J 2015

Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases using in Silico Screening

DANIEL, Lukáš, Tomáš BURYŠKA, Zbyněk PROKOP, Jiří DAMBORSKÝ, Jan BREZOVSKÝ et. al.

Basic information

Original name

Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases using in Silico Screening

Authors

DANIEL, Lukáš (203 Czech Republic, belonging to the institution), Tomáš BURYŠKA (203 Czech Republic, belonging to the institution), Zbyněk PROKOP (203 Czech Republic, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, belonging to the institution) and Jan BREZOVSKÝ (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Chemical Information and Modeling, 2015, 1549-9596

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 3.657

RIV identification code

RIV/00216224:14310/15:00081404

Organization unit

Faculty of Science

DOI

UT WoS

000348619400005

Keywords in English

in Silico Screening;Haloalkane Dehalogenases

Tags

Změněno: 7/4/2016 10:10, Ing. Andrea Mikešková

Abstract

V originále

The substrate specificity is a key feature of enzymes determining their applicability in biomaterials and biotechnologies. Experimental testing of activities with novel substrates is a time-consuming and inefficient process, typically resulting in many failures. Here, we present an experimentally validated in silico method for the discovery of novel substrates of enzymes with known reaction mechanism. The method was developed for a model system of biotechnologically relevant enzymes, haloalkane dehalogenases. Based on the parameterization of six different haloalkane dehalogenases with 30 halogenated substrates, mechanism-based geometric criteria for reactivity approximation were defined. These criteria were subsequently applied to the previously experimentally uncharacterized haloalkane dehalogenase DmmA. The enzyme was computationally screened against 42,000 compounds, yielding 548 structurally unique compounds as potential substrates. Eight out of sixteen experimentally tested top-ranking compounds were active with DmmA, indicating a 50% success rate for the prediction of substrates. The remaining eight compounds were able to bind to the active site and inhibit enzymatic activity. These results confirmed good applicability of the method for prioritizing active compounds – true substrates and binders – for experimental testing.

Links

EE2.3.30.0037, research and development project
Name: Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce
GAP503/12/0572, research and development project
Name: Konstrukce syntetické metabolické dráhy pro degradaci důležitého environmentálního polutantu proteinovým a metabolickým inženýrstvím
Investor: Czech Science Foundation
LO1214, research and development project
Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)
Investor: Ministry of Education, Youth and Sports of the CR