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Jha T, Jana R, Banerjee S, Baidya SK, Amin SA, Gayen S, Ghosh B, Adhikari N. Exploring different classification-dependent QSAR modelling strategies for HDAC3 inhibitors in search of meaningful structural contributors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:367-389. [PMID: 38757181 DOI: 10.1080/1062936x.2024.2350504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024]
Abstract
Histone deacetylase 3 (HDAC3), a Zn2+-dependent class I HDACs, contributes to numerous disorders such as neurodegenerative disorders, diabetes, cardiovascular disease, kidney disease and several types of cancers. Therefore, the development of novel and selective HDAC3 inhibitors might be promising to combat such diseases. Here, different classification-based molecular modelling studies such as Bayesian classification, recursive partitioning (RP), SARpy and linear discriminant analysis (LDA) were conducted on a set of HDAC3 inhibitors to pinpoint essential structural requirements contributing to HDAC3 inhibition followed by molecular docking study and molecular dynamics (MD) simulation analyses. The current study revealed the importance of hydroxamate function for Zn2+ chelation as well as hydrogen bonding interaction with Tyr298 residue. The importance of hydroxamate function for higher HDAC3 inhibition was noticed in the case of Bayesian classification, recursive partitioning and SARpy models. Also, the importance of substituted thiazole ring was revealed, whereas the presence of linear alkyl groups with carboxylic acid function, any type of ester function, benzodiazepine moiety and methoxy group in the molecular structure can be detrimental to HDAC3 inhibition. Therefore, this study can aid in the design and discovery of effective novel HDAC3 inhibitors in the future.
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Affiliation(s)
- T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - R Jana
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S A Amin
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - B Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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2
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Jiang F, Xu M, Bei W, Cheng K, Huang L. Palladium-catalyzed native α-amino acid derivative-directed arylation/oxidation of benzylic C-H bonds: synthesis of 5-aryl-1,4-benzodiazepin-2-ones. Chem Commun (Camb) 2022; 58:9638-9641. [PMID: 35938553 DOI: 10.1039/d2cc03266j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A Pd-catalyzed, native α-amino acid derivative-directed benzylic C-H bond arylation/oxidation with aryl iodides was developed. The natural amino acid auxiliary could serve as a desired building block for formation of 5-aryl-1,4-benzodiazepin-2-ones after removal of the trifluoroacetyl protecting group. The bifunctional reaction probably proceeded through a sequential benzylic arylation/oxidation process.
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Affiliation(s)
- Fengxuan Jiang
- Key Laboratory of Alternative Technologies for Fine Chemicals Process, Institute of Applied Chemistry, Shaoxing University, Shaoxing, Zhejiang Province 312000, People's Republic of China.,School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, Zhejiang Province 325035, People's Republic of China.
| | - Menghua Xu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Wenfeng Bei
- Key Laboratory of Alternative Technologies for Fine Chemicals Process, Institute of Applied Chemistry, Shaoxing University, Shaoxing, Zhejiang Province 312000, People's Republic of China
| | - Kai Cheng
- Key Laboratory of Alternative Technologies for Fine Chemicals Process, Institute of Applied Chemistry, Shaoxing University, Shaoxing, Zhejiang Province 312000, People's Republic of China
| | - Lehao Huang
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, Zhejiang Province 325035, People's Republic of China.
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3
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Dalovai P, Karunakar GV, Damodaran Nadar V, Doddi VR, Kanaparthy S. Gold-catalyzed formation of substituted aminobenzophenone derivatives via intramolecular 6-endo-dig cyclization. J CHEM SCI 2021. [DOI: 10.1007/s12039-020-01860-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Knutson DE, Roni R, Mian Y, Cook JM, Stafford DC, Arnold LA. Improved scale-up synthesis and purification of clinical asthma candidate MIDD0301. Org Process Res Dev 2020; 24:1467-1476. [PMID: 32952391 DOI: 10.1021/acs.oprd.0c00200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report an improved and scalable synthesis of MIDD0301, a positive GABAA receptor modulator that is under development as oral and inhaled treatments for asthma. In contrast to other benzodiazepines in clinical use, MIDD0301 is a chiral compound that has limited brain absorption. The starting material to generate MIDD0301 is 2-amino-5-bromo-2'-fluorobenzophenone, which has a non-basic nitrogen due to electron withdrawing substituents in the ortho and para positions, reducing its reactivity towards activated carboxylic acids. Investigations of peptide coupling reagents on multigram scale resulted in moderate yields due to incomplete conversions. Secondly, basic conditions used for the formation of the seven-membered 1,4-diazepine ring resulted in racemization of the chiral center. We found that neutral conditions comparable to the pKa of the primary amine were sufficient to support the formation of the intramolecular imine but did not enable the simultaneous removal of the protecting group. Both difficulties were overcome with the application of the N-carboxyanhydride of D-alanine. Activated in the presence of acid, this compound reacted with non-basic 2-amino-5-bromo-2'-fluorobenzophenone and formed the 1,4-diazepine upon neutralization with triethylamine. Carefully designed workup procedures and divergent solubility of the synthetic intermediates in solvents and solvent combinations were utilized to eliminate the need for column chromatography. To improve compatibility with large scale reactors, temperature-controlled slow addition of reagents generated the imidazodiazepine at -20 °C. All intermediates were isolated with a purity of >97% and impurities were identified and quantified. After the final hydrolysis step, MIDD0301 was isolated in a 44% overall yield and purity of 98.9% after recrystallization. The enantiomeric excess was greater than 99.0%.
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Affiliation(s)
- Daniel E Knutson
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Rashid Roni
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Yeunus Mian
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - James M Cook
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Douglas C Stafford
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, United States.,Pantherics Incorporated, La Jolla, California 92037, United States
| | - Leggy A Arnold
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, United States.,Pantherics Incorporated, La Jolla, California 92037, United States
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5
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Amin SA, Banerjee S, Adhikari N, Jha T. Discriminations of active from inactive HDAC8 inhibitors Part II: Bayesian classification study to find molecular fingerprints. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:245-260. [PMID: 32073312 DOI: 10.1080/1062936x.2020.1723136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
In continuation of our earlier work (Doi: 10.1080/07391102.2019.1661876), a statistically validated and robust Bayesian model was developed on a large diverse set of HDAC8 inhibitors. The training set comprised of 676 small molecules and 293 compounds were considered as test set molecules. The findings of this analysis will help to explore some major directions regarding the HDAC8 inhibitor designing approach. Acrylamide (G1-G3, G9), N-substituted 2-phenylimidazole (G4-G8, G9, G12-G13, G16-G19), benzimidazole (G10-G11), piperidine substituted pyrrole (G13-G14) groups, alkyl/aryl amide (G15) and aryloxy carboxamide (G20) fingerprints were found to play a crucial role in HDAC8 inhibitory activity whereas -CH-N=CH- (B1, B4-B6, B14) motif, benzamide (B2-B3, B9-B13, B16-B17) groups and heptazepine (B7-B8, B15, B18-B20) group were found to influence negatively the HDAC8 inhibitory activity. The importance of such fingerprints was further validated by the HDAC8 enzyme and related inhibitor interactions at the receptor level. These results are in close agreement with those of our previous work that validate each other. Moreover, this comparative learning may enrich future endeavours regarding the designing strategy of HDAC8 inhibitors.
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Affiliation(s)
- S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Arora N, Dhiman P, Kumar S, Singh G, Monga V. Recent advances in synthesis and medicinal chemistry of benzodiazepines. Bioorg Chem 2020; 97:103668. [PMID: 32106040 DOI: 10.1016/j.bioorg.2020.103668] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 12/11/2022]
Abstract
Benzodiazepines (BZDs) represent a diverse class of bicyclic heterocyclic molecules. In the last few years, benzodiazepines have emerged as potential therapeutic agents. As a result, several mild, efficient and high yielding protocols have been developed that offer access to various functionalized benzodiazepines (BZDs). They are known to possess a wide array of biological activities such as anxiolytic, anticancer, anticonvulsant, antipsychotics, muscle relaxant, anti-tuberculosis, and antimicrobial activities. The fascinating spectrum of biological activities exhibited by BZDs in various fields has prompted the medicinal chemist to design and discover novel benzodiazepine-based analogs as potential therapeutic candidates with the desired biological profile. In this review, an attempt has been made by to summarize (1) Recent advances in the synthetic chemistry of benzodiazepines which enable their synthesis with desired substitution pattern; (2) Medicinal chemistry of BZDs as therapeutic candidates with promising biological profile including insight of mechanistic studies; (3) The correlation of biological data with the structure i.e. structure-activity relationship studies were also included to provide an insight into the rational design of more active agents.
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Affiliation(s)
- Nidhi Arora
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, G.T. Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Prashant Dhiman
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, G.T. Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Shubham Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, G.T. Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, G.T. Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, G.T. Road, Ghal Kalan, Moga 142001, Punjab, India.
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7
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Ahmed N, Shamsabadi A, Chudasama V. Formation of Synthetically Versatile 2-Aminobenzophenones from Readily Accessed Acyl Hydrazides. ACS OMEGA 2019; 4:22601-22612. [PMID: 31909344 PMCID: PMC6941372 DOI: 10.1021/acsomega.9b03417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
Herein, we report the transformation of readily accessed acyl hydrazides into protected 2-aminobenzophenones via a two-step process involving an aryne-based molecular rearrangement followed by a one-pot addition-elimination procedure. The assembly of the scaffold is tolerant of a wide variety of functional groups, and the carbamate group on the product can be facilely removed to afford highly valuable 2-aminobenzophenones. Application of the protocol was demonstrated in the synthesis of neurological medicine phenazepam.
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8
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Daniel L, Gotsbacher MP, Richardson-Sanchez T, Tieu W, Codd R. Exploring hydroxamic acid inhibitors of HDAC1 and HDAC2 using small molecule tools and molecular or homology modelling. Bioorg Med Chem Lett 2019; 29:2581-2586. [PMID: 31400937 DOI: 10.1016/j.bmcl.2019.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
Hydroxamic acid compounds 1-10 containing a N-hydroxycinnamamide scaffold and a 4-(benzylamino)methyl cap group that was either unsubstituted (1) or substituted with one (2-4) or two (5-10) methoxy groups in variable positions were prepared as inhibitors of Zn(II)-containing histone deacetylases (HDACs). The 3,4- (9) and 3,5- (10) bis-methoxy-substituted compounds were the least potent against HeLa nuclear extract, HDAC1 and HDAC2. Molecular modelling showed methoxy groups in the 3-, 4- and 5-position, but not the 2-position, had unfavourable steric interactions with the G32-H33-P34 triad on a loop at the surface of the HDAC2 active site cavity. An HDAC1 homology model showed potential ionic (E243..K288) and cation-pi (K247..F292) interactions between helix 10 and helix 11 that were absent in HDAC2 ((G243..K288) and (K247..V292)). This surface-located interhelical constraint could inform the design of bitopic HDAC1 and HDAC2 selective ligands using an allosteric approach, and/or protein-protein interaction (PPI) inhibitors.
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Affiliation(s)
- Lydia Daniel
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Michael P Gotsbacher
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Tomas Richardson-Sanchez
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - William Tieu
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia.
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9
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Laconde G, Amblard M, Martinez J. Unexpected Reactivity of N
-Acyl-Benzotriazoles with Aromatic Amines in Acidic Medium (ABAA Reaction). European J Org Chem 2018. [DOI: 10.1002/ejoc.201801567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guillaume Laconde
- Department of Amino Acids, Peptides and Proteins; Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS; Université Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier France
| | - Muriel Amblard
- Department of Amino Acids, Peptides and Proteins; Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS; Université Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier France
| | - Jean Martinez
- Department of Amino Acids, Peptides and Proteins; Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS; Université Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier France
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10
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Rabal O, Sánchez-Arias JA, Cuadrado-Tejedor M, de Miguel I, Pérez-González M, García-Barroso C, Ugarte A, Estella-Hermoso de Mendoza A, Sáez E, Espelosin M, Ursua S, Haizhong T, Wei W, Musheng X, Garcia-Osta A, Oyarzabal J. Design, synthesis, biological evaluation and in vivo testing of dual phosphodiesterase 5 (PDE5) and histone deacetylase 6 (HDAC6)-selective inhibitors for the treatment of Alzheimer's disease. Eur J Med Chem 2018; 150:506-524. [PMID: 29549837 DOI: 10.1016/j.ejmech.2018.03.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 02/06/2023]
Abstract
We have identified chemical probes that act as dual phosphodiesterase 5 (PDE5) and histone deacetylase 6 (HDAC6)-selective inhibitors (>1 log unit difference versus class I HDACs) to decipher the contribution of HDAC isoforms to the positive impact of dual-acting PDE5 and HDAC inhibitors on mouse models of Alzheimer's disease (AD) and fine-tune this systems therapeutics approach. Structure- and knowledge-based approaches led to the design of first-in-class molecules with the desired target compound profile: dual PDE5 and HDAC6-selective inhibitors. Compound 44b, which fulfilled the biochemical, functional and ADME-Tox profiling requirements and exhibited adequate pharmacokinetic properties, was selected as pharmacological tool compound and tested in a mouse model of AD (Tg2576) in vivo.
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Affiliation(s)
- Obdulia Rabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Juan A Sánchez-Arias
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Mar Cuadrado-Tejedor
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain; Anatomy Department, School of Medicine, University of Navarra, Irunlarrea 1, E-31008, Pamplona, Spain
| | - Irene de Miguel
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Marta Pérez-González
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Carolina García-Barroso
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Ana Ugarte
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Ander Estella-Hermoso de Mendoza
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Elena Sáez
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Maria Espelosin
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Susana Ursua
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Tan Haizhong
- WuXi Apptec (Tianjin) Co. Ltd., TEDA, No. 111 HuangHai Road, 4th Avenue, Tianjin, 300456, PR China
| | - Wu Wei
- WuXi Apptec (Tianjin) Co. Ltd., TEDA, No. 111 HuangHai Road, 4th Avenue, Tianjin, 300456, PR China
| | - Xu Musheng
- WuXi Apptec (Tianjin) Co. Ltd., TEDA, No. 111 HuangHai Road, 4th Avenue, Tianjin, 300456, PR China
| | - Ana Garcia-Osta
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain
| | - Julen Oyarzabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pio XII 55, E-31008, Pamplona, Spain.
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12
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Ballante F. Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection. Methods Mol Biol 2018; 1824:67-88. [PMID: 30039402 DOI: 10.1007/978-1-4939-8630-9_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Main goal in drug discovery is the identification of drug-like compounds capable to modulate specific biological targets. Thus, the prediction of reliable binding poses of candidate ligands, through molecular docking simulations, represents a key step to be pursued in structure-based drug design (SBDD). Since the increasing number of resolved three-dimensional ligand-protein structures, together with the expansion of computational power and software development, the comprehensive and systematic use of experimental data can be proficiently employed to validate the docking performance. This allows to select and refine the protocol to adopt when predicting the binding pose of trial compounds in a target. Given the availability of multiple docking software, a comparative docking assessment in an early research stage represents a must-use step to minimize fails in molecular modeling. This chapter describes how to perform a docking assessment, using freely available tools, in a semiautomated fashion.
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Affiliation(s)
- Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA. .,Department of Cell and Molecular Biology, Uppsala Biomedicinska Centrum BMC, Uppsala University, Uppsala, Sweden.
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13
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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14
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Structural insights of SmKDAC8 inhibitors: Targeting Schistosoma epigenetics through a combined structure-based 3D QSAR, in vitro and synthesis strategy. Bioorg Med Chem 2017; 25:2105-2132. [DOI: 10.1016/j.bmc.2017.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/06/2017] [Accepted: 02/09/2017] [Indexed: 11/24/2022]
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