Rational, computer-enabled peptide drug design: principles, methods, applications and future directions

Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides

(2015) Douglas H. Pike et al.   BIOPOLYMERS

PepT1, ASBT-Linked Prodrug Strategy to Improve Oral Bioavailability and Tissue Targeting Distribution

(2015) Xiaopeng Han et al.   CURRENT DRUG METABOLISM

Construction and screening of vast libraries of natural product-like macrocyclic peptides using in vitro display technologies

(2015) Nasir K Bashiruddin et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Peptide therapeutics: current status and future directions

(2015) Keld Fosgerau et al.   DRUG DISCOVERY TODAY

Exploring experimental and computational markers of cyclic peptides: Charting islands of permeability

(2015) Conan K. Wang et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Peptide therapeutics: Targeting the undruggable space

(2015) Natia Tsomaia   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products

(2015) Andrew T. Bockus et al.   JOURNAL OF MEDICINAL CHEMISTRY

Rational Design of Dual Peptides Targeting Ghrelin and Y2 Receptors to Regulate Food Intake and Body Weight

(2015) Tom-Marten Kilian et al.   JOURNAL OF MEDICINAL CHEMISTRY

Cell-Permeable Cyclic Peptides from Synthetic Libraries Inspired by Natural Products

(2015) William M. Hewitt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Recent Development of Peptide Drugs and Advance on Theory and Methodology of Peptide Inhibitor Design

(2015) Qi-Shi Du et al.   Medicinal Chemistry

Vascular endothelial growth factor is an autocrine growth factor, signaling through neuropilin-1 in non-small cell lung cancer

(2015) Martin P Barr et al.   Molecular Cancer

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization

(2015) Hasup Lee et al.   NUCLEIC ACIDS RESEARCH

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

(2015) Mateusz Kurcinski et al.   NUCLEIC ACIDS RESEARCH

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking

(2015) Avraham Ben-Shimon et al.   STRUCTURE

Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery

(2015) Sébastien Giguère et al.   PLoS Computational Biology

Bond distances in polypeptide backbones depend on the local conformation

(2015) Roberto Improta et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Toxin acidic residue evolutionary function-guided design of de novo peptide drugs for the immunotherapeutic target, the Kv1.3 channel

(2015) Zongyun Chen et al.   Scientific Reports

Improving on Nature: Making a Cyclic Heptapeptide Orally Bioavailable

(2014) Daniel S. Nielsen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Specific STAT3-Binding Peptide Exerts Antiproliferative Effects and Antitumor Activity by Inhibiting STAT3 Phosphorylation and Signaling

(2014) Daejin Kim et al.   CANCER RESEARCH

Modulation, Bioinformatic Screening, and Assessment of Small Molecular Peptides Targeting the Vascular Endothelial Growth Factor Receptor

(2014) Shibin Feng et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Derivation of ligands for the complement C3a receptor from the C-terminus of C5a

(2014) Reena Halai et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Novel expression of Neuropilin 1 on human tumor-infiltrating lymphocytes in colorectal cancer liver metastases

(2014) Belal Chaudhary et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Conjugation of a brain-penetrant peptide with neurotensin provides antinociceptive properties

(2014) Michel Demeule et al.   JOURNAL OF CLINICAL INVESTIGATION

Predicting peptide binding sites on protein surfaces by clustering chemical interactions

(2014) Chengfei Yan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Identification of Tetrapeptides from a Mixture Based Positional Scanning Library That Can Restore nM Full Agonist Function of the L106P, I69T, I102S, A219V, C271Y, and C271R Human Melanocortin-4 Polymorphic Receptors (hMC4Rs)

(2014) Erica M. Haslach et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of a Potent Stapled Helix Peptide That Binds to the 70N Domain of Replication Protein A

(2014) Andreas O. Frank et al.   JOURNAL OF MEDICINAL CHEMISTRY

New Compstatin Peptides Containing N-Terminal Extensions and Non-Natural Amino Acids Exhibit Potent Complement Inhibition and Improved Solubility Characteristics

(2014) Ronald D. Gorham et al.   JOURNAL OF MEDICINAL CHEMISTRY

Hydrocarbon-Stapled Peptides: Principles, Practice, and Progress

(2014) Loren D. Walensky et al.   JOURNAL OF MEDICINAL CHEMISTRY

Combination of Amino Acid/Dipeptide with Nitric Oxide Donating Oleanolic Acid Derivatives as PepT1 Targeting Antitumor Prodrugs

(2014) Lei Fang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Transferrin Receptor-Mediated Endocytosis: A Useful Target for Cancer Therapy

(2014) Stephanie Tortorella et al.   JOURNAL OF MEMBRANE BIOLOGY

Tumor-Penetrating iRGD Peptide Inhibits Metastasis

(2014) K. N. Sugahara et al.   MOLECULAR CANCER THERAPEUTICS

Anaphylaxis and Hypotension after Administration of Peginesatide

(2014) Charles L. Bennett et al.   NEW ENGLAND JOURNAL OF MEDICINE

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

(2014) Adrien Saladin et al.   NUCLEIC ACIDS RESEARCH

Correction: De Novo Peptide Design and Experimental Validation of Histone Methyltransferase Inhibitors

(2014)   PLoS One

PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta

(2014) Haiou Li et al.   PLoS One

Rational design and synthesis of an orally bioavailable peptide guided by NMR amide temperature coefficients

(2014) Conan K. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions

(2014) Q.S. Du et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

An endocytosis pathway initiated through neuropilin-1 and regulated by nutrient availability

(2014) Hong-Bo Pang et al.   Nature Communications

Serum Stable Natural Peptides Designed by mRNA Display

(2014) Shannon M. Howell et al.   Scientific Reports

Molecular Grafting onto a Stable Framework Yields Novel Cyclic Peptides for the Treatment of Multiple Sclerosis

(2013) Conan K. Wang et al.   ACS Chemical Biology

Conformational investigation of antibiotic proximicin by X-ray structure analysis and quantum studies suggest a stretched conformation of this type of γ-peptide

(2013) Alexander Denisiuk et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Cyclotides as grafting frameworks for protein engineering and drug design applications

(2013) Aaron G. Poth et al.   BIOPOLYMERS

A Brief Overview of Antimicrobial Peptides Containing Unnatural Amino Acids and Ligand-Based Approaches for Peptide Ligands

(2013) Jayendra Bhonsle et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Future directions for peptide therapeutics development

(2013) Allan A. Kaspar et al.   DRUG DISCOVERY TODAY

Development of an Informatics Platform for Therapeutic Protein and Peptide Analytics

(2013) Mark R. Hansen et al.   Journal of Chemical Information and Modeling

Constrained H-Phe-Phe-NH2 Analogues with High Affinity to the Substance P 1–7 Binding Site and with Improved Metabolic Stability and Cell Permeability

(2013) Rebecca Fransson et al.   JOURNAL OF MEDICINAL CHEMISTRY

A General Method for Making Peptide Therapeutics Resistant to Serine Protease Degradation: Application to Dipeptidyl Peptidase IV Substrates

(2013) Kathryn R. Heard et al.   JOURNAL OF MEDICINAL CHEMISTRY

Screening Bicyclic Peptide Libraries for Protein–Protein Interaction Inhibitors: Discovery of a Tumor Necrosis Factor-α Antagonist

(2013) Wenlong Lian et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

(2013) Mikael Trellet et al.   PLoS One

Targeting Caspase-3 as Dual Therapeutic Benefits by RNAi Facilitating Brain-Targeted Nanoparticles in a Rat Model of Parkinson’s Disease

(2013) Yang Liu et al.   PLoS One

Protein-Peptide Complex Prediction through Fragment Interaction Patterns

(2013) Erik Verschueren et al.   STRUCTURE

Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening

(2013) Arnab Bhattacherjee et al.   PLoS Computational Biology

PepBind: A Comprehensive Database and Computational Tool for Analysis of Protein–peptide Interactions

(2013) Arindam Atanu Das et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Tumor-Penetrating Peptides

(2013) Tambet Teesalu et al.   Frontiers in Oncology

Orally Active Peptidic Bradykinin B1 Receptor Antagonists Engineered from a Cyclotide Scaffold for Inflammatory Pain Treatment

(2012) Clarence T. T. Wong et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Rationally Engineered Anti-HIV Peptide Fusion Inhibitor with Greatly Reduced Immunogenicity

(2012) F. Brauer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

In Silico and in Vitro Elucidation of BH3 Binding Specificity toward Bcl-2

(2012) Nir London et al.   BIOCHEMISTRY

Protease-resistant peptide design-empowering nature's fragile warriors against HIV

(2012) Matthew T. Weinstock et al.   BIOPOLYMERS

De Novo Design of a Tumor-Penetrating Peptide

(2012) L. Alberici et al.   CANCER RESEARCH

Peptide Bicycles that Inhibit the Grb2 SH2 Domain

(2012) Justin S. Quartararo et al.   CHEMBIOCHEM

Synthesis, Characterization and Pharmacodynamics of Vitamin-B12-Conjugated Glucagon-Like Peptide-1

(2012) Susan Clardy-James et al.   ChemMedChem

Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides

(2012) Chen Han et al.   CHEMPHYSCHEM

Recent work in the development and application of protein–peptide docking

(2012) Joseph Audie et al.   Future Medicinal Chemistry

De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation

(2012) Meghan L. Bellows-Peterson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predicting and Improving the Membrane Permeability of Peptidic Small Molecules

(2012) Salma B. Rafi et al.   JOURNAL OF MEDICINAL CHEMISTRY

PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides

(2012) P. Thevenet et al.   NUCLEIC ACIDS RESEARCH

TumorHoPe: A Database of Tumor Homing Peptides

(2012) Pallavi Kapoor et al.   PLoS One

Phage selection of cyclic peptide antagonists with increased stability toward intestinal proteases

(2012) V. Baeriswyl et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Computer-aided antibody design

(2012) D. Kuroda et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance

(2012) Arthur C. Rand et al.   MedChemComm

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

(2012) Kyle E. Roberts et al.   PLoS Computational Biology

Brainpeps: the blood–brain barrier peptide database

(2011) Sylvia Van Dorpe et al.   Brain Structure & Function

Drug-permeability and transporter assays in Caco-2 and MDCK cell lines

(2011) Donna A Volpe   Future Medicinal Chemistry

Novel Peptide-Specific Quantitative Structure–Activity Relationship (QSAR) Analysis Applied to Collagen IV Peptides with Antiangiogenic Activity

(2011) Corban G. Rivera et al.   JOURNAL OF MEDICINAL CHEMISTRY

Backbone Cyclic Peptide Inhibitors of Protein Kinase B (PKB/Akt)

(2011) Yftah Tal-Gan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Oral Delivery of the Appetite Suppressing Peptide hPYY(3–36) through the Vitamin B12Uptake Pathway

(2011) Christopher H. Fazen et al.   JOURNAL OF MEDICINAL CHEMISTRY

In silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues

(2011) Jérôme Beaufays et al.   JOURNAL OF PEPTIDE SCIENCE

Elucidation of the Contribution of Active Site and Exosite Interactions to Affinity and Specificity of Peptidylic Serine Protease Inhibitors Using Non-Natural Arginine Analogs

(2011) M. Hosseini et al.   MOLECULAR PHARMACOLOGY

Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes

(2011) Lydia Alvarez-Erviti et al.   NATURE BIOTECHNOLOGY

On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds

(2011) Tina R White et al.   Nature Chemical Biology

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

(2011) Nir London et al.   NUCLEIC ACIDS RESEARCH

Transtumoral targeting enabled by a novel neuropilin-binding peptide

(2011) L Roth et al.   ONCOGENE

Four Small Puzzles That Rosetta Doesn't Solve

(2011) Rhiju Das   PLoS One

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

(2011) Barak Raveh et al.   PLoS One

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Discovery of Entry Inhibitors for HIV-1 via a New De Novo Protein Design Framework

(2010) M.L. Bellows et al.   BIOPHYSICAL JOURNAL

Cyclotides, a promising molecular scaffold for peptide-based therapeutics

(2010) Krishnappa Jagadish et al.   BIOPOLYMERS

Systemic combinatorial peptide selection yields a non-canonical iron-mimicry mechanism for targeting tumors in a mouse model of human glioblastoma

(2010) Fernanda I. Staquicini et al.   JOURNAL OF CLINICAL INVESTIGATION

Targeted brain delivery of itraconazole via RVG29 anchored nanoparticles

(2010) Wei Chen et al.   JOURNAL OF DRUG TARGETING

VitAL: Viterbi Algorithm for de novo Peptide Design

(2010) E. Besray Unal et al.   PLoS One

Discovery of High-Affinity Protein Binding Ligands – Backwards

(2010) Chris W. Diehnelt et al.   PLoS One

Serum Stabilities of Short Tryptophan- and Arginine-Rich Antimicrobial Peptide Analogs

(2010) Leonard T. Nguyen et al.   PLoS One

Coadministration of a Tumor-Penetrating Peptide Enhances the Efficacy of Cancer Drugs

(2010) K. N. Sugahara et al.   SCIENCE

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-based Design of High Affinity Peptides Inhibiting the Interaction of p53 with MDM2 and MDMX

(2009) Jason Phan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Creating Protein Affinity Reagents by Combining Peptide Ligands on Synthetic DNA Scaffolds

(2009) Berea A. R. Williams et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PepX: a structural database of non-redundant protein–peptide complexes

(2009) Peter Vanhee et al.   NUCLEIC ACIDS RESEARCH

Physiochemical drug properties associated with in vivo toxicological outcomes

(2008) Jason D. Hughes et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Antitumour activity of ANG1005, a conjugate between paclitaxel and the new brain delivery vector Angiopep-2

(2008) A Régina et al.   BRITISH JOURNAL OF PHARMACOLOGY

Recent Advances in QSAR and Their Applications in Predicting the Activities of Chemical Molecules, Peptides and Proteins for Drug Design

(2008) Qi-Shi Du et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Backbone Cyclic Peptidomimetic Melanocortin-4 Receptor Agonist as a Novel Orally Administrated Drug Lead for Treating Obesity

(2008) Shmuel Hess et al.   JOURNAL OF MEDICINAL CHEMISTRY

Toward Full-Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2

(2007) Ho Ki Fung et al.   BIOPHYSICAL JOURNAL