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Mohammadi Y, Emadi R, Maddahi A, Shirdel S, Morowvat MH. Identifying potential Alzheimer's disease therapeutics through GSK-3β inhibition: A molecular docking and dynamics approach. Comput Biol Chem 2024; 111:108095. [PMID: 38805865 DOI: 10.1016/j.compbiolchem.2024.108095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
Abstract
Emerging as a promising drug target for Alzheimer's disease (AD) therapy, glycogen synthase kinase 3β (GSK-3β) has garnered attention. This study sought to rigorously scrutinize a compendium of natural compounds retrieved from the ZINC database through pharmacodynamic experiments, employing a 1 H-indazole-3-carboxamide (INDZ) scaffold, to identify compounds capable of inhibiting the GSK-3β protein. Utilizing a multi-step approach, the study involved pharmacophore analysis, followed by molecular docking to select five promising ligands for further investigation. Subsequently, ESMACS simulations were employed to assess the stability of the ligand-protein interactions. Evaluation of the binding modes and free energy of the ligands revealed that five compounds (2a-6a) exhibited crucial interactions with the active site residues. Furthermore, various methodologies, including hydrogen bond and clustering analyses, were utilized to ascertain their inhibitory potential and elucidate the factors contributing to ligand binding in the protein's active site. The findings from MMPBSA/GBSA analysis indicated that these five selected small molecules closely approached the IC50 value of the reference ligand (OH8), yielding energy values of -34.85, -32.58, -31.71, and -30.39 kcal/mol, respectively. Additionally, an assessment of the interactions using hydrogen bond and dynamic analyses delineated the effective binding of the ligands with the binding pockets in the protein. Through computational analysis, we obtained valuable insights into the molecular mechanisms of GSK-3β, aiding in the development of more potent inhibitors.
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Affiliation(s)
- Yasaman Mohammadi
- Faculty of Dentistry, Islamic Azad University, Shiraz Branch, Shiraz, Iran
| | - Reza Emadi
- Department of Biochemistry, Institute of Biochemistry & Biophsysics (IBB), University of Tehran, Tehran, Iran
| | - Arman Maddahi
- Department of Microbiology, Islamic Azad University, Shiraz Branch, Shiraz, Iran
| | - Shiva Shirdel
- Department of Psychology, Faculty of Education and Psychology, University of Tabriz, Tabriz, Iran
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Turkistani A, Al-Kuraishy HM, Al-Gareeb AI, Albuhadily AK, Alexiou A, Papadakis M, Elfiky MM, Saad HM, Batiha GES. Therapeutic Potential Effect of Glycogen Synthase Kinase 3 Beta (GSK-3β) Inhibitors in Parkinson Disease: Exploring an Overlooked Avenue. Mol Neurobiol 2024:10.1007/s12035-024-04003-z. [PMID: 38367137 DOI: 10.1007/s12035-024-04003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/20/2024] [Indexed: 02/19/2024]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease of the brain due to degeneration of dopaminergic neurons in the substantia nigra (SN). Glycogen synthase kinase 3 beta (GSK-3β) is implicated in the pathogenesis of PD. Therefore, the purpose of the present review was to revise the mechanistic role of GSK-3β in PD neuropathology, and how GSK-3β inhibitors affect PD neuropathology. GSK-3 is a conserved threonine/serine kinase protein that is intricate in the regulation of cellular anabolic and catabolic pathways by modulating glycogen synthase. Over-expression of GSK-3β is also interconnected with the development of different neurodegenerative diseases. However, the underlying mechanism of GSK-3β in PD neuropathology is not fully clarified. Over-expression of GSK-3β induces the development of PD by triggering mitochondrial dysfunction and oxidative stress in the dopaminergic neurons of the SN. NF-κB and NLRP3 inflammasome are activated in response to dysregulated GSK-3β in PD leading to progressive neuronal injury. Higher expression of GSK-3β in the early stages of PD neuropathology might contribute to the reduction of neuroprotective brain-derived neurotrophic factor (BDNF). Thus, GSK-3β inhibitors may be effective in PD by reducing inflammatory and oxidative stress disorders which are associated with degeneration of dopaminergic in the SN.
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Affiliation(s)
- Areej Turkistani
- Department of Pharmacology and Toxicology, College of Medicine, Taif University, 21944, Taif, Saudi Arabia
| | - Hayder M Al-Kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, Mustansiriyah University, P.O. Box 14132, Baghdad, Iraq
| | - Ali I Al-Gareeb
- Department of Clinical Pharmacology and Medicine, College of Medicine, Mustansiriyah University, P.O. Box 14132, Baghdad, Iraq
| | - Ali K Albuhadily
- Department of Clinical Pharmacology and Medicine, College of Medicine, Mustansiriyah University, P.O. Box 14132, Baghdad, Iraq
| | - Athanasios Alexiou
- University Centre for Research & Development, Chandigarh University, Chandigarh-Ludhiana Highway, Mohali, Punjab, India
- Department of Research & Development, Funogen, Athens, Greece
- Department of Research & Development, AFNP Med, 1030, Vienna, Austria
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, 2770, Australia
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten-Herdecke, Heusnerstrasse 40, University of Witten-Herdecke, 42283, Wuppertal, Germany.
| | - Mohamed M Elfiky
- Anatomy Department, General Medicine Practice Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Anatomy Department, Faculty of Medicine, Menoufia University, Shibin El Kom, Al Minufya, Egypt
| | - Hebatallah M Saad
- Department of Pathology, Faculty of Veterinary Medicine, Matrouh University, Matrouh, 51744, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
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Cheng Z, Han T, Yao J, Wang K, Dong X, Yu F, Huang H, Han M, Liao Q, He S, Lyu W, Li Q. Targeting glycogen synthase kinase-3β for Alzheimer's disease: Recent advances and future Prospects. Eur J Med Chem 2024; 265:116065. [PMID: 38160617 DOI: 10.1016/j.ejmech.2023.116065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
Senile plaques induced by β-amyloid (Aβ) abnormal aggregation and neurofibrillary tangles (NFT) caused by tau hyperphosphorylation are important pathological manifestations of Alzheimer's disease (AD). Glycogen synthase kinase-3 (GSK-3) is a conserved kinase; one member GSK-3β is highly expressed in the AD brain and involved in the formation of NFT. Hence, pharmacologically inhibiting GSK-3β activity and expression is a good approach to treat AD. As summarized in this article, multiple GSK-3β inhibitors has been comprehensively summarized over recent five years. However, only lithium carbonate and Tideglusib have been studied in clinical trials of AD. Besides ATP-competitive and non-ATP-competitive inhibitors, peptide inhibitors, allosteric inhibitors and other types of inhibitors have gradually attracted more interest. Moreover, considering the close relationship between GSK-3β and other targets involved in cholinergic hypothesis, Aβ aggregation hypothesis, tau hyperphosphorylation hypothesis, oxidative stress hypothesis, neuro-inflammation hypothesis, etc., diverse multifunctional molecules and multi-target directed ligands (MTDLs) have also been disclosed. We hope that these recent advances and critical perspectives will facilitate the discovery of safe and effective GSK-3β inhibitors for AD treatment.
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Affiliation(s)
- Zimeng Cheng
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Tianyue Han
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Jingtong Yao
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Kaixuan Wang
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Xue Dong
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Fan Yu
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - He Huang
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Menglin Han
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China
| | - Qinghong Liao
- Shandong Kangqiao Biotechnology Co., Ltd, Qingdao, 266033, Shandong, People's Republic of China
| | - Siyu He
- Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Weiping Lyu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, People's Republic of China
| | - Qi Li
- Department of Medical Pharmacy, School of Basic Medicine, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China.
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Sai Varshini M, Reddy RA, Krishnamurthy PT, Selvaraj D. Rational Design of Dual Inhibitors for Alzheimer's Disease: Insights from Computational Screening of BACE1 and GSK-3β. Curr Comput Aided Drug Des 2024; 20:998-1012. [PMID: 37921183 DOI: 10.2174/0115734099270256231018072007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is one of the most concerned neurodegenerative disorders across the world characterized by amyloid-beta (Aβ) plaques and neurofibrillary tangles (NFTs), leading to cognitive decline and memory loss. Targeting key pathways involved in AD like Aβ and NFT pathways, are crucial for the development of effective therapeutic strategies. In this study, we aimed to identify and establish promising dual inhibitors targeting BACE1 and GSK-3β, two proteins implicated in Aβ and NFT formation respectively. METHODS We have used molecular docking, ADME property analysis, and MMGBSA calculations for the identification of hit molecules and further evaluation of binding affinity, drug-like properties, and stability against BACE1 and GSK-3β. RESULTS Our results demonstrated strong binding affinities of ZINC000034853956 towards the active sites of both proteins, with favorable interactions involving key residues crucial for inhibitory activity. Additionally, ZINC000034853956 exhibited favorable drug-like properties. MD simulations revealed the stable binding of ZINC000034853956 to both BACE1 and GSK-3β over a 50 ns period, with consistent ligand-protein interactions, such as hydrogen bonding and hydrophobic contacts. These findings highlight the potential of ZINC000034853956 as a promising candidate for AD treatment, acting as a dual inhibitor targeting both BACE1 and GSK-3β. Overall, our study provides valuable insights into the potential of ZINC000034853956 as a dual inhibitor for AD. The strong binding affinity, favorable drug-like properties, and stability observed in MD simulations support its suitability for further optimization and preclinical studies. CONCLUSION Further investigations are warranted to elucidate the precise molecular mechanisms and therapeutic benefits of ZINC000034853956. Our findings offer hope for the development of novel therapeutic interventions targeting crucial pathways involved in AD neurodegeneration.
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Affiliation(s)
- Magham Sai Varshini
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, 643001, TN, India
| | - Ramakkamma Aishwarya Reddy
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, 643001, TN, India
| | | | - Divakar Selvaraj
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, 643001, TN, India
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Kaur A, Goyal B. In silico design and identification of new peptides for mitigating hIAPP aggregation in type 2 diabetes. J Biomol Struct Dyn 2023:1-16. [PMID: 37691445 DOI: 10.1080/07391102.2023.2254411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023]
Abstract
The aberrant misfolding and self-aggregation of human islet amyloid polypeptide (hIAPP or amylin) into cytotoxic aggregates are implicated in the pathogenesis of type 2 diabetes (T2D). Among various inhibitors, short peptides derived from the amyloidogenic regions of hIAPP have been employed as hIAPP aggregation inhibitors due to their low immunogenicity, biocompatibility, and high chemical diversity. Recently, hIAPP fragment HSSNN18-22 was identified as an amyloidogenic sequence and displayed higher antiproliferative activity to RIN-5F cells. Various hIAPP aggregation inhibitors have been designed by chemical modifications of the highly amyloidogenic sequence (NFGAIL) of hIAPP. In this work, a library of pentapeptides based on fragment HSSNN18-22 was designed and assessed for their efficacy in blocking hIAPP aggregation using an integrated computational screening approach. The binding free energy calculations by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method identified HSSQN and HSSNQ that bind to hIAPP monomer with a binding affinity of -21.25 ± 4.90 and -19.73 ± 3.10 kcal/mol, respectively, which is notably higher as compared to HSSNN (-11.90 ± 4.12 kcal/mol). The sampling of the non aggregation-prone helical conformation was notably increased from 23.5 ± 3.0 in the hIAPP monomer to 38.1 ± 3.6, and 33.8 ± 3.0% on the incorporation of HSSQN, and HSSNQ, respectively, which indicate reduced aggregation propensity of hIAPP monomer. The pentapeptides, HSSQN and HSSNQ, identified as hIAPP aggregation inhibitors in this work can be further conjugated with various metal chelating peptides to yield more efficacious and clinically relevant multifunctional modulators for targeting various pathological hallmarks of T2D.
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Affiliation(s)
- Apneet Kaur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, India
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Kaur R, Narang SS, Singh P, Goyal B. Structural and molecular insights into tacrine-benzofuran hybrid induced inhibition of amyloid-β peptide aggregation and BACE1 activity. J Biomol Struct Dyn 2023; 41:13211-13227. [PMID: 37013977 DOI: 10.1080/07391102.2023.2191722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/16/2023] [Indexed: 04/05/2023]
Abstract
Amyloid-β (Aβ) aggregation and β-amyloid precursor protein cleaving enzyme 1 (BACE1) are the potential therapeutic drug targets for Alzheimer's disease (AD). A recent study highlighted that tacrine-benzofuran hybrid C1 displayed anti-aggregation activity against Aβ42 peptide and inhibit BACE1 activity. However, the inhibition mechanism of C1 against Aβ42 aggregation and BACE1 activity remains unclear. Thus, molecular dynamics (MD) simulations of Aβ42 monomer and BACE1 with and without C1 were performed to inspect the inhibitory mechanism of C1 against Aβ42 aggregation and BACE1 activity. In addition, a ligand-based virtual screening followed by MD simulations was employed to explore potent new small-molecule dual inhibitors of Aβ42 aggregation and BACE1 activity. MD simulations highlighted that C1 promotes the non aggregating helical conformation in Aβ42 and destabilizes D23-K28 salt bridge that plays a vital role in the self-aggregation of Aβ42. C1 displays a favourable binding free energy (-50.7 ± 7.3 kcal/mol) with Aβ42 monomer and preferentially binds to the central hydrophobic core (CHC) residues. MD simulations highlighted that C1 strongly interacted with the BACE1 active site (Asp32 and Asp228) and active pockets. The scrutiny of interatomic distances among key residues of BACE1 highlighted the close flap (non-active) position in BACE1 on the incorporation of C1. The MD simulations explain the observed high inhibitory activity of C1 against Aβ aggregation and BACE1 in the in vitro studies. The ligand-based virtual screening followed by MD simulations identified CHEMBL2019027 (C2) as a promising dual inhibitor of Aβ42 aggregation and BACE1 activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajdeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Pritpal Singh
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Nisa N, Rasmita B, Arati C, Uditraj C, Siddhartha R, Dinata R, Bhanushree B, Bidanchi RM, Manikandan B, Laskar SA, Abinash G, Pori B, Roy VK, Gurusubramanian G. Repurposing of phyto-ligand molecules from the honey bee products for Alzheimer's disease as novel inhibitors of BACE-1: small molecule bioinformatics strategies as amyloid-based therapy. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:51143-51169. [PMID: 36808033 DOI: 10.1007/s11356-023-25943-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/10/2023] [Indexed: 04/16/2023]
Abstract
Alzheimer's disease (AD) is one of the neurodegenerative diseases, manifesting dementia, spatial disorientation, language, cognitive, and functional impairment, mainly affects the elderly population with a growing concern about the financial burden on society. Repurposing can improve the traditional progress of drug design applications and could speed up the identification of innovative remedies for AD. The pursuit of potent anti-BACE-1 drugs for AD treatment has become a pot boiler topic in the recent past and to instigate the design of novel improved inhibitors from the bee products. Drug-likeness characteristics (ADMET: absorption, distribution, metabolism, excretion, and toxicity), docking (AutoDock Vina), simulation (GROMACS), and free energy interaction (MM-PBSA, molecular mechanics Poisson-Boltzmann surface area) analyses were performed to identify the lead candidates from the bee products (500 bioactives from the honey, royal jelly, propolis, bee bread, bee wax, and bee venom) for Alzheimer's disease as novel inhibitors of BACE-1 (beta-site amyloid precursor protein cleaving enzyme (1) receptor using appropriate bioinformatics tools. Forty-four bioactive lead compounds were screened from the bee products through high throughput virtual screening on the basis of their pharmacokinetic and pharmacodynamics characteristics, showing favorable intestinal and oral absorption, bioavailability, blood brain barrier penetration, less skin permeability, and no inhibition of cytochrome P450 inhibitors. The docking score of the forty-four ligand molecules was found to be between -4 and -10.3 kcal/mol, respectively, exhibiting strong binding affinity to BACE1 receptor. The highest binding affinity was observed in the rutin (-10.3 kcal/mol), 3,4-dicaffeoylquinic acid (-9.5 kcal/mol), nemorosone (-9.5 kcal/mol), and luteolin (-8.9 kcal/mol). Furthermore, these compounds demonstrated high total binding energy -73.20 to -105.85 kJ/mol), and low root mean square deviation (0.194-0.202 nm), root mean square fluctuation (0.0985-0.1136 nm), radius of gyration (2.12 nm), number of H-bonds (0.778-5.436), and eigenvector values (2.39-3.54 nm2) in the molecular dynamic simulation, signifying restricted motion of Cα atoms, proper folding and flexibility, and highly stable with compact of the BACE1 receptor with the ligands. Docking and simulation studies concluded that rutin, 3,4-dicaffeoylquinic acid, nemorosone, and luteolin are plausibly used as novel inhibitors of BACE1 to combat AD, but further in-depth experimental investigations are warranted to prove these in silico findings.
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Affiliation(s)
- Nisekhoto Nisa
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Borgohain Rasmita
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Chettri Arati
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Chetia Uditraj
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | - Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Baishya Bhanushree
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | - Bose Manikandan
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Saeed Ahmed Laskar
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Giri Abinash
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Buragohain Pori
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Vikas Kumar Roy
- Department of Zoology, Mizoram University, Aizawl, Mizoram, 796004, India
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Lauro FV, Marcela RN, Maria LR, Francisco DC, Magdalena AR, Virginia MAM, Montserrat MG. Effect Produced by a Cyclooctyne Derivative on Both Infarct Area and Left Ventricular Pressure via Calcium Channel Activation. Drug Res (Stuttg) 2023; 73:105-112. [PMID: 36446591 DOI: 10.1055/a-1967-2004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND There are reports which indicate that some cyclooctyne derivatives may exert changes in cardiovascular system; however, its molecular mechanism is not very clear. OBJECTIVE The aim of this study was to evaluate the biological activity of four cyclooctyne derivatives (compounds 1: to 4: ) produced on infarct area and left ventricular pressure. METHODS Biological activity produced by cyclooctyne derivatives on infarct area was determinate using an ischemia/reperfusion injury model. In addition, to characterize the molecular mechanism of this effect, the following strategies were carried out as follows; i) biological activity produced by cyclooctyne derivative (compound 4: ) on either perfusion pressure or left ventricular pressure was evaluated using an isolated rat heart; ii) theoretical interaction of cyclooctyne derivative with calcium channel (1t0j protein surface) using a docking model. RESULTS The results showed that cyclooctyne derivative (compound 4: ) decrease infarct area of in a dose-dependent manner compared with compound 1: to 3: . Besides, this cyclooctyne derivative increase both perfusion pressure and left ventricular pressure which was inhibited by nifedipine. Other theoretical data suggests that cyclooctyne derivative could interact with some aminoacid residues (Met83, Ile85, Ser86, Leu108, Glu114) involved in 1t0j protein surface. CONCLUSIONS All these data indicate that cyclooctyne derivative increase left ventricular pressure via calcium channel activation and this phenomenon could be translated as a decrease of infarct area.
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Affiliation(s)
- Figueroa-Valverde Lauro
- Laboratory of Pharmaco-Chemistry, Faculty of Chemical Biological Sciences, University Autonomous of Campeche, Av. Agustín Melgar s/n, Col Buenavista C.P. Campeche, Camp., México
| | - Rosas-Nexticapa Marcela
- Facultad de Nutrición, Universidad Veracruzana, Médicos y Odontologos s/n C.P. Unidad del Bosque Xalapa Veracruz, México
| | - López-Ramos Maria
- Laboratory of Pharmaco-Chemistry, Faculty of Chemical Biological Sciences, University Autonomous of Campeche, Av. Agustín Melgar s/n, Col Buenavista C.P. Campeche, Camp., México
| | - Díaz-Cedillo Francisco
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala s/n Col. Santo Tomas, México, D.F. C.P
| | - Alvarez-Ramirez Magdalena
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala s/n Col. Santo Tomas, México, D.F. C.P
| | - Mateu-Armad Maria Virginia
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala s/n Col. Santo Tomas, México, D.F. C.P
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Dharmasivam M, Kaya B, Wijesinghe T, Gholam Azad M, Gonzálvez MA, Hussaini M, Chekmarev J, Bernhardt PV, Richardson DR. Designing Tailored Thiosemicarbazones with Bespoke Properties: The Styrene Moiety Imparts Potent Activity, Inhibits Heme Center Oxidation, and Results in a Novel "Stealth Zinc(II) Complex". J Med Chem 2023; 66:1426-1453. [PMID: 36649565 DOI: 10.1021/acs.jmedchem.2c01600] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A novel, potent, and selective antitumor agent, namely (E)-3-phenyl-1-(2-pyridinyl)-2-propen-1-one 4,4-dimethyl-3-thiosemicarbazone (PPP44mT), and its analogues were synthesized and characterized and displayed strikingly distinctive properties. This activity was mediated by the inclusion of a styrene moiety, which through steric and electrochemical mechanisms prevented deleterious oxy-myoglobin or oxy-hemoglobin oxidation relative to other potent thiosemicarbazones, i.e., di-2-pyridylketone-4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC) or di-2-pyridylketone-4,4-dimethyl-3-thiosemicarbazone (Dp44mT). Structure-activity relationship analysis demonstrated specific tuning of PPP44mT electrochemistry further inhibited oxy-myoglobin or oxy-hemoglobin oxidation. Both PPP44mT and its Cu(II) complexes showed conspicuous almost immediate cytotoxicity against SK-N-MC tumor cells (within 3 h). In contrast, [Zn(PPP44mT)2] demonstrated a pronounced delay in activity, taking 48 h before marked antiproliferative efficacy was apparent. As such, [Zn(PPP44mT)2] was designated as a "stealth Zn(II) complex" that overcomes the near immediate cytotoxicity of PPP44mT or its copper complexes. Upon examination of the suppression of oncogenic signaling, [Zn(PPP44mT)2] was superior at inhibiting cyclin D1 expression compared to DpC or Dp44mT.
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Affiliation(s)
- Mahendiran Dharmasivam
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan4111, Australia
| | - Busra Kaya
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan4111, Australia.,Department of Chemistry, Istanbul University-Cerrahpasa, Avcilar, 34320Istanbul, Turkey
| | - Tharushi Wijesinghe
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan4111, Australia
| | - Mahan Gholam Azad
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan4111, Australia
| | - Miguel A Gonzálvez
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane4072, Australia
| | - Mohammad Hussaini
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan4111, Australia
| | - Jason Chekmarev
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan4111, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane4072, Australia
| | - Des R Richardson
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan4111, Australia.,Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya466-8550, Japan
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Arzani H, Rafii-Tabar H, Ramezani F. The investigation into the effect of the length of RGD peptides and temperature on the interaction with the αIIbβ3 integrin: a molecular dynamic study. J Biomol Struct Dyn 2022; 40:9701-9712. [PMID: 34060983 DOI: 10.1080/07391102.2021.1932602] [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: 12/16/2022]
Abstract
The tripeptide Arg-Gly-Asp acid (RGD) is a protein sequence in the binding of proteins to cell surfaces, and is involved in various biological processes such as cell adhesion to the extracellular matrix, platelet activation, hemostasis, etc. The C2 domain of the Von Willebrand Factor (VWF), containing the RGD motif, plays an important role in the initial homeostasis process. It binds to the αIIbβ3 integrin and stimulates platelet aggregation. We have investigated, using the molecular Dynamic (MD) simulation method, the effect of the RGD-peptide length, and temperature variation, on the binding to the αIIbβ3 integrin receptor. We examined 10 different structural modes of the αIIbβ3 at three different temperatures; 237 K, 310 K and 318 K. Our findings show that the amino acids that form a binding pocket include Asp224, Tyr234, Ser226, Tyr190, Tyr189, Trp260, Trp262, Asp259, Lys253, Arg214, Asp217, Ser161 and Ala218 and that the ligand-receptor interaction was increased at higher temperatures. It was also found that the increase in the number of ligands' amino acids and their types (% glycine) plays an important role in the stability, conformation, and ligand-receptor interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hossein Arzani
- Department of Medical Physics and Biomedical Engineering, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,The Physics Branch of Iran Academy of Sciences, Tehran, Iran
| | - Fatemeh Ramezani
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
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11
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Bingöl EN, Taştekil I, Yay C, Keskin N, Ozbek P. How Epstein-Barr virus envelope glycoprotein gp350 tricks the CR2? A molecular dynamics study. J Mol Graph Model 2022; 114:108196. [DOI: 10.1016/j.jmgm.2022.108196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
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12
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Yadav M, Abdalla M, Madhavi M, Chopra I, Bhrdwaj A, Soni L, Shaheen U, Prajapati L, Sharma M, Sikarwar MS, Albogami S, Hussain T, Nayarisseri A, Singh SK. Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2068799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manasi Yadav
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, PR People’s Republic of China
| | - Maddala Madhavi
- Department of Zoology, Osmania University, Hyderabad, Telangana State, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Lovely Soni
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Uzma Shaheen
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Leena Prajapati
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Megha Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | | | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Tajamul Hussain
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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13
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Mass Spectrometric Behavior and Molecular Mechanisms of Fermented Deoxyanthocyanidins to Alleviate Ulcerative Colitis Based on Network Pharmacology. Int J Anal Chem 2022; 2022:9293208. [PMID: 35356765 PMCID: PMC8960007 DOI: 10.1155/2022/9293208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
Aims. Ulcerative colitis (UC) is a type of chronic idiopathic inflammatory bowel disease with a multifactorial pathogenesis and limited treatment options. The aim of the present study is to investigate the hydrogen deuterium exchange mass spectrometry (HDX-MS) behaviors of fermented deoxyanthocyanidins and their molecular mechanisms to alleviate UC by using quantum chemistry and network pharmacology. Methods. Tandem MS indicated at least two fragmentation pathways through which deuterated vinylphenol-deoxyanthocyanidins could generate different product ions. Quantum calculations were conducted to determine the transition states of the relevant molecules and analyze their optimized configuration, vibrational characteristics, intrinsic reaction coordinates, and corresponding energies. The potential targets of deoxyanthocyanidins in UC were screened from a public database. The R package was used for Gene Ontology (GO) and KEGG pathway analyses, and the protein–protein interactions (PPIs) of the targets were assessed using Search Tool for the Retrieval of Interacting Genes (STRING). Finally, molecular docking was implemented to analyze the binding energies and action modes of the target compounds through the online tool CB-Dock. Results. Quantum calculations indicated two potential fragmentation pathways involving the six-membered ring and dihydrogen cooperative transfer reactions of the vinylphenol-deoxyanthocyanidins. A total of 146 and 57 intersecting targets of natural and fermented deoxyanthocyanidins were separately screened out from the UC database and significant overlaps in GO terms and KEGG pathways were noted. Three shared hub targets (i.e., PTGS2, ESR1, and EGFR) were selected from the two PPI networks by STRING. Molecular docking results showed that all deoxyanthocyanidins have a good binding potential with the hub target proteins and that fermented deoxyanthocyanidins have lower binding energies and more stable conformations compared with natural ones. Conclusions. Deoxyanthocyanidins may provide anti-inflammatory, antioxidative, and immune system regulatory effects to suppress UC progression. It is proposed for the first time that fermentation of deoxyanthocyanidins can help adjust the structure of the intestinal microbiota and increase the biological activity of the natural compounds against UC. Furthermore, HDX-MS is a helpful strategy to analyze deoxyanthocyanidin metabolites with unknown structures.
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [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: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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15
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Wadhwa P, Jain P, Jadhav HR. Glycogen Synthase Kinase 3 (GSK3): Its Role and Inhibitors. Curr Top Med Chem 2021; 20:1522-1534. [PMID: 32416693 DOI: 10.2174/1568026620666200516153136] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 12/23/2022]
Abstract
Glycogen Synthase Kinase 3 (GSK3) is one of the Serine/Threonine protein kinases, which has gained a lot of attention for its role in a variety of pathways. It has two isoforms, GSK3α and GSK3β. However, GSK3β is highly expressed in different areas of the brain and has been implicated in Alzheimer's disease as it is involved in tau phosphorylation. Due to its high specificity concerning substrate recognition, GSK3 has been considered as an important target. In the last decade, several GSK3 inhibitors have been reported and two molecules are in clinical trials. This review collates the information published in the last decade about the role of GSK3 in Alzheimer's disease and progress in the development of its inhibitors. Using this collated information, medicinal chemists can strategize and design novel GSK3 inhibitors that could be useful in the treatment of Alzheimer's disease.
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Affiliation(s)
- Pankaj Wadhwa
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani- 333031, Rajasthan, India
| | - Priti Jain
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani- 333031, Rajasthan, India
| | - Hemant R Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani- 333031, Rajasthan, India
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16
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del Hierro I, Mélida H, Broyart C, Santiago J, Molina A. Computational prediction method to decipher receptor-glycoligand interactions in plant immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1710-1726. [PMID: 33316845 PMCID: PMC8048873 DOI: 10.1111/tpj.15133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 05/22/2023]
Abstract
Microbial and plant cell walls have been selected by the plant immune system as a source of microbe- and plant damage-associated molecular patterns (MAMPs/DAMPs) that are perceived by extracellular ectodomains (ECDs) of plant pattern recognition receptors (PRRs) triggering immune responses. From the vast number of ligands that PRRs can bind, those composed of carbohydrate moieties are poorly studied, and only a handful of PRR/glycan pairs have been determined. Here we present a computational screening method, based on the first step of molecular dynamics simulation, that is able to predict putative ECD-PRR/glycan interactions. This method has been developed and optimized with Arabidopsis LysM-PRR members CERK1 and LYK4, which are involved in the perception of fungal MAMPs, chitohexaose (1,4-β-d-(GlcNAc)6 ) and laminarihexaose (1,3-β-d-(Glc)6 ). Our in silico results predicted CERK1 interactions with 1,4-β-d-(GlcNAc)6 whilst discarding its direct binding by LYK4. In contrast, no direct interaction between CERK1/laminarihexaose was predicted by the model despite CERK1 being required for laminarihexaose immune activation, suggesting that CERK1 may act as a co-receptor for its recognition. These in silico results were validated by isothermal titration calorimetry binding assays between these MAMPs and recombinant ECDs-LysM-PRRs. The robustness of the developed computational screening method was further validated by predicting that CERK1 does not bind the DAMP 1,4-β-d-(Glc)6 (cellohexaose), and then probing that immune responses triggered by this DAMP were not impaired in the Arabidopsis cerk1 mutant. The computational predictive glycan/PRR binding method developed here might accelerate the discovery of protein-glycan interactions and provide information on immune responses activated by glycoligands.
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Affiliation(s)
- Irene del Hierro
- Centro de Biotecnología y Genómica de Plantas (CBGP)Universidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo‐UPM28223Pozuelo de Alarcón, MadridSpain
- Departamento de Biotecnología‐Biología VegetalEscuela Técnica Superior de Ingeniería AgronómicaAlimentaria y de BiosistemasUniversidad Politécnica de Madrid (UPM)28040MadridSpain
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas (CBGP)Universidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo‐UPM28223Pozuelo de Alarcón, MadridSpain
- Present address:
Área de Fisiología VegetalDepartamento de Ingeniería y Ciencias AgrariasUniversidad de León24071LeónSpain
| | - Caroline Broyart
- Département de Biologie Moléculaire Végétale (DBMV)University of Lausanne (UNIL)Biophore Building, UNIL SorgeCH‐1015LausanneSwitzerland
| | - Julia Santiago
- Département de Biologie Moléculaire Végétale (DBMV)University of Lausanne (UNIL)Biophore Building, UNIL SorgeCH‐1015LausanneSwitzerland
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (CBGP)Universidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo‐UPM28223Pozuelo de Alarcón, MadridSpain
- Departamento de Biotecnología‐Biología VegetalEscuela Técnica Superior de Ingeniería AgronómicaAlimentaria y de BiosistemasUniversidad Politécnica de Madrid (UPM)28040MadridSpain
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Ahmadi K, Farasat A, Rostamian M, Johari B, Madanchi H. Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study. J Biomol Struct Dyn 2021; 40:5566-5576. [PMID: 33438525 PMCID: PMC7814568 DOI: 10.1080/07391102.2021.1871958] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Regarding the urgency of therapeutic measures for coronavirus disease 2019 (COVID-19) pandemic, the use of available drugs with FDA approval is preferred because of the less time and cost required for their development. In silico drug repurposing is an accurate way to speed up the screening of the existing FDA-approved drugs to find a therapeutic option for COVID-19. The similarity in SARS-CoV-2 and HIV-1 fusion mechanism to host cells can be a key point for Inhibit SARS-CoV-2 entry into host cells by HIV fusion inhibitors. Accordingly, in this study, an HIV-1 fusion inhibitor called Enfuvirtide (Enf) was selected. The affinity and essential residues involving in the Enf binding to the S2 protein of SARS-CoV-2, HIV-1 gp41 protein and angiotensin-converting enzyme 2 (ACE-2) as a negative control, was evaluated using molecular docking. Eventually, Enf-S2 and Enf-gp41 protein complexes were simulated by molecular dynamics (MD) in terms of binding affinity and stability. Based on the most important criteria such as docking score, cluster size, energy and dissociation constant, the strongest interaction was observed between Enf with the S2 protein. In addition, MD results confirmed that Enf-S2 protein interaction was remarkably stable and caused the S2 protein residues to undergo the fewest fluctuations. In conclusion, it can be stated that Enf can act as a strong SARS-CoV-2 fusion inhibitor and demonstrates the potential to enter the clinical trial phase of COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Alireza Farasat
- Cellular and Molecular Research Center, Research Institute for Prevention of Non Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran.,Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Behrooz Johari
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hamid Madanchi
- Department of Biotechnology, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran.,Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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18
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Yang Y, Sun M, Yu Z, Liu J, Yan W, Liu Z, Wei M, Wang H. Designing high affinity target-binding peptides to HLA-E: a key membrane antigen of multiple myeloma. Aging (Albany NY) 2020; 12:20457-20470. [PMID: 33115963 PMCID: PMC7655190 DOI: 10.18632/aging.103858] [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: 04/23/2020] [Accepted: 07/21/2020] [Indexed: 01/10/2023]
Abstract
Multiple myeloma (MM) is a plasma cell malignancy that is currently incurable. Finding new targets and designing drugs are crucial for the treatment of MM. The two datasets (GSE6691 and GSE39754) are used to screen highly expressed antigen on MM cells. HLA-E was an ideal target for it was a hub gene, and also located in one of the key clusters. Highly expression of HLA-E mRNA on MM cells was also confirmed by real-time qPCR testing the MM patients' samples in Shengjing hospital. Crystal structure of HLA-E was obtained from Protein Data Bank (PDB ID: 3CDG) which was used to design targeting peptides with Molecular Operating Environment software. By analyzing interaction between CD94/NKG2A and HLA-E, a peptide with twelve amino acids was screened as a model peptide. Peptides library was constructed by randomly replaced non-key amino acid. Peptide-protein docking method was used to identify high affinity peptides. PEPTIDE 1-3 and model peptide were synthesized and identified the affinity to HLA-E by flow cytometer and confocal laser microscopy. At last, PEPTIDE3 (NALDEYCEDKNR) was found with the highest affinity. Taking all, HLA-E is a new treatment target, and PEPTIDE 3 is an ideal high affinity target-binding peptide candidate.
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Affiliation(s)
- Ying Yang
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Mingli Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Zhaojin Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Jinwei Liu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
- Department of Pharmacy, Chifeng Municipal Hospital, Chifeng Inner Mongolia, China
| | - Wei Yan
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhuogang Liu
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Hongtao Wang
- Department of Hematology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Gheibi N, Ghorbani M, Shariatifar H, Farasat A. Effects of unsaturated fatty acids (Arachidonic/Oleic Acids) on stability and structural properties of Calprotectin using molecular docking and molecular dynamics simulation approach. PLoS One 2020; 15:e0230780. [PMID: 32214349 PMCID: PMC7098580 DOI: 10.1371/journal.pone.0230780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Calprotectin is a heterodimeric protein complex with two subunits called S100A8/A9. The protein has an essential role in inflammation process and various human diseases. It has the ability to bind to unsaturated fatty acids including Arachidonic acid, Oleic acid and etc., which could be considered as a major carrier for fatty acids. In this study we aimed to appraise the thermodynamics and structural changes of Calprotectin in presence of Arachidonic acid/Oleic acid) using docking and molecular dynami simulation method. To create the best conformation of Calprotectin-Oleic acid/Arachidonic acid complexes, the docking process was performed. The complexes with the best binding energy were selected as the models for molecular dynamics simulation process. Furthermore, the structural and thermodynamics properties of the complexes were evaluated too. The Root Mean Square Deviation and Root Mean Square Fluctuation results showed that the binding of Arachidonic acid/Oleic acid to Calprotectin can cause the protein structural changes which was confirmed by Define Secondary Structure of Proteins results. Accordingly, the binding free energy results verified that binding of Oleic acid to Calprotectin leads to instability of S100A8/A9 subunits in the protein. Moreover, the electrostatic energy contribution of the complexes (Calprotectin-Oleic acid/Arachidonic acid) was remarkably higher than van der Waals energy. Thus, the outcome of this study confirm that Oleic acid has a stronger interaction with Calprotectin in comparison with Arachidonic acid. Our findings indicated that binding of unsaturated fatty acids to Calprotectin leads to structural changes of the S100A8/A9 subunits which could be beneficial to play a biological role in inflammation process.
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Affiliation(s)
- Nematollah Gheibi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohamad Ghorbani
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Hanifeh Shariatifar
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Farasat
- Cellular and Molecular Research Center, Research Institute for Prevention of Non Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
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20
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Gheibi N, Ghorbani M, Shariatifar H, Farasat A. In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach. PLoS One 2019; 14:e0224095. [PMID: 31622441 PMCID: PMC6797115 DOI: 10.1371/journal.pone.0224095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022] Open
Abstract
Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+. Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+. The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes.
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Affiliation(s)
- Nematollah Gheibi
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Ghorbani
- Department of Nanobiotechnology/ Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Hanifeh Shariatifar
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Farasat
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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21
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Sivakumar M, Saravanan K, Saravanan V, Sugarthi S, kumar SM, Alhaji Isa M, Rajakumar P, Aravindhan S. Discovery of new potential triplet acting inhibitor for Alzheimer’s disease via X-ray crystallography, molecular docking and molecular dynamics. J Biomol Struct Dyn 2019; 38:1903-1917. [DOI: 10.1080/07391102.2019.1620128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Kandasamy Saravanan
- X-Ray Crystallography and Computational Molecular Biology Lab, Department of Physics, Periyar University, Salem, India
| | | | - Srinivasan Sugarthi
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram, Tamil Nadu, India
| | | | - Mustafa Alhaji Isa
- Bioinformatics and Computational Biology Lab, Department of Microbiology, Faculty of Sciences, University of Maiduguri, Maiduguri, Nigeria
| | - Perumal Rajakumar
- Department of Organic Chemistry, University of Madras, Chennai, India
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22
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Sharma S, Singh N, Nepovimova E, Korabecny J, Kuca K, Satnami ML, Ghosh KK. Interaction of synthesized nitrogen enriched graphene quantum dots with novel anti-Alzheimer’s drugs: spectroscopic insights. J Biomol Struct Dyn 2019; 38:1822-1837. [DOI: 10.1080/07391102.2019.1619625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Srishti Sharma
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, India
| | - Namrata Singh
- Ramrao Adik Institute of Technology, DY Patil University, Navi Mumbai, India
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Korabecny
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- National Institute of Mental Health, Klecany, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Manmohan L. Satnami
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, India
| | - Kallol K. Ghosh
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, India
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23
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Jonniya NA, Kar P. Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations. J Biomol Struct Dyn 2019; 38:1306-1321. [DOI: 10.1080/07391102.2019.1602079] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Nisha A. Jonniya
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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24
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Shuaib S, Saini RK, Goyal D, Goyal B. Impact of K16A and K28A mutation on the structure and dynamics of amyloid-β42 peptide in Alzheimer’s disease: key insights from molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:708-721. [DOI: 10.1080/07391102.2019.1586587] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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25
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Sriroopreddy R, Raghuraman P, Sudandiradoss C. Structural debilitation of mutation G322D associated with MSH2 and their role in triple negative breast cancer. J Biomol Struct Dyn 2019; 38:771-780. [DOI: 10.1080/07391102.2019.1587512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ramireddy Sriroopreddy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - P. Raghuraman
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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26
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Ece A. Towards more effective acetylcholinesterase inhibitors: a comprehensive modelling study based on human acetylcholinesterase protein–drug complex. J Biomol Struct Dyn 2019; 38:565-572. [DOI: 10.1080/07391102.2019.1583606] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul, Turkey
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27
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Saravanan K, Sivanandam M, Hunday G, Mathiyalagan L, Kumaradhas P. Investigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis. J Biomol Struct Dyn 2018; 37:2339-2354. [DOI: 10.1080/07391102.2018.1479661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Magudeeswaran Sivanandam
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Govindasamy Hunday
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Lakshmanan Mathiyalagan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, Tamil Nadu, India
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28
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Loza-Mejía MA, Salazar JR, Sánchez-Tejeda JF. In Silico Studies on Compounds Derived from Calceolaria: Phenylethanoid Glycosides as Potential Multitarget Inhibitors for the Development of Pesticides. Biomolecules 2018; 8:E121. [PMID: 30360548 PMCID: PMC6322355 DOI: 10.3390/biom8040121] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 11/25/2022] Open
Abstract
An increasing occurrence of resistance in insect pests and high mammal toxicity exhibited by common pesticides increase the need for new alternative molecules. Among these alternatives, bioinsecticides are considered to be environmentally friendly and safer than synthetic insecticides. Particularly, plant extracts have shown great potential in laboratory conditions. However, the lack of studies that confirm their mechanisms of action diminishes their potential applications on a large scale. Previously, we have reported the insect growth regulator and insecticidal activities of secondary metabolites isolated from plants of the Calceolaria genus. Herein, we report an in silico study of compounds isolated from Calceolaria against acetylcholinesterase, prophenoloxidase, and ecdysone receptor. The molecular docking results are consistent with the previously reported experimental results, which were obtained during the bioevaluation of Calceolaria extracts. Among the compounds, phenylethanoid glycosides, such as verbascoside, exhibited good theoretical affinity to all the analyzed targets. In light of these results, we developed an index to evaluate potential multitarget insecticides based on docking scores.
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29
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Ahmad S, Shaker B, Ahmad F, Raza S, Azam SS. Moleculer dynamics simulaiton revealed reciever domain of Acinetobacter baumannii BfmR enzyme as the hot spot for future antibiotics designing. J Biomol Struct Dyn 2018; 37:2897-2912. [DOI: 10.1080/07391102.2018.1498805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Bilal Shaker
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Faisal Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Saad Raza
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
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30
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Yan W, Li SX, Wei M, Gao H. Identification of MMP9 as a novel key gene in mantle cell lymphoma based on bioinformatic analysis and design of cyclic peptides as MMP9 inhibitors based on molecular docking. Oncol Rep 2018; 40:2515-2524. [PMID: 30226602 PMCID: PMC6151885 DOI: 10.3892/or.2018.6682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive disease. MCL is associated with poor patient prognosis and limited survival. To identify key genes and explore targeting cyclic peptide inhibitors for the treatment of MCL, we downloaded two gene expression profiles (GSE32018 and GSE9327) from the Gene Expression Omnibus (GEO) database. We screened 84 differentially expressed genes (DEGs). Pathway analysis showed that DEMs were mainly enriched in the ‘Pathway in cancer’, ‘PI3K-Akt signaling pathway’, ‘Cytokine-cytokine receptor interaction’, ‘Rap1 signaling pathway’, ‘NF-κB signaling pathway’ and ‘Leukocyte trans-endothelial migration’. We subsequently constructed a protein-protein interaction (PPI) network of DEGs. In addition, matrix metalloproteinase 9 (MMP9) with a high degree in the PPI network was identified as a hub gene in MCL. Meanwhile in the Molecular Complex Detection (MCODE) analysis, MMP9 was located in the important cluster. Thus, MMP9 can be used as a therapeutic target for MCL and we designed cyclic peptides as MMP9 inhibitors. MMP9 protein structure was gathered from the Protein Data Bank (PDB), with a PDB ID: 1L6J. MMP9 and cyclic peptides were docked using Molecular Operating Environment (MOE) software after structural optimization. It was revealed that cyclic peptide 2 bound deeply in the binding pocket of MMP9 and had interaction with the active-site Zn2+ ion in the catalytic domain. Cyclic peptides 1, 2, 4–6 also displayed potential interaction with active residues of MMP9; thus, these cyclic peptides can serve as potential drug candidates to block MMP9 activity and future studies are warranted to confirm their efficacy.
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Affiliation(s)
- Wei Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Shawn Xiang Li
- International College, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Hua Gao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P.R. China
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31
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Ahmad S, Raza S, Abro A, Liedl KR, Azam SS. Toward novel inhibitors against KdsB: a highly specific and selective broad-spectrum bacterial enzyme. J Biomol Struct Dyn 2018; 37:1326-1345. [DOI: 10.1080/07391102.2018.1459318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Saad Raza
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Asma Abro
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Faculty of Life Sciences and Informatics, Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Klaus R. Liedl
- Institute for General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, Innsbruck 6020, Austria
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
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32
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Sharma T, Siddiqi MI. In silico identification and design of potent peptide inhibitors against PDZ-3 domain of Postsynaptic Density Protein (PSD-95). J Biomol Struct Dyn 2018; 37:1241-1253. [PMID: 29557723 DOI: 10.1080/07391102.2018.1454851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Unique intrinsic properties of peptides like low toxicity, high biological activity, and specificity make them attractive therapeutic agents. PDZ-binding peptide inhibitors have been demonstrated for curing of Alzheimer, Parkinson, Dementia, and other central nervous system ailments. In this article, we report the successful use of an integrated computational protocol to analyze the structural basis of how peptides bind to the shallow groove of the third PDZ domain (PDZ-3) from the postsynaptic density (PSD-95) protein. This protocol employs careful and precise computational techniques for design of new strategy for predicting novel and potent peptides against PDZ protein. We attempted to generate a pharmacophore model using crystal structure of peptide inhibitor bound to the PDZ-3. A highly specific and sensitive generated pharmacophore model was used for screening virtual database generated using different combination of amino acid substitutions as well as decoy peptide database for its sensitivity and specificity. Identified hit peptides were further analyzed by docking studies, and their stability analyzed using solvated molecular dynamics. Quantum Mechanics/Molecular Mechanics (QM/MM) interaction energy and GMX-PBSA scoring schemes were used for ranking of stable peptides. Computational approach applied here generated encouraging results for identifying peptides against PDZ interaction model. The workflow can be further exercised as a virtual screening technique for reducing the search space for candidate target peptides against PDZ domains.
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Affiliation(s)
- Tanuj Sharma
- a Laboratory of Computational Biology and Bioinformatics, Division of Molecular and Structural Biology , CSIR-Central Drug Research Institute , Lucknow 226031 , India
| | - Mohammad Imran Siddiqi
- a Laboratory of Computational Biology and Bioinformatics, Division of Molecular and Structural Biology , CSIR-Central Drug Research Institute , Lucknow 226031 , India.,b Academy of Scientific and Innovative Research (AcSIR) , CSIR-Central Drug Research Institute , Campus, Lucknow 226031 , India
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