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Ledneczki I, Némethy Z, Molnár KD, Tapolcsányi P, Ilkei V, Vágó I, Kolok S, Thán M, Laszy J, Balázs O, Krámos B, Szigetvári Á, Bata I, Makó A, Visegrády A, Fodor L, Vastag M, Lévay G, Lendvai B, Greiner I, Éles J. Optimization of Novel α7 Nicotinic Acetylcholine Receptor Positive Allosteric Modulators and the Discovery of a Preclinical Development Candidate Molecule (RGH-560). J Med Chem 2023; 66:16276-16302. [PMID: 37989278 DOI: 10.1021/acs.jmedchem.3c01635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
During optimization of a previously identified lead compound, attempts were made to optimize the reactive indole structural element, the suboptimal metabolic stability, as well as the low kinetic solubility. It was concluded that the indole was important for in vitro activity. With the aim of further improvements, more thorough modifications were also carried out. As a result, a new chemotype (the azetidinespirochromone family) was identified, which proved to be 1 order of magnitude less lipophilic retaining the same high level of in vitro potency as the lead series itself, however, with improved metabolic stability and kinetic solubility. Compound 53 showed the most balanced physicochemical and pharmacological profile with significant in vivo efficacy in the scopolamine-induced amnesia test. Based on these promising results, cognitive enhancement through the positive modulation of α7 nAChRs appears to be a viable approach. Compound 53 was selected to be a preclinical development candidate (as RGH-560).
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Affiliation(s)
| | - Zsolt Némethy
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | | | - Pál Tapolcsányi
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Viktor Ilkei
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - István Vágó
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Sándor Kolok
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Márta Thán
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Judit Laszy
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Ottilia Balázs
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Balázs Krámos
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Áron Szigetvári
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Imre Bata
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Attila Makó
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | | | - László Fodor
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Mónika Vastag
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - György Lévay
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Balázs Lendvai
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - István Greiner
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - János Éles
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
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Liu K, Zhang Y, Zhang W, Liu L, Yu Z. A Study on the Interactions of Proteinase K with Myricetin and Myricitrin by Multi-Spectroscopy and Molecular Modeling. Int J Mol Sci 2023; 24:ijms24065317. [PMID: 36982397 PMCID: PMC10048853 DOI: 10.3390/ijms24065317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Myricetin (MYR) and myricitrin (MYT) are well recognized for their nutraceutical value, such as antioxidant, hypoglycemic, and hypotensive effects. In this work, fluorescence spectroscopy and molecular modeling were adopted to investigate the conformational and stability changes of proteinase K (PK) in the presence of MYR and MYT. The experimental results showed that both MYR and MYT could quench fluorescence emission via a static quenching mechanism. Further investigation demonstrated that both hydrogen bonding and van der Waals forces play significant roles in the binding of complexes, which is consistent with the conclusions of molecular modeling. Synchronous fluorescence spectroscopy, Förster resonance energy transfer, and site-tagged competition experiments were performed to prove that the binding of MYR or MYT to PK could alter its micro-environment and conformation. Molecular docking results revealed that either MYR or MYT spontaneously interacted with PK at a single binding site via hydrogen bonding and hydrophobic interactions, which is consistent with the results of spectroscopic measurements. A 30 ns molecular dynamics simulation was conducted for both PK-MYR and PK-MYT complexes. The calculation results showed that no large structural distortions or interaction changes occurred during the entire simulation time span. The average RMSD changes of PK in PK-MYR and PK-MYT were 2.06 and 2.15 Å, respectively, indicating excellent stability of both complexes. The molecular simulation results suggested that both MYR and MYT could interact with PK spontaneously, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results indicates that the method herein could be feasible and worthwhile for protein–ligand complex studies.
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Affiliation(s)
- Kefan Liu
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Yubo Zhang
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Wei Zhang
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Liyan Liu
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Zhan Yu
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
- Provincial Key Laboratory for Separation and Analysis of Complex Systems in Liaoning Universities, Shenyang Normal University, Shenyang 110034, China
- Correspondence:
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Rachmawati D, Fahmi MZ, Abdjan MI, Wasito EB, Siswanto I, Mazlan N, Rohmah J, Baktir A. In Vitro Assessment on Designing Novel Antibiofilms of Pseudomonas aeruginosa Using a Computational Approach. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248935. [PMID: 36558064 PMCID: PMC9784811 DOI: 10.3390/molecules27248935] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
An anti-biofilm that can inhibit the matrix of biofilm formation is necessary to prevent recurrent and chronic Pseudomonas aeruginosa infection. This study aimed to design compounds with a new mechanism through competitive inhibitory activity against phosphomannomutase/phosphoglucomutase (PMM/PGM), using in vitro assessment and a computational (in silico) approach. The active site of PMM/PGM was assessed through molecular redocking using L-tartaric acid as the native ligand and other small molecules, such as glucaric acid, D-sorbitol, and ascorbic acid. The docking program set the small molecules to the active site, showing a stable complex formation. Analysis of structural similarity, bioavailability, absorption, distribution, metabolism, excretion, and toxicity properties proved the potential application of ligands as an anti-biofilm. In vitro assessment with crystal violet showed that the ligands could reach up to 95.87% inhibition at different concentrations. The nitrocellulose membrane and scanning electron microscopic visualization showed that the untreated P. aeruginosa biofilm was denser than the ligand-treated biofilm.
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Affiliation(s)
- Dian Rachmawati
- Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Mochammad Zakki Fahmi
- Supramodification Nano-Micro Engineering (SPANENG) Research Group, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Muhammad Ikhlas Abdjan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Eddy Bagus Wasito
- Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Imam Siswanto
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Nurzafirah Mazlan
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
| | - Jazirotur Rohmah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Afaf Baktir
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
- Correspondence: ; Tel.: +62-823-3481-7019
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Wardana AP, Abdjan MI, Aminah NS, Fahmi MZ, Siswanto I, Kristanti AN, Saputra MA, Takaya Y. 3,4,3'-Tri- O-methylellagic acid as an anticancer agent: in vitro and in silico studies. RSC Adv 2022; 12:29884-29891. [PMID: 36321100 PMCID: PMC9580503 DOI: 10.1039/d2ra05246f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022] Open
Abstract
We report a natural product compound isolated from Syzygium polycephalum known as 3,4,3'-tri-O-methylellagic acid (T-EA) as a candidate drug for cancer treatment. The characterization of the isolated T-EA compound was carried out using various spectroscopic methods. The in vitro evaluation showcased the inhibition activity of T-EA towards the T47D and HeLa cell lines with EC50 values of 55.35 ± 6.28 μg mL-1 and 12.57 ± 2.22 μg mL-1, respectively. Meanwhile, the in silico evaluation aimed to understand the interaction of T-EA with enzymes responsible for cancer regulation at the molecular level by targeting the hindrance of cyclin-dependent kinase 9 (CDK9) and sirtuin 1 (SIRT1) enzymes. T-EA showed a binding free energy towards the SIRT1 protein of ΔG bind (MM-GBSA): -30.98 ± 0.25 kcal mol-1 and ΔG bind (MM-PBSA): -24.07 ± 0.30 kcal mol-1, while that of CDK9 was ΔG bind (MM-GBSA): -29.50 ± 0.22 kcal mol-1 and ΔG bind (MM-PBSA): -25.87 ± 0.40 kcal mol-1. The obtained results from this research could be considered as important information on 3,4,3'-tri-O-methylellagic acid as a drug to treat cervical and breast cancers.
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Affiliation(s)
- Andika Pramudya Wardana
- PhD Student of Mathematics and Natural Sciences, Faculty of Science and Technology, Universitas AirlanggaSurabaya 60115Indonesia,Department of Chemistry, Faculty of Science and Technology, Universitas AirlanggaSurabaya 60115Indonesia+62-31-5936502+62-31-5936501
| | - Muhammad Ikhlas Abdjan
- Department of Chemistry, Faculty of Science and Technology, Universitas AirlanggaSurabaya 60115Indonesia+62-31-5936502+62-31-5936501
| | - Nanik Siti Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas AirlanggaSurabaya 60115Indonesia+62-31-5936502+62-31-5936501,Biotechnology of Tropical Medicinal Plants Research Group, Universitas AirlanggaIndonesia
| | - Mochamad Zakki Fahmi
- Department of Chemistry, Faculty of Science and Technology, Universitas AirlanggaSurabaya 60115Indonesia+62-31-5936502+62-31-5936501
| | - Imam Siswanto
- Department of Chemistry, Faculty of Science and Technology, Universitas AirlanggaSurabaya 60115Indonesia+62-31-5936502+62-31-5936501,Bioinformatic Laboratory, UCoE Research Center for Bio-Molecule Engineering, Universitas AirlanggaSurabayaIndonesia
| | - Alfinda Novi Kristanti
- Department of Chemistry, Faculty of Science and Technology, Universitas AirlanggaSurabaya 60115Indonesia+62-31-5936502+62-31-5936501,Biotechnology of Tropical Medicinal Plants Research Group, Universitas AirlanggaIndonesia
| | - Mirza Ardella Saputra
- Nanotechnology Engineering, Faculty of Advanced Technology and Multidiscipline, Universitas AirlanggaSurabaya 60115Indonesia
| | - Yoshiaki Takaya
- Faculty of Pharmacy, Meijo University150 Yagotoyama, TempakuNagoya468-8503Japan
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A Versatile Class of 1,4,4-Trisubstituted Piperidines Block Coronavirus Replication In Vitro. Pharmaceuticals (Basel) 2022; 15:ph15081021. [PMID: 36015168 PMCID: PMC9416004 DOI: 10.3390/ph15081021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
There is a clear need for novel antiviral concepts to control SARS-CoV-2 infection. Based on the promising anti-coronavirus activity observed for a class of 1,4,4-trisubstituted piperidines, we here conducted a detailed analysis of the structure–activity relationship of these structurally unique inhibitors. Despite the presence of five points of diversity, the synthesis of an extensive series of analogues was readily achieved by Ugi four-component reaction from commercially available reagents. After evaluating 63 analogues against human coronavirus 229E, four of the best molecules were selected and shown to have micromolar activity against SARS-CoV-2. Since the action point was situated post virus entry and lying at the stage of viral polyprotein processing and the start of RNA synthesis, enzymatic assays were performed with CoV proteins involved in these processes. While no inhibition was observed for SARS-CoV-2 nsp12-nsp7-nsp8 polymerase, nsp14 N7-methyltransferase and nsp16/nsp10 2’-O-methyltransferase, nor the nsp3 papain-like protease, the compounds clearly inhibited the nsp5 main protease (Mpro). Although the inhibitory activity was quite modest, the plausibility of binding to the catalytic site of Mpro was established by in silico studies. Therefore, the 1,4,4-trisubstituted piperidines appear to represent a novel class of non-covalent CoV Mpro inhibitors that warrants further optimization and development.
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Borges EL, Goulart HA, Perin G, Schneider PH, Rieder GS, Nogara PA, da Rocha JBT. One-Pot Synthesis and in Silico Molecular Docking Studies of Arylselanyl Hydrazides as Potential Antituberculosis Agents. Chem Biodivers 2022; 19:e202100793. [PMID: 35293125 DOI: 10.1002/cbdv.202100793] [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: 10/01/2021] [Accepted: 03/14/2022] [Indexed: 11/06/2022]
Abstract
The present study reports a simple two-step method for the synthesis of arylselanyl hydrazide derivatives using hypophosphorous acid and polyethylene glycol (H3 PO2 /PEG-400) as an alternative reducing system and hydrazine hydrate (NH2 NH2 ⋅xH2 O/50-60 %). This single-vessel procedure was employed with methyl acrylate 2a and methyl bromoacetate 2b using diaryl diselenides to generate the nucleophile species to produce, respectively, 3-(arylselanyl)propane-hydrazides 4a-e and 2-(arylselanyl)acetohydrazides 5a-e with good yields by accelerating the reduction of -Se-Se- bond, when compared to available methods. The synthesized molecules are structurally similar to the isoniazid (INH). Therefore, we perform in silico molecular docking studies, using the lactoperoxidase enzyme, in order to verify whether the INH Se derivatives could interact in a similar way to INH at the active site of the mammalian enzyme. The in silico results indicated a similar type of interaction of the arylselanyl hydrazide derivatives with that of INH. In view of the similar in silico interaction of the selenium derivatives of INH, the arylselanyl hydrazide derivatives reported here should be tested against Mycobacterium tuberculosis in vitro.
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Affiliation(s)
- Elton L Borges
- Grupo de Pesquisa em Síntese Orgânica da Região Amazônica (LASORA, DAEPA), Fundação Universidade Federal de Rondônia (UNIR), Rua da Paz 4376, 76916-000, Presidente Médici, RO, Brazil
| | - Helen A Goulart
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Gelson Perin
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Paulo H Schneider
- Instituto de Química, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Guilherme S Rieder
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - Pablo A Nogara
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - João B T da Rocha
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
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Ladefoged LK, Koch R, Biggin PC, Schiøtt B. Binding and Activation of Serotonergic G-Protein Coupled Receptors by the Multimodal Antidepressant Vortioxetine. ACS Chem Neurosci 2022; 13:1129-1142. [PMID: 35348335 DOI: 10.1021/acschemneuro.1c00029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are important pharmacological targets. Despite substantial progress, important questions still remain concerning the details of activation: how can a ligand act as an agonist in one receptor but as an antagonist in a homologous receptor, and how can agonists activate a receptor despite lacking polar functional groups able to interact with helix 5 as is the case for the related adrenergic receptors? Studying vortioxetine (VXT), an important multimodal antidepressant drug, may elucidate both questions. Herein, we present a thorough in silico analysis of VXT binding to 5-HT1A, 5-HT1B, and 5-HT7 receptors and compare it with available experimental data. We are able to rationalize the differential mode of action of VXT at different receptors, but also, in the case of the 5-HT1A receptor, we observe the initial steps of activation that inform about an activation mechanism that does not involve polar interaction with helix 5. The results extend our current understanding of agonist and antagonist action at aminergic GPCRs.
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Affiliation(s)
- Lucy Kate Ladefoged
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Rebekka Koch
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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Aminah NS, Abdjan MI, Wardana AP, Kristanti AN, Siswanto I, Rakhman KA, Takaya Y. The dolabellane diterpenes as potential inhibitors of the SARS-CoV-2 main protease: molecular insight of the inhibitory mechanism through computational studies. RSC Adv 2021; 11:39455-39466. [PMID: 35492446 PMCID: PMC9044469 DOI: 10.1039/d1ra07584e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
An investigation has been carried out on natural products from dolabellane derivatives to understand their potential in inhibiting the SARS-CoV-2 main protease (3CLpro) using an in silico approach. Inhibition of the 3CLpro enzyme is a promising target in stopping the replication of the SARS-CoV-2 virus through inhibition of the subsite binding pocket. The redocking process aims to determine the 3CLpro active sites. The redocking requirement showed a good pose with an RMSD value of 1.39 Å. The combination of molecular docking and MD simulation shows the results of DD13 as a candidate which had a good binding affinity (kcal mol-1) to inhibit the 3CLpro enzyme activity. Prediction of binding free energy (kcal mol-1) of DD13 using the Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PB/GBSA) approach shows the results ΔG bind(MM-GBSA): -52.33 ± 0.34 and ΔG bind(MM-PBSA): -43.52 ± 0.42. The key residues responsible for the inhibition mechanism are Hie41, Ser46, Met49, Asn142, Cys145, Hie163, Met165, and Gln189. Additionally, pharmacokinetic prediction recommended that DD13 had promising criteria as a drug candidate. The results demonstrated in this study provide theoretical information to obtain a potential inhibitor against the SARS-CoV-2 main protease.
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Affiliation(s)
- Nanik Siti Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga Indonesia
| | - Muhammad Ikhlas Abdjan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Ph.D. Student of Mathematics and Natural Sciences, Faculty of Science and Technology, Universitas Airlangga Komplek Kampus C UNAIR, Jl. Mulyorejo 60115 Surabaya Indonesia
| | - Andika Pramudya Wardana
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Ph.D. Student of Mathematics and Natural Sciences, Faculty of Science and Technology, Universitas Airlangga Komplek Kampus C UNAIR, Jl. Mulyorejo 60115 Surabaya Indonesia
| | - Alfinda Novi Kristanti
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga Indonesia
| | - Imam Siswanto
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga Surabaya 60115 Indonesia
- Bioinformatic Laboratory, UCoE Research Center for Bio-Molecule Engineering, Universitas Airlangga Surabaya Indonesia
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Hatmal MM, Abuyaman O, Taha M. Docking-generated multiple ligand poses for bootstrapping bioactivity classifying Machine Learning: Repurposing covalent inhibitors for COVID-19-related TMPRSS2 as case study. Comput Struct Biotechnol J 2021; 19:4790-4824. [PMID: 34426763 PMCID: PMC8373588 DOI: 10.1016/j.csbj.2021.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/03/2021] [Accepted: 08/16/2021] [Indexed: 01/10/2023] Open
Abstract
In the present work we introduce the use of multiple docked poses for bootstrapping machine learning-based QSAR modelling. Ligand-receptor contact fingerprints are implemented as descriptor variables. We implemented this method for the discovery of potential inhibitors of the serine protease enzyme TMPRSS2 involved the infectivity of coronaviruses. Several machine learners were scanned, however, Xgboost, support vector machines (SVM) and random forests (RF) were the best with testing set accuracies reaching 90%. Three potential hits were identified upon using the method to scan known untested FDA approved drugs against TMPRSS2. Subsequent molecular dynamics simulation and covalent docking supported the results of the new computational approach.
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Affiliation(s)
- Ma'mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, PO Box 330127, Zarqa 13133, Jordan
| | - Omar Abuyaman
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, PO Box 330127, Zarqa 13133, Jordan
| | - Mutasem Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
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Orro A, Uggeri M, Rusnati M, Urbinati C, Pedemonte N, Pesce E, Moscatelli M, Padoan R, Cichero E, Fossa P, D'Ursi P. In silico drug repositioning on F508del-CFTR: A proof-of-concept study on the AIFA library. Eur J Med Chem 2021; 213:113186. [PMID: 33472120 DOI: 10.1016/j.ejmech.2021.113186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 12/14/2022]
Abstract
Computational drug repositioning is of growing interest to academia and industry, for its ability to rapidly screen a huge number of candidates in silico (exploiting comprehensive drug datasets) together with reduced development cost and time. The potential of drug repositioning has not been fully evaluated yet for cystic fibrosis (CF), a disease mainly caused by deletion of Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein. F508del-CFTR is thus withheld in the endoplasmic reticulum and rapidly degraded by the ubiquitin/proteasome system. CF is still a fatal disease. Nowadays, it is treatable by some CFTR-rescuing drugs, but new-generation drugs with stronger therapeutic benefits and fewer side effects are still awaited. In this manuscript we report about the results of a pilot computational drug repositioning screening in search of F508del-CFTR-targeted drugs performed on AIFA library by means of a dedicated computational pipeline and surface plasmon resonance binding assay to experimentally validate the computational findings.
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Affiliation(s)
- Alessandro Orro
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, Italy
| | - Matteo Uggeri
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, Italy; Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Genova, Italy
| | - Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Chiara Urbinati
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Emanuela Pesce
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Marco Moscatelli
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, Italy
| | - Rita Padoan
- Department of Pediatrics, Regional Support Centre for Cystic Fibrosis, Children's Hospital-ASST Spedali Civili, University of Brescia, Brescia, Italy
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Genova, Italy
| | - Paola Fossa
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Genova, Italy
| | - Pasqualina D'Ursi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, Italy.
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Abdjan MI, Aminah NS, Siswanto I, Kristanti AN, Takaya Y, Choudhary MI. Exploration of stilbenoid trimers as potential inhibitors of sirtuin1 enzyme using a molecular docking and molecular dynamics simulation approach. RSC Adv 2021; 11:19323-19332. [PMID: 35478645 PMCID: PMC9033617 DOI: 10.1039/d1ra02233d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 05/21/2021] [Indexed: 12/25/2022] Open
Abstract
A combination of molecular docking and molecular dynamics simulation (250 ns) has been carried out to study the interaction of stilbenoid trimer compounds with the SIRT1 enzyme as the target protein. SIRT1 expression regulates cellular stress responses that lead to the development of cancer. Redocking showed a good native ligand pose with an RMSD value of 1.40 Å at the receptor active site's coordinates. The molecular docking score uses a grid score functional (kcal mol−1), which shows results of 1NS: 79.56, TS1: −26.83, TS2: −87.77, and TS3: −83.67. The TS2 and TS3 candidates were chosen for further analysis because they had a lower grid score than the native ligand (1NS). Furthermore, prediction of binding free energy (kcal mol−1) using the Quantum Mechanics/generalized Born Surface Area (QM/MM-GBSA) method shows the results of 1NS: −31.52 ± 0.39, TS2: −58.99 ± 0.34, and TS3: −43.38 ± 0.35. These results indicate that the TS2 and TS3 compounds have good potential as inhibitors of the SIRT1 enzyme. Additionally, the amino acid residues were responsible for the inhibition mechanism through hydrogen bond interactions at the molecular level, including ASP22, PHE91, PRO11, ILE165, ASP166, and VAL230. The observations made in this study provide theoretical information for exploring the stilbenoid trimers as anticancer agents by targeting the SIRT1 enzyme. A combination of molecular docking and molecular dynamics simulation (250 ns) has been carried out to study the interaction of stilbenoid trimer compounds with the SIRT1 enzyme as the target protein.![]()
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Affiliation(s)
- Muhammad Ikhlas Abdjan
- Departement of Chemistry
- Faculty of Science and Technology
- Universitas Airlangga
- Surabaya 60115
- Indonesia
| | - Nanik Siti Aminah
- Departement of Chemistry
- Faculty of Science and Technology
- Universitas Airlangga
- Surabaya 60115
- Indonesia
| | - Imam Siswanto
- Departement of Chemistry
- Faculty of Science and Technology
- Universitas Airlangga
- Surabaya 60115
- Indonesia
| | - Alfinda Novi Kristanti
- Departement of Chemistry
- Faculty of Science and Technology
- Universitas Airlangga
- Surabaya 60115
- Indonesia
| | - Yoshiaki Takaya
- Faculty of Pharmacy
- Meijo University
- Nagoya
- Japan
- Adjunct Professor Department of Chemistry
| | - Muhammad Iqbal Choudhary
- H. E. J. Research Institute of Chemistry
- International Center for Chemical and Biological Sciences
- University of Karachi
- Karachi-75270
- Pakistan
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