cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery

被引：2

作者：

Santini, Brianda L. ^{[1
]}

Wendel, Stephanie ^{[1
]}

Halbwedl, Niklas ^{[1
]}

Knipp, Asha ^{[1
]}

Zacharias, Martin ^{[1
]}

机构：

[1] Tech Univ Munich, Ctr Funct Prot Assemblies, Ernst Otto Fischer Str 8, Garching, Germany

来源：

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL | 2024年 / 23卷

关键词：

Cyclic peptides; Rational drug design; Molecular dynamics; Protein-protein complexes; Protein binding modulation; PROTEIN-PROTEIN INTERACTIONS; COMPLEX; REFINEMENT; LIBRARIES; RECEPTOR; REVEALS;

D O I：

10.1016/j.csbj.2024.08.008

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Cyclic peptides have emerged as versatile scaffolds in drug discovery due to their stability and specificity. Here, we present the cPEPmatch webserver (accessible at https://t38webservices.nat.tum.de/cpepmatch/), an easy-touse interface for the rational design of cyclic peptides targeting protein-protein interactions combined with a semi-quantitative evaluation of binding stability. This platform also offers access to a comprehensive database of cyclic peptide crystal structures. We demonstrate the webserver's utility through a series of case studies involving medically relevant protein systems, highlighting its potential to significantly advance drug discovery efforts.

引用

页码：3155 / 3162

页数：8

共 37 条

[1] Design of cyclic peptides as novel inhibitors of ICOS/ICOSL interaction [J].

Abdel-Rahman, Somaya A. ;

Santini, Brianda L. ;

Calvo-Barreiro, Laura ;

Zacharias, Martin ;

Gabr, Moustafa .

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 2024, 99

[2] The structure of an MDM2-Nutlin-3a complex solved by the use of a validated MDM2 surface-entropy reduction mutant [J].

Anil, Burcu ;

Riedinger, Christiane ;

Endicott, Jane A. ;

Noble, Martin E. M. .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2013, 69 :1358-1366

[3] The interface of protein-protein complexes: Analysis of contacts and prediction of interactions [J].

Bahadur, R. P. ;

Zacharias, M. .

CELLULAR AND MOLECULAR LIFE SCIENCES, 2008, 65 (7-8) :1059-1072

[4] The Amber biomolecular simulation programs [J].

Case, DA ;

Cheatham, TE ;

Darden, T ;

Gohlke, H ;

Luo, R ;

Merz, KM ;

Onufriev, A ;

Simmerling, C ;

Wang, B ;

Woods, RJ .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) :1668-1688

[5] The exploration of macrocycles for drug discovery - an underexploited structural class [J].

Driggers, Edward M. ;

Hale, Stephen P. ;

Lee, Jinbo ;

Terrett, Nicholas K. .

NATURE REVIEWS DRUG DISCOVERY, 2008, 7 (07) :608-624

[6] Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides [J].

Duffy, Fergal J. ;

O'Donovan, Darragh ;

Devocelle, Marc ;

Moran, Niamh ;

O'Connell, David J. ;

Shields, Denis C. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2015, 55 (03) :600-613

[7] CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids [J].

Duffy, Fergal J. ;

Verniere, Melanie ;

Devocelle, Marc ;

Bernard, Elise ;

Shields, Denis C. ;

Chubb, Anthony J. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2011, 51 (04) :829-836

[8] MODELLER: Generation and refinement of homology-based protein structure models [J].

Fiser, A ;

Sali, A .

MACROMOLECULAR CRYSTALLOGRAPHY, PT D, 2003, 374 :461-491

[9] Pharmacological manipulation of transcription factor protein-protein interactions: Opportunities and obstacles [J].

Fontaine F. ;

Overman J. ;

François M. .

Cell Regeneration, 4 (1) :4:2

[10] The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities [J].

Genheden, Samuel ;

Ryde, Ulf .

EXPERT OPINION ON DRUG DISCOVERY, 2015, 10 (05) :449-461

← 1 2 3 4 →