Drugging the ‘undruggable’. Therapeutic targeting of protein–DNA interactions with the use of computer-aided drug discovery methods

GPU-Accelerated Flexible Molecular Docking

(2021) Mengran Fan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hedgehog signaling pathway inhibitors: an updated patent review (2015–present)

(2020) Deborah Quaglio et al.   EXPERT OPINION ON THERAPEUTIC PATENTS

Target gene-independent functions of MYC oncoproteins

(2020) Apoorva Baluapuri et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery

(2020) Xiaonan Yang et al.   Frontiers in Genetics

Pharmacophore-Based Virtual Screening for Identification of Negative Modulators of GLI1 as Potential Anticancer Agents

(2020) Fabrizio Manetti et al.   ACS Medicinal Chemistry Letters

Industry-scale application and evaluation of deep learning for drug target prediction

(2020) Noé Sturm et al.   Journal of Cheminformatics

Deep Docking: A Deep Learning Platform for Augmentation of Structure Based Drug Discovery

(2020) Francesco Gentile et al.   ACS Central Science

Targeting Intrinsically Disordered Proteins through Dynamic Interactions

(2020) Jianlin Chen et al.   Biomolecules

Drugging “undruggable” genes for cancer treatment: Are we making progress?

(2020) Michael J. Duffy et al.   INTERNATIONAL JOURNAL OF CANCER

Targeting STAT3 in Cancer Immunotherapy

(2020) Sailan Zou et al.   Molecular Cancer

STAT3, the Challenge for Chemotherapeutic and Radiotherapeutic Efficacy

(2020) Ping-Lian Yang et al.   Cancers

Effects of MTX-23, a Novel PROTAC of Androgen Receptor Splice Variant-7 and Androgen Receptor, on CRPC resistant to Second-Line Antiandrogen Therapy

(2020) Geun Taek Lee et al.   MOLECULAR CANCER THERAPEUTICS

‘The game has changed.’ AI triumphs at protein folding

(2020) Robert F. Service   SCIENCE

Signal Transducer and Activator of Transcription (STATs) Proteins in Cancer and Inflammation: Functions and Therapeutic Implication

(2019) Chin-Yap Loh et al.   Frontiers in Oncology

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

Inhibition of pancreatic cancer stem cell characteristics by α‐Mangostin: Molecular mechanisms involving Sonic hedgehog and Nanog

(2019) Yiming Ma et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Diarylidenylpiperidones, H-4073 and HO-3867, Induce G2/M Cell-Cycle Arrest, Apoptosis and Inhibit STAT3 Phosphorylation in Human Pancreatic Cancer Cells

(2019) Jesse M. Mast et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

ETS transcription factors as emerging drug targets in cancer

(2019) Michael Hsing et al.   MEDICINAL RESEARCH REVIEWS

PrankWeb: a web server for ligand binding site prediction and visualization

(2019) Lukas Jendele et al.   NUCLEIC ACIDS RESEARCH

Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA

(2019) Susan Sammak et al.   BIOCHEMISTRY

AP-1 Transcription Factors as Regulators of Immune Responses in Cancer

(2019) Vasileios Atsaves et al.   Cancers

1H-NMR metabolomics reveals the Glabrescione B exacerbation of glycolytic metabolism beside the cell growth inhibitory effect in glioma

(2019) Giuseppina D’Alessandro et al.   Cell Communication and Signaling

Omomyc reveals new mechanisms to inhibit the MYC oncogene

(2019) Mark J. Demma et al.   MOLECULAR AND CELLULAR BIOLOGY

Computer-Aided Discovery of Small Molecule Inhibitors of Thymocyte Selection-Associated High Mobility Group Box Protein (TOX) as Potential Therapeutics for Cutaneous T-Cell Lymphomas

(2019) Vibudh Agrawal et al.   MOLECULES

Advances in protein structure prediction and design

(2019) Brian Kuhlman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mechanism of Small Molecules Inhibiting Activator Protein-1 DNA Binding Probed with Induced Fit Docking and Metadynamics Simulations

(2019) Zhou Yin   Journal of Chemical Information and Modeling

Ensemble Docking in Drug Discovery

(2018) Rommie E. Amaro et al.   BIOPHYSICAL JOURNAL

The prognostic significance of topoisomerase II alpha protein in early stage luminal breast cancer

(2018) Xin An et al.   BMC CANCER

Cancer statistics, 2018

(2018) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

A highlight on Sonic hedgehog pathway

(2018) Gabriela Basile Carballo et al.   Cell Communication and Signaling

Inhibitors of protein–protein interactions (PPIs): an analysis of scaffold choices and buried surface area

(2018) Xu Ran et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Advancing drug discovery via GPU-based deep learning

(2018) Erik Gawehn et al.   Expert Opinion on Drug Discovery

Untying the knot of transcription factor druggability: Molecular modeling study of FOXM1 inhibitors

(2018) S. Amirhossein Tabatabaei-Dakhili et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Targeting Transcription Factors for Cancer Treatment

(2018) Mélanie Lambert et al.   MOLECULES

The Expanding World of N-MYC–Driven Tumors

(2018) David S. Rickman et al.   Cancer Discovery

Overexpression of topoisomerase II alpha protein is a factor for poor prognosis in patients with luminal B breast cancer

(2018) Hideo Shigematsu et al.   Oncotarget

The genetic landscape of a physical interaction

(2018) Guillaume Diss et al.   eLife

The Role of Activator Protein-1 (AP-1) Family Members in CD30-Positive Lymphomas

(2018) Ines Garces de los Fayos Alonso et al.   Cancers

Current trends in Hedgehog signaling pathway inhibition by small molecules

(2018) Francesca Ghirga et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Regulation of the master regulator FOXM1 in cancer

(2018) Guo-Bin Liao et al.   Cell Communication and Signaling

Small-molecule compounds targeting the STAT3 DNA-binding domain suppress survival of cisplatin-resistant human ovarian cancer cells by inducing apoptosis

(2018) Wei Huang et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Computer-aided drug discovery of Myc-Max inhibitors as potential therapeutics for prostate cancer

(2018) Lavinia A. Carabet et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Emerging roles of Myc in stem cell biology and novel tumor therapies

(2018) Go J. Yoshida   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

The nuclear receptor superfamily: A structural perspective

(2018) Emily R. Weikum et al.   PROTEIN SCIENCE

Therapeutic Inhibition of Myc in Cancer. Structural Bases and Computer-Aided Drug Discovery Approaches

(2018) Lavinia Carabet et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Androgen Receptor Rearrangement and Splicing Variants in Resistance to Endocrine Therapies in Prostate Cancer

(2017) Yeung Ho et al.   ENDOCRINOLOGY

Targeting STAT3 by HO3867 induces apoptosis in ovarian clear cell carcinoma

(2017) Kristin Bixel et al.   INTERNATIONAL JOURNAL OF CANCER

Bypassing Drug Resistance Mechanisms of Prostate Cancer with Small Molecules that Target Androgen Receptor–Chromatin Interactions

(2017) Kush Dalal et al.   MOLECULAR CANCER THERAPEUTICS

Sequence-specific DNA binding by MYC/MAX to low-affinity non-E-box motifs

(2017) Michael Allevato et al.   PLoS One

FoxM1: Repurposing an oncogene as a biomarker

(2017) Deeptashree Nandi et al.   SEMINARS IN CANCER BIOLOGY

Discovery and characterization of small molecules targeting the DNA-binding ETS domain of ERG in prostate cancer

(2017) Miriam S. Butler et al.   Oncotarget

MMPP Attenuates Non-Small Cell Lung Cancer Growth by Inhibiting the STAT3 DNA-Binding Activity via Direct Binding to the STAT3 DNA-Binding Domain

(2017) Dong Ju Son et al.   Theranostics

Origins of Allostery and Evolvability in Proteins: A Case Study

(2016) Arjun S. Raman et al.   CELL

OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors

(2016) L A Jung et al.   ONCOGENE

Androgen receptor variant-driven prostate cancer: clinical implications and therapeutic targeting

(2016) E S Antonarakis et al.   PROSTATE CANCER AND PROSTATIC DISEASES

α-Mangostin-encapsulated PLGA nanoparticles inhibit pancreatic carcinogenesis by targeting cancer stem cells in human, and transgenic (KrasG12D, and KrasG12D/tp53R270H) mice

(2016) Raj Kumar Verma et al.   Scientific Reports

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

Perturbation of the c-Myc–Max Protein–Protein Interaction via Synthetic α-Helix Mimetics

(2015) Kwan-Young Jung et al.   JOURNAL OF MEDICINAL CHEMISTRY

Switching and withdrawing hormonal agents for castration-resistant prostate cancer

(2015) David Lorente et al.   Nature Reviews Urology

Small-molecule inhibitors targeting the DNA-binding domain of STAT3 suppress tumor growth, metastasis and STAT3 target gene expression in vivo

(2015) W Huang et al.   ONCOGENE

The oncogene ERG: a key factor in prostate cancer

(2015) P Adamo et al.   ONCOGENE

Binding cavities and druggability of intrinsically disordered proteins

(2015) Yugang Zhang et al.   PROTEIN SCIENCE

A small-molecule inhibitor of the aberrant transcription factor CBF -SMMHC delays leukemia in mice

(2015) A. Illendula et al.   SCIENCE

MYC, Metabolism, and Cancer

(2015) Z. E. Stine et al.   Cancer Discovery

Catalytic inhibitors of DNA topoisomerase II suppress the androgen receptor signaling and prostate cancer progression

(2015) Haolong Li et al.   Oncotarget

Antitumor activity of the c-Myc inhibitor KSI-3716 in gemcitabine-resistant bladder cancer

(2015) Ho Kyung Seo et al.   Oncotarget

Thymocyte selection-associated high mobility group box gene (TOX) is aberrantly over-expressed in mycosis fungoides and correlates with poor prognosis

(2015) Yuanshen Huang et al.   Oncotarget

A Small Molecule Compound Targeting STAT3 DNA-Binding Domain Inhibits Cancer Cell Proliferation, Migration, and Invasion

(2014) Wei Huang et al.   ACS Chemical Biology

(E)-2,4-Bis(p-hydroxyphenyl)-2-butenal enhanced TRAIL-induced apoptosis in ovarian cancer cells through downregulation of NF-κB/STAT3 pathway

(2014) Seung Hee Cho et al.   ARCHIVES OF PHARMACAL RESEARCH

Evidence of an oncogenic role of aberrant TOX activation in cutaneous T-cell lymphoma

(2014) Y. Huang et al.   BLOOD

Anti-arthritis effects of (E)-2,4-bis(p-hydroxyphenyl)-2-butenal are mediated by inhibition of the STAT3 pathway

(2014) Jung Ok Ban et al.   BRITISH JOURNAL OF PHARMACOLOGY

Drugging MYCN through an Allosteric Transition in Aurora Kinase A

(2014) William Clay Gustafson et al.   CANCER CELL

HO-3867, a Safe STAT3 Inhibitor, Is Selectively Cytotoxic to Ovarian Cancer

(2014) Kellie S. Rath et al.   CANCER RESEARCH

Orphan nuclear receptors as drug targets for the treatment of prostate and breast cancers

(2014) Mani Roshan-Moniri et al.   CANCER TREATMENT REVIEWS

Molecular Pathways: Targeting ETS Gene Fusions in Cancer

(2014) F. Y. Feng et al.   CLINICAL CANCER RESEARCH

Introduction to RNA-Seq and its Applications to Drug Discovery and Development

(2014) Zainab Khatoon et al.   DRUG DEVELOPMENT RESEARCH

Gli1/DNA interaction is a druggable target for Hedgehog-dependent tumors

(2014) P. Infante et al.   EMBO JOURNAL

Mechanisms of acquired resistance to androgen receptor targeting drugs in castration-resistant prostate cancer

(2014) David D Chism et al.   Expert Review of Anticancer Therapy

Selectively Targeting the DNA-binding Domain of the Androgen Receptor as a Prospective Therapy for Prostate Cancer

(2014) Kush Dalal et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovery of Small-Molecule Inhibitors Selectively Targeting the DNA-Binding Domain of the Human Androgen Receptor

(2014) Huifang Li et al.   JOURNAL OF MEDICINAL CHEMISTRY

Hot spots in protein–protein interfaces: Towards drug discovery

(2014) Engin Cukuroglu et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition

(2014) Michael V. Gormally et al.   Nature Communications

Therapeutic Strategies to Inhibit MYC

(2014) M. R. McKeown et al.   Cold Spring Harbor Perspectives in Medicine

MYC Activation Is a Hallmark of Cancer Initiation and Maintenance

(2014) M. Gabay et al.   Cold Spring Harbor Perspectives in Medicine

Ectopic expression of embryonic stem cell and other developmental genes in cutaneous T-cell lymphoma

(2014) Ivan V Litvinov et al.   OncoImmunology

Cancer statistics, 2013

(2013) Rebecca Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

TOP2A is overexpressed and is a therapeutic target for adrenocortical carcinoma

(2013) Meenu Jain et al.   ENDOCRINE-RELATED CANCER

Discovery of RG7388, a Potent and Selective p53–MDM2 Inhibitor in Clinical Development

(2013) Qingjie Ding et al.   JOURNAL OF MEDICINAL CHEMISTRY

Intravesical Instillation of c-MYC Inhibitor KSI-3716 Suppresses Orthotopic Bladder Tumor Growth

(2013) Kyung-Chae Jeong et al.   JOURNAL OF UROLOGY

The mechanisms of Hedgehog signalling and its roles in development and disease

(2013) James Briscoe et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MYC, Metabolism, Cell Growth, and Tumorigenesis

(2013) C. V. Dang   Cold Spring Harbor Perspectives in Medicine

Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins

(2013) Fan Jin et al.   PLoS Computational Biology

Overcoming mutation-based resistance to antiandrogens with rational drug design

(2013) Minna D Balbas et al.   eLife

Targeting FOXM1 in cancer

(2012) Marianna Halasi et al.   BIOCHEMICAL PHARMACOLOGY

Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure

(2012) David Ryan Koes et al.   BIOINFORMATICS

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein–Protein Interfaces

(2012) Brandon S. Zerbe et al.   Journal of Chemical Information and Modeling

Molecular Markers of Early-Stage Mycosis Fungoides

(2012) Yaohua Zhang et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

The Structure of DNA-Bound Human Topoisomerase II Alpha: Conformational Mechanisms for Coordinating Inter-Subunit Interactions with DNA Cleavage

(2012) Timothy J. Wendorff et al.   JOURNAL OF MOLECULAR BIOLOGY

The DNA topoisomerase II catalytic inhibitor merbarone is genotoxic and induces endoreduplication

(2012) Nuria Pastor et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

First-in-Human Trial of a STAT3 Decoy Oligonucleotide in Head and Neck Tumors: Implications for Cancer Therapy

(2012) Malabika Sen et al.   Cancer Discovery

Alkylation of Cysteine 468 in Stat3 Defines a Novel Site for Therapeutic Development

(2011) Ralf Buettner et al.   ACS Chemical Biology

Genomic and Biochemical Insights into the Specificity of ETS Transcription Factors

(2011) Peter C. Hollenhorst et al.   Annual Review of Biochemistry

FOXM1: From cancer initiation to progression and treatment

(2011) Chuay-Yeng Koo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

HO-3867, a curcumin analog, sensitizes cisplatin-resistant ovarian carcinoma, leading to therapeutic synergy through STAT3 inhibition

(2011) Karuppaiyah Selvendiran et al.   CANCER BIOLOGY & THERAPY

BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc

(2011) Jake E. Delmore et al.   CELL

The many roles of TOX in the immune system

(2011) Parinaz Aliahmad et al.   CURRENT OPINION IN IMMUNOLOGY

Isolation and identification of an antiproliferative substance from fructose–tyrosine Maillard reaction products

(2011) In Guk Hwang et al.   FOOD CHEMISTRY

Update of PAX2 mutations in renal coloboma syndrome and establishment of a locus-specific database

(2011) Matthew Bower et al.   HUMAN MUTATION

The transcription factor FOXM1 is a cellular target of the natural product thiostrepton

(2011) Nagaratna S. Hegde et al.   Nature Chemistry

Canonical hedgehog signaling augments tumor angiogenesis by induction of VEGF-A in stromal perivascular cells

(2011) W. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A complex task? Direct modulation of transcription factors with small molecules

(2010) Angela N Koehler   CURRENT OPINION IN CHEMICAL BIOLOGY

Fluorescence polarization assays in small molecule screening

(2010) Wendy A Lea et al.   Expert Opinion on Drug Discovery

Safe and targeted anticancer efficacy of a novel class of antioxidant-conjugated difluorodiarylidenyl piperidones: Differential cytotoxicity in healthy and cancer cells

(2010) Karuppaiyah Selvendiran et al.   FREE RADICAL BIOLOGY AND MEDICINE

Small-molecule inhibitors of c-Myc transcriptional factor suppress proliferation and induce apoptosis of promyelocytic leukemia cell via cell cycle arrest

(2010) Kyung-Chae Jeong et al.   Molecular BioSystems

Sonic Hedgehog/GLI1 signaling pathway inhibition restricts cell migration and invasion in human gliomas

(2010) Ke Wang et al.   NEUROLOGICAL RESEARCH

Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence

(2010) D. R. Littler et al.   NUCLEIC ACIDS RESEARCH

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Direct inhibition of the NOTCH transcription factor complex

(2009) Raymond E. Moellering et al.   NATURE

A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma

(2009) Hayriye V Erkizan et al.   NATURE MEDICINE

In vivo validation of PAX2 as a target for renal cancer therapy

(2008) Pierre-Alain Hueber et al.   CANCER LETTERS

Targeting STAT3 in cancer: how successful are we?

(2008) Peibin Yue et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores

(2008) Caterina Barillari et al.   Journal of Chemical Information and Modeling

Treatment of arthritis with a selective inhibitor of c-Fos/activator protein-1

(2008) Yukihiko Aikawa et al.   NATURE BIOTECHNOLOGY

Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

(2008) Shandar Ahmad et al.   NUCLEIC ACIDS RESEARCH

Role of the TMPRSS2-ERG Gene Fusion in Prostate Cancer

(2008) Scott A. Tomlins et al.   NEOPLASIA