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Article ; Online: Correction to: BRADSHAW: a system for automated molecular design.

Green, Darren V S / Pickett, Stephen / Luscombe, Chris / Senger, Stefan / Marcus, David / Meslamani, Jamel / Brett, David / Powell, Adam / Masson, Jonathan

Journal of computer-aided molecular design

2019 Volume 34, Issue 7, Page(s) 767

Abstract: The original version of this article unfortunately contained some mistakes in the references. ...

Abstract	The original version of this article unfortunately contained some mistakes in the references.
Language	English
Publishing date	2019-11-06
Publishing country	Netherlands
Document type	Published Erratum
ZDB-ID	808166-9
ISSN	1573-4951 ; 0920-654X
ISSN (online)	1573-4951
ISSN	0920-654X
DOI	10.1007/s10822-019-00243-7
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Article ; Online: Structural features and inhibitors of bromodomains.

Meslamani, Jamel / Smith, Steven G / Sanchez, Roberto / Zhou, Ming-Ming

Drug discovery today. Technologies

2016 Volume 19, Page(s) 3–15

Abstract: Bromodomains are conserved structural modules responsible for recognizing acetylated-lysine residues on histone tails and other transcription-associated proteins, such as transcription factors and co-factors. Owing to their important functions in the ... ...

Abstract	Bromodomains are conserved structural modules responsible for recognizing acetylated-lysine residues on histone tails and other transcription-associated proteins, such as transcription factors and co-factors. Owing to their important functions in the regulation of ordered gene transcription in chromatin, bromodomains of the BET family proteins have recently been shown as druggable targets for a wide array of human diseases, including cancer and inflammation. Here we review the structural and functional features of the bromodomains and their small-molecule inhibitors. Additional new insights provided herein highlight the landscape of the ligand binding sites in the bromodomains that will hopefully facilitate further development of new inhibitors with optimal affinity and selectivity.
MeSH term(s)	Animals ; Humans ; Nuclear Proteins/chemistry ; Protein Domains ; Transcription Factors/chemistry
Chemical Substances	Nuclear Proteins ; Transcription Factors
Language	English
Publishing date	2016-09-22
Publishing country	England
Document type	Journal Article ; Review
ISSN	1740-6749
ISSN (online)	1740-6749
DOI	10.1016/j.ddtec.2016.09.001
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Article ; Online: HIPK2 directs cell type-specific regulation of STAT3 transcriptional activity in Th17 cell differentiation.

Cheung, Ka Lung / Jaganathan, Anbalagan / Hu, Yuan / Xu, Feihong / Lejeune, Alannah / Sharma, Rajal / Caescu, Cristina I / Meslamani, Jamel / Vincek, Adam / Zhang, Fan / Lee, Kyung / Zaware, Nilesh / Qayum, Amina Abdul / Ren, Chunyan / Kaplan, Mark H / He, John Cijiang / Xiong, Huabao / Zhou, Ming-Ming

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 14, Page(s) e2117112119

Abstract: SignificanceSTAT3 (signal transducer and activator of transcription 3) is a master transcription factor that organizes cellular responses to cytokines and growth factors and is implicated in inflammatory disorders. STAT3 is a well-recognized therapeutic ... ...

Abstract	SignificanceSTAT3 (signal transducer and activator of transcription 3) is a master transcription factor that organizes cellular responses to cytokines and growth factors and is implicated in inflammatory disorders. STAT3 is a well-recognized therapeutic target for human cancer and inflammatory disorders, but how its function is regulated in a cell type-specific manner has been a major outstanding question. We discovered that Stat3 imposes self-directed regulation through controlling transcription of its own regulator homeodomain-interacting protein kinase 2 (
MeSH term(s)	Animals ; Cell Differentiation/genetics ; Colitis/genetics ; Colitis/metabolism ; Lymphocyte Activation ; Mice ; Protein Serine-Threonine Kinases/genetics ; STAT3 Transcription Factor/genetics ; STAT3 Transcription Factor/metabolism ; Th17 Cells
Chemical Substances	STAT3 Transcription Factor ; Stat3 protein, mouse ; Hipk2 protein, mouse (EC 2.7.1.-) ; Protein Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2022-03-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2117112119
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Article ; Online: Enhancing the accuracy of chemogenomic models with a three-dimensional binding site kernel.

Meslamani, Jamel / Rognan, Didier

Journal of chemical information and modeling

2011 Volume 51, Issue 7, Page(s) 1593–1603

Abstract: Computational chemogenomic (or proteochemometric) methods predict target-ligand interactions by training machine learning algorithms on known experimental data in order to distinguish attributes of true from false target-ligand pairs. Many ligand and ... ...

Abstract	Computational chemogenomic (or proteochemometric) methods predict target-ligand interactions by training machine learning algorithms on known experimental data in order to distinguish attributes of true from false target-ligand pairs. Many ligand and target descriptors can be used for training and predicting binary associations or even binding affinities. Several chemogenomic studies have not noticed any real benefit in using 3-D structural target descriptors with respect to simpler sequence-based or property-based information. To assess whether this observation results from inaccurate target description or from the fact that 3-D information is simply not required in chemogenomic modeling, we used a target kernel measuring the distance between target-ligand binding sites of known X-ray structures. When used in combination with a standard ligand kernel in a support vector machine (SVM) classifier, the 3-D target kernel significantly outperforms a sequence-based target kernel in discriminating 2882 target-ligand PDB complexes from 9128 false pairs, whatever the modeling procedure (local or global). The best SVM models could be successfully applied to predict, with very high recall (70%), precision (99%), and specificity (99%), target-ligand associations for an external set of 14,117 ligands and 531 targets. In most of the cases, pooling all data in a global model gave better statistics than just discretizing specific target-ligand subspaces in local models. The current study clearly demonstrates that chemogenomic models taking both ligand and target information outperform simpler ligand-based models. It also permits one to design good modeling practices in predicting target-ligand pairing for a large array of targets: (i) ligand-based models are precise enough if sufficient ligand information (>40-50 diverse ligands) is known; (ii) if not, structure-based chemogenomic models (associating a ligand kernel to a structure-based target kernel) are recommended for proteins of known holostructures; (iii) sequence-based chemogenomic models (associating a ligand kernel to a sequence-based target kernel) can still be used with a very good accuracy for the remaining targets.
MeSH term(s)	Algorithms ; Binding Sites ; Drug Delivery Systems ; Genomics ; Ligands ; Models, Genetic ; Protein Binding
Chemical Substances	Ligands
Language	English
Publishing date	2011-07-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/ci200166t
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Article: The bromodomain: from epigenome reader to druggable target.

Sanchez, Roberto / Meslamani, Jamel / Zhou, Ming-Ming

Biochimica et biophysica acta

2014 Volume 1839, Issue 8, Page(s) 676–685

Abstract: Lysine acetylation is a fundamental post-translational modification that plays an important role in the control of gene transcription in chromatin in an ordered fashion. The bromodomain, the conserved structural module present in transcription-associated ...

Abstract	Lysine acetylation is a fundamental post-translational modification that plays an important role in the control of gene transcription in chromatin in an ordered fashion. The bromodomain, the conserved structural module present in transcription-associated proteins, functions exclusively to recognize acetyl-lysine on histones and non-histone proteins. The structural analyses of bromodomains' recognition of lysine-acetylated peptides derived from histones and cellular proteins provide detailed insights into the differences and unifying features of biological ligand binding selectivity by the bromodomains. Newly developed small-molecule inhibitors targeting bromodomain proteins further highlight the functional importance of bromodomain/acetyl-lysine binding as a key mechanism in orchestrating molecular interactions and regulation in chromatin biology and gene transcription. These new studies argue that modulating bromodomain/acetyl-lysine interactions with small-molecule chemicals offer new opportunities to control gene expression in a wide array of human diseases including cancer and inflammation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
MeSH term(s)	Acetylation ; Cardiovascular Diseases/drug therapy ; Cardiovascular Diseases/genetics ; Cardiovascular Diseases/metabolism ; Epigenesis, Genetic ; HIV Infections/drug therapy ; HIV Infections/genetics ; HIV Infections/metabolism ; HIV Infections/virology ; Histones/chemistry ; Histones/genetics ; Histones/metabolism ; Humans ; Lysine/metabolism ; Models, Molecular ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology ; Transcription Factors/antagonists & inhibitors ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Histones ; Small Molecule Libraries ; Transcription Factors ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2014-03-28
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbagrm.2014.03.011
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Article ; Online: BRADSHAW: a system for automated molecular design.

Green, Darren V S / Pickett, Stephen / Luscombe, Chris / Senger, Stefan / Marcus, David / Meslamani, Jamel / Brett, David / Powell, Adam / Masson, Jonathan

Journal of computer-aided molecular design

2019 Volume 34, Issue 7, Page(s) 747–765

Abstract: This paper introduces BRADSHAW (Biological Response Analysis and Design System using an Heterogenous, Automated Workflow), a system for automated molecular design which integrates methods for chemical structure generation, experimental design, active ... ...

Abstract	This paper introduces BRADSHAW (Biological Response Analysis and Design System using an Heterogenous, Automated Workflow), a system for automated molecular design which integrates methods for chemical structure generation, experimental design, active learning and cheminformatics tools. The simple user interface is designed to facilitate access to large scale automated design whilst minimising software development required to introduce new algorithms, a critical requirement in what is a very fast moving field. The system embodies a philosophy of automation, best practice, experimental design and the use of both traditional cheminformatics and modern machine learning algorithms.
MeSH term(s)	Adenosine A2 Receptor Antagonists/chemistry ; Algorithms ; Cheminformatics/methods ; Cheminformatics/statistics & numerical data ; Cheminformatics/trends ; Computer-Aided Design/statistics & numerical data ; Computer-Aided Design/trends ; Deep Learning ; Drug Design ; Drug Discovery/methods ; Drug Discovery/statistics & numerical data ; Drug Discovery/trends ; Humans ; Machine Learning ; Matrix Metalloproteinase Inhibitors/chemistry ; Quantitative Structure-Activity Relationship ; Small Molecule Libraries ; Software ; User-Computer Interface ; Workflow
Chemical Substances	Adenosine A2 Receptor Antagonists ; Matrix Metalloproteinase Inhibitors ; Small Molecule Libraries
Language	English
Publishing date	2019-10-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	808166-9
ISSN	1573-4951 ; 0920-654X
ISSN (online)	1573-4951
ISSN	0920-654X
DOI	10.1007/s10822-019-00234-8
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Article ; Online: Computational profiling of bioactive compounds using a target-dependent composite workflow.

Meslamani, Jamel / Bhajun, Ricky / Martz, Francois / Rognan, Didier

Journal of chemical information and modeling

2013 Volume 53, Issue 9, Page(s) 2322–2333

Abstract: Computational target fishing is a chemoinformatic method aimed at determining main and secondary targets of bioactive compounds in order to explain their mechanism of action, anticipate potential side effects, or repurpose existing drugs for novel ... ...

Abstract	Computational target fishing is a chemoinformatic method aimed at determining main and secondary targets of bioactive compounds in order to explain their mechanism of action, anticipate potential side effects, or repurpose existing drugs for novel therapeutic indications. Many existing successes in this area have been based on a use of a single computational method to estimate potentially new target-ligand associations. We herewith present an automated workflow using several methods to optimally browse target-ligand space according to existing knowledge on either ligand and target space under investigation. The protocol uses four ligand-based (SVM classification, SVR affinity prediction, nearest neighbors interpolation, shape similarity) and two structure-based approaches (docking, protein-ligand pharmacophore match) in series, according to well-defined ligand and target property checks. The workflow was remarkably accurate (72%) in identifying the main target of 189 clinical candidates and proposed two novel off-targets which could be experimentally validated. Rolofylline, an adenosine A1 receptor antagonist, was confirmed to inhibit phosphodiesterase 5 with a moderate affinity (IC50 = 13.8 μM). More interestingly, we describe a strong binding (IC50 = 142 nM) of a claimed selective phosphodiesterase 10 A inhibitor (PF-2545920) with the cysteinyl leukotriene type 1 G protein-coupled receptor.
MeSH term(s)	Computational Biology/methods ; Humans ; Ligands ; Pharmaceutical Preparations/metabolism ; Reproducibility of Results ; Support Vector Machine
Chemical Substances	Ligands ; Pharmaceutical Preparations
Language	English
Publishing date	2013-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/ci400303n
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Article ; Online: Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin.

Liu, Nan / Konuma, Tsuyoshi / Sharma, Rajal / Wang, Deyu / Zhao, Nan / Cao, Lingling / Ju, Ying / Liu, Di / Wang, Shuai / Bosch, Almudena / Sun, Yifei / Zhang, Siwei / Ji, Donglei / Nagatoishi, Satoru / Suzuki, Noa / Kikuchi, Masaki / Wakamori, Masatoshi / Zhao, Chengcheng / Ren, Chunyan /

Zhou, Thomas Jiachi / Xu, Yaoyao / Meslamani, Jamel / Fu, Shibo / Umehara, Takashi / Tsumoto, Kouhei / Akashi, Satoko / Zeng, Lei / Roeder, Robert G / Walsh, Martin J / Zhang, Qiang / Zhou, Ming-Ming

Molecular cell

2023 Volume 83, Issue 13, Page(s) 2206–2221.e11

Abstract: Histone lysine acylation, including acetylation and crotonylation, plays a pivotal role in gene transcription in health and diseases. However, our understanding of histone lysine acylation has been limited to gene transcriptional activation. Here, we ... ...

Abstract	Histone lysine acylation, including acetylation and crotonylation, plays a pivotal role in gene transcription in health and diseases. However, our understanding of histone lysine acylation has been limited to gene transcriptional activation. Here, we report that histone H3 lysine 27 crotonylation (H3K27cr) directs gene transcriptional repression rather than activation. Specifically, H3K27cr in chromatin is selectively recognized by the YEATS domain of GAS41 in complex with SIN3A-HDAC1 co-repressors. Proto-oncogenic transcription factor MYC recruits GAS41/SIN3A-HDAC1 complex to repress genes in chromatin, including cell-cycle inhibitor p21. GAS41 knockout or H3K27cr-binding depletion results in p21 de-repression, cell-cycle arrest, and tumor growth inhibition in mice, explaining a causal relationship between GAS41 and MYC gene amplification and p21 downregulation in colorectal cancer. Our study suggests that H3K27 crotonylation signifies a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for transcriptional silencing and H3K27 acetylation for transcriptional activation.
MeSH term(s)	Mice ; Animals ; Chromatin/genetics ; Histones/metabolism ; Lysine/metabolism ; Transcription Factors/metabolism ; Gene Expression Regulation ; Acetylation
Chemical Substances	Chromatin ; Histones ; Lysine (K3Z4F929H6) ; Transcription Factors
Language	English
Publishing date	2023-06-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.05.022
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Article ; Online: ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains.

Meslamani, Jamel / Smith, Steven G / Sanchez, Roberto / Zhou, Ming-Ming

Bioinformatics (Oxford, England)

2014 Volume 30, Issue 10, Page(s) 1481–1483

Abstract: Context: Epigenome reader domains are rapidly emerging as a new class of drug targets for a wide array of human diseases. To facilitate study of structure-activity relationship and small-molecule ligand design for these domains, we have created ChEpiMod. ...

Abstract	Context: Epigenome reader domains are rapidly emerging as a new class of drug targets for a wide array of human diseases. To facilitate study of structure-activity relationship and small-molecule ligand design for these domains, we have created ChEpiMod. ChEpiMod is a free knowledgebase of chemical modulators with documented modulatory activity for epigenome reader domains. Methods: ChEpiMod organizes information about chemical modulators and their associated binding-affinity data, as well as available structures of epigenome readers from the Protein Data Bank. The data are gathered from the literature and patents. Entries are supplemented by annotation. The current version of ChEpiMod covers six epigenome reader domain families (Bromodomain, PHD finger, Chromodomain, MBT, PWWP and Tudor). The database can be used to browse existing chemical modulators and bioactivity data, as well as, all available structures of readers and their molecular interactions. The database is updated weekly. Availability: ChEpiMod is freely available at http://chepimod.org Contact: ming-ming.zhou@mssm.edu Supplementary information: Supplementary data is available at Bioinformatics online.
MeSH term(s)	Amino Acid Sequence ; Databases, Genetic ; Epigenesis, Genetic ; Genomics/methods ; Humans ; Ligands ; Molecular Sequence Data ; Small Molecule Libraries/metabolism ; Structure-Activity Relationship
Chemical Substances	Ligands ; Small Molecule Libraries
Language	English
Publishing date	2014-01-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btu052
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Article ; Online: sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins.

Meslamani, Jamel / Rognan, Didier / Kellenberger, Esther

Bioinformatics (Oxford, England)

2011 Volume 27, Issue 9, Page(s) 1324–1326

Abstract: Background: The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein-ligand complexes, chosen for their geometrical and physico-chemical properties. ... ...

Abstract	Background: The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein-ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the detailed intermolecular interactions for complexes. The sc-PDB now includes a hierarchical classification of all the binding sites within a functional class. Method: The sc-PDB entries were first clustered according to the protein name indifferent of the species. For each cluster, we identified dissimilar sites (e.g. catalytic and allosteric sites of an enzyme). SCOPE AND APPLICATIONS: The classification of sc-PDB targets by binding site diversity was intended to facilitate chemogenomics approaches to drug design. In ligand-based approaches, it avoids comparing ligands that do not share the same binding site. In structure-based approaches, it permits to quantitatively evaluate the diversity of the binding site definition (variations in size, sequence and/or structure). Availability: The sc-PDB database is freely available at: http://bioinfo-pharma.u-strasbg.fr/scPDB.
MeSH term(s)	Binding Sites ; Databases, Protein ; Drug Design ; Ligands ; Proteins/chemistry ; Proteins/classification ; Proteins/metabolism
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2011-05-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btr120
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