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George N, Xiao J. Inhibiting sphingosine 1-phosphate lyase: From efficacy to mechanism. Neurobiol Dis 2024; 199:106585. [PMID: 38955289 DOI: 10.1016/j.nbd.2024.106585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024] Open
Abstract
Sphingosine-1 phosphate (S1P) is a lipid metabolite regulating diverse biological processes, including proliferation, differentiation, migration, and apoptosis, highlighting its physiological and therapeutic significance. Current S1P-based therapeutic approaches primarily focus on modulating the downstream signalling via targeting S1P receptors, however, this is challenged by incomplete receptor internalisation. Sphingosine-1-phosphate lyase (SPL) is a highly conserved enzyme that "gatekeeps" the final step of S1P degradation. Cognisant of the complex ligand and receptor interaction and dynamic metabolic networks, the selective modulation of SPL activity presents a new opportunity to regulate S1P biosynthesis and reveal its role in various systems. Over the past decade, an evolving effort has been made to identify new molecules that could block SPL activity in vitro or in vivo. This review focuses on summarising the current understanding of the reported SPL inhibitors identified through various screening approaches, discussing their efficacy in diverse model systems and the possible mechanism of action. Whilst effective modulation of S1P levels via inhibiting SPL is feasible, the specificity of those inhibitors remains inconclusive, presenting a clear challenge for future implications. Yet, none of the currently available SPL inhibitors is proven effective in elevating S1P levels within the central nervous system. This review article embraces future research focusing on investigating selective SPL inhibitors with high potency and possibly blood-brain-barrier permeability, which would aid the development of new S1P-based therapeutics for neurological disorders.
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Affiliation(s)
- Nelson George
- Department of Health Sciences and Biostatistics, School of Health Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Junhua Xiao
- Department of Health Sciences and Biostatistics, School of Health Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia.
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Lambring CB, Fiadjoe H, Behera SK, Basha R. Docking and molecular dynamic simulations of Mithramycin-A and Tolfenamic acid against Sp1 and survivin. Process Biochem 2024; 137:207-216. [PMID: 38912413 PMCID: PMC11192519 DOI: 10.1016/j.procbio.2023.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Therapeutic targeting of Sp1 transcription factor and survivin, are studied in various cancers due to their consistent overexpression. These markers result in poorer cancer prognoses and their downregulation has been investigated as an effective treatment approach. Mithramycin-A and Tolfenamic acid are two drugs with innate anti-cancer properties and are suggested to be able to target Sp1 through GC/GT DNA binding interference, however in-depth binding and mechanistic studies are lacking. Through docking analysis, we investigated Mithramycin-A and Tolfenamic acid in terms of their specific binding interactions with Sp1 and survivin. Through further molecular dynamics simulations including Root Mean Square (RMS) Fluctuation and RMS Deviation, rGYr, and H-bond analysis, we identified critical residues involved in drug interactions with each protein in question. We show Mithramycin-A as the superior binding candidate to each protein and found that it exhibited stronger binding with Sp1, and then survivin. Subsequent molecular dynamics simulations followed the same trend as initial binding energy calculations and showed crucial amino acids involved in each Mithramycin-A-protein complex. Our findings warrant further investigation into Mithramycin-A and its specific interaction with Sp1 and their downstream targets giving a better understanding of Mithramycin-A and its potential as an effective cancer treatment.
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Affiliation(s)
| | - Hope Fiadjoe
- UNT Health Science Center at Fort Worth, Fort Worth, TX 76107, USA
| | | | - Riyaz Basha
- UNT Health Science Center at Fort Worth, Fort Worth, TX 76107, USA
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Xiao J. Sphingosine 1-Phosphate Lyase in the Developing and Injured Nervous System: a Dichotomy? Mol Neurobiol 2023; 60:6869-6882. [PMID: 37507574 PMCID: PMC10657793 DOI: 10.1007/s12035-023-03524-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Sphingosine 1-phosphate lyase (SPL) is the terminal enzyme that controls the degradation of the bioactive lipid sphingosine 1-phosphate (S1P) within an interconnected sphingolipid metabolic network. The unique metabolic position of SPL in maintaining S1P levels implies SPL could be an emerging new therapeutic target. Over the past decade, an evolving effort has been made to unravel the role of SPL in the nervous system; however, to what extent SPL influences the developing and mature nervous system through altering S1P biosynthesis remains opaque. While congenital SPL deletion is associated with deficits in the developing nervous system, the loss of SPL activity in adults appears to be neuroprotective in acquired neurological disorders. The controversial findings concerning SPL's role in the nervous system are further constrained by the current genetic and pharmacological tools. This review attempts to focus on the multi-faceted nature of SPL function in the mammalian nervous systems, implying its dichotomy in the developing and adult central nervous system (CNS). This article also highlights SPL is emerging as a therapeutic molecule that can be selectively targeted to modulate S1P for the treatment of acquired neurodegenerative diseases, raising new questions for future investigation. The development of cell-specific inducible conditional SPL mutants and selective pharmacological tools will allow the precise understanding of SPL's function in the adult CNS, which will aid the development of a new strategy focusing on S1P-based therapies for neuroprotection.
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Affiliation(s)
- Junhua Xiao
- Department of Health Sciences and Biostatistics, School of Health Sciences, Swinburne University of Technology, John Street, Hawthorn, VIC, 3022, Australia.
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Landeros-Martínez LL, Campos-Almazán MI, Sánchez-Bojorge NA, Flores R, Palomares-Báez JP, Rodríguez-Valdez LM. Theoretical Studies for the Discovery of Potential Sucrase-Isomaltase Inhibitors from Maize Silk Phytochemicals: An Approach to Treatment of Type 2 Diabetes. Molecules 2023; 28:6778. [PMID: 37836621 PMCID: PMC10574772 DOI: 10.3390/molecules28196778] [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: 08/09/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
A theoretical analysis of the potential inhibition of human sucrase-isomaltase (SI) by flavonoids was carried out with the aim of identifying potential candidates for an alternative treatment of type 2 diabetes. Two compounds from maize silks, maysin and luteolin, were selected to be studied with the structure-based density functional theory (DFT), molecular docking (MDock), and molecular dynamics (MD) approaches. The docking score and MD simulations suggested that the compounds maysin and luteolin presented higher binding affinities in N-terminal sucrase-isomaltase (NtSI) than in C-terminal sucrase-isomaltase (CtSI). The reactivity parameters, such as chemical hardness (η) and chemical potential (µ), of the ligands, as well as of the active site amino acids of the NtSI, were calculated by the meta-GGA M06 functional in combination with the 6-31G(d) basis set. The lower value of chemical hardness calculated for the maysin molecule indicated that this might interact more easily with the active site of NtSI, in comparison with the values of the acarbose and luteolin structures. Additionally, a possible oxidative process was proposed through the quantum chemical calculations of the electronic charge transfer values (∆N) between the active site amino acids of the NtSI and the ligands. In addition, maysin displayed a higher ability to generate more oxidative damage in the NtSI active site. Our results suggest that maysin and luteolin can be used to develop novel α-glucosidase inhibitors via NtSI inhibition.
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Affiliation(s)
| | | | | | | | | | - Luz María Rodríguez-Valdez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua 31125, Mexico; (L.-L.L.-M.); (M.I.C.-A.); (N.-A.S.-B.); (R.F.); (J.P.P.-B.)
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Pamarthy D, Behera SK, Swain S, Yadav S, Suresh S, Jain N, Bhadra MP. Diaryl ether derivative inhibits GPX4 expression levels to induce ferroptosis in thyroid cancer cells. Drug Dev Res 2023; 84:861-887. [PMID: 37070554 DOI: 10.1002/ddr.22059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 03/20/2023] [Accepted: 04/01/2023] [Indexed: 04/19/2023]
Abstract
Papillary thyroid carcinoma contributes to about 80% of the total thyroid cancer cases. BRAFV600E is a frequently occurring mutation in PTCs. Although several BRAF inhibitors are available, many thyroid cancer patients acquire resistance to BRAF inhibitors. Therefore, new targets and drugs need to be identified as therapies. Ferroptosis is a recently discovered type of cell death, and inhibiting glutathione peroxidase 4 (GPX4) using small molecules was found to trigger ferroptosis. But it is unknown whether inhibiting GPX4 renders thyroid cancer cells susceptible to ferroptosis. To identify novel GPX4 inhibitors, we focused on our previously reported cohort of diaryl ether and dibenzoxepine molecules. In this study, we asked whether diaryl ether and dibenzoxepine derivatives trigger ferroptosis in thyroid cancer cells. To answer this question, we screened diaryl ether and dibenzoxepine derivatives in cell-based assays and performed mechanism of action studies. We found that a diaryl ether derivative, 16 decreased thyroid cell proliferation and triggered ferroptosis by inhibiting GPX4 expression levels. Molecular modeling and dynamics simulations showed that 16 binds to the active site of GPX4. Upon deciphering the mode of 16-induced ferroptosis, we found that 16 treatments decrease mitochondrial polarization and reduce mitochondrial respiration similar to a ferroptosis inducer, RSL3. We conclude that the diaryl ether derivative, 16 inhibits GPX4 expression levels to induce ferroptosis in thyroid cancer cells. Based on our observations, we suggest that 16 can be lead-optimized and developed as a ferroptosis-inducing agent to treat thyroid cancers.
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Affiliation(s)
- Deepika Pamarthy
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Santosh Kumar Behera
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, (NIPER), Ahmedabad, Gujarat, India
| | - Sonam Swain
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Yadav
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, Telangana, India
| | - Surisetti Suresh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, Telangana, India
| | - Nishant Jain
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manika Pal Bhadra
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Pradhan S, Behera SK, Samal SK, Panda I, Sahu PK, Priyadarshini S. Interaction Between 2‐Methylimidazole and 1‐Butanol/1‐Octanol: Thermophysical and Computational Studies. ChemistrySelect 2023. [DOI: 10.1002/slct.202204931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Sanghamitra Pradhan
- Department of Chemistry Institute of Technical Education and Research (FET) Siksha ‘O' Anusandhan Deemed to be University Khandagiri square Bhubaneswar 751030 Odisha India
| | - Santosh Kumar Behera
- Department of Biotechnology National Institute of Pharmaceutical Education and Research Ahmedabad Gujarat 382355 India
| | - Sangram Keshari Samal
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies ICMR-Regional Medical Research Center Bhubaneswar 751 023 Odisha India
| | - Itishree Panda
- Department of Chemistry Institute of Technical Education and Research (FET) Siksha ‘O' Anusandhan Deemed to be University Khandagiri square Bhubaneswar 751030 Odisha India
| | - Pratyush Kumar Sahu
- Department of Chemistry Institute of Technical Education and Research (FET) Siksha ‘O' Anusandhan Deemed to be University Khandagiri square Bhubaneswar 751030 Odisha India
| | - Swayamprabha Priyadarshini
- Department of Chemistry Institute of Technical Education and Research (FET) Siksha ‘O' Anusandhan Deemed to be University Khandagiri square Bhubaneswar 751030 Odisha India
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Kumar S, Ahmad K, Behera SK, Nagrale DT, Chaurasia A, Yadav MK, Murmu S, Jha Y, Rajawat MVS, Malviya D, Singh UB, Shankar R, Tripathy M, Singh HV. Biocomputational Assessment of Natural Compounds as a Potent Inhibitor to Quorum Sensors in Ralstonia solanacearum. Molecules 2022; 27:molecules27093034. [PMID: 35566383 PMCID: PMC9102662 DOI: 10.3390/molecules27093034] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/24/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Ralstonia solanacearum is among the most damaging bacterial phytopathogens with a wide number of hosts and a broad geographic distribution worldwide. The pathway of phenotype conversion (Phc) is operated by quorum-sensing signals and modulated through the (R)-methyl 3-hydroxypalmitate (3-OH PAME) in R. solanacearum. However, the molecular structures of the Phc pathway components are not yet established, and the structural consequences of 3-OH PAME on quorum sensing are not well studied. In this study, 3D structures of quorum-sensing proteins of the Phc pathway (PhcA and PhcR) were computationally modeled, followed by the virtual screening of the natural compounds library against the predicted active site residues of PhcA and PhcR proteins that could be employed in limiting signaling through 3-OH PAME. Two of the best scoring common ligands ZINC000014762512 and ZINC000011865192 for PhcA and PhcR were further analyzed utilizing orbital energies such as HOMO and LUMO, followed by molecular dynamics simulations of the complexes for 100 ns to determine the ligands binding stability. The findings indicate that ZINC000014762512 and ZINC000011865192 may be capable of inhibiting both PhcA and PhcR. We believe that, after further validation, these compounds may have the potential to disrupt bacterial quorum sensing and thus control this devastating phytopathogenic bacterial pathogen.
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Affiliation(s)
- Sunil Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, India; (K.A.); (M.V.S.R.); (D.M.); (U.B.S.)
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India;
- Correspondence: (S.K.); (H.V.S.)
| | - Khurshid Ahmad
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, India; (K.A.); (M.V.S.R.); (D.M.); (U.B.S.)
| | - Santosh Kumar Behera
- National Institute of Pharmaceutical Education and Research, Ahmedabad 382355, India;
| | - Dipak T. Nagrale
- ICAR-Central Institute for Cotton Research, Nagpur 440010, India;
| | - Anurag Chaurasia
- ICAR-Indian Institute of Vegetable Research, Varanasi 221305, India;
| | - Manoj Kumar Yadav
- Department of Bioinformatics, SRM University, Sonepat 131029, India;
| | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India;
| | - Yachana Jha
- N. V. Patel College of Pure and Applied Sciences, S.P. University, Anand 388315, India;
| | - Mahendra Vikram Singh Rajawat
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, India; (K.A.); (M.V.S.R.); (D.M.); (U.B.S.)
| | - Deepti Malviya
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, India; (K.A.); (M.V.S.R.); (D.M.); (U.B.S.)
| | - Udai B. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, India; (K.A.); (M.V.S.R.); (D.M.); (U.B.S.)
| | - Raja Shankar
- ICAR-IIHR, Hessaraghatta Lake Post, Bengaluru 560089, India;
| | - Minaketan Tripathy
- Department of Pharmacy, Sitaram Kashyap College of Pharmacy, Rahod 495556, India;
| | - Harsh Vardhan Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, India; (K.A.); (M.V.S.R.); (D.M.); (U.B.S.)
- Correspondence: (S.K.); (H.V.S.)
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Mahata S, Behera SK, Kumar S, Sahoo PK, Sarkar S, Fazil MHUT, Nasare VD. In-silico and in-vitro investigation of STAT3-PIM1 heterodimeric complex: Its mechanism and inhibition by curcumin for cancer therapeutics. Int J Biol Macromol 2022; 208:356-366. [DOI: 10.1016/j.ijbiomac.2022.03.137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 01/19/2023]
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Computational identification of 2,4-disubstituted amino-pyrimidines as L858R/T790M-EGFR double mutant inhibitors using pharmacophore mapping, molecular docking, binding free energy calculation, DFT study and molecular dynamic simulation. In Silico Pharmacol 2021; 9:54. [PMID: 34631361 DOI: 10.1007/s40203-021-00113-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022] Open
Abstract
Pharmacophore modelling studies have been performed for a series of 2,4-disubstituted-pyrimidines derivatives as EGFR L858R/T790M tyrosine kinase inhibitors. The high scoring AARR.15 hypothesis was selected as the best pharmacophore model with the highest survival score of 3.436 having two hydrogen bond acceptors and two aromatic ring features. Pharmacophore-based virtual screening followed by structure-based yielded the six molecules (ZINC17013227, ZINC17013215, ZINC9573324, ZINC9573445, ZINC24023331 and ZINC17013503) from the ZINC database with significant in silico predicted activity and strong binding affinity towords the EGFR L858R/T790M tyrosine kinase. In silico toxicity and cytochrome profiling indicates that all the 06 virtually screened compounds were substrate/inhibitors of the CYP-3A4 metabolizing enzyme and were non-carcinogenic and devoid of Ames mutagenesis. Density functional theory (DFT) and molecular dynamic (MD) simulation further validated the obtained hits. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00113-x.
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Safarizadeh H, Garkani-Nejad Z. Investigation of MI-2 analogues as MALT1 inhibitors to treat of diffuse large B-Cell lymphoma through combined molecular dynamics simulation, molecular docking and QSAR techniques and design of new inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Yagci ZB, Esvap E, Ozkara HA, Ulgen KO, Olmez EO. Inflammatory response and its relation to sphingolipid metabolism proteins: Chaperones as potential indirect anti-inflammatory agents. MOLECULAR CHAPERONES IN HUMAN DISORDERS 2019; 114:153-219. [DOI: 10.1016/bs.apcsb.2018.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Vora J, Patel S, Sinha S, Sharma S, Srivastava A, Chhabria M, Shrivastava N. Structure based virtual screening, 3D-QSAR, molecular dynamics and ADMET studies for selection of natural inhibitors against structural and non-structural targets of Chikungunya. J Biomol Struct Dyn 2018; 37:3150-3161. [PMID: 30114965 DOI: 10.1080/07391102.2018.1509732] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The transmission of mosquito-borne Chikungunya virus (CHIKV) has large epidemics worldwide. Till date, there are neither anti-viral drugs nor vaccines available for the treatment of Chikungunya. Accumulated evidences suggest that some natural compounds i.e., Epigallocatechin gallate, Harringtonine, Apigenin, Chrysin, Silybin, etc. have the capability to inhibit CHIKV replication in vitro. Natural compounds are known to possess less or no side effects. Therefore, natural compound in its purified or crude extracts form could be the preeminent and safe mode of therapies for Chikungunya. Wet lab screening and identification of natural compounds against Chikungunya targets is a time consuming and expensive exercise. In the present study, we used in silico techniques like receptor-ligand docking, Molecular dynamic (MD), Three Dimensional Quantitative Structure Activity Relation (3D-QSAR) and ADME properties to screen out potential compounds. Aim of the study is to identify potential lead/s from natural sources using in silico techniques that can be developed as a drug like molecule against Chikungunya infection and replication. Three softwares were used for molecular docking studies. Potential ligands selected by docking studies were subsequently subjected 3D-QSAR studies to predict biological activity. Based on docking scores and pIC50 value, potential anti-Chikungunya compounds were identified. Best docked receptor-ligands were also subjected to MD for more accurate estimation. Lipinski's rule and ADME studies of the identified compounds were also studied to assess their drug likeness properties. Results of in silico findings, led to identification of few best fit compounds of natural origin against targets of Chikungunya virus which may lead to discovery of new drugs for Chikungunya. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jaykant Vora
- a Department of Pharmacognosy and Phytochemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Ahmedabad , Gujarat , India.,b Registered Ph.D. student of Gujarat University , Ahmedabad , Gujarat , India
| | - Shivani Patel
- c Department of Pharmaceutical Chemistry , L.M. College of Pharmacy , Ahmedabad , Gujarat , India
| | - Sonam Sinha
- a Department of Pharmacognosy and Phytochemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Ahmedabad , Gujarat , India.,b Registered Ph.D. student of Gujarat University , Ahmedabad , Gujarat , India
| | - Sonal Sharma
- a Department of Pharmacognosy and Phytochemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Ahmedabad , Gujarat , India
| | - Anshu Srivastava
- a Department of Pharmacognosy and Phytochemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Ahmedabad , Gujarat , India
| | - Mahesh Chhabria
- c Department of Pharmaceutical Chemistry , L.M. College of Pharmacy , Ahmedabad , Gujarat , India
| | - Neeta Shrivastava
- a Department of Pharmacognosy and Phytochemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Ahmedabad , Gujarat , India
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Makhouri FR, Ghasemi JB. In Silico Studies in Drug Research Against Neurodegenerative Diseases. Curr Neuropharmacol 2018; 16:664-725. [PMID: 28831921 PMCID: PMC6080098 DOI: 10.2174/1570159x15666170823095628] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/24/2017] [Accepted: 08/16/2017] [Indexed: 01/14/2023] Open
Abstract
Background Neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral sclerosis, Parkinson's disease (PD), spinal cerebellar ataxias, and spinal and bulbar muscular atrophy are described by slow and selective degeneration of neurons and axons in the central nervous system (CNS) and constitute one of the major challenges of modern medicine. Computer-aided or in silico drug design methods have matured into powerful tools for reducing the number of ligands that should be screened in experimental assays. Methods In the present review, the authors provide a basic background about neurodegenerative diseases and in silico techniques in the drug research. Furthermore, they review the various in silico studies reported against various targets in neurodegenerative diseases, including homology modeling, molecular docking, virtual high-throughput screening, quantitative structure activity relationship (QSAR), hologram quantitative structure activity relationship (HQSAR), 3D pharmacophore mapping, proteochemometrics modeling (PCM), fingerprints, fragment-based drug discovery, Monte Carlo simulation, molecular dynamic (MD) simulation, quantum-mechanical methods for drug design, support vector machines, and machine learning approaches. Results Detailed analysis of the recently reported case studies revealed that the majority of them use a sequential combination of ligand and structure-based virtual screening techniques, with particular focus on pharmacophore models and the docking approach. Conclusion Neurodegenerative diseases have a multifactorial pathoetiological origin, so scientists have become persuaded that a multi-target therapeutic strategy aimed at the simultaneous targeting of multiple proteins (and therefore etiologies) involved in the development of a disease is recommended in future.
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Affiliation(s)
| | - Jahan B Ghasemi
- Chemistry Department, Faculty of Sciences, University of Tehran, Tehran, Iran
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Patel S, Modi P, Ranjan V, Chhabria M. Structure-based design, synthesis and evaluation of 2,4-diaminopyrimidine derivatives as novel caspase-1 inhibitors. Bioorg Chem 2018; 78:258-268. [DOI: 10.1016/j.bioorg.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/12/2018] [Accepted: 03/18/2018] [Indexed: 12/20/2022]
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Patel S, Modi P, Chhabria M. Rational approach to identify newer caspase-1 inhibitors using pharmacophore based virtual screening, docking and molecular dynamic simulation studies. J Mol Graph Model 2018; 81:106-115. [DOI: 10.1016/j.jmgm.2018.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/11/2018] [Accepted: 02/18/2018] [Indexed: 10/17/2022]
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Yilmazer B, Yagci ZB, Bakar E, Ozden B, Ulgen K, Ozkirimli E. Investigation of novel pharmacological chaperones for Gaucher Disease. J Mol Graph Model 2017; 76:364-378. [DOI: 10.1016/j.jmgm.2017.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/16/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
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Bayraktar O, Ozkirimli E, Ulgen K. Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site. Comput Biol Chem 2017; 69:64-76. [PMID: 28587987 DOI: 10.1016/j.compbiolchem.2017.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/29/2017] [Accepted: 05/24/2017] [Indexed: 02/03/2023]
Abstract
The sphingosine kinase 1 (SK1)/sphingosine-1-phosphate (S1P) signaling pathway is a crucial target for numerous human diseases from cancer to cardiovascular diseases. However, available SK1 inhibitors that target the active site suffer from poor potency, selectivity and pharmacokinetic properties. The selectivity issue of the kinases, which share a highly-conserved ATP-pocket, can be overcome by targeting the less-conserved allosteric sites. SK1 is known to function minimally as a dimer; however, the crystal structure of the SK1 dimer has not been determined. In this study, a template-based algorithm implemented in PRISM was used to predict the SK1 dimer structure and then the possible allosteric sites at the dimer interface were determined via SiteMap. These sites were used in a virtual screening campaign that includes an integrated workflow of structure-based pharmacophore modeling, virtual screening, molecular docking, re-screening of common scaffolds to propose a series of compounds with different scaffolds as potential allosteric SK1 inhibitors. Finally, the stability of the SK1-ligand complexes was analyzed by molecular dynamics simulations. As a final outcome, ligand 7 having a 4,9-dihydro-1H-purine scaffold and ligand 12 having a 2,3,4,9-tetrahydro-1H-β-carboline scaffold were found to be potential selective inhibitors for SK1.
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Affiliation(s)
- Ozge Bayraktar
- Department of Computational Science and Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey
| | - Elif Ozkirimli
- Department of Computational Science and Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey; Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey.
| | - Kutlu Ulgen
- Department of Computational Science and Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey; Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey.
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Sanllehí P, Abad JL, Casas J, Bujons J, Delgado A. Bacterial versus human sphingosine-1-phosphate lyase (S1PL) in the design of potential S1PL inhibitors. Bioorg Med Chem 2016; 24:4381-4389. [DOI: 10.1016/j.bmc.2016.07.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 12/28/2022]
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Blankenbach KV, Schwalm S, Pfeilschifter J, Meyer Zu Heringdorf D. Sphingosine-1-Phosphate Receptor-2 Antagonists: Therapeutic Potential and Potential Risks. Front Pharmacol 2016; 7:167. [PMID: 27445808 PMCID: PMC4914510 DOI: 10.3389/fphar.2016.00167] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/03/2016] [Indexed: 12/26/2022] Open
Abstract
The sphingosine-1-phosphate (S1P) signaling system with its specific G-protein-coupled S1P receptors, the enzymes of S1P metabolism and the S1P transporters, offers a multitude of promising targets for drug development. Until today, drug development in this area has nearly exclusively focused on (functional) antagonists at the S1P1 receptor, which cause a unique phenotype of immunomodulation. Accordingly, the first-in class S1P1 receptor modulator, fingolimod, has been approved for the treatment of relapsing-remitting multiple sclerosis, and novel S1P1 receptor (functional) antagonists are being developed for autoimmune and inflammatory diseases such as psoriasis, inflammatory bowel disease, lupus erythematodes, or polymyositis. Besides the S1P1 receptor, also S1P2 and S1P3 are widely expressed and regulate many diverse functions throughout the body. The S1P2 receptor, in particular, often exerts cellular functions which are opposed to the functions of the S1P1 receptor. As a consequence, antagonists at the S1P2 receptor have the potential to be useful in a contrasting context and different areas of indication compared to S1P1 antagonists. The present review will focus on the therapeutic potential of S1P2 receptor antagonists and discuss their opportunities as well as their potential risks. Open questions and areas which require further investigations will be emphasized in particular.
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Affiliation(s)
- Kira V Blankenbach
- Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany
| | - Stephanie Schwalm
- Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany
| | - Josef Pfeilschifter
- Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany
| | - Dagmar Meyer Zu Heringdorf
- Institut für Allgemeine Pharmakologie und Toxikologie, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Germany
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