little toxicity. All these findings support the notion that the compounds can be used in experiments to test their anti-cancer activities.
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Affiliation(s)
- Ziyad Tariq Muhseen
- School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China;
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710062, China
| | - Mustafa Hussein Ali
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
| | - Nawar Rushdi Jaber
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad 00964, Iraq;
| | - Dheyaa Shakir Mashrea
- Educational Directorate of Babylon Province, Ministry of Education, Babylon 51002, Iraq;
| | - Ali Mamoon Alfalki
- Department of Health Professional Graduate, University of New England, Biddeford, Portland, ME 04005, USA;
| | - Guanglin Li
- School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China;
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710062, China
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10
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Muneer I, Ahmad S, Naz A, Abbasi SW, Alblihy A, Aloliqi AA, Aba Alkhayl FF, Alrumaihi F, Ahmad S, El Bakri Y, Tahir Ul Qamar M. Discovery of Novel Inhibitors From Medicinal Plants for V-Domain Ig Suppressor of T-Cell Activation. Front Mol Biosci 2021; 8:716735. [PMID: 34765641 PMCID: PMC8576517 DOI: 10.3389/fmolb.2021.716735] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
V-domain Ig suppressor of T cell activation (VISTA) is an immune checkpoint and is a type I transmembrane protein. VISTA is linked to immunotherapy resistance, and it is a potential immune therapeutic target, especially for triple-negative breast cancer. It expresses at a high concentration in regulatory T cells and myeloid-derived suppressor cells, and its functional blockade is found to delay tumor growth. A useful medicinal plant database for drug designing (MPD3), which is a collection of phytochemicals from diverse plant families, was employed in virtual screening against VISTA to prioritize natural inhibitors against VISTA. Three compounds, Paratocarpin K (PubChem ID: 14187087), 3-(1H-Indol-3-yl)-2-(trimethylazaniumyl)propanoate (PubChem ID: 3861164), and 2-[(5-Benzyl-4-ethyl-1,2,4-triazol-3-yl)sulfanylmethyl]-5-methyl-1,3,4-oxadiazole (PubChem ID: 6494266), having binding energies stronger than -6 kcal/mol were found to have two common hydrogen bond interactions with VISTA active site residues: Arg54 and Arg127. The dynamics of the compound-VISTA complexes were further explored to infer binding stability of the systems. Results revealed that the compound 14187087 and 6494266 systems are highly stable with an average RMSD of 1.31 Å. Further affirmation on the results was achieved by running MM-GBSA on the MD simulation trajectories, which re-ranked 14187087 as the top-binder with a net binding energy value of -33.33 kcal/mol. In conclusion, the present study successfully predicted natural compounds that have the potential to block the function of VISTA and therefore can be utilized further in experimental studies to validate their real anti-VISTA activity.
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Affiliation(s)
- Iqra Muneer
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Adel Alblihy
- Medical Center, King Fahad Security College (KFSC), Riyadh, Saudi Arabia
| | - Abdulaziz A Aloliqi
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Sarfraz Ahmad
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
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11
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In Silico Core Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pyogenes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111355. [PMID: 34769873 PMCID: PMC8582943 DOI: 10.3390/ijerph182111355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 12/18/2022]
Abstract
Streptococcus pyogenes is a significant pathogen that causes skin and upper respiratory tract infections and non-suppurative complications, such as acute rheumatic fever and post-strep glomerulonephritis. Multidrug resistance has emerged in S. pyogenes strains, making them more dangerous and pathogenic. Hence, it is necessary to identify and develop therapeutic methods that would present novel approaches to S. pyogenes infections. In the current study, a subtractive proteomics approach was employed to core proteomes of four strains of S. pyogenes using several bioinformatic software tools and servers. The core proteome consists of 1324 proteins, and 302 essential proteins were predicted from them. These essential proteins were analyzed using BLASTp against human proteome, and the number of potential targets was reduced to 145. Based on subcellular localization prediction, 46 proteins with cytoplasmic localization were chosen for metabolic pathway analysis. Only two cytoplasmic proteins, i.e., chromosomal replication initiator protein DnaA and two-component response regulator (TCR), were discovered to have the potential to be novel drug target candidates. Three-dimensional (3D) structure prediction of target proteins was carried out via the Swiss Model server. Molecular docking approach was employed to screen the library of 1000 phytochemicals against the interacting residues of the target proteins through the MOE software. Further, the docking studies were validated by running molecular dynamics simulation and highly popular binding free energy approaches of MM-GBSA and MM-PBSA. The findings revealed a promising candidate as a novel target against S. pyogenes infections.
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12
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Alrumaihi F. A Comprehensive Computational Screening of Phytochemicals Derived from Saudi Medicinal Plants against Human CC Chemokine Receptor 7 to Identify Potential Anti-Cancer Therapeutics. Molecules 2021; 26:6354. [PMID: 34770763 PMCID: PMC8588288 DOI: 10.3390/molecules26216354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 01/03/2023] Open
Abstract
Homeostatic trafficking of immune cells by CC chemokine receptor 7 (CCR7) keeps immune responses and tolerance in a balance. The involvement of this protein in lymph node metastasis in cancer marks CCR7 as a penitential drug target. Using the crystal structure of CCR7, herein, a comprehensive virtual screening study is presented to filter novel strong CCR7 binding phytochemicals from Saudi medicinal plants that have a higher binding affinity for the intracellular allosteric binding pocket. By doing so, three small natural molecules named as Hit-1 (1,8,10-trihydroxy-3-methoxy-6-methylanthracen-9(4H)-one), Hit-2 (4-(3,4-dimethoxybenzyl)-3-(4-hydroxy-3-methoxybenzyl)dihydrofuran-2(3H)-one), and Hit-3 (10-methyl-12,13-dihydro-[1,2]dioxolo[3,4,5-de]furo[3,2-g]isochromeno[4,3-b]chromen-8-ol) are predicted showing strong binding potential for the CC chemokine receptor 7 allosteric pocket. During molecular dynamics simulations, the compounds were observed in the formation of several chemical bonding of short bond distances. Additionally, the molecules remained in strong contact with the active pocket residues and experienced small conformation changes that seemed to be mediated by the CCR7 loops to properly engage the ligands. Two types of binding energy methods (MM/GBPBSA and WaterSwap) were additionally applied to further validate docking and simulation findings. Both analyses complement the good affinity of compounds for CCR7, the electrostatic and van der Waals energies being the most dominant in intermolecular interactions. The active pocket residue's role in compounds binding was further evaluated via alanine scanning, which highlighted their importance in natural compounds binding. Additionally, the compounds fulfilled all drug-like rules: Lipinski, Ghose, Veber, Egan, and Muegge passed many safety parameters, making them excellent anti-cancer candidates for experimental testing.
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Affiliation(s)
- Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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13
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Suleman M, Tahir Ul Qamar M, Saleem S, Ahmad S, Ali SS, Khan H, Akbar F, Khan W, Alblihy A, Alrumaihi F, Waseem M, Allemailem KS. Mutational Landscape of Pirin and Elucidation of the Impact of Most Detrimental Missense Variants That Accelerate the Breast Cancer Pathways: A Computational Modelling Study. Front Mol Biosci 2021; 8:692835. [PMID: 34262943 PMCID: PMC8273169 DOI: 10.3389/fmolb.2021.692835] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022] Open
Abstract
Pirin (PIR) protein is highly conserved in both prokaryotic and eukaryotic organisms. Recently, it has been identified that PIR positively regulates breast cancer cell proliferation, xenograft tumor formation, and metastasis, through an enforced transition of G1/S phase of the cell cycle by upregulation of E2F1 expression at the transcriptional level. Keeping in view the importance of PIR in many crucial cellular processes in humans, we used a variety of computational tools to identify non-synonymous single-nucleotide polymorphisms (SNPs) in the PIR gene that are highly deleterious for the structure and function of PIR protein. Out of 173 SNPs identified in the protein, 119 are non-synonymous, and by consensus, 24 mutations were confirmed to be deleterious in nature. Mutations such as V257A, I28T, and I264S were unveiled as highly destabilizing due to a significant stability fold change on the protein structure. This observation was further established through molecular dynamics (MD) simulation that demonstrated the role of the mutation in protein structure destability and affecting its internal dynamics. The findings of this study are believed to open doors to investigate the biological relevance of the mutations and drugability potential of the protein.
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Affiliation(s)
- Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | | | - Shoaib Saleem
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Haji Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Fazal Akbar
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Wajid Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Adel Alblihy
- Medical Center, King Fahad Security College (KFSC), Riyadh, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad, Pakistan
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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14
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Chukwuemeka PO, Umar HI, Iwaloye O, Oretade OM, Olowosoke CB, Elabiyi MO, Igbe FO, Oretade OJ, Eigbe JO, Adeojo FJ. Targeting p53-MDM2 interactions to identify small molecule inhibitors for cancer therapy: beyond "Failure to rescue". J Biomol Struct Dyn 2021; 40:9158-9176. [PMID: 33988074 DOI: 10.1080/07391102.2021.1924267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
At present, disrupting p53-MDM2 interactions through small molecule ligands is a promising approach to safe treatment and management of human cancer. Tumor cells unlike the normal cells, are rapidly evolving affecting the efficacy of many approved anti-cancer agents due to drug resistance. Therefore, identifying a potential anticancer compound is crucial. Pharmacophore based virtual screening, followed by molecular docking, ADMET evaluation, and molecular dynamics studies against MDM2 protein was investigated to identify potential ligands that may act as inhibitors. The model (AHRR_1) with survival score (4.176) was selected among the top ranked generated Pharmacophore hypothesis. Validation of the model hypothesis by an external dataset of actives and inactive compounds produced significant validation attributes including; AUC = 0.85, BEDROC = 0.56 at α = 20.0, RIE = 8.18, AUAC = 0.88, and EF of 6.2 at the top 2% of the dataset. The model was use for screening the ZINC database, and the top 1375 hits satisfying the model hypothesis were subjected to molecular docking studies to understand the molecular and structural basis of selectivity of compounds for MDM2 protein. A sub-set of 25 compounds with binding energy lower than the reference inhibitors were evaluated for pharmacokinetic properties. Four compounds (ZINC02639178, ZINC06752762, ZINC38933175, and ZINC77969611) showed the most desired pharmacokinetic profile. Lastly, investigation of the dynamic behaviour of leads-protein complexes through MD simulation showed similar RMSD, RMSF, and H-bond occupancy profile compared to a reference inhibitor, suggesting stability throughout the simulation time. However, ZINC02639178 was found to satisfy the molecular enumeration the most compared to the other three leads. It may emerge as potential treatment option after extensive experimental studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prosper Obed Chukwuemeka
- Department of Biotechnology, School of Sciences (SOS), Federal University of Technology Akure, Akure, Nigeria
| | - Haruna Isiyaku Umar
- Department of Biochemistry, School of Sciences (SOS), Federal University of Technology Akure, Akure, Nigeria
| | - Opeyemi Iwaloye
- Bioinformatics and Molecular biology unit, Department of Biochemistry, School of Sciences (SOS), Federal University of Technology Akure, Akure, Nigeria
| | - Oluwaseyi Matthew Oretade
- Department of Biotechnology, School of Sciences (SOS), Federal University of Technology Akure, Akure, Nigeria
| | | | - Michael Omoniyi Elabiyi
- Department of Microbiology, School of Sciences (SOS), Federal University of Technology Akure, Akure, Nigeria
| | - Festus Omotere Igbe
- Department of Biochemistry, School of Sciences (SOS), Federal University of Technology Akure, Akure, Nigeria
| | - Oyeyemi Janet Oretade
- Department of Physiology, College of Health Science (CHS), Osun State University, Osogbo, Nigeria
| | - Joy Oseme Eigbe
- Department of Biomedical Technology, School of Health and Health Technology (SHHT), Federal University of Technology Akure, Akure, Nigeria
| | - Funmilayo Janet Adeojo
- Department of Biotechnology, School of Sciences (SOS), Federal University of Technology Akure, Akure, Nigeria
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15
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Muhseen ZT, Ahmad S, Li G. Structural basis of UDP-N-acetylglucosamine pyrophosphorylase and identification of promising terpenes to control Aedes aegypti. Colloids Surf B Biointerfaces 2021; 204:111820. [PMID: 33964525 DOI: 10.1016/j.colsurfb.2021.111820] [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: 04/06/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
According to the world health organization (WHO) 2020 report, vector borne diseases account for 17 % of all infections with reported 700 thousand death each year. They are of considerable importance to health professionals as they are posing a serious health threat and include dengue fever, Zika fever, chikungunya, yellow fever, and other disease agents. Aedes aegypti serve as a vector for transmitting several of these tropical fevers. In the present study, UDP-N-acetylglucosamine pyrophosphorylase enzyme (Aa-UAP) of A. aegypti which plays a significant contribution in chitin metabolism is targeted with natural terpenes to propose an eco-friendly and novel candidates for the development of new insecticides. The three dimensional Aa-UAP structure was constructed via a comparative homology approach and validated, followed by structure-based virtual screening against 1000 terpenes collected from natural MDP3 and NPACT databases. Top hits were subjected to molecular dynamics (MD) simulations and binding free energies analysis to elucidate complex intermolecular stability and affinity over simulated time. The results demonstrated that Aa-UAP possesses a homodimer state and its active site residues are well conserved. Three compounds (NPACT00138, NPACT00452, and NPACT00839) were prioritized as they are establishing conserved and stable interactions with the active binding-site residues of Aa-UAP. Conclusively, the reported Aa-UAP specific terpenes could serve as promising leads in order to develop potential insecticides. Importantly, the FDA approved drug NPACT00839 (Paclitaxel) could be used further in the fast-track experimental testing pipeline for biological optimization.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China; School of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China; School of Life Sciences, Shaanxi Normal University, Xi'an, China.
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16
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Muhseen ZT, Hameed AR, Al-Bhadly O, Ahmad S, Li G. Natural products for treatment of Plasmodium falciparum malaria: An integrated computational approach. Comput Biol Med 2021; 134:104415. [PMID: 33910128 DOI: 10.1016/j.compbiomed.2021.104415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022]
Abstract
Malaria is a life-threatening infectious disease with an estimated 229 million cases in the year 2019 worldwide. Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate reductoisomerase (PfDXR) is one of the key enzymes in the biosynthetic pathway of isoprenoid, (required for parasite growth and survival) and considered as an attractive target for designing anti-malarial drugs. Fosmidomycin is an effective DXR inhibitor and has been proven effective and safe against P. falciparum in clinical trials. However, due to low bioavailability and inappropriate drug attributes, it is not a preferred option. The present study was performed to identify PfDXR inhibitors with improved pharmacology/safety. For this purpose, an integrated computational framework, comprising of pharmacophore modeling, virtual screening, molecular docking, molecular dynamics (MD) simulation and MM/PBSA, was used. The binding free energy analysis was performed using a focused library of phytochemicals established from medicinal plants. The study identified four bioactive compounds namely, Myricetin 3-rhamnoside, 7-O-Galloyltricetiflavan, (25S)-5-beta-spirostan-3-beta-ol 3-O-beta-d-glucopyranosyl-(1->2)-beta-d-glucopyranoside, and Oleanolic acid 28-O-beta-d-glucopyranoside as potential inhibitors of PfDXR. The selection of these four compounds was based on pharmacophore mapping, docking score, binding stability, molecular interactions with the residues of PfDXR active site, binding stability and free energy estimation. In conclusion, medicinal plant-based scaffolds were predicted with enhanced efficacy and adequate physiochemical/pharmacokinetic profile that might be helpful in controlling malaria.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China; School of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Alaa R Hameed
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad, Iraq.
| | - Ola Al-Bhadly
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad, Iraq.
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China; School of Life Sciences, Shaanxi Normal University, Xi'an, China.
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17
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Zhao J, Blayney A, Liu X, Gandy L, Jin W, Yan L, Ha JH, Canning AJ, Connelly M, Yang C, Liu X, Xiao Y, Cosgrove MS, Solmaz SR, Zhang Y, Ban D, Chen J, Loh SN, Wang C. EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction. Nat Commun 2021; 12:986. [PMID: 33579943 PMCID: PMC7881117 DOI: 10.1038/s41467-021-21258-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/11/2021] [Indexed: 12/19/2022] Open
Abstract
Epigallocatechin gallate (EGCG) from green tea can induce apoptosis in cancerous cells, but the underlying molecular mechanisms remain poorly understood. Using SPR and NMR, here we report a direct, μM interaction between EGCG and the tumor suppressor p53 (KD = 1.6 ± 1.4 μM), with the disordered N-terminal domain (NTD) identified as the major binding site (KD = 4 ± 2 μM). Large scale atomistic simulations (>100 μs), SAXS and AUC demonstrate that EGCG-NTD interaction is dynamic and EGCG causes the emergence of a subpopulation of compact bound conformations. The EGCG-p53 interaction disrupts p53 interaction with its regulatory E3 ligase MDM2 and inhibits ubiquitination of p53 by MDM2 in an in vitro ubiquitination assay, likely stabilizing p53 for anti-tumor activity. Our work provides insights into the mechanisms for EGCG's anticancer activity and identifies p53 NTD as a target for cancer drug discovery through dynamic interactions with small molecules.
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Affiliation(s)
- Jing Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Alan Blayney
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Lauren Gandy
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Weihua Jin
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Lufeng Yan
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ashley J Canning
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Michael Connelly
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Chao Yang
- Department of Chemistry, New York University, New York, NY, USA
| | - Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Yuanyuan Xiao
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Sozanne R Solmaz
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
| | - David Ban
- Merck Research Laboratories, Mass Spectrometry and Biophysics, Kenilworth, NJ, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemistry and Chemical Biology, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
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18
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Muhseen ZT, Hameed AR, Al-Hasani HMH, Ahmad S, Li G. Computational Determination of Potential Multiprotein Targeting Natural Compounds for Rational Drug Design Against SARS-COV-2. Molecules 2021; 26:674. [PMID: 33525411 PMCID: PMC7865386 DOI: 10.3390/molecules26030674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/21/2022] Open
Abstract
SARS-CoV-2 caused the current COVID-19 pandemic and there is an urgent need to explore effective therapeutics that can inhibit enzymes that are imperative in virus reproduction. To this end, we computationally investigated the MPD3 phytochemical database along with the pool of reported natural antiviral compounds with potential to be used as anti-SARS-CoV-2. The docking results demonstrated glycyrrhizin followed by azadirachtanin, mycophenolic acid, kushenol-w and 6-azauridine, as potential candidates. Glycyrrhizin depicted very stable binding mode to the active pocket of the Mpro (binding energy, -8.7 kcal/mol), PLpro (binding energy, -7.9 kcal/mol), and Nucleocapsid (binding energy, -7.9 kcal/mol) enzymes. This compound showed binding with several key residues that are critical to natural substrate binding and functionality to all the receptors. To test docking prediction, the compound with each receptor was subjected to molecular dynamics simulation to characterize the molecule stability and decipher its possible mechanism of binding. Each complex concludes that the receptor dynamics are stable (Mpro (mean RMSD, 0.93 Å), PLpro (mean RMSD, 0.96 Å), and Nucleocapsid (mean RMSD, 3.48 Å)). Moreover, binding free energy analyses such as MMGB/PBSA and WaterSwap were run over selected trajectory snapshots to affirm intermolecular affinity in the complexes. Glycyrrhizin was rescored to form strong affinity complexes with the virus enzymes: Mpro (MMGBSA, -24.42 kcal/mol and MMPBSA, -10.80 kcal/mol), PLpro (MMGBSA, -48.69 kcal/mol and MMPBSA, -38.17 kcal/mol) and Nucleocapsid (MMGBSA, -30.05 kcal/mol and MMPBSA, -25.95 kcal/mol), were dominated mainly by vigorous van der Waals energy. Further affirmation was achieved by WaterSwap absolute binding free energy that concluded all the complexes in good equilibrium and stability (Mpro (mean, -22.44 kcal/mol), PLpro (mean, -25.46 kcal/mol), and Nucleocapsid (mean, -23.30 kcal/mol)). These promising findings substantially advance our understanding of how natural compounds could be shaped to counter SARS-CoV-2 infection.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an 710062, China
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Alaa R Hameed
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad 00964, Iraq
| | - Halah M H Al-Hasani
- Department of Biotechnology, College of Science, University of Diyala, Baqubah 32001, Iraq
| | - Sajjad Ahmad
- Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an 710062, China
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
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19
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Promising Terpenes as Natural Antagonists of Cancer: An In-Silico Approach. Molecules 2019; 25:molecules25010155. [PMID: 31906032 PMCID: PMC6983034 DOI: 10.3390/molecules25010155] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/13/2019] [Accepted: 12/19/2019] [Indexed: 01/10/2023] Open
Abstract
Overexpression of murine double minute 2 (MDM2) results in the inactivation of p53 and causes cancer which is a leading cause of death in recent era. In recent decades, much attention has been paid to discover potential inhibitors against MDM2 in order to cure cancer. Outcomes from studies proposes that the MDM2 is a hot target to screen potent antagonists. Thus, this study aims at discovering natural compounds using several computational approaches to inhibit the MDM2 and to eliminate p53-MDM2 interaction, which would result in the reactivation of p53 activity. A library of 500 terpenes was prepared and several virtual screening approaches were employed to find out the best hits which could serve as p53-MDM2 antagonists. On the basis of the designed protocol, three terpenes were selected. In the present study, for the stability and validation of selected three protein-ligand complexes 20 ns molecular dynamics simulations and principal component analyses (PCA) were performed. Results found that the selected terpenes hits (3-trans-p-coumaroyl maslinic acid, Silvestrol and Betulonic acid) are potential inhibitors of p53–MDM2 interaction and could serve as potent antagonists.
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