4.7 Review

Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs

Journal

DRUG DISCOVERY TODAY
Volume 21, Issue 5, Pages 712-717

Publisher

ELSEVIER SCI LTD
DOI: 10.1016/j.drudis.2016.02.005

Keywords

-

Funding

  1. NIH [1R01GM094551]

Ask authors/readers for more resources

Key to the pharmaceutical utility of certain macrocyclic drugs is a 'chameleonic' ability to change their conformation to expose polar groups in aqueous solution, but bury them when traversing lipid membranes. Based on analysis of the structures of 20 macrocyclic compounds that are approved oral drugs, we propose that good solubility requires a topological polar surface area (TPSA, in angstrom(2)) of >= 0.2 x molecular weight (MW). Meanwhile, good passive membrane permeability requires a molecular (i.e., 3D) PSA in nonpolar environments of <= 140 angstrom(2). We show that one or other of these limits is almost invariably violated for compounds with MW > 600 Da, suggesting that some degree of chameleonic behavior is required for most high MW oral drugs.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Biochemistry & Molecular Biology

Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core

Vinita Lukose, Lingqi Luo, Dima Kozakov, Sandor Vajda, Karen N. Allen, Barbara Imperiali

BIOCHEMISTRY (2015)

Editorial Material Oncology

Fragments and hot spots in drug discovery

Sandor Vajda, Adrian Whitty, Dima Kozakov

ONCOTARGET (2015)

Article Biochemical Research Methods

Accounting for pairwise distance restraints in FFT-based protein-protein docking

Bing Xia, Sandor Vajda, Dima Kozakov

BIOINFORMATICS (2016)

Article Chemistry, Multidisciplinary

Focused Grid-Based Resampling for Protein Docking and Mapping

Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov

JOURNAL OF COMPUTATIONAL CHEMISTRY (2016)

Article Multidisciplinary Sciences

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds

Dzmitry Padhorny, Andrey Kazennov, Brandon S. Zerbe, Kathryn A. Porter, Bing Xia, Scott E. Mottarella, Yaroslav Kholodov, David W. Ritchie, Sandor Vajda, Dima Kozakov

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Biochemistry & Molecular Biology

A benchmark testing ground for integrating homology modeling and protein docking

Tanggis Bohnuud, Lingqi Luo, Shoshana J. Wodak, Alexandre M. J. J. Bonvin, Zhiping Weng, Sandor Vajda, Ora Schueler-Furman, Dima Kozakov

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking

Christine Yueh, David R. Hall, Bing Xia, Dzmitry Padhorny, Dima Kozakov, Sandor Vajda

JOURNAL OF MOLECULAR BIOLOGY (2017)

Article Biochemical Research Methods

The ClusPro web server for protein-protein docking

Dima Kozakov, David R. Hall, Bing Xia, Kathryn A. Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda

NATURE PROTOCOLS (2017)

Article Chemistry, Organic

Progress towards the broad use of non-peptide synthetic macrocycles in drug discovery

Adrian Whitty, Lauren A. Viarengo, Mengqi Zhong

ORGANIC & BIOMOLECULAR CHEMISTRY (2017)

Article Biochemistry & Molecular Biology

New additions to the ClusPro server motivated by CAPRI

Sandor Vajda, Christine Yueh, Dmitri Beglov, Tanggis Bohnuud, Scott E. Mottarella, Bing Xia, David R. Hall, Dima Kozakov

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2017)

Article Chemistry, Multidisciplinary

Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning

Paula C. Ortet, Samantha N. Muellers, Lauren A. Viarengo-Baker, Kristina Streu, Blair R. Szymczyna, Aaron B. Beeler, Karen N. Allen, Adrian Whitty

Summary: Research shows that the binding affinity of Nrf2 for KEAP1 can be replicated in a cyclic 7-mer peptide, achieved through optimizing the conformation of the cyclic compound; Analysis using X-ray crystal structures and machine learning indicates that strain locations in the bound ligand can be identified by observing patterns of subangstrom distortions; Optimizing the cyclic peptide affinity is driven by conformational preorganization associated with specific substitutions and geometries, as well as by reducing strain in the ETGE motif.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Biochemistry & Molecular Biology

Novel p.G250A Mutation Associated with Chronic Pancreatitis Highlights Misfolding-Prone Region in Carboxypeptidase A1 (CPA1)

Mate Sandor, Franziska G. Thiel, Margit Schmid, Alexandra Demcsak, Nataly C. Morales Granda, Balazs Csaba Nemeth, Sandor Vajda, Andre Hoerning, Miklos Sahin-Toth

Summary: Inborn mutations in the CPA1 gene may lead to misfolding of the protein and are associated with chronic pancreatitis. A novel mutation, p.G250A, was identified in a patient with pancreatic disorder, and its functional properties were similar to another mutation, p.N256K, confirming its pathogenic nature. These mutations result in reduced secretion of CPA1 and endoplasmic reticulum stress. Mutations affecting a specific loop in the protein structure exhibit secretion defects and ER stress in varying degrees, and the severity of ER stress correlates with the secretion defect.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Chemistry, Multidisciplinary

Defining and navigating macrocycle chemical space

Lauren A. Viarengo-Baker, Lauren E. Brown, Anna A. Rzepiela, Adrian Whitty

Summary: Macrocyclic compounds are increasingly studied for inhibiting challenging drug targets. This study identifies distinct regions in structure-property space for oral and non-oral macrocycle drugs, as well as commercially available synthetic MCs. Thirteen properties are identified for designing synthetic MCs that overlap with oral MC drugs, advancing understanding of bioactive and orally bioavailable MCs.

CHEMICAL SCIENCE (2021)

Review Pharmacology & Pharmacy

Illuminating the druggable genome: Pathways to progress

Karlie R. Sharma, Christine M. Colvis, Griffih P. Rodgers, Douglas M. Sheeley

Summary: There are many genes within the druggable genome that have not been studied, and the US National Institutes of Health's program provides resources to explore these genes, with the potential for rapid impact on human health.

DRUG DISCOVERY TODAY (2024)

Review Pharmacology & Pharmacy

Unravelling the potential of mitochondria-targeted liposomes for enhanced cancer treatment

Mohammad Sameer Khan, B. H. Jaswanth Gowda, Waleed H. Almalki, Tanuja Singh, Amirhossein Sahebkar, Prashant Kesharwani

Summary: Mitochondria-specific functional liposomes hold great potential for cancer therapy. This review discusses the association between mitochondria and tumor formation, as well as the advantages of liposomes in delivering drugs to mitochondria.

DRUG DISCOVERY TODAY (2024)

Review Pharmacology & Pharmacy

Multiorgan locked-state model of chronic diseases and systems pharmacology opportunities

Choong Yong Ung, Cristina Correia, Hu Li, Christopher M. Adams, Jennifer J. Westendorf, Shizhen Zhu

Summary: With increasing human life expectancy, the global medical burden of chronic diseases is growing. Chronic diseases often involve malfunctioning of multiple organs, and understanding the interorgan crosstalk is crucial to understanding the etiology of chronic diseases. Researchers have proposed the locked-state model (LoSM) and cutting-edge systems biology and artificial intelligence strategies to decipher chronic multiorgan locked states. The findings have important clinical implications for improving treatments for chronic diseases.

DRUG DISCOVERY TODAY (2024)