1
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Joshi N, Alavala RR. Sulfonamido, amido heterocyclic adducts of tetrazole derivatives as BACE1 inhibitors: in silico exploration. Mol Divers 2024:10.1007/s11030-023-10792-7. [PMID: 38267751 DOI: 10.1007/s11030-023-10792-7] [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: 11/01/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Alzheimer's disease is a neurodegenerative disorder accounting for 60-80% of dementia cases and is accompanied by a high mortality rate in patients above 70 years of age. The formation of senile plaques composed of amyloid-β protein is a hallmark of Alzheimer's disease. Beta-site APP cleaving enzyme 1 (BACE1) is a proteolytic enzyme involved in the degradation of amyloid precursor protein, which further degrades to form toxic amyloid-β fragments. Hence, inhibition of BACE1 was stated to be an effective strategy for Alzheimer's therapeutics. Keeping in mind the structures of different BACE1 inhibitors that had reached the clinical trials, we designed a library of compounds (total 164) based on a substituted 5-amino tetrazole scaffold which was an isosteric replacement of the cyclic amidine moiety, a common component of the BACE1 inhibitors which reached the clinical trials. The scaffold was linked to different structural moieties with the aid of an amide or sulfonamide bond to design some novel molecules. Molecular docking was initially performed and the top 5 molecules were selected based on docking scores and protein-ligand interactions. Furthermore, molecular dynamic simulations were performed for these molecules (3g, 7k, 8n, 9d, 9g) for 100 ns and MM-GBSA calculations were performed for each of these complexes. After critical evaluation of the obtained results, three potential molecules (9d, 8n, and 7k) were forwarded for prolonged stability studies by performing molecular dynamic simulations for 250 ns and simultaneous MM-GBSA calculations. It was observed that the compounds (9d, 8n, and 7k) were forming good interactions with the amino acid residues of the catalytic site of the enzyme with multiple non-covalent interactions. In MD simulations, the compounds have shown better stability and better binding energy throughout the runtime.
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Affiliation(s)
- Nachiket Joshi
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS, V L Mehta Road, Vile Parle West, Mumbai, Maharashtra, 400056, India
| | - Rajasekhar Reddy Alavala
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS, V L Mehta Road, Vile Parle West, Mumbai, Maharashtra, 400056, India.
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2
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Stern N, Gacs A, Tátrai E, Flachner B, Hajdú I, Dobi K, Bágyi I, Dormán G, Lőrincz Z, Cseh S, Kígyós A, Tóvári J, Goldblum A. Dual Inhibitors of AChE and BACE-1 for Reducing Aβ in Alzheimer's Disease: From In Silico to In Vivo. Int J Mol Sci 2022; 23:13098. [PMID: 36361906 PMCID: PMC9655245 DOI: 10.3390/ijms232113098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 07/30/2023] Open
Abstract
Alzheimer's disease (AD) is a complex and widespread condition, still not fully understood and with no cure yet. Amyloid beta (Aβ) peptide is suspected to be a major cause of AD, and therefore, simultaneously blocking its formation and aggregation by inhibition of the enzymes BACE-1 (β-secretase) and AChE (acetylcholinesterase) by a single inhibitor may be an effective therapeutic approach, as compared to blocking one of these targets or by combining two drugs, one for each of these targets. We used our ISE algorithm to model each of the AChE peripheral site inhibitors and BACE-1 inhibitors, on the basis of published data, and constructed classification models for each. Subsequently, we screened large molecular databases with both models. Top scored molecules were docked into AChE and BACE-1 crystal structures, and 36 Molecules with the best weighted scores (based on ISE indexes and docking results) were sent for inhibition studies on the two enzymes. Two of them inhibited both AChE (IC50 between 4-7 μM) and BACE-1 (IC50 between 50-65 μM). Two additional molecules inhibited only AChE, and another two molecules inhibited only BACE-1. Preliminary testing of inhibition by F681-0222 (molecule 2) on APPswe/PS1dE9 transgenic mice shows a reduction in brain tissue of soluble Aβ42.
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Affiliation(s)
- Noa Stern
- Molecular Modeling and Drug Design Lab, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Alexandra Gacs
- Department of Experimental Pharmacology, National Institute of Oncology, H-1122 Budapest, Hungary
| | - Enikő Tátrai
- Department of Experimental Pharmacology, National Institute of Oncology, H-1122 Budapest, Hungary
- KINETO Lab Ltd., H-1032 Budapest, Hungary
| | | | - István Hajdú
- TargetEx Ltd., H-2120 Dunakeszi, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | | | | | | | | | | | | | - József Tóvári
- KINETO Lab Ltd., H-1032 Budapest, Hungary
- Department of Tumor Biology, National Korányi Institute of TB and Pulmonology, H-1121 Budapest, Hungary
| | - Amiram Goldblum
- Molecular Modeling and Drug Design Lab, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
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3
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L-DOPA and Droxidopa: From Force Field Development to Molecular Docking into Human β2-Adrenergic Receptor. Life (Basel) 2022; 12:life12091393. [PMID: 36143429 PMCID: PMC9501711 DOI: 10.3390/life12091393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/10/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
The increasing interest in the molecular mechanism of the binding of different agonists and antagonists to β2-adrenergic receptor (β2AR) inactive and active states has led us to investigate protein–ligand interactions using molecular docking calculations. To perform this study, the 3.2 Å X-ray crystal structure of the active conformation of human β2AR in the complex with the endogenous agonist adrenaline has been used as a template for investigating the binding of two exogenous catecholamines to this adrenergic receptor. Here, we show the derivation of L-DOPA and Droxidopa OPLS all atom (AA) force field (FF) parameters via quantum mechanical (QM) calculations, molecular dynamics (MD) simulations in aqueous solutions of the two catecholamines and the molecular docking of both ligands into rigid and flexible β2AR models. We observe that both ligands share with adrenaline similar experimentally observed binding anchor sites, which are constituted by Asp113/Asn312 and Ser203/Ser204/Ser207 side chains. Moreover, both L-DOPA and Droxidopa molecules exhibit binding affinities comparable to that predicted for adrenaline, which is in good agreement with previous experimental and computational results. L-DOPA and Droxidopa OPLS AA FFs have also been tested by performing MD simulations of these ligands docked into β2AR proteins embedded in lipid membranes. Both hydrogen bonds and hydrophobic interaction networks observed over the 1 μs MD simulation are comparable with those derived from molecular docking calculations and MD simulations performed with the CHARMM FF.
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4
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Biswas AD, Catte A, Mancini G, Barone V. Analysis of L-DOPA and droxidopa binding to human β 2-adrenergic receptor. Biophys J 2021; 120:5631-5643. [PMID: 34767786 PMCID: PMC8715240 DOI: 10.1016/j.bpj.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/29/2022] Open
Abstract
Over the last two decades, an increasing number of studies has been devoted to a deeper understanding of the molecular process involved in the binding of various agonists and antagonists to active and inactive conformations of β2-adrenergic receptor (β2AR). The 3.2 Å x-ray crystal structure of human β2AR active state in combination with the endogenous low affinity agonist adrenaline offers an ideal starting structure for studying the binding of various catecholamines to adrenergic receptors. We show that molecular docking of levodopa (L-DOPA) and droxidopa into rigid and flexible β2AR models leads for both ligands to binding anchor sites comparable to those experimentally reported for adrenaline, namely D113/N312 and S203/S204/S207 side chains. Both ligands have a hydrogen bond network that is extremely similar to those of noradrenaline and dopamine. Interestingly, redocking neutral and protonated versions of adrenaline to rigid and flexible β2AR models results in binding poses that are more energetically stable and distinct from the x-ray crystal structure. Similarly, lowest energy conformations of noradrenaline and dopamine generated by docking into flexible β2AR models had binding free energies lower than those of best poses in rigid receptor models. Furthermore, our findings show that L-DOPA and droxidopa molecules have binding affinities comparable to those predicted for adrenaline, noradrenaline, and dopamine, which are consistent with previous experimental and computational findings and supported by the molecular dynamics simulations of β2AR-ligand complexes performed here.
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5
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Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proc Natl Acad Sci U S A 2021; 118:e2106195118. [PMID: 34475217 PMCID: PMC8433570 DOI: 10.1073/pnas.2106195118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
Protein flexibility remains a major challenge in library docking because of difficulties in sampling conformational ensembles with accurate probabilities. Here, we use the model cavity site of T4 lysozyme L99A to test flexible receptor docking with energy penalties from molecular dynamics (MD) simulations. Crystallography with larger and smaller ligands indicates that this cavity can adopt three major conformations: open, intermediate, and closed. Since smaller ligands typically bind better to the cavity site, we anticipate an energy penalty for the cavity opening. To estimate its magnitude, we calculate conformational preferences from MD simulations. We find that including a penalty term is essential for retrospective ligand enrichment; otherwise, high-energy states dominate the docking. We then prospectively docked a library of over 900,000 compounds for new molecules binding to each conformational state. Absent a penalty term, the open conformation dominated the docking results; inclusion of this term led to a balanced sampling of ligands against each state. High ranked molecules were experimentally tested by Tm upshift and X-ray crystallography. From 33 selected molecules, we identified 18 ligands and determined 13 crystal structures. Most interesting were those bound to the open cavity, where the buried site opens to bulk solvent. Here, highly unusual ligands for this cavity had been predicted, including large ligands with polar tails; these were confirmed both by binding and by crystallography. In docking, incorporating protein flexibility with thermodynamic weightings may thus access new ligand chemotypes. The MD approach to accessing and, crucially, weighting such alternative states may find general applicability.
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Affiliation(s)
- Anna S Kamenik
- Institute of General, Inorganic, and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Isha Singh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Klaus R Liedl
- Institute of General, Inorganic, and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria;
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
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6
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Stanzione F, Giangreco I, Cole JC. Use of molecular docking computational tools in drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:273-343. [PMID: 34147204 DOI: 10.1016/bs.pmch.2021.01.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular docking has become an important component of the drug discovery process. Since first being developed in the 1980s, advancements in the power of computer hardware and the increasing number of and ease of access to small molecule and protein structures have contributed to the development of improved methods, making docking more popular in both industrial and academic settings. Over the years, the modalities by which docking is used to assist the different tasks of drug discovery have changed. Although initially developed and used as a standalone method, docking is now mostly employed in combination with other computational approaches within integrated workflows. Despite its invaluable contribution to the drug discovery process, molecular docking is still far from perfect. In this chapter we will provide an introduction to molecular docking and to the different docking procedures with a focus on several considerations and protocols, including protonation states, active site waters and consensus, that can greatly improve the docking results.
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Affiliation(s)
| | - Ilenia Giangreco
- Cambridge Crystallographic Data Centre, Cambridge, United Kingdom
| | - Jason C Cole
- Cambridge Crystallographic Data Centre, Cambridge, United Kingdom
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7
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Amendola G, Ettari R, Previti S, Di Chio C, Messere A, Di Maro S, Hammerschmidt SJ, Zimmer C, Zimmermann RA, Schirmeister T, Zappalà M, Cosconati S. Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening. J Chem Inf Model 2021; 61:2062-2073. [PMID: 33784094 PMCID: PMC8029447 DOI: 10.1021/acs.jcim.1c00184] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Indexed: 12/13/2022]
Abstract
During almost all 2020, coronavirus disease 2019 (COVID-19) pandemic has constituted the major risk for the worldwide health and economy, propelling unprecedented efforts to discover drugs for its prevention and cure. At the end of the year, these efforts have culminated with the approval of vaccines by the American Food and Drug Administration (FDA) and the European Medicines Agency (EMA) giving new hope for the future. On the other hand, clinical data underscore the urgent need for effective drugs to treat COVID-19 patients. In this work, we embarked on a virtual screening campaign against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mpro chymotrypsin-like cysteine protease employing our in-house database of peptide and non-peptide ligands characterized by different types of warheads acting as Michael acceptors. To this end, we employed the AutoDock4 docking software customized to predict the formation of a covalent adduct with the target protein. In vitro verification of the inhibition properties of the most promising candidates allowed us to identify two new lead inhibitors that will deserve further optimization. From the computational point of view, this work demonstrates the predictive power of AutoDock4 and suggests its application for the in silico screening of large chemical libraries of potential covalent binders against the SARS-CoV-2 Mpro enzyme.
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Affiliation(s)
- Giorgio Amendola
- DiSTABiF, University of Campania Luigi
Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical,
and Environmental Sciences, University of Messina, Viale
Annunziata, Messina 98168, Italy
| | - Santo Previti
- Department of Chemical, Biological, Pharmaceutical,
and Environmental Sciences, University of Messina, Viale
Annunziata, Messina 98168, Italy
| | - Carla Di Chio
- Department of Chemical, Biological, Pharmaceutical,
and Environmental Sciences, University of Messina, Viale
Annunziata, Messina 98168, Italy
| | - Anna Messere
- DiSTABiF, University of Campania Luigi
Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania Luigi
Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Stefan J. Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences,
University of Mainz, Staudingerweg 5, Mainz 55128,
Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences,
University of Mainz, Staudingerweg 5, Mainz 55128,
Germany
| | - Robert A. Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences,
University of Mainz, Staudingerweg 5, Mainz 55128,
Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences,
University of Mainz, Staudingerweg 5, Mainz 55128,
Germany
| | - Maria Zappalà
- Department of Chemical, Biological, Pharmaceutical,
and Environmental Sciences, University of Messina, Viale
Annunziata, Messina 98168, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi
Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
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8
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Ensemble docking-based virtual screening toward identifying inhibitors against Wee1 kinase. Future Med Chem 2020; 11:1889-1906. [PMID: 31517534 DOI: 10.4155/fmc-2019-0022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: Wee1 kinase plays a key role in the arrest of G2/M checkpoint that prevents mitotic entry in response to DNA damage. This work is to discover potent Wee1 inhibitors which can be considered valuable. Materials & Methods: Herein, Ensemble docking using multiple crystal structures was considered an effective strategy in the virtual screening. The performance of 17 scoring functions obtained from different docking software was evaluated for molecular docking. Results: Two novel compounds B1 and A2 were identified as Wee1 inhibitors with IC50 values of 10.23 ± 0.505 and 8.72 ± 0.323 μM, respectively. Further cell viability assay demonstrated that the two active compounds exhibited good anticancer activities. Conclusion: This provides a meaningful starting point for further structure optimization to discover more potent Wee1 inhibitors.
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9
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Rallabandi HR, Ganesan P, Kim YJ. Targeting the C-Terminal Domain Small Phosphatase 1. Life (Basel) 2020; 10:life10050057. [PMID: 32397221 PMCID: PMC7281111 DOI: 10.3390/life10050057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
The human C-terminal domain small phosphatase 1 (CTDSP1/SCP1) is a protein phosphatase with a conserved catalytic site of DXDXT/V. CTDSP1’s major activity has been identified as dephosphorylation of the 5th Ser residue of the tandem heptad repeat of the RNA polymerase II C-terminal domain (RNAP II CTD). It is also implicated in various pivotal biological activities, such as acting as a driving factor in repressor element 1 (RE-1)-silencing transcription factor (REST) complex, which silences the neuronal genes in non-neuronal cells, G1/S phase transition, and osteoblast differentiation. Recent findings have denoted that negative regulation of CTDSP1 results in suppression of cancer invasion in neuroglioma cells. Several researchers have focused on the development of regulating materials of CTDSP1, due to the significant roles it has in various biological activities. In this review, we focused on this emerging target and explored the biological significance, challenges, and opportunities in targeting CTDSP1 from a drug designing perspective.
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10
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Wang Z, Sun H, Shen C, Hu X, Gao J, Li D, Cao D, Hou T. Combined strategies in structure-based virtual screening. Phys Chem Chem Phys 2020; 22:3149-3159. [PMID: 31995074 DOI: 10.1039/c9cp06303j] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The identification and optimization of lead compounds are inalienable components in drug design and discovery pipelines. As a powerful computational approach for the identification of hits with novel structural scaffolds, structure-based virtual screening (SBVS) has exhibited a remarkably increasing influence in the early stages of drug discovery. During the past decade, a variety of techniques and algorithms have been proposed and tested with different purposes in the scope of SBVS. Although SBVS has been a common and proven technology, it still shows some challenges and problems that are needed to be addressed, where the negative influence regardless of protein flexibility and the inaccurate prediction of binding affinity are the two major challenges. Here, focusing on these difficulties, we summarize a series of combined strategies or workflows developed by our group and others. Furthermore, several representative successful applications from recent publications are also discussed to demonstrate the effectiveness of the combined SBVS strategies in drug discovery campaigns.
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Affiliation(s)
- Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
| | - Chao Shen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
| | - Xueping Hu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
| | - Junbo Gao
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
| | - Dan Li
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410004, Hunan, P. R. China.
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
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11
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Monet D, Desdouits N, Nilges M, Blondel A. mkgridXf: Consistent Identification of Plausible Binding Sites Despite the Elusive Nature of Cavities and Grooves in Protein Dynamics. J Chem Inf Model 2019; 59:3506-3518. [DOI: 10.1021/acs.jcim.9b00103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Damien Monet
- Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, CNRS-USR 3756, Institut Pasteur, 28 rue du Dr. Roux, 75015 Paris, France
- Sorbonne Université, Collège doctoral, ED515 - Complexité du Vivant, 75005 Paris, France
| | - Nathan Desdouits
- Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, CNRS-USR 3756, Institut Pasteur, 28 rue du Dr. Roux, 75015 Paris, France
- Sorbonne Université, Collège doctoral, ED515 - Complexité du Vivant, 75005 Paris, France
| | - Michael Nilges
- Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, CNRS-USR 3756, Institut Pasteur, 28 rue du Dr. Roux, 75015 Paris, France
| | - Arnaud Blondel
- Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, CNRS-USR 3756, Institut Pasteur, 28 rue du Dr. Roux, 75015 Paris, France
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12
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Salerno S, García-Argáez AN, Barresi E, Taliani S, Simorini F, La Motta C, Amendola G, Tomassi S, Cosconati S, Novellino E, Da Settimo F, Marini AM, Via LD. New insights in the structure-activity relationships of 2-phenylamino-substituted benzothiopyrano[4,3-d]pyrimidines as kinase inhibitors. Eur J Med Chem 2018; 150:446-456. [PMID: 29547832 DOI: 10.1016/j.ejmech.2018.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 01/14/2023]
Abstract
Inhibition of angiogenesis via blocking vascular endothelial growth factor receptor (VEGFR) signaling pathway emerged as an established approach in anticancer therapy. So far, many monoclonal antibodies and ATP-competitive small molecule inhibitors have been clinically validated and approved. In this study, structure-activity relationships (SAR) within the 2-phenylamino-substituted benzothiopyrano[4,3-d]pyrimidine class of kinase inhibitors were further refined by the synthesis and biological evaluation of new compounds 1-21 featuring different substitution patterns on the pendant phenyl moiety, combined with H, OCH3, or Cl at 8-position. Most compounds showed a promising human kinase insert domain receptor (KDR) inhibition profile, with IC50 values in the submicromolar/low micromolar range, and promising antiproliferative activity on human umbilical vein endothelial cells (HUVECs) as well as on a panel of three human tumor cell lines. The angio-kinase selectivity profile was assessed for the most promising compound 16 against a set of six human kinases. Finally, computational studies allowed clarifying at molecular level the interaction pattern established by the compounds with KDR, highlighting key stable cation-π interactions, and thus providing the basis for further designing novel inhibitors.
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Affiliation(s)
- Silvia Salerno
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | | | - Elisabetta Barresi
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Sabrina Taliani
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy.
| | - Francesca Simorini
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Concettina La Motta
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Giorgio Amendola
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100, Caserta, Italy
| | - Stefano Tomassi
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100, Caserta, Italy
| | - Sandro Cosconati
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100, Caserta, Italy.
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Federico Da Settimo
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Anna Maria Marini
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Lisa Dalla Via
- Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
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13
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Nnadi CI, Jenkins ML, Gentile DR, Bateman LA, Zaidman D, Balius TE, Nomura DK, Burke JE, Shokat KM, London N. Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. J Chem Inf Model 2018; 58:464-471. [PMID: 29320178 DOI: 10.1021/acs.jcim.7b00399] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The success of targeted covalent inhibitors in the global pharmaceutical industry has led to a resurgence of covalent drug discovery. However, covalent inhibitor design for flexible binding sites remains a difficult task due to a lack of methodological development. Here, we compared covalent docking to empirical electrophile screening against the highly dynamic target K-RasG12C. While the overall hit rate of both methods was comparable, we were able to rapidly progress a docking hit to a potent irreversible covalent binder that modifies the inactive, GDP-bound state of K-RasG12C. Hydrogen-deuterium exchange mass spectrometry was used to probe the protein dynamics of compound binding to the switch-II pocket and subsequent destabilization of the nucleotide-binding region. SOS-mediated nucleotide exchange assays showed that, contrary to prior switch-II pocket inhibitors, these new compounds appear to accelerate nucleotide exchange. This study highlights the efficiency of covalent docking as a tool for the discovery of chemically novel hits against challenging targets.
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Affiliation(s)
- Chimno I Nnadi
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco , San Francisco, California 94158, United States
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology. University of Victoria , Victoria, BC V8W 2Y2, Canada
| | - Daniel R Gentile
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco , San Francisco, California 94158, United States
| | - Leslie A Bateman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley , Berkeley, California 94720, United States
| | - Daniel Zaidman
- Department of Organic Chemistry, The Weizmann Institute of Science , Rehovot, 7610001, Israel
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94158, United States
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley , Berkeley, California 94720, United States
| | - John E Burke
- Department of Biochemistry and Microbiology. University of Victoria , Victoria, BC V8W 2Y2, Canada
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco , San Francisco, California 94158, United States
| | - Nir London
- Department of Organic Chemistry, The Weizmann Institute of Science , Rehovot, 7610001, Israel
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14
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Kumar A, Tiwari A, Sharma A. Changing Paradigm from one Target one Ligand Towards Multi-target Directed Ligand Design for Key Drug Targets of Alzheimer Disease: An Important Role of In Silico Methods in Multi-target Directed Ligands Design. Curr Neuropharmacol 2018; 16:726-739. [PMID: 29542413 PMCID: PMC6080096 DOI: 10.2174/1570159x16666180315141643] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/01/2017] [Accepted: 05/01/2017] [Indexed: 12/14/2022] Open
Abstract
Alzheimer disease (AD) is now considered as a multifactorial neurodegenerative disorder and rapidly increasing to an alarming situation and causing higher death rate. One target one ligand hypothesis does not provide complete solution of AD due to multifactorial nature of the disease and one target one drug fails to provide better treatment against AD. Moreover, currently available treatments are limited and most of the upcoming treatments under clinical trials are based on modulating single target. So, the current AD drug discovery research is shifting towards a new approach for a better solution that simultaneously modulates more than one targets in the neurodegenerative cascade. This can be achieved by network pharmacology, multi-modal therapies, multifaceted, and/or the more recently proposed term "multi-targeted designed drugs". Drug discovery project is a tedious, costly and long-term project. Moreover, multi-target AD drug discovery added extra challenges such as the good binding affinity of ligands for multiple targets, optimal ADME/T properties, no/less off-target side effect and crossing of the blood-brain barrier. These hurdles may be addressed by insilico methods for an efficient solution in less time and cost as computational methods successfully applied to single target drug discovery project. Here, we are summarizing some of the most prominent and computationally explored single targets against AD and further, we discussed a successful example of dual or multiple inhibitors for same targets. Moreover, we focused on ligand and structure-based computational approach to design MTDL against AD. However, it is not an easy task to balance dual activity in a single molecule but computational approach such as virtual screening docking, QSAR, simulation and free energy is useful in future MTDLs drug discovery alone or in combination with a fragment-based method. However, rational and logical implementations of computational drug designing methods are capable of assisting AD drug discovery and play an important role in optimizing multi-target drug discovery.
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Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
| | - Ashish Tiwari
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow-226015, (U.P.), India
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15
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Prati F, Bottegoni G, Bolognesi ML, Cavalli A. BACE-1 Inhibitors: From Recent Single-Target Molecules to Multitarget Compounds for Alzheimer’s Disease. J Med Chem 2017; 61:619-637. [DOI: 10.1021/acs.jmedchem.7b00393] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Federica Prati
- Drug Discovery Unit,
Division of Biological Chemistry and Drug Discovery, College of Life
Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, U.K
| | - Giovanni Bottegoni
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Maria Laura Bolognesi
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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16
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Xia J, Hsieh JH, Hu H, Wu S, Wang XS. The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening. J Chem Inf Model 2017; 57:1414-1425. [PMID: 28511009 DOI: 10.1021/acs.jcim.6b00749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based virtual screening (SBVS) has become an indispensable technique for hit identification at the early stage of drug discovery. However, the accuracy of current scoring functions is not high enough to confer success to every target and thus remains to be improved. Previously, we had developed binary pose filters (PFs) using knowledge derived from the protein-ligand interface of a single X-ray structure of a specific target. This novel approach had been validated as an effective way to improve ligand enrichment. Continuing from it, in the present work we attempted to incorporate knowledge collected from diverse protein-ligand interfaces of multiple crystal structures of the same target to build PF ensembles (PFEs). Toward this end, we first constructed a comprehensive data set to meet the requirements of ensemble modeling and validation. This set contains 10 diverse targets, 118 well-prepared X-ray structures of protein-ligand complexes, and large benchmarking actives/decoys sets. Notably, we designed a unique workflow of two-layer classifiers based on the concept of ensemble learning and applied it to the construction of PFEs for all of the targets. Through extensive benchmarking studies, we demonstrated that (1) coupling PFE with Chemgauss4 significantly improves the early enrichment of Chemgauss4 itself and (2) PFEs show greater consistency in boosting early enrichment and larger overall enrichment than our prior PFs. In addition, we analyzed the pairwise topological similarities among cognate ligands used to construct PFEs and found that it is the higher chemical diversity of the cognate ligands that leads to the improved performance of PFEs. Taken together, the results so far prove that the incorporation of knowledge from diverse protein-ligand interfaces by ensemble modeling is able to enhance the screening competence of SBVS scoring functions.
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Affiliation(s)
- Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Jui-Hua Hsieh
- Kelly Government Solutions , Research Triangle Park, North Carolina 27709, United States
| | - Huabin Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Xiang Simon Wang
- Molecular Modeling and Drug Discovery Core Laboratory for District of Columbia Center for AIDS Research (DC CFAR), Department of Pharmaceutical Sciences, College of Pharmacy, Howard University , Washington, D.C. 20059, United States
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17
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Hernández-Rodríguez M, Correa-Basurto J, Gutiérrez A, Vitorica J, Rosales-Hernández MC. Asp32 and Asp228 determine the selective inhibition of BACE1 as shown by docking and molecular dynamics simulations. Eur J Med Chem 2016; 124:1142-1154. [DOI: 10.1016/j.ejmech.2016.08.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 08/10/2016] [Accepted: 08/13/2016] [Indexed: 11/28/2022]
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18
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Moitessier N, Pottel J, Therrien E, Englebienne P, Liu Z, Tomberg A, Corbeil CR. Medicinal Chemistry Projects Requiring Imaginative Structure-Based Drug Design Methods. Acc Chem Res 2016; 49:1646-57. [PMID: 27529781 DOI: 10.1021/acs.accounts.6b00185] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Computational methods for docking small molecules to proteins are prominent in drug discovery. There are hundreds, if not thousands, of documented examples-and several pertinent cases within our research program. Fifteen years ago, our first docking-guided drug design project yielded nanomolar metalloproteinase inhibitors and illustrated the potential of structure-based drug design. Subsequent applications of docking programs to the design of integrin antagonists, BACE-1 inhibitors, and aminoglycosides binding to bacterial RNA demonstrated that available docking programs needed significant improvement. At that time, docking programs primarily considered flexible ligands and rigid proteins. We demonstrated that accounting for protein flexibility, employing displaceable water molecules, and using ligand-based pharmacophores improved the docking accuracy of existing methods-enabling the design of bioactive molecules. The success prompted the development of our own program, Fitted, implementing all of these aspects. The primary motivation has always been to respond to the needs of drug design studies; the majority of the concepts behind the evolution of Fitted are rooted in medicinal chemistry projects and collaborations. Several examples follow: (1) Searching for HDAC inhibitors led us to develop methods considering drug-zinc coordination and its effect on the pKa of surrounding residues. (2) Targeting covalent prolyl oligopeptidase (POP) inhibitors prompted an update to Fitted to identify reactive groups and form bonds with a given residue (e.g., a catalytic residue) when the geometry allows it. Fitted-the first fully automated covalent docking program-was successfully applied to the discovery of four new classes of covalent POP inhibitors. As a result, efficient stereoselective syntheses of a few screening hits were prioritized rather than synthesizing large chemical libraries-yielding nanomolar inhibitors. (3) In order to study the metabolism of POP inhibitors by cytochrome P450 enzymes (CYPs)-for toxicology studies-the program Impacts was derived from Fitted and helped us to reveal a complex metabolism with unforeseen stereocenter isomerizations. These efforts, combined with those of other docking software developers, have strengthened our understanding of the complex drug-protein binding process while providing the medicinal chemistry community with useful tools that have led to drug discoveries. In this Account, we describe our contributions over the past 15 years-within their historical context-to the design of drug candidates, including BACE-1 inhibitors, POP covalent inhibitors, G-quadruplex binders, and aminoglycosides binding to nucleic acids. We also remark the necessary developments of docking programs, specifically Fitted, that enabled structure-based design to flourish and yielded multiple fruitful, rational medicinal chemistry campaigns.
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Affiliation(s)
- Nicolas Moitessier
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Joshua Pottel
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Eric Therrien
- Molecular Forecaster Inc., 969
Marc-Aurèle-Fortin, Laval, Québec, Canada H7L 6H9
| | - Pablo Englebienne
- Royal HaskoningDHV, Laan 1914
35, 3818 EX Amersfoort, The Netherlands
| | - Zhaomin Liu
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Anna Tomberg
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Christopher R. Corbeil
- Human
Health Therapeutics, National Research Council Canada, 6100 Royalmount
Avenue, Montréal, Québec, Canada H4P 2R2
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19
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Estrada M, Pérez C, Soriano E, Laurini E, Romano M, Pricl S, Morales-García JA, Pérez-Castillo A, Rodríguez-Franco MI. New neurogenic lipoic-based hybrids as innovative Alzheimer's drugs with σ-1 agonism and β-secretase inhibition. Future Med Chem 2016; 8:1191-207. [PMID: 27402296 DOI: 10.4155/fmc-2016-0036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Neurogenic agents emerge as innovative drugs for the treatment of Alzheimer's disease (AD), whose pathological complexity suggests strengthening research in the multi-target directed ligands strategy. RESULTS By combining the lipoic acid structure with N-benzylpiperidine or N,N-dibenzyl(N-methyl)amine fragments, new multi-target directed ligands were obtained that act at three relevant targets in AD: σ-1 receptor (σ1R), β-secretase-1 (BACE1) and acetylcholinesterase (AChE). Moreover, they show potent neurogenic properties, good antioxidant capacity and favorable CNS permeability. Molecular modeling studies on AChE, σ1R and BACE1 highlight relevant drug-protein interactions that may contribute to the development of new disease-modifying drugs. CONCLUSION New lipoic-based σ1 agonists endowed with neurogenic, antioxidant, cholinergic and amyloid β-peptide-reducing properties have been discovered for the potential treatment of AD.
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Affiliation(s)
- Martín Estrada
- Instituto de Química Médica (IQM-CSIC), C/Juan de la Cierva 3, 28006-Madrid, Spain
| | - Concepción Pérez
- Instituto de Química Médica (IQM-CSIC), C/Juan de la Cierva 3, 28006-Madrid, Spain
| | - Elena Soriano
- Instituto de Química Orgánica General (IQOG-CSIC), C/Juan de la Cierva 3, 28006-Madrid, Spain
| | - Erik Laurini
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 - Trieste, Italy
| | - Sabrina Pricl
- Molecular Simulation Engineering (MOSE) Laboratory, DEA, Piazzale Europa 1, University of Trieste, 34127 Trieste, Italy
- National Interuniversity Consortium for Material Science & Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Trieste, Italy
| | - José A Morales-García
- Instituto de Investigaciones Biomédicas "Alberto Sols" (IIB-CSIC), C/Arturo Duperier 4, 28029-Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), C/Valderrebollo 5, 28031-Madrid, Spain
| | - Ana Pérez-Castillo
- Instituto de Investigaciones Biomédicas "Alberto Sols" (IIB-CSIC), C/Arturo Duperier 4, 28029-Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), C/Valderrebollo 5, 28031-Madrid, Spain
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20
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Amendola G, Di Maio D, La Pietra V, Cosconati S. Best Matching Protein Conformations and Docking Programs for a Virtual Screening Campaign Against SMO Receptor. Mol Inform 2016; 35:340-9. [DOI: 10.1002/minf.201501021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/14/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Giorgio Amendola
- DiSTABiF; Seconda Università degli Studi di Napoli; Via Vivaldi 43 81100 Caserta Italy
| | - Danilo Di Maio
- Istituto Nazionale di Fisica Nucleare (INFN); sezione di Pisa; Largo Bruno Pontecorvo 3 56127 Pisa Italy
- Scuola Normale Superiore; Piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Valeria La Pietra
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Via D. Montesano 49 80131 Naples Italy
| | - Sandro Cosconati
- DiSTABiF; Seconda Università degli Studi di Napoli; Via Vivaldi 43 81100 Caserta Italy
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21
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Abstract
Computational docking can be used to predict bound conformations and free energies of binding for small-molecule ligands to macromolecular targets. Docking is widely used for the study of biomolecular interactions and mechanisms, and it is applied to structure-based drug design. The methods are fast enough to allow virtual screening of ligand libraries containing tens of thousands of compounds. This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction and docking with explicit hydration. The entire protocol will require ∼5 h.
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22
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Johnson DK, Karanicolas J. Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein-Protein Interactions. J Chem Inf Model 2016; 56:399-411. [PMID: 26726827 DOI: 10.1021/acs.jcim.5b00572] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions play important roles in virtually all cellular processes, making them enticing targets for modulation by small-molecule therapeutics: specific examples have been well validated in diseases ranging from cancer and autoimmune disorders, to bacterial and viral infections. Despite several notable successes, however, overall these remain a very challenging target class. Protein interaction sites are especially challenging for computational approaches, because the target protein surface often undergoes a conformational change to enable ligand binding: this confounds traditional approaches for virtual screening. Through previous studies, we demonstrated that biased "pocket optimization" simulations could be used to build collections of low-energy pocket-containing conformations, starting from an unbound protein structure. Here, we demonstrate that these pockets can further be used to identify ligands that complement the protein surface. To do so, we first build from a given pocket its "exemplar": a perfect, but nonphysical, pseudoligand that would optimally match the shape and chemical features of the pocket. In our previous studies, we used these exemplars to quantitatively compare protein surface pockets to one another. Here, we now introduce this exemplar as a template for pharmacophore-based screening of chemical libraries. Through a series of benchmark experiments, we demonstrate that this approach exhibits comparable performance as traditional docking methods for identifying known inhibitors acting at protein interaction sites. However, because this approach is predicated on ligand/exemplar overlays, and thus does not require explicit calculation of protein-ligand interactions, exemplar screening provides a tremendous speed advantage over docking: 6 million compounds can be screened in about 15 min on a single 16-core, dual-GPU computer. The extreme speed at which large compound libraries can be traversed easily enables screening against a "pocket-optimized" ensemble of protein conformations, which in turn facilitates identification of more diverse classes of active compounds for a given protein target.
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Affiliation(s)
- David K Johnson
- Center for Computational Biology, and ‡Department of Molecular Biosciences, University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - John Karanicolas
- Center for Computational Biology, and ‡Department of Molecular Biosciences, University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
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23
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Bietz S, Rarey M. SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. J Chem Inf Model 2016; 56:248-59. [PMID: 26759067 DOI: 10.1021/acs.jcim.5b00588] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Structural flexibility of proteins has an important influence on molecular recognition and enzymatic function. In modeling, structure ensembles are therefore often applied as a valuable source of alternative protein conformations. However, their usage is often complicated by structural artifacts and inconsistent data annotation. Here, we present SIENA, a new computational approach for the automated assembly and preprocessing of protein binding site ensembles. Starting with an arbitrarily defined binding site in a single protein structure, SIENA searches for alternative conformations of the same or sequentially closely related binding sites. The method is based on an indexed database for identifying perfect k-mer matches and a recently published algorithm for the alignment of protein binding site conformations. Furthermore, SIENA provides a new algorithm for the interaction-based selection of binding site conformations which aims at covering all known ligand-binding geometries. Various experiments highlight that SIENA is able to generate comprehensive and well selected binding site ensembles improving the compatibility to both known and unconsidered ligand molecules. Starting with the whole PDB as data source, the computation time of the whole ensemble generation takes only a few seconds. SIENA is available via a Web service at www.zbh.uni-hamburg.de/siena .
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Affiliation(s)
- Stefan Bietz
- Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany
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24
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Discovery of Novel ROCK1 Inhibitors via Integrated Virtual Screening Strategy and Bioassays. Sci Rep 2015; 5:16749. [PMID: 26568382 PMCID: PMC4645114 DOI: 10.1038/srep16749] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/19/2015] [Indexed: 12/22/2022] Open
Abstract
Rho-associated kinases (ROCKs) have been regarded as promising drug targets for the treatment of cardiovascular diseases, nervous system diseases and cancers. In this study, a novel integrated virtual screening protocol by combining molecular docking and pharmacophore mapping based on multiple ROCK1 crystal structures was utilized to screen the ChemBridge database for discovering potential inhibitors of ROCK1. Among the 38 tested compounds, seven of them exhibited significant inhibitory activities of ROCK1 (IC50 < 10 μM) and the most potent one (compound TS-f22) with the novel scaffold of 4-Phenyl-1H-pyrrolo [2,3-b] pyridine had an IC50 of 480 nM. Then, the structure-activity relationships of 41 analogues of TS-f22 were examined. Two potent inhibitors were proven effective in inhibiting the phosphorylation of the downstream target in the ROCK signaling pathway in vitro and protecting atorvastatin-induced cerebral hemorrhage in vivo. The high hit rate (28.95%) suggested that the integrated virtual screening strategy was quite reliable and could be used as a powerful tool for identifying promising active compounds for targets of interest.
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25
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Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis. Future Med Chem 2015; 7:2317-31. [DOI: 10.4155/fmc.15.150] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based and normal mode analysis-based protocols combined with conformational pocket classifications to efficiently generate RCEs. Materials & Methods: We assessed our protocols on two well-characterized protein targets showing local active site flexibility, dihydrofolate reductase and large collective movements, CDK2. The performance of the RCEs was validated by distinguishing known ligands of dihydrofolate reductase and CDK2 among a dataset of diverse chemical decoys. Results & discussion: Our results show that different simulation protocols can be efficient for generation of RCEs depending on different kind of protein flexibility.[Formula: see text]
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26
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Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem 2015; 36:1132-56. [PMID: 25914306 DOI: 10.1002/jcc.23905] [Citation(s) in RCA: 450] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 03/01/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
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Affiliation(s)
- William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, 11794
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27
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Xiong X, Yuan H, Zhang Y, Xu J, Ran T, Liu H, Lu S, Xu A, Li H, Jiang Y, Lu T, Chen Y. Protein flexibility oriented virtual screening strategy for JAK2 inhibitors. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Zeng H, Wu X. Alzheimer's disease drug development based on Computer-Aided Drug Design. Eur J Med Chem 2015; 121:851-863. [PMID: 26415837 DOI: 10.1016/j.ejmech.2015.08.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/01/2015] [Accepted: 08/21/2015] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder characterized by the excessive deposition of amyloids in the brain. The pathological features mainly include the extracellular amyloid plaques and intracellular neurofibrillary tangles, which are the production of amyloid precursor protein (APP) processed by the α-, β- and γ-secretases. Based on the amyloid cascade hypotheses of AD, a large number of amyloid-β agents and secretase inhibitors against AD have been recently developed by using computational methods. This review article describes pathophysiology of AD and the structure of the Aβ plaques, β- and γ-secretases, and discusses the recent advances in the development of the amyloid agents for AD therapy and diagnosis by using Computer-Aided Drug Design approach.
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Affiliation(s)
- Huahui Zeng
- Science & Technology Department, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China; Department of Nuclear Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China.
| | - Xiangxiang Wu
- Science & Technology Department, Henan University of Traditional Chinese Medicine, Zhengzhou 450046, China.
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29
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Gowthaman R, Miller SA, Rogers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aubé J, Roy A, Karanicolas J. DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites. J Med Chem 2015; 59:4152-70. [PMID: 26126123 DOI: 10.1021/acs.jmedchem.5b00150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions represent an exciting and challenging target class for therapeutic intervention using small molecules. Protein interaction sites are often devoid of the deep surface pockets presented by "traditional" drug targets, and crystal structures reveal that inhibitors typically engage these sites using very shallow binding modes. As a consequence, modern virtual screening tools developed to identify inhibitors of traditional drug targets do not perform as well when they are instead deployed at protein interaction sites. To address the need for novel inhibitors of important protein interactions, here we introduce an alternate docking strategy specifically designed for this regime. Our method, termed DARC (Docking Approach using Ray-Casting), matches the topography of a surface pocket "observed" from within the protein to the topography "observed" when viewing a potential ligand from the same vantage point. We applied DARC to carry out a virtual screen against the protein interaction site of human antiapoptotic protein Mcl-1 and found that four of the top-scoring 21 compounds showed clear inhibition in a biochemical assay. The Ki values for these compounds ranged from 1.2 to 21 μM, and each had ligand efficiency comparable to promising small-molecule inhibitors of other protein-protein interactions. These hit compounds do not resemble the natural (protein) binding partner of Mcl-1, nor do they resemble any known inhibitors of Mcl-1. Our results thus demonstrate the utility of DARC for identifying novel inhibitors of protein-protein interactions.
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Affiliation(s)
- Ragul Gowthaman
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Sven A Miller
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Steven Rogers
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Jittasak Khowsathit
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Lan Lan
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Nan Bai
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - David K Johnson
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Chunjing Liu
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Liang Xu
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Asokan Anbanandam
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Jeffrey Aubé
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Anuradha Roy
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - John Karanicolas
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
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Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015; 28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.
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Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, 3084, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia.,School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
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Theory and applications of covalent docking in drug discovery: merits and pitfalls. Molecules 2015; 20:1984-2000. [PMID: 25633330 PMCID: PMC6272664 DOI: 10.3390/molecules20021984] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/19/2014] [Accepted: 01/12/2015] [Indexed: 11/17/2022] Open
Abstract
The present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages over non-covalent inhibitors such as covalent warheads can target rare, non-conserved residue of a particular target protein and thus led to development of highly selective inhibitors, covalent inhibitors can be effective in targeting proteins with shallow binding cleavage which will led to development of novel inhibitors with increased potency than non-covalent inhibitors. Several computational approaches have been developed to simulate covalent interactions; however, this is still a challenging area to explore. Covalent molecular docking has been recently implemented in the computer-aided drug design workflows to describe covalent interactions between inhibitors and biological targets. In this review we highlight: (i) covalent interactions in biomolecular systems; (ii) the mathematical framework of covalent molecular docking; (iii) implementation of covalent docking protocol in drug design workflows; (iv) applications covalent docking: case studies and (v) shortcomings and future perspectives of covalent docking. To the best of our knowledge; this review is the first account that highlights different aspects of covalent docking with its merits and pitfalls. We believe that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors.
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Manoharan P, Chennoju K, Ghoshal N. Target specific proteochemometric model development for BACE1 – protein flexibility and structural water are critical in virtual screening. MOLECULAR BIOSYSTEMS 2015; 11:1955-72. [DOI: 10.1039/c5mb00088b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Structural water and protein plasticity are important factors for BACE1 targeted ligand virtual screening.
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Affiliation(s)
- Prabu Manoharan
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Kiranmai Chennoju
- National Institute of Pharmaceutical Education and Research
- Kolkata 700032
- India
| | - Nanda Ghoshal
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
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33
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Forli S, Olson AJ. Computational challenges of structure-based approaches applied to HIV. Curr Top Microbiol Immunol 2015; 389:31-51. [PMID: 25711462 DOI: 10.1007/82_2015_432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Here, we review some of the opportunities and challenges that we face in computational modeling of HIV therapeutic targets and structural biology, both in terms of methodology development and structure-based drug design (SBDD). Computational methods have provided fundamental support to HIV research since the initial structural studies, helping to unravel details of HIV biology. Computational models have proved to be a powerful tool to analyze and understand the impact of mutations and to overcome their structural and functional influence in drug resistance. With the availability of structural data, in silico experiments have been instrumental in exploiting and improving interactions between drugs and viral targets, such as HIV protease, reverse transcriptase, and integrase. Issues such as viral target dynamics and mutational variability, as well as the role of water and estimates of binding free energy in characterizing ligand interactions, are areas of active computational research. Ever-increasing computational resources and theoretical and algorithmic advances have played a significant role in progress to date, and we envision a continually expanding role for computational methods in our understanding of HIV biology and SBDD in the future.
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Affiliation(s)
- Stefano Forli
- MGL, Department of Integrative Structural and Computational Biology and HIV Interaction and Viral Evolution Center, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
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Tian S, Sun H, Pan P, Li D, Zhen X, Li Y, Hou T. Assessing an ensemble docking-based virtual screening strategy for kinase targets by considering protein flexibility. J Chem Inf Model 2014; 54:2664-79. [PMID: 25233367 DOI: 10.1021/ci500414b] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, to accommodate receptor flexibility, based on multiple receptor conformations, a novel ensemble docking protocol was developed by using the naïve Bayesian classification technique, and it was evaluated in terms of the prediction accuracy of docking-based virtual screening (VS) of three important targets in the kinase family: ALK, CDK2, and VEGFR2. First, for each target, the representative crystal structures were selected by structural clustering, and the capability of molecular docking based on each representative structure to discriminate inhibitors from non-inhibitors was examined. Then, for each target, 50 ns molecular dynamics (MD) simulations were carried out to generate an ensemble of the conformations, and multiple representative structures/snapshots were extracted from each MD trajectory by structural clustering. On average, the representative crystal structures outperform the representative structures extracted from MD simulations in terms of the capabilities to separate inhibitors from non-inhibitors. Finally, by using the naïve Bayesian classification technique, an integrated VS strategy was developed to combine the prediction results of molecular docking based on different representative conformations chosen from crystal structures and MD trajectories. It was encouraging to observe that the integrated VS strategy yields better performance than the docking-based VS based on any single rigid conformation. This novel protocol may provide an improvement over existing strategies to search for more diverse and promising active compounds for a target of interest.
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Affiliation(s)
- Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University , Suzhou, Jiangsu 215123, P. R. China
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Bai Q, Shao Y, Pan D, Zhang Y, Liu H, Yao X. Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations. PLoS One 2014; 9:e107837. [PMID: 25229694 PMCID: PMC4168136 DOI: 10.1371/journal.pone.0107837] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 08/23/2014] [Indexed: 11/19/2022] Open
Abstract
We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD) simulations and free energy calculations. To test the effectiveness of MolGridCal, we screened potential ligands for β2 adrenergic receptor (β2AR) from a database containing 50,000 small molecules. MolGridCal can not only send tasks to the grid server automatically, but also can distribute tasks using the screensaver function. As for the results of virtual screening, the known agonist BI-167107 of β2AR is ranked among the top 2% of the screened candidates, indicating MolGridCal program can give reasonable results. To further study the binding mode and refine the results of MolGridCal, more accurate docking and scoring methods are used to estimate the binding affinity for the top three molecules (agonist BI-167107, neutral antagonist alprenolol and inverse agonist ICI 118,551). The results indicate agonist BI-167107 has the best binding affinity. MD simulation and free energy calculation are employed to investigate the dynamic interaction mechanism between the ligands and β2AR. The results show that the agonist BI-167107 also has the lowest binding free energy. This study can provide a new way to perform virtual screening effectively through integrating molecular docking based on grid computing, MD simulations and free energy calculations. The source codes of MolGridCal are freely available at http://molgridcal.codeplex.com.
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Affiliation(s)
- Qifeng Bai
- Department of Chemistry, Lanzhou University, Lanzhou, China
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Yonghua Shao
- Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Dabo Pan
- Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Yang Zhang
- School of Information Science & Engineering, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- Department of Chemistry, Lanzhou University, Lanzhou, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
- * E-mail:
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Santos-Martins D, Forli S, Ramos MJ, Olson AJ. AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins. J Chem Inf Model 2014; 54:2371-9. [PMID: 24931227 PMCID: PMC4144784 DOI: 10.1021/ci500209e] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 12/14/2022]
Abstract
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer's disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code.
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Affiliation(s)
- Diogo Santos-Martins
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
- REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Stefano Forli
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Maria João Ramos
- REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Arthur J. Olson
- Department of Integrative Structural and Computational
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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Fischer M, Coleman RG, Fraser JS, Shoichet BK. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem 2014; 6:575-83. [PMID: 24950326 PMCID: PMC4144196 DOI: 10.1038/nchem.1954] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/11/2014] [Indexed: 12/04/2022]
Abstract
Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.
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Affiliation(s)
- Marcus Fischer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
- Faculty of Pharmacy, Donnelly Center, University of Toronto, 160 College St. Toronto Ontario M5S 3E1
| | - Ryan G. Coleman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
- Faculty of Pharmacy, Donnelly Center, University of Toronto, 160 College St. Toronto Ontario M5S 3E1
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Kalászi A, Szisz D, Imre G, Polgár T. Screen3D: a novel fully flexible high-throughput shape-similarity search method. J Chem Inf Model 2014; 54:1036-49. [PMID: 24568118 DOI: 10.1021/ci400620f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
3D shape- or volume-based virtual screening is a broadly used approach in drug discovery. In recent years a large number of publications have appeared in which these tools were compared not only to competitive methods but to docking studies as well. Studies often showed that the effectiveness of docking could be highly variable due to a large number of possible confounding factors, while ligand-based, shape-based approaches were more consistent. Here, we describe a novel, fully flexible shape-based virtual screening algorithm that does not require previous 3D conformation or conformer generation. Due to its solid consistency it can easily be used on desktop computers by non-expert scientists. The algorithm is demonstrated in a study for the investigation of β-secretase inhibitors and benchmarked on the Directory of Useful Decoys data set.
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Affiliation(s)
- Adrián Kalászi
- ChemAxon Ltd., Graphisoft park, Zahony u. 7, Budapest, Hungary , 1037
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Butini S, Gabellieri E, Brindisi M, Giovani S, Maramai S, Kshirsagar G, Guarino E, Brogi S, La Pietra V, Giustiniano M, Marinelli L, Novellino E, Campiani G, Cappelli A, Gemma S. A stereoselective approach to peptidomimetic BACE1 inhibitors. Eur J Med Chem 2013; 70:233-47. [DOI: 10.1016/j.ejmech.2013.09.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/25/2013] [Accepted: 09/28/2013] [Indexed: 11/16/2022]
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Abstract
INTRODUCTION Alzheimer's disease (AD), which is characterized by progressive intellectual deterioration, is the most common cause of dementia. β-Secretase (or BACE1) expression is a trigger for amyloid β peptide formation, a cause of AD, and thus is a molecular target for the development of drugs against AD. Many BACE1 inhibitors have been identified by academic and pharmaceutical research groups and a number of advanced technologies in drug discovery have been applied to the drug discovery. AREAS COVERED The purpose of this review is to present and discuss the methodologies used for BACE1 inhibitor drug discovery via substrate- and structure-based design, high-throughput screening and fragment-based drug design. The authors also review the advantages and disadvantages of these methodologies. EXPERT OPINION Many BACE1 inhibitors have been designed using X-ray crystal structure-based drug design as well as through in silico screening. Nevertheless, there are serious problems with regards to deciding the best X-ray crystal structure for designing BACE1 inhibitors through computational approaches. There are two prominent configurations of BACE1 but there is still room for improvement. Future developments may make it possible to identify BACE1 inhibitors as potential drug candidates.
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Affiliation(s)
- Yoshio Hamada
- Kobe Gakuin University, Faculty of Pharmaceutical Sciences, Minatojima, Chuo-ku, Kobe 650-8586, Japan
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Fukunishi Y, Nakamura H. Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking. Pharmaceuticals (Basel) 2012; 5:1332-45. [PMID: 24281339 PMCID: PMC3816669 DOI: 10.3390/ph5121332] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 11/24/2012] [Accepted: 11/30/2012] [Indexed: 01/05/2023] Open
Abstract
Ligand-based and structure-based drug screening methods were integrated for in silico drug development by combining the maximum-volume overlap (MVO) method with a protein-compound docking program. The MVO method is used to select reliable docking poses by calculating volume overlaps between the docking pose in question and the known ligand docking pose, if at least a single protein-ligand complex structure is known. In the present study, the compounds in a database were docked onto a target protein that had a known protein-ligand complex structure. The new score is the summation of the docking score and the MVO score, which is the measure of the volume overlap between the docking poses of the compound in question and the known ligand. The compounds were sorted according to the new score. The in silico screening results were improved by comparing the MVO score to the original docking score only. The present method was also applied to some target proteins with known ligands, and the results demonstrated that it worked well.
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Affiliation(s)
- Yoshifumi Fukunishi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-3-3599-8290; Fax: +81-3-3599-8099
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail: (H.N.)
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