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Mavroeidi P, Zorba LP, Tzouras NV, Neofotistos SP, Georgiou N, Sahin K, Şentürk M, Durdagi S, Vougioukalakis GC, Mavromoustakos T. Are Terminal Alkynes Necessary for MAO-A/MAO-B Inhibition? A New Scaffold Is Revealed. Molecules 2024; 29:2486. [PMID: 38893361 PMCID: PMC11174103 DOI: 10.3390/molecules29112486] [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: 04/03/2024] [Revised: 05/15/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
A versatile family of quaternary propargylamines was synthesized employing the KA2 multicomponent reaction, through the single-step coupling of a number of amines, ketones, and terminal alkynes. Sustainable synthetic procedures using transition metal catalysts were employed in all cases. The inhibitory activity of these molecules was evaluated against human monoaminoxidase (hMAO)-A and hMAO-B enzymes and was found to be significant. The IC50 values for hMAO-B range from 152.1 to 164.7 nM while the IC50 values for hMAO-A range from 765.6 to 861.6 nM. Furthermore, these compounds comply with Lipinski's rule of five and exhibit no predicted toxicity. To understand their binding properties with the two target enzymes, key interactions were studied using molecular docking, all-atom molecular dynamics (MD) simulations, and MM/GBSA binding free energy calculations. Overall, herein, the reported family of propargylamines exhibits promise as potential treatments for neurodegenerative disorders, such as Parkinson's disease. Interestingly, this is the first time a propargylamine scaffold bearing an internal alkyne has been reported to show activity against monoaminoxidases.
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Affiliation(s)
- Panagiou Mavroeidi
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (P.M.); (L.P.Z.); (N.V.T.); (S.P.N.); (N.G.)
| | - Leandros P. Zorba
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (P.M.); (L.P.Z.); (N.V.T.); (S.P.N.); (N.G.)
| | - Nikolaos V. Tzouras
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (P.M.); (L.P.Z.); (N.V.T.); (S.P.N.); (N.G.)
| | - Stavros P. Neofotistos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (P.M.); (L.P.Z.); (N.V.T.); (S.P.N.); (N.G.)
| | - Nikitas Georgiou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (P.M.); (L.P.Z.); (N.V.T.); (S.P.N.); (N.G.)
| | - Kader Sahin
- Department of Analytical Chemistry, School of Pharmacy, Bahcesehir University, 34349 Istanbul, Turkey;
| | - Murat Şentürk
- Department of Biochemistry, Faculty of Pharmacy, Agri Ibrahim Cecen University, 04100 Agri, Turkey;
| | - Serdar Durdagi
- Molecular Therapy Laboratory, Department of Pharmaceutical Chemistry, School of Pharmacy, Bahcesehir University, 34349 Istanbul, Turkey
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
- Laboratory for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahcesehir University, 34349 Istanbul, Turkey
| | - Georgios C. Vougioukalakis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (P.M.); (L.P.Z.); (N.V.T.); (S.P.N.); (N.G.)
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (P.M.); (L.P.Z.); (N.V.T.); (S.P.N.); (N.G.)
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Mousavi H, Rimaz M, Zeynizadeh B. Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[ h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases. ACS Chem Neurosci 2024; 15:1828-1881. [PMID: 38647433 DOI: 10.1021/acschemneuro.4c00055] [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] [Indexed: 04/25/2024] Open
Abstract
Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3β, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.
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Affiliation(s)
- Hossein Mousavi
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran 19395-3697, Iran
| | - Behzad Zeynizadeh
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
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3
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Haddad S, Oktay L, Erol I, Şahin K, Durdagi S. Utilizing Heteroatom Types and Numbers from Extensive Ligand Libraries to Develop Novel hERG Blocker QSAR Models Using Machine Learning-Based Classifiers. ACS OMEGA 2023; 8:40864-40877. [PMID: 37929100 PMCID: PMC10620895 DOI: 10.1021/acsomega.3c06074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/13/2023] [Indexed: 11/07/2023]
Abstract
The human ether-à-go-go-related gene (hERG) channel plays a crucial role in membrane repolarization. Any disruptions in its function can lead to severe cardiovascular disorders such as long QT syndrome (LQTS), which increases the risk of serious cardiovascular problems such as tachyarrhythmia and sudden cardiac death. Drug-induced LQTS is a significant concern and has resulted in drug withdrawals from the market in the past. The main objective of this study is to pinpoint crucial heteroatoms present in ligands that initiate interactions leading to the effective blocking of the hERG channel. To achieve this aim, ligand-based quantitative structure-activity relationships (QSAR) models were constructed using extensive ligand libraries, considering the heteroatom types and numbers, and their associated hERG channel blockage pIC50 values. Machine learning-assisted QSAR models were developed to analyze the key structural components influencing compound activity. Among the various methods, the KPLS method proved to be the most efficient, allowing the construction of models based on eight distinct fingerprints. The study delved into investigating the influence of heteroatoms on the activity of hERG blockers, revealing their significant role. Furthermore, by quantifying the effect of heteroatom types and numbers on ligand activity at the hERG channel, six compound pairs were selected for molecular docking. Subsequent molecular dynamics simulations and per residue MM/GBSA calculations were performed to comprehensively analyze the interactions of the selected pair compounds.
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Affiliation(s)
- Safa Haddad
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahçeşehir
University, Istanbul 34353, Turkey
- Computational
Drug Design Center (HITMER), Bahçeşehir
University, Istanbul 34353, Turkey
| | - Lalehan Oktay
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahçeşehir
University, Istanbul 34353, Turkey
- Computational
Drug Design Center (HITMER), Bahçeşehir
University, Istanbul 34353, Turkey
| | - Ismail Erol
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahçeşehir
University, Istanbul 34353, Turkey
- Computational
Drug Design Center (HITMER), Bahçeşehir
University, Istanbul 34353, Turkey
| | - Kader Şahin
- Department
of Analytical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul 34734, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahçeşehir
University, Istanbul 34353, Turkey
- Computational
Drug Design Center (HITMER), Bahçeşehir
University, Istanbul 34353, Turkey
- Molecular
Therapy Lab, Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul 34353, Turkey
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Abstract
Proper elucidation of drug-target interaction is one of the most significant steps at the early stages of the drug development research. Computer-aided drug design tools have substantial contribution to this stage. In this chapter, we specifically concentrate on the computational methods widely used to develop reversible inhibitors for monoamine oxidase (MAO) isozymes. In this context, current computational techniques in identifying the best drug candidates showing high potency are discussed. The protocols of structure-based drug design methodologies, namely, molecular docking, in silico screening, and molecular dynamics simulations, are presented. Employing case studies of safinamide binding to MAO B, we demonstrate how to use AutoDock 4.2.6 and NAMD software packages.
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Affiliation(s)
- Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey.
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, Istanbul, Turkey
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Dehghan M, Fathinejad F, Farzaei MH, Barzegari E. In silico unraveling of molecular anti-neurodegenerative profile of Citrus medica flavonoids against novel pharmaceutical targets. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02496-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jalal K, Khan F, Nawaz S, Afroz R, Khan K, Ali SB, Hao L, Khan SA, Kazi M, Uddin R, Haleem DJ. Anxiolytic, anti-nociceptive and body weight reducing effects of L-lysine in rats: Relationship with brain serotonin an In-Vivo and In-Silico study. Biomed Pharmacother 2022; 152:113235. [PMID: 35696944 DOI: 10.1016/j.biopha.2022.113235] [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: 03/24/2022] [Revised: 05/26/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
L-lysine (L-lys) had long been comprehended as an essential amino acid for humans. There were reports that the absence or inadequate availability of L-lys in the diet may lead to mental and physical impairments. The present study was designed to explore the effects of L-lys on body weight changes, cumulative food intake, anxiety-like behavior and pain perception in rats. 5-Hydroxytryptamine (5-HT, serotonin) metabolism, and tryptophan (Trp) levels in the midbrain (MB), hippocampus (HP), and prefrontal cortex (PFC) were also determined. Animals were treated with L-lys in doses of 0.5 g/kg and 1 g/kg for 20 days and behavioral studies were performed on day 1st and day 20th. After monitoring behaviors on day 20th, animals were killed to collect the serum and brain regions MB, HP and PFC. 5-HT metabolism and Trp levels were determined by HPLC-EC. The treatment produce no effect on food intakes but body weights were reduced. 20 days administration of L-lys produced an anxiolytic effect and increased exploratory activity on day 1st. Repeated administration of L-lys increased 5-HT levels in the PFC and HP. 5-Hydroxyindoleacetic acid (5-HIAA), the metabolite of 5-HT, decreased in the HP. Trp, the precourser of 5-HT, decreased in the PFC. Results suggested a decrease in 5-HT degredation in enhancing 5-HT levels. Results of in-silico analysis showed that lysine had a potential binding affinity for MAO (monoamine oxidase) A and B with an energy of (-4.8 kcal/mol and -5.3 kcal/mol) respectively. The molecular dynamic simulation study revealed the stability of L-lys after 10 ns for each protein. Conclusively, the present study showed that L-lys produced an anxiolytic effect and reduced body weight. These beneficial effects were associated with an increase in 5-HT levels in the PFC and HP. In-silico analysis suggested that 5-HT increase were due to the binding of L-lys with MAOs resulting in an inhibition of the degradation of monoamine.
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Affiliation(s)
- Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Faisal Khan
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Shazia Nawaz
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Rushda Afroz
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sadia Basharat Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Liangliang Hao
- Hospital of Chengdu University of Traditional Chinese Medicine, No.39 Shi-er-qiao Road, Chengdu, PR China
| | - Saeed Ahmad Khan
- Department of Pharmacy, Kohat University of Science and Technology, KP, Pakistan; Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin,78712, USA
| | - Mohsin Kazi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Darakhshan Jabeen Haleem
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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Durdagi S, Orhan MD, Aksoydan B, Calis S, Dogan B, Sahin K, Shahraki A, Iyison NB, Avsar T. Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2: A Combined in silico and in vitro Study. Mol Inform 2022; 41:e2100062. [PMID: 34529322 PMCID: PMC8646260 DOI: 10.1002/minf.202100062] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022]
Abstract
In the current study, we used 7922 FDA approved small molecule drugs as well as compounds in clinical investigation from NIH's NPC database in our drug repurposing study. SARS-CoV-2 main protease as well as Spike protein/ACE2 targets were used in virtual screening and top-100 compounds from each docking simulations were considered initially in short molecular dynamics (MD) simulations and their average binding energies were calculated by MM/GBSA method. Promising hit compounds selected based on average MM/GBSA scores were then used in long MD simulations. Based on these numerical calculations following compounds were found as hit inhibitors for the SARS-CoV-2 main protease: Pinokalant, terlakiren, ritonavir, cefotiam, telinavir, rotigaptide, and cefpiramide. In addition, following 3 compounds were identified as inhibitors for Spike/ACE2: Denopamine, bometolol, and rotigaptide. In order to verify the predictions of in silico analyses, 4 compounds (ritonavir, rotigaptide, cefotiam, and cefpiramide) for the main protease and 2 compounds (rotigaptide and denopamine) for the Spike/ACE2 interactions were tested by in vitro experiments. While the concentration-dependent inhibition of the ritonavir, rotigaptide, and cefotiam was observed for the main protease; denopamine was effective at the inhibition of Spike/ACE2 binding.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations LaboratoryDepartment of BiophysicsSchool of MedicineBahcesehir University34734IstanbulTurkey
- Neuroscience ProgramGraduate School of Health SciencesBahçeşehir University34353IstanbulTurkey
- Virtual Drug Screening and Development LaboratorySchool of MedicineBahcesehir University34734IstanbulTurkey
- Head of Department of Basic Medical SciencesHead of Department of BiophysicsSchool of MedicineBahcesehir UniversityDurdagi Research Group (DRG)34734IstanbulTurkey
| | - Muge Didem Orhan
- Department of Medical BiologySchool of MedicineBahcesehir University34734IstanbulTurkey
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations LaboratoryDepartment of BiophysicsSchool of MedicineBahcesehir University34734IstanbulTurkey
- Neuroscience ProgramGraduate School of Health SciencesBahçeşehir University34353IstanbulTurkey
| | - Seyma Calis
- Department of Medical BiologySchool of MedicineBahcesehir University34734IstanbulTurkey
| | - Berna Dogan
- Computational Biology and Molecular Simulations LaboratoryDepartment of BiophysicsSchool of MedicineBahcesehir University34734IstanbulTurkey
| | - Kader Sahin
- Computational Biology and Molecular Simulations LaboratoryDepartment of BiophysicsSchool of MedicineBahcesehir University34734IstanbulTurkey
| | - Aida Shahraki
- Computational Biology and Molecular Simulations LaboratoryDepartment of BiophysicsSchool of MedicineBahcesehir University34734IstanbulTurkey
- Department of Molecular Biology and GeneticsBogazici University34470IstanbulTurkey
| | - Necla Birgül Iyison
- Department of Molecular Biology and GeneticsBogazici University34470IstanbulTurkey
| | - Timucin Avsar
- Department of Medical BiologySchool of MedicineBahcesehir University34734IstanbulTurkey
- Head of Department of Medical Biology
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Dhanabalan AK, Subaraja M, Palanichamy K, Velmurugan D, Gunasekaran K. Identification of a Chlorogenic Ester as a Monoamine Oxidase (MAO-B) Inhibitor by Integrating "Traditional and Machine Learning" Virtual Screening and In Vitro as well as In Vivo Validation: A Lead against Neurodegenerative Disorders? ACS Chem Neurosci 2021; 12:3690-3707. [PMID: 34553601 DOI: 10.1021/acschemneuro.1c00430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Parkinson's disease (PD) is the furthermost motor disorder of adult-onset dementia connected to memory and other cognitive abilities. Monoamine oxidases (MAOs) have gained significant attention in recent years owing to their possible therapeutic use against PD. Expression of MAO-B has been found to be elevated in PD patients for increased uptake of dopamine, producing hydrogen peroxide and finally causing neuronal injury. In this work, two new compounds have been identified as leads against MAO-B, and one of those compounds has been validated in vitro and in vivo. From the Protein Data Bank, MAO-B protein structures complexed with selegiline, 6-hydroxy-N-propargyl-1(R)-aminoindan, or a chromen derivative have been selected as templates for shape-based virtual screening (SB-VS) against the Traditional Chinese Medicinal (TCM) natural database. In parallel, using machine learning, a molecular-descriptor-based support vector model (SVM) was prepared and screened. For this purpose, naïve Bayesian, logistic regression, and random forest strategies were employed with the best specific molecular descriptor, which yielded a model with an overall accuracy (Q) of 0.81. Two common hit compounds lead-1 and lead-2 resulting from both shape and SVM screenings were analyzed through molecular docking and molecular dynamics (MD) simulation (200 ns). Also, from trajectory analysis such as molecular mechanics generalized Born surface area (MMGB/SA) and the residual interaction network (RIN) analyzer, both leads were found to bind at the active site with a favorable correlated motion, including domain movements. Lead-2, which is a chlorogenic ester, was synthesized and found to have no cytotoxic effect up to 50 μg/mL on Neuro-2A cells. The significant reactive oxygen species (ROS) scavenging activity by lead-2 could be correlated to its neuroprotective efficacy. Its capacity to inhibit human MAO-B through a competitive mode could be observed. An experimental zebra fish model confirms the neuroprotection by lead-2 by assessing the locomotor activities under malathion influence and treatment of lead-2. Also, histopathology analysis revealed that lead-2 could slow down degeneration in the brain. The present study emphasizes that integrating machine learning in parallel with traditional virtual screening may be useful to identify effective lead compounds for a given target.
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Affiliation(s)
- Anantha Krishnan Dhanabalan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Mamangam Subaraja
- Vivekanandha College of Arts and Sciences for Women (Autonomous), Tiruchengode 637205, Tamil Nadu, India
| | - Kuppusamy Palanichamy
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Krishnasamy Gunasekaran
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
- Bioinformatics Infrastructure Facility, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
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9
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Cruz-Vicente P, Passarinha LA, Silvestre S, Gallardo E. Recent Developments in New Therapeutic Agents against Alzheimer and Parkinson Diseases: In-Silico Approaches. Molecules 2021; 26:2193. [PMID: 33920326 PMCID: PMC8069930 DOI: 10.3390/molecules26082193] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
Neurodegenerative diseases (ND), including Alzheimer's (AD) and Parkinson's Disease (PD), are becoming increasingly more common and are recognized as a social problem in modern societies. These disorders are characterized by a progressive neurodegeneration and are considered one of the main causes of disability and mortality worldwide. Currently, there is no existing cure for AD nor PD and the clinically used drugs aim only at symptomatic relief, and are not capable of stopping neurodegeneration. Over the last years, several drug candidates reached clinical trials phases, but they were suspended, mainly because of the unsatisfactory pharmacological benefits. Recently, the number of compounds developed using in silico approaches has been increasing at a promising rate, mainly evaluating the affinity for several macromolecular targets and applying filters to exclude compounds with potentially unfavorable pharmacokinetics. Thus, in this review, an overview of the current therapeutics in use for these two ND, the main targets in drug development, and the primary studies published in the last five years that used in silico approaches to design novel drug candidates for AD and PD treatment will be presented. In addition, future perspectives for the treatment of these ND will also be briefly discussed.
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Affiliation(s)
- Pedro Cruz-Vicente
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Sciences and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Luís A. Passarinha
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Sciences and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
| | - Samuel Silvestre
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Eugenia Gallardo
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6201-001 Covilhã, Portugal;
- Laboratory of Pharmaco-Toxicology—UBIMedical, University of Beira Interior, 6200-001 Covilhã, Portugal
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Comert Onder F, Kahraman N, Bellur Atici E, Cagir A, Kandemir H, Tatar G, Taskin Tok T, Kara G, Karliga B, Durdagi S, Ay M, Ozpolat B. Target-Driven Design of a Coumarinyl Chalcone Scaffold Based Novel EF2 Kinase Inhibitor Suppresses Breast Cancer Growth In Vivo. ACS Pharmacol Transl Sci 2021; 4:926-940. [PMID: 33860211 DOI: 10.1021/acsptsci.1c00030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Indexed: 11/28/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K) is an unusual alpha kinase involved in protein synthesis through phosphorylation of elongation factor 2 (EF2). eEF-2K is highly overexpressed in breast cancer, and its activity is associated with significantly shortened patient survival and proven to be a potential molecular target in breast cancer. The crystal structure of eEF-2K remains unknown, and there is no potent, safe, and effective inhibitor available for clinical applications. We designed and synthesized several generations of potential inhibitors. The effect of the inhibitors at the binding pocket of eEF-2K was analyzed after developing a 3D target model by using a domain of another α-kinase called myosin heavy-chain kinase A (MHCKA) that closely resembles eEF-2K. In silico studies showed that compounds with a coumarin-chalcone core have high predicted binding affinities for eEF-2K. Using in vitro studies in highly aggressive and invasive (MDA-MB-436, MDA-MB-231, and BT20) and noninvazive (MCF-7) breast cancer cells, we identified a lead compound that was highly effective in inhibiting eEF-2K activity at submicromolar concentrations and at inhibiting cell proliferation by induction of apoptosis with no toxicity in normal breast epithelial cells. In vivo systemic administration of the lead compound encapsulated in single lipid-based liposomal nanoparticles twice a week significantly suppressed growth of MDA-MB-231 tumors in orthotopic breast cancer models in nude mice with no observed toxicity. In conclusion, our study provides a highly potent and in vivo effective novel small-molecule eEF-2K inhibitor that may be used as a molecularly targeted therapy breast cancer or other eEF-2K-dependent tumors.
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Affiliation(s)
- Ferah Comert Onder
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States.,Department of Medical Biology, Çanakkale Onsekiz Mart University, Faculty of Medicine, 17020 Canakkale, Turkey.,Department of Chemistry, Natural Products and Drug Research Laboratory, Faculty of Science and Arts, Çanakkale Onsekiz Mart University, 17020 Canakkale, Turkey
| | - Nermin Kahraman
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States
| | | | - Ali Cagir
- Izmir Institute of Technology, Department of Chemistry, Bioorganic and Medicinal Chemistry Laboratory, 35430 Urla, Turkey
| | - Hakan Kandemir
- Tekirdag Namik Kemal University, Department of Chemistry, 59030 Tekirdag, Turkey
| | - Gizem Tatar
- Gaziantep University, Institute of Health Sciences, Department of Bioinformatics and Computational Biology, 27310 Gaziantep, Turkey
| | - Tugba Taskin Tok
- Gaziantep University, Institute of Health Sciences, Department of Bioinformatics and Computational Biology, 27310 Gaziantep, Turkey.,Gaziantep University, Faculty of Arts and Sciences, Department of Chemistry, 27310 Gaziantep, Turkey
| | - Goknur Kara
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States
| | | | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory, Bahcesehir University, 34734 Istanbul, Turkey
| | - Mehmet Ay
- Department of Chemistry, Natural Products and Drug Research Laboratory, Faculty of Science and Arts, Çanakkale Onsekiz Mart University, 17020 Canakkale, Turkey
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States.,Center for RNA Interference and Non-Coding RNAs, The University of Texas, MD Anderson Cancer Center, Houston, Texas 77030, United States
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11
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Is YS, Aksoydan B, Senturk M, Yurtsever M, Durdagi S. Integrated Binary QSAR-Driven Virtual Screening and In Vitro Studies for Finding Novel hMAO-B-Selective Inhibitors. J Chem Inf Model 2020; 60:4047-4055. [PMID: 32672456 DOI: 10.1021/acs.jcim.0c00169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The increased activity of monoamine oxidase (MAO) enzymes may lead to serious consequences since they reduce the level of neurotransmitters and are associated with severe neurodegenerative diseases. The inhibition of this enzyme, especially the B isoform, plays a vital role in the treatment of Parkinson's disease (PD). This study is aimed to find novel human MAO-B (hMAO-B) selective inhibitors. A total of 256.750 compounds from the Otava small molecules database were virtually screened gradually by employing several screening techniques for this purpose. Initially, a high-throughput virtual screening (HTVS) method was employed, and 10% of the molecules having high docking scores were subjected to binary QSAR models for further screening of their therapeutic activities against PD, Alzheimer's disease (AD), and depression as well as for their toxicity and pharmacokinetic properties. Then, enzyme selectivity of the ligands towards the A and B forms that passed through all the filters were studied using the induced-fit docking method and molecular dynamics simulations. At the end of this exhaustive research, we identified two hit molecules ligand 3 (Otava ID: 7131545) and ligand 4 (Otava ID: 7566820). Based on the in vitro results, these two compounds (ligands 3 and 4) together with ligands 1 and 2 found in our previous study showed activity at the nanomolar (nM) level, and the results indicated that these four ligands inhibit hMAO-B better than the FDA-approved drug selegiline.
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Affiliation(s)
- Yusuf Serhat Is
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734 Istanbul, Turkey.,Department of Chemistry, Istanbul Technical University, 34467 Istanbul, Turkey.,Department of Chemical Technology, Istanbul Gedik University, 34876 Istanbul, Turkey
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734 Istanbul, Turkey.,Neuroscience Program, Graduate School of Health Sciences, Bahçeşehir University, 34349 Istanbul, Turkey
| | - Murat Senturk
- Department of Biochemistry, Faculty of Pharmacy, Agri Ibrahim Cecen University, 04100 Agri, Turkey
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, 34467 Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734 Istanbul, Turkey.,Neuroscience Program, Graduate School of Health Sciences, Bahçeşehir University, 34349 Istanbul, Turkey.,Virtual Drug Screening and Development Laboratory, School of Medicine, Bahcesehir University, 34734 Istanbul, Turkey
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12
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Abstract
Currently, the world suffers from a new coronavirus SARS-CoV-2 that causes COVID-19. Therefore, there is a need for the urgent development of novel drugs and vaccines for COVID-19. Since it can take years to develop new drugs against this disease, here we used a hybrid combined molecular modeling approach in virtual drug screening repurposing study to identify new compounds against this disease. One of the important SARS-CoV-2 targets namely type 2 transmembrane serine protease (TMPRSS2) was screened with NPC’s NIH small molecule library which includes approved drugs by FDA and compounds in clinical investigation. We used 6654 small molecules in molecular docking and top-50 docking scored compounds were initially used in short (10-ns) molecular dynamics (MD) simulations. Based on average MM/GBSA binding free energy results, long (100-ns) MD simulations were employed for the identified hits. Both binding energy results as well as crucial residues in ligand binding were also compared with a positive control TMPRSS2 inhibitor, Camostat mesylate. Based on these numerical calculations we proposed a compound (benzquercin) as strong TMPRSS2 inhibitor. If these results can be validated by in vitro and in vivo studies, benzquercin can be considered to be used as inhibitor of TMPRSS2 at the clinical studies.
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Affiliation(s)
- Serdar DurdaĞi
- Department of Biophysics, Computational Biology and Molecular Simulations Laboratory, School of Medicine, Bahçeşehir University, İstanbul Turkey
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13
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Tutumlu G, Dogan B, Avsar T, Orhan MD, Calis S, Durdagi S. Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2. Front Chem 2020; 8:167. [PMID: 32328476 PMCID: PMC7160371 DOI: 10.3389/fchem.2020.00167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Antiapoptotic members of B-cell leukemia/lymphoma-2 (BCL-2) family proteins are one of the overexpressed proteins in cancer cells that are oncogenic targets. As such, targeting of BCL-2 family proteins raises hopes for new therapeutic discoveries. Thus, we used multistep screening and filtering approaches that combine structure and ligand-based drug design to identify new, effective BCL-2 inhibitors from a small molecule database (Specs SC), which includes more than 210,000 compounds. This database is first filtered based on binary “cancer-QSAR” model constructed with 886 training and 167 test set compounds and common 26 toxicity quantitative structure-activity relationships (QSAR) models. Predicted non-toxic compounds are considered for target-driven studies. Here, we applied two different approaches to filter and select hit compounds for further in vitro biological assays and human cell line experiments. In the first approach, a molecular docking and filtering approach is used to rank compounds based on their docking scores and only a few top-ranked molecules are selected for further long (100-ns) molecular dynamics (MD) simulations and in vitro tests. While docking algorithms are promising in predicting binding poses, they can be less prone to precisely predict ranking of compounds leading to decrease in the success rate of in silico studies. Hence, in the second approach, top-docking poses of each compound filtered through QSAR studies are subjected to initially short (1 ns) MD simulations and their binding energies are calculated via molecular mechanics generalized Born surface area (MM/GBSA) method. Then, the compounds are ranked based on their average MM/GBSA energy values to select hit molecules for further long MD simulations and in vitro studies. Additionally, we have applied text-mining approaches to identify molecules that contain “indol” phrase as many of the approved drugs contain indole and indol derivatives. Around 2700 compounds are filtered based on “cancer-QSAR” model and are then docked into BCL-2. Short MD simulations are performed for the top-docking poses for each compound in complex with BCL-2. The complexes are again ranked based on their MM/GBSA values to select hit molecules for further long MD simulations and in vitro studies. In total, seven molecules are subjected to biological activity tests in various human cancer cell lines as well as Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) assay. Inhibitory concentrations are evaluated, and biological activities and apoptotic potentials are assessed by cell culture studies. Four molecules are found to be limiting the proliferation capacity of cancer cells while increasing the apoptotic cell fractions.
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Affiliation(s)
- Gurbet Tutumlu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Timucin Avsar
- Department of Medical Biology, Bahcesehir University, School of Medicine, Istanbul, Turkey.,Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
| | - Muge Didem Orhan
- Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
| | - Seyma Calis
- Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Molecular Biology, Genetics and Biotechnology Graduate Program, Istanbul Technical University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.,Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
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14
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Ramesh M, Muthuraman A. Quantitative Structure-Activity Relationship (QSAR) Studies for the Inhibition of MAOs. Comb Chem High Throughput Screen 2020; 23:887-897. [PMID: 32208114 DOI: 10.2174/1386207323666200324173231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/20/2020] [Accepted: 02/04/2020] [Indexed: 11/22/2022]
Abstract
Monoamine oxidases are the crucial drug targets for the treatment of neurodegenerative disorders like depression, Parkinson's disease, and Alzheimer's disease. The enzymes catalyze the oxidative deamination of several monoamine containing neurotransmitters, i.e. serotonin (5-HT), melatonin, epinephrine, norepinephrine, phenylethylamine, benzylamine, dopamine, tyramine, etc. The oxidative reaction of monoamine oxidases results in the production of hydrogen peroxide that leads to the neurodegeneration process. Therefore, the inhibition of monoamine oxidases has shown a profound effect against neurodegenerative diseases. At present, the design and development of newer lead molecules for the inhibition of monoamine oxidases are under intensive research in the field of medicinal chemistry. Recently, the advancement in QSAR methodologies has shown considerable interest in the development of monoamine oxidase inhibitors. The present review describes the development of QSAR methodologies, and their role in the design of newer monoamine oxidase inhibitors. It will assist the medicinal chemist in the identification of selective and potent monoamine oxidase inhibitors from various chemical scaffolds.
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Affiliation(s)
- Muthusamy Ramesh
- Department of Pharmaceutical Analysis, Omega College of Pharmacy, Hyderabad-501 301, India
| | - Arunachalam Muthuraman
- Pharmacology Unit, Faculty of Pharmacy, AIMST University, Semeling, 08100 Bedong, Kedah Darul Aman, Malaysia
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15
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Comert Onder F, Durdagi S, Sahin K, Ozpolat B, Ay M. Design, Synthesis, and Molecular Modeling Studies of Novel Coumarin Carboxamide Derivatives as eEF-2K Inhibitors. J Chem Inf Model 2020; 60:1766-1778. [PMID: 32027127 DOI: 10.1021/acs.jcim.9b01083] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eukaryotic elongation factor-2 kinase (eEF-2K) is an unusual alpha kinase commonly upregulated in various human cancers, including breast, pancreatic, lung, and brain tumors. We have demonstrated that eEF-2K is relevant to poor prognosis and shorter patient survival in breast and lung cancers and validated it as a molecular target using genetic methods in related in vivo tumor models. Although several eEF-2K inhibitors have been published, none of them have shown to be potent and specific enough for translation into clinical trials. Therefore, development of highly effective novel inhibitors targeting eEF-2K is needed for clinical applications. However, currently, the crystal structure of eEF-2K is not known, limiting the efforts for designing novel inhibitor compounds. Therefore, using homology modeling of eEF-2K, we designed and synthesized novel coumarin-3-carboxamides including compounds A1, A2, and B1-B4 and evaluated their activity by performing in silico analysis and in vitro biological assays in breast cancer cells. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) area results showed that A1 and A2 have interaction energies with eEF-2K better than those of B1-B4 compounds. Our in vitro results indicated that compounds A1 and A2 were highly effective in inhibiting eEF-2K at 1.0 and 2.5 μM concentrations compared to compounds B1-B4, supporting the in silico findings. In conclusion, the results of this study suggest that our homology modeling along with in silico analysis may be effectively used to design inhibitors for eEF-2K. Our newly synthesized compounds A1 and A2 may be used as novel eEF-2K inhibitors with potential therapeutic applications.
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Affiliation(s)
- Ferah Comert Onder
- Department of Chemistry, Faculty of Science and Arts, Natural Products and Drug Research Laboratory, Canakkale Onsekiz Mart University, 17020 Canakkale, Turkey.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory, Bahcesehir University, Kadikoy, 34734 Istanbul, Turkey
| | - Kader Sahin
- Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory, Bahcesehir University, Kadikoy, 34734 Istanbul, Turkey
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Mehmet Ay
- Department of Chemistry, Faculty of Science and Arts, Natural Products and Drug Research Laboratory, Canakkale Onsekiz Mart University, 17020 Canakkale, Turkey
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16
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Naidoo D, Roy A, Slavětínská LP, Chukwujekwu JC, Gupta S, Van Staden J. New role for crinamine as a potent, safe and selective inhibitor of human monoamine oxidase B: In vitro and in silico pharmacology and modeling. JOURNAL OF ETHNOPHARMACOLOGY 2020; 248:112305. [PMID: 31639490 DOI: 10.1016/j.jep.2019.112305] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The development of selective inhibitors of monoamine oxidase B (MAO-B) has been essential in treating Parkinson's disease. However, the apparent hepatotoxicity and drug-drug interactions of current inhibitors accentuate the need for the development of novel pharmacotherapies. Crossyne guttata (L.) D. & U. Müll-Doblies is used frequently by Rastafarian bush doctors to treat alcoholism, a disorder which is also accentuated by MAO. OBJECTIVE The study sought to isolate, identify and characterise the biologically active constituents of C. guttata based on their ability to inhibit the MAO enzymes. MATERIALS AND METHODS Column chromatography was used to isolate the biologically active alkaloids of C. guttata. The ability of the alkaloids to inhibit the biotransformation of 4-aminoantipyrine by the MAO enzymes was evaluated in vitro. In silico docking was conducted using AutoDock Vina server while the pharmacokinetic properties of the compounds were evaluated using SwissADME. RESULTS Chromatographic separation of an ethanolic fraction of C. guttata yielded the alkaloids crinamine 1 and epibuphanisine 2. 1 and 2 along with structurally related alkaloids haemanthamine 3 and haemanthidine 4 were evaluated for their ability to inhibit the action of isozymes of MAO in vitro. Alkaloids effected submicromolar IC50 values against MAO-B, the most potent of which being crinamine 1 (0.014 μM) > haemanthidine 4 (0.017 μM) > epibuphanisine 2 (0.039 μM) > haemanthamine 3 (0.112 μM). Binding energies of the alkaloids correlated well with their inhibitory potential with crinamine displaying the best binding efficacy and binding energy score with MAO-B. DISCUSSION AND CONCLUSION Crinamine and epibuphanisine exhibited potent and selective inhibitory activity towards MAO-B. After comprehensive in silico investigations encompassing robust molecular docking analysis, the drug-like attributes and safety of the alkaloids suggest the crinamine is a potentially safe drug for human application.
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Affiliation(s)
- D Naidoo
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal Pietermaritzburg, Private Bag X01, Scottsville 3209, South Africa
| | - A Roy
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal Pietermaritzburg, Private Bag X01, Scottsville 3209, South Africa
| | - L Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Nám. 2, 16610 Prague-6, Czech Republic
| | - J C Chukwujekwu
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal Pietermaritzburg, Private Bag X01, Scottsville 3209, South Africa
| | - S Gupta
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal Pietermaritzburg, Private Bag X01, Scottsville 3209, South Africa
| | - J Van Staden
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal Pietermaritzburg, Private Bag X01, Scottsville 3209, South Africa.
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17
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Wang D, Hong RY, Guo M, Liu Y, Chen N, Li X, Kong DX. Novel C7-Substituted Coumarins as Selective Monoamine Oxidase Inhibitors: Discovery, Synthesis and Theoretical Simulation. Molecules 2019; 24:molecules24214003. [PMID: 31694262 PMCID: PMC6864482 DOI: 10.3390/molecules24214003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/02/2022] Open
Abstract
There is a continued need to develop new selective human monoamine oxidase (hMAO) inhibitors that could be beneficial for the treatment of neurological diseases. However, hMAOs are closely related with high sequence identity and structural similarity, which hinders the development of selective MAO inhibitors. “Three-Dimensional Biologically Relevant Spectrum (BRS-3D)” method developed by our group has demonstrated its effectiveness in subtype selectivity studies of receptor and enzyme ligands. Here, we report a series of novel C7-substituted coumarins, either synthesized or commercially purchased, which were identified as selective hMAO inhibitors. Most of the compounds demonstrated strong activities with IC50 values (half-inhibitory concentration) ranging from sub-micromolar to nanomolar. Compounds, FR1 and SP1, were identified as the most selective hMAO-A inhibitors, with IC50 values of 1.5 nM (selectivity index (SI) < −2.82) and 19 nM (SI < −2.42), respectively. FR4 and FR5 showed the most potent hMAO-B inhibitory activity, with IC50 of 18 nM and 15 nM (SI > 2.74 and SI > 2.82). Docking calculations and molecular dynamic simulations were performed to elucidate the selectivity preference and SAR profiles.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
| | - Ren-Yuan Hong
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji’nan 250012, Shandong, China;
| | - Mengyao Guo
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
| | - Yi Liu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
| | - Nianhang Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
| | - Xun Li
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, No 18877, Jingshi Road, Ji’nan 250002, Shandong, China
- Correspondence: (X.L.); (D.-X.K.); Tel.: +86-531-88382005 (X.L.); +86-27-8728 0877 (D.-X.K.)
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
- Correspondence: (X.L.); (D.-X.K.); Tel.: +86-531-88382005 (X.L.); +86-27-8728 0877 (D.-X.K.)
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18
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Jones HBL, Crean RM, Mullen A, Kendrick EG, Bull SD, Wells SA, Carbery DR, MacMillan F, van der Kamp MW, Pudney CR. Exposing the Interplay Between Enzyme Turnover, Protein Dynamics, and the Membrane Environment in Monoamine Oxidase B. Biochemistry 2019; 58:2362-2372. [PMID: 30964996 DOI: 10.1021/acs.biochem.9b00213] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is an increasing realization that structure-based drug design may show improved success by understanding the ensemble of conformations accessible to an enzyme and how the environment affects this ensemble. Human monoamine oxidase B (MAO-B) catalyzes the oxidation of amines and is inhibited for the treatment of both Parkinson's disease and depression. Despite its clinical importance, its catalytic mechanism remains unclear, and routes to drugging this target would be valuable. Evidence of a radical in either the transition state or the resting state of MAO-B is present throughout the literature and is suggested to be a flavin semiquinone, a tyrosyl radical, or both. Here we see evidence of a resting-state flavin semiquinone, via absorption redox studies and electron paramagnetic resonance, suggesting that the anionic semiquinone is biologically relevant. On the basis of enzyme kinetic studies, enzyme variants, and molecular dynamics simulations, we find evidence for the importance of the membrane environment in mediating the activity of MAO-B and that this mediation is related to the protein dynamics of MAO-B. Further, our MD simulations identify a hitherto undescribed entrance for substrate binding, membrane modulated substrate access, and indications for half-site reactivity: only one active site is accessible to binding at a time. Our study combines both experimental and computational evidence to illustrate the subtle interplay between enzyme activity and protein dynamics and the immediate membrane environment. Understanding key biomedical enzymes to this level of detail will be crucial to inform strategies (and binding sites) for rational drug design for these targets.
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Affiliation(s)
| | | | - Anna Mullen
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
| | | | | | | | | | - Fraser MacMillan
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
| | - Marc W van der Kamp
- School of Biochemistry , University of Bristol , Biomedical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
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19
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Synthesis and evaluation of chromone derivatives as inhibitors of monoamine oxidase. Mol Divers 2019; 23:897-913. [DOI: 10.1007/s11030-019-09917-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/06/2019] [Indexed: 12/30/2022]
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20
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Tripathi RKP, Ayyannan SR. Monoamine oxidase-B inhibitors as potential neurotherapeutic agents: An overview and update. Med Res Rev 2019; 39:1603-1706. [PMID: 30604512 DOI: 10.1002/med.21561] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 12/23/2022]
Abstract
Monoamine oxidase (MAO) inhibitors have made significant contributions and remain an indispensable approach of molecular and mechanistic diversity for the discovery of antineurodegenerative drugs. However, their usage has been hampered by nonselective and/or irreversible action which resulted in drawbacks like liver toxicity, cheese effect, and so forth. Hence, the search for selective MAO inhibitors (MAOIs) has become a substantial focus in current drug discovery. This review summarizes our current understanding on MAO-A/MAO-B including their structure, catalytic mechanism, and biological functions with emphases on the role of MAO-B as a potential therapeutic target for the development of medications treating neurodegenerative disorders. It also highlights the recent developments in the discovery of potential MAO-B inhibitors (MAO-BIs) belonging to diverse chemical scaffolds, arising from intensive chemical-mechanistic and computational studies documented during past 3 years (2015-2018), with emphases on their potency and selectivity. Importantly, readers will gain knowledge of various newly established MAO-BI scaffolds and their development potentials. The comprehensive information provided herein will hopefully accelerate ideas for designing novel selective MAO-BIs with superior activity profiles and critical discussions will inflict more caution in the decision-making process in the MAOIs discovery.
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Affiliation(s)
- Rati Kailash Prasad Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India.,Department of Pharmaceutical Chemistry, Parul Institute of Pharmacy, Parul University, Vadodara, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
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21
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Gao Y, Chen Y, Tian Y, Zhao Y, Wu F, Luo X, Ju X, Liu G. In silico study of 3-hydroxypyrimidine-2,4-diones as inhibitors of HIV RT-associated RNase H using molecular docking, molecular dynamics, 3D-QSAR, and pharmacophore models. NEW J CHEM 2019. [DOI: 10.1039/c9nj03353j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rational design and virtual screening of novel inhibitors of HIV reverse transcriptase associated ribonuclease H based on a combined molecular modeling study.
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Affiliation(s)
- Ya Gao
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Yanming Chen
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Yafeng Tian
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Yilan Zhao
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Fengshou Wu
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Xiaogang Luo
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Xiulian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Genyan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
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