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Yakoubi S. Synergistic integration of deep learning with protein docking in cardiovascular disease treatment strategies. IUBMB Life 2024; 76:666-696. [PMID: 38748776 DOI: 10.1002/iub.2819] [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: 02/11/2024] [Accepted: 03/13/2024] [Indexed: 08/31/2024]
Abstract
This research delves into the exploration of the potential of tocopherol-based nanoemulsion as a therapeutic agent for cardiovascular diseases (CVD) through an in-depth molecular docking analysis. The study focuses on elucidating the molecular interactions between tocopherol and seven key proteins (1O8a, 4YAY, 4DLI, 1HW9, 2YCW, 1BO9 and 1CX2) that play pivotal roles in CVD development. Through rigorous in silico docking investigations, assessment was conducted on the binding affinities, inhibitory potentials and interaction patterns of tocopherol with these target proteins. The findings revealed significant interactions, particularly with 4YAY, displaying a robust binding energy of -6.39 kcal/mol and a promising Ki value of 20.84 μM. Notable interactions were also observed with 1HW9, 4DLI, 2YCW and 1CX2, further indicating tocopherol's potential therapeutic relevance. In contrast, no interaction was observed with 1BO9. Furthermore, an examination of the common residues of 4YAY bound to tocopherol was carried out, highlighting key intermolecular hydrophobic bonds that contribute to the interaction's stability. Tocopherol complies with pharmacokinetics (Lipinski's and Veber's) rules for oral bioavailability and proves safety non-toxic and non-carcinogenic. Thus, deep learning-based protein language models ESM1-b and ProtT5 were leveraged for input encodings to predict interaction sites between the 4YAY protein and tocopherol. Hence, highly accurate predictions of these critical protein-ligand interactions were achieved. This study not only advances the understanding of these interactions but also highlights deep learning's immense potential in molecular biology and drug discovery. It underscores tocopherol's promise as a cardiovascular disease management candidate, shedding light on its molecular interactions and compatibility with biomolecule-like characteristics.
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Affiliation(s)
- Sana Yakoubi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Alliance for Research on the Mediterranean North Africa (ARENA), University of Tsukuba, Ibaraki, Japan
- University of Tunis El Manar, Tunis, Tunisia
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Ali S, Ali U, Qamar A, Zafar I, Yaqoob M, Ain QU, Rashid S, Sharma R, Nafidi HA, Bin Jardan YA, Bourhia M. Predicting the effects of rare genetic variants on oncogenic signaling pathways: A computational analysis of HRAS protein function. Front Chem 2023; 11:1173624. [PMID: 37153521 PMCID: PMC10160440 DOI: 10.3389/fchem.2023.1173624] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
The HRAS gene plays a crucial role in regulating essential cellular processes for life, and this gene's misregulation is linked to the development of various types of cancers. Nonsynonymous single nucleotide polymorphisms (nsSNPs) within the coding region of HRAS can cause detrimental mutations that disrupt wild-type protein function. In the current investigation, we have employed in-silico methodologies to anticipate the consequences of infrequent genetic variations on the functional properties of the HRAS protein. We have discovered a total of 50 nsSNPs, of which 23 were located in the exon region of the HRAS gene and denoting that they were expected to cause harm or be deleterious. Out of these 23, 10 nsSNPs ([G60V], [G60D], [R123P], [D38H], [I46T], [G115R], [R123G], [P11OL], [A59L], and [G13R]) were identified as having the most delterious effect based on results of SIFT analysis and PolyPhen2 scores ranging from 0.53 to 69. The DDG values -3.21 kcal/mol to 0.87 kcal/mol represent the free energy change associated with protein stability upon mutation. Interestingly, we identified that the three mutations (Y4C, T58I, and Y12E) were found to improve the structural stability of the protein. We performed molecular dynamics (MD) simulations to investigate the structural and dynamic effects of HRAS mutations. Our results showed that the stable model of HRAS had a significantly lower energy value of -18756 kj/mol compared to the initial model of -108915 kj/mol. The RMSD value for the wild-type complex was 4.40 Å, and the binding energies for the G60V, G60D, and D38H mutants were -107.09 kcal/mol, -109.42 kcal/mol, and -107.18 kcal/mol, respectively as compared to wild-type HRAS protein had -105.85 kcal/mol. The result of our investigation presents convincing corroboration for the potential functional significance of nsSNPs in augmenting HRAS expression and adding to the activation of malignant oncogenic signalling pathways.
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Affiliation(s)
- Sadaqat Ali
- Medical Department, DHQ Hospital Bhawalnagr, Punjab, Pakistan
| | | | - Adeem Qamar
- Department of Pathology, Sahiwal Medical College Sahiwal, Punjab, Pakistan
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Punjab, Pakistan
| | - Muhammad Yaqoob
- Department of Life Sciences, ARID University-Barani Institute of Sciences Burewala Campus, Punjab, Pakistan
| | - Qurat ul Ain
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Summya Rashid
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Punjab, Pakistan
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- *Correspondence: Mohammed Bourhia, ; Rohit Sharma,
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Yousef A. Bin Jardan
- 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, Agadir, Morocco
- *Correspondence: Mohammed Bourhia, ; Rohit Sharma,
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Jovanović JĐ, Antonijević M, Vojinović R, Filipović ND, Marković Z. In silico study of inhibitory capacity of sacubitril/valsartan toward neprilysin and angiotensin receptor. RSC Adv 2022; 12:29719-29726. [PMID: 36321085 PMCID: PMC9575392 DOI: 10.1039/d2ra04226f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023] Open
Abstract
Heart failure (HF) is a life-threatening condition that occurs when the heart cannot pump enough blood and oxygen to meet the body's needs. It affects mostly the elderly, commonly from the male population, especially those with obesity, diabetes, or some other chronic condition. It can be treated with different medications, and promising results were shown by a relatively new medicament called Entresto. Results obtained from molecular docking and molecular dynamics simulations to examine the inhibitory capacity of Entresto are presented in this study. Parameters obtained by the molecular docking simulations show that both parts of Entresto (sacubitril (SAC) and valsartan (VAL)) interact with targeted proteins, and inhibit their physiological function. Simulations of molecular dynamics revealed some interesting inhibitory patterns. SAC was discovered to produce structural alterations in neprilysin by binding to it, reducing neprilysin's physiological activity. In addition to blocking the active site, SAC binding causes the enzyme's structure to become less compact over time, causing changes in its biochemical characteristics and preventing the enzyme from performing its biological function. Similar to SAC, VAL also causes deviations in the structure of angiotensin receptors. The angiotensin receptor GPCR (G-protein-coupled receptors) is immersed in the lipid bilayer, and changes in the tertiary structure are only visible through RMSD and RMSF, not by examining R g. In this regard, MD simulations validated the results of molecular docking simulations, demonstrating that both SAC and VAL had inhibitory potential towards the neprilysin and angiotensin receptors, respectively.
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Affiliation(s)
- Jelena Đorović Jovanović
- Department of Science, Institute for Information Technologies, University of Kragujevac Jovana Cvijića bb 34000 Kragujevac Republic of Serbia
| | - Marko Antonijević
- Department of Science, Institute for Information Technologies, University of Kragujevac Jovana Cvijića bb 34000 Kragujevac Republic of Serbia
| | - Radiša Vojinović
- Faculty of Medical Sciences, University of Kragujevac Svetozara Markovića 69 34000 Kragujevc Republic of Serbia
| | - Nenad D Filipović
- Faculty of Engineering, University of Kragujevac Sestre Janjić 6 34000 Kragujevac Republic of Serbia
| | - Zoran Marković
- Department of Science, Institute for Information Technologies, University of Kragujevac Jovana Cvijića bb 34000 Kragujevac Republic of Serbia
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Goyzueta-Mamani LD, Barazorda-Ccahuana HL, Chávez-Fumagalli MA, F. Alvarez KL, Aguilar-Pineda JA, Vera-Lopez KJ, Lino Cardenas CL. In Silico Analysis of Metabolites from Peruvian Native Plants as Potential Therapeutics against Alzheimer's Disease. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030918. [PMID: 35164183 PMCID: PMC8838509 DOI: 10.3390/molecules27030918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/19/2022]
Abstract
Background: Despite research on the molecular bases of Alzheimer’s disease (AD), effective therapies against its progression are still needed. Recent studies have shown direct links between AD progression and neurovascular dysfunction, highlighting it as a potential target for new therapeutics development. In this work, we screened and evaluated the inhibitory effect of natural compounds from native Peruvian plants against tau protein, amyloid beta, and angiotensin II type 1 receptor (AT1R) pathologic AD markers. Methods: We applied in silico analysis, such as virtual screening, molecular docking, molecular dynamics simulation (MD), and MM/GBSA estimation, to identify metabolites from Peruvian plants with inhibitory properties, and compared them to nicotinamide, telmisartan, and grapeseed extract drugs in clinical trials. Results: Our results demonstrated the increased bioactivity of three plants’ metabolites against tau protein, amyloid beta, and AT1R. The MD simulations indicated the stability of the AT1R:floribundic acid, amyloid beta:rutin, and tau:brassicasterol systems. A polypharmaceutical potential was observed for rutin due to its high affinity to AT1R, amyloid beta, and tau. The metabolite floribundic acid showed bioactivity against the AT1R and tau, and the metabolite brassicasterol showed bioactivity against the amyloid beta and tau. Conclusions: This study has identified molecules from native Peruvian plants that have the potential to bind three pathologic markers of AD.
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Affiliation(s)
- Luis Daniel Goyzueta-Mamani
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
- Correspondence: (L.D.G.-M.); (C.L.L.C.)
| | - Haruna Luz Barazorda-Ccahuana
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru;
| | - Miguel Angel Chávez-Fumagalli
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
| | - Karla Lucia F. Alvarez
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
| | - Jorge Alberto Aguilar-Pineda
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
| | - Karin Jannet Vera-Lopez
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
| | - Christian Lacks Lino Cardenas
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Correspondence: (L.D.G.-M.); (C.L.L.C.)
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Design, Synthesis, and In Vitro Evaluation of Novel Indolyl DiHydropyrazole Derivatives as Potential Anticancer Agents. Molecules 2021; 26:molecules26175235. [PMID: 34500672 PMCID: PMC8434462 DOI: 10.3390/molecules26175235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Indoles derived from both natural sources or artificial synthetic methods have been known to interact with aryl hydrocarbon receptors (AhR), and exhibit anticancer activity. In light of these attractive properties, a series of hybrid molecules with structural features of indoles, i.e., those bearing a pyrazoline nucleus, were evaluated for their enhanced anticancer activity. The designed molecules were subjected to molecular docking in order to screen for potential AhR interacting compounds, and the identified indolyl dihydropyrazole derivatives were synthesized. The synthesized compounds were characterized, and their cytotoxicity was evaluated against four human cancer cell lines using the MTT assay. Based on the Glide g-score, H-bonding interactions and bonding energy of 20 candidate molecules were selected for further analysis from the 64 initially designed molecules. These candidate molecules have shown promising anti-proliferative activity against the cell lines tested. Among these candidate molecules, the compounds with hydroxy phenyl substitution on the pyrazoline ring have shown potent activity across all the tested cell lines. The designed scaffold was proven effective for screening potential candidate molecules with anticancer properties, and may be further optimized structurally for yielding the ideal anti-tumorigenic compound for the treatment of various cancers.
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A.S. Murad H, S. Al-Kayy S, A. Alkaabi T. Are the Newest Angiotensin Receptor Blockers Preferred than the Old Members in COVID-19 Patients with Cardiovascular Comorbidity? INT J PHARMACOL 2021. [DOI: 10.3923/ijp.2021.435.441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Mittal L, Kumari A, Srivastava M, Singh M, Asthana S. Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. J Biomol Struct Dyn 2021; 39:3662-3680. [PMID: 32396769 PMCID: PMC7256355 DOI: 10.1080/07391102.2020.1768151] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/07/2020] [Indexed: 12/23/2022]
Abstract
The pandemic caused by novel coronavirus disease 2019 (COVID-19) infecting millions of populations worldwide and counting, has demanded quick and potential therapeutic strategies. Current approved drugs or molecules under clinical trials can be a good pool for repurposing through in-silico techniques to quickly identify promising drug candidates. The structural information of recently released crystal structures of main protease (Mpro) in APO and complex with inhibitors, N3, and 13b molecules was utilized to explore the binding site architecture through Molecular dynamics (MD) simulations. The stable state of Mpro was used to conduct extensive virtual screening of the aforementioned drug pool. Considering the recent success of HIV protease molecules, we also used anti-protease molecules for drug repurposing purposes. The identified top hits were further evaluated through MD simulations followed by the binding free energy calculations using MM-GBSA. Interestingly, in our screening, several promising drugs stand out as potential inhibitors of Mpro. However, based on control (N3 and 13b), we have identified six potential molecules, Leupeptin Hemisulphate, Pepstatin A, Nelfinavir, Birinapant, Lypression and Octreotide which have shown the reasonably significant MM-GBSA score. Further insight shows that the molecules form stable interactions with hot-spot residues, that are mainly conserved and can be targeted for structure- and pharmacophore-based designing. The pharmacokinetic annotations and therapeutic importance have suggested that these molecules possess drug-like properties and pave their way for in-vitro studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster 3rd Milestone, Faridabad, Haryana, India
| | - Anita Kumari
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster 3rd Milestone, Faridabad, Haryana, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster 3rd Milestone, Faridabad, Haryana, India
| | - Mrityunjay Singh
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster 3rd Milestone, Faridabad, Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster 3rd Milestone, Faridabad, Haryana, India
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Mannino G, Iovino P, Lauria A, Genova T, Asteggiano A, Notarbartolo M, Porcu A, Serio G, Chinigò G, Occhipinti A, Capuzzo A, Medana C, Munaron L, Gentile C. Bioactive Triterpenes of Protium heptaphyllum Gum Resin Extract Display Cholesterol-Lowering Potential. Int J Mol Sci 2021; 22:ijms22052664. [PMID: 33800828 PMCID: PMC7961947 DOI: 10.3390/ijms22052664] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
Hypercholesterolemia is one of the major causes of cardiovascular disease, the risk of which is further increased if other forms of dyslipidemia occur. Current therapeutic strategies include changes in lifestyle coupled with drug administration. Statins represent the most common therapeutic approach, but they may be insufficient due to the onset of resistance mechanisms and side effects. Consequently, patients with mild hypercholesterolemia prefer the use of food supplements since these are perceived to be safer. Here, we investigate the phytochemical profile and cholesterol-lowering potential of Protium heptaphyllum gum resin extract (PHE). Chemical characterization via HPLC-APCI-HRMS2 and GC-FID/MS identified 13 compounds mainly belonging to ursane, oleanane, and tirucallane groups. Studies on human hepatocytes have revealed how PHE is able to reduce cholesterol production and regulate the expression of proteins involved in its metabolism. (HMGCR, PCSK9, LDLR, FXR, IDOL, and PPAR). Moreover, measuring the inhibitory activity of PHE against HMGR, moderate inhibition was recorded. Finally, molecular docking studies identified acidic tetra- and pentacyclic triterpenoids as the main compounds responsible for this action. In conclusion, our study demonstrates how PHE may be a useful alternative to contrast hypercholesterolemia, highlighting its potential as a sustainable multitarget natural extract for the nutraceutical industry that is rapidly gaining acceptance as a source of health-promoting compounds.
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Affiliation(s)
- Giuseppe Mannino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
| | - Piera Iovino
- Biosfered S.R.L., 10148 Turin, Italy; (P.I.); (A.A.)
| | - Antonino Lauria
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
| | - Tullio Genova
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (T.G.); (G.C.); (L.M.)
| | - Alberto Asteggiano
- Biosfered S.R.L., 10148 Turin, Italy; (P.I.); (A.A.)
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10125 Torino, Italy (C.M.)
| | - Monica Notarbartolo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
| | - Alessandra Porcu
- Abel Nutraceuticals S.R.L., 10148 Turin, Italy; (A.P.); (A.O.); (A.C.)
| | - Graziella Serio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
| | - Giorgia Chinigò
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (T.G.); (G.C.); (L.M.)
| | - Andrea Occhipinti
- Abel Nutraceuticals S.R.L., 10148 Turin, Italy; (A.P.); (A.O.); (A.C.)
| | - Andrea Capuzzo
- Abel Nutraceuticals S.R.L., 10148 Turin, Italy; (A.P.); (A.O.); (A.C.)
| | - Claudio Medana
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10125 Torino, Italy (C.M.)
| | - Luca Munaron
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (T.G.); (G.C.); (L.M.)
| | - Carla Gentile
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
- Correspondence: ; Tel.: +39-091-2388-6472
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Targeting the Autophagy Specific Lipid Kinase VPS34 for Cancer Treatment: An Integrative Repurposing Strategy. Protein J 2021; 40:41-53. [PMID: 33400087 DOI: 10.1007/s10930-020-09955-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The impact of autophagy on cancer treatment and its corresponding responsiveness has galvanized the scientific community to develop novel inhibitors for cancer treatment. Importantly, the discovery of inhibitors that targets the early phase of autophagy was identified as a beneficial choice. Despite the number of research in recent years, screening of the DrugBank repository (9591 molecules) for the Vacuolar protein sorting 34 (VPS34) has not been reported earlier. Therefore, the present study was designed to identify potential VPS34 antagonists using integrated pharmacophore strategies. Primarily, an energy-based pharmacophore and receptor cavity-based analysis yielded five (DHRRR) and seven featured (AADDHRR) pharmacophore hypotheses respectively, which were utilized for the database screening process. The glide score, the binding free energy, pharmacokinetics and pharmacodynamics properties were examined to narrow down the screened compounds. This analysis yielded a hit molecule, DB03916 that exhibited a better docking score, higher binding affinity and better drug-like properties in contrast to the reference compound that suffers from a toxicity property. Importantly, the result was validated using a 50 ns molecular dynamics simulation study. Overall, we conclude that the identified hit molecule DB03916 is believed to serve as a prospective antagonist against VPS34 for cancer treatment.
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Esmaile SC, Bezerra KS, de Oliveira Campos DM, da Silva MK, Neto JXL, Manzoni V, Fulco UL, Oliveira JIN. Quantum binding energy features of the drug olmesartan bound to angiotensin type-1 receptors in the therapeutics of stroke. NEW J CHEM 2021. [DOI: 10.1039/d1nj03975j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the binding energies of 105 residues within a 10 Å pocket radius, predicted the energetic relevance of olmesartan regions, and the influence of individual protein segments on OLM -AT1 binding.
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Affiliation(s)
- Stephany Campanelli Esmaile
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - Katyanna Sales Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | | | - Maria Karolaynne da Silva
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - José Xavier Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - Vinicius Manzoni
- Instituto de Física, Universidade Federal de Alagoas, 57072-970, Maceio, AL, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - Jonas Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
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Rosário-Ferreira N, Marques-Pereira C, Gouveia RP, Mourão J, Moreira IS. Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View. Methods Mol Biol 2021; 2315:3-28. [PMID: 34302667 DOI: 10.1007/978-1-0716-1468-6_1] [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: 01/06/2023]
Abstract
Membrane proteins (MPs) encompass a large family of proteins with distinct cellular functions, and although representing over 50% of existing pharmaceutical drug targets, their structural and functional information is still very scarce. Over the last years, in silico analysis and algorithm development were essential to characterize MPs and overcome some limitations of experimental approaches. The optimization and improvement of these methods remain an ongoing process, with key advances in MPs' structure, folding, and interface prediction being continuously tackled. Herein, we discuss the latest trends in computational methods toward a deeper understanding of the atomistic and mechanistic details of MPs.
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Affiliation(s)
- Nícia Rosário-Ferreira
- Coimbra Chemistry Center, Department of Chemistry, University of Coimbra, Coimbra, Portugal.,Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Catarina Marques-Pereira
- Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Raquel P Gouveia
- Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Joana Mourão
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Irina S Moreira
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
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Saranyadevi S, Shanthi V. Molecular simulation strategies for the discovery of selective inhibitors of β-catenin. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tumor dissemination and relapse in lung cancer were found to be due to the existence of cancer stem cells. In particular, the [Formula: see text]-catenin pathway is found to be one of the crucial pathways in maintaining the stem-like properties of the cells. Thus, targeting the [Formula: see text]-catenin family of proteins is a significant therapeutic route in the treatment of lung cancer. Therefore, in the present study, a pharmacophore-based drug repurposing approach was accomplished to pinpoint potent [Formula: see text]-catenin inhibitors from the DrugBank database. Primarily, ligand-based pharmacophore hypothesis (AAHHR) was generated using existing [Formula: see text]-catenin inhibitors available in the literature and utilized for library screening. Subsequently, the inhibitory activity of the screened compounds was examined by the hierarchical docking process and the Prime MM-GBSA algorithm. Moreover, quantum chemical calculations and molecular dynamics simulations were executed to analyze the inhibitory effects of the screened hit molecule. The results indicate that hit molecule, DB08047 was found to possess better binding free energy, favorable ligand strain energy, satisfactory pharmacokinetic properties and superior free energy landscape profile. Eventually, the pIC[Formula: see text] values of the lead compounds were predicted by the AutoQSAR algorithm. It is noteworthy to mention that DB08047 was found to possess pyrazole scaffolds which could downregulate [Formula: see text]-catenin pathway and thus facilitate the controlled cell growth/inhibit tumor growth.
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Affiliation(s)
- S. Saranyadevi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - V. Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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Takezako T, Unal H, Karnik SS, Node K. The non-biphenyl-tetrazole angiotensin AT 1 receptor antagonist eprosartan is a unique and robust inverse agonist of the active state of the AT 1 receptor. Br J Pharmacol 2018; 175:2454-2469. [PMID: 29570771 PMCID: PMC5980637 DOI: 10.1111/bph.14213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/26/2018] [Accepted: 03/06/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND AND PURPOSE Conditions such as hypertension and renal allograft rejection are accompanied by chronic, agonist-independent, signalling by angiotensin II AT1 receptors. The current treatment paradigm for these diseases entails the preferred use of inverse agonist AT1 receptor blockers (ARBs). However, variability in the inverse agonist activities of common biphenyl-tetrazole ARBs for the active state of AT1 receptors often leads to treatment failure. Therefore, characterization of robust inverse agonist ARBs for the active state of AT1 receptors is necessary. EXPERIMENTAL APPROACH To identify the robust inverse agonist for active state of AT1 receptors and its molecular mechanism, we performed site-directed mutagenesis, competition binding assay, inositol phosphate production assay and molecular modelling for both ground-state wild-type AT1 receptors and active-state N111G mutant AT1 receptors. KEY RESULTS Although candesartan and telmisartan exhibited weaker inverse agonist activity for N111G- compared with WT-AT1 receptors, only eprosartan exhibited robust inverse agonist activity for both N111G- and WT- AT1 receptors. Specific ligand-receptor contacts for candesartan and telmisartan are altered in the active-state N111G- AT1 receptors compared with the ground-state WT-AT1 receptors, suggesting an explanation of their attenuated inverse agonist activity for the active state of AT1 receptors. In contrast, interactions between eprosartan and N111G-AT1 receptors were not significantly altered, and the inverse agonist activity of eprosartan was robust. CONCLUSIONS AND IMPLICATIONS Eprosartan may be a better therapeutic option than other ARBs. Comparative studies investigating eprosartan and other ARBs for the treatment of diseases caused by chronic, agonist-independent, AT1 receptor activation are warranted.
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Affiliation(s)
- Takanobu Takezako
- Department of Advanced Heart ResearchSaga UniversitySagaJapan
- Department of Internal MedicineNadeshiko Lady's HospitalKobeJapan
| | - Hamiyet Unal
- Department of Molecular Cardiology, Lerner Research InstituteCleveland Clinic FoundationClevelandOHUSA
| | - Sadashiva S Karnik
- Department of Molecular Cardiology, Lerner Research InstituteCleveland Clinic FoundationClevelandOHUSA
| | - Koichi Node
- Department of Cardiovascular MedicineSaga UniversitySagaJapan
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Publisher's note. J Mol Graph Model 2017; 77:240-249. [DOI: 10.1016/j.jmgm.2017.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/17/2022]
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15
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Moschonas IC, Kellici TF, Mavromoustakos T, Stathopoulos P, Tsikaris V, Magafa V, Tzakos AG, Tselepis AD. Molecular requirements involving the human platelet protease-activated receptor-4 mechanism of activation by peptide analogues of its tethered-ligand. Platelets 2017; 28:812-821. [DOI: 10.1080/09537104.2017.1282607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- I. C. Moschonas
- Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - T. F. Kellici
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece
| | - T. Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece
- Department of Chemistry, York College and the Graduate Center of the City University of New York, Jamaica, NY, USA
| | - P. Stathopoulos
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - V. Tsikaris
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - V. Magafa
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, University of Patras, Patras, Greece
| | - A. G. Tzakos
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - A. D. Tselepis
- Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
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