Michal H. Kolář

Michal H. Kolář
University of Chemistry and Technology, Prague | VSCHT · Department of Physical Chemistry (ÚFCH)

Ph.D.

About

37
Publications
47,868
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,461
Citations
Introduction
I run computer simulations to understand phenomena at atomic and subatomic level, and write about it occasionally on http://mhko.science. In addition, I like travelling by train and dislike tomatoes.
Additional affiliations
January 2018 - present
University of Chemistry and Technology, Prague
Position
  • Professor (Assistant)
January 2016 - December 2017
Max Planck Institute for Biophysical Chemistry
Position
  • Fellow
January 2014 - December 2015
Forschungszentrum Jülich
Position
  • PostDoc Position
Education
September 2009 - May 2013
Charles University in Prague
Field of study
  • Molecular Modeling
September 2007 - June 2009
Charles University in Prague
Field of study
  • Molecular Modeling
September 2004 - June 2007
Charles University in Prague
Field of study
  • Chemistry

Publications

Publications (37)
Article
Full-text available
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM), the structure of the ribosome was resolved at atomic resolution in many functional and conformational states....
Article
The effect of polar flattening on the stability of 32 halogen-bonded complexes was investigated by utilizing CCSD(T)/CBS, DFT and DFT-SAPT/CBS methods. It is shown that the value of polar flattening increases with the decreasing value of studied isodensity. For the complexes investigated, the polar flattening based on the isodensity of 0.001 a.u. r...
Article
To contribute to the understanding of noncovalent binding of halogenated molecules with biological activity, electrostatic potential (ESP) maps of more than 2500 compounds were thoroughly analysed. A peculiar region of positive ESP, called the σ-hole, is a concept of central importance for halogen bonding. We aim to simplify the view on σ-holes and...
Article
Until recently, the description of halogen bonding by standard molecular mechanics has been poor, owing to the lack of the so-called σ hole localized at the halogen. This region of positive electrostatic potential located on top of a halogen atom explains the counterintuitive attraction of halogenated compounds interacting with Lewis bases. In mole...
Article
A novel approach in molecular docking was successfully used to reproduce protein-ligand experimental geometries. When dealing with halogenated compounds the correct description of halogen bonds between the ligand and the protein is shown to be essential. Applying a simple molecular mechanistic model for halogen bonds improved the protein-ligand geo...
Article
Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the σ‐hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the σ‐hole is often modeled as a pseudo‐atom with a posit...
Article
Full-text available
The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arres...
Preprint
Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the $\sigma$-hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the $\sigma$-hole is often modeled as a pseudo-ato...
Preprint
Full-text available
The ribosome is a fundamental biomolecular complex responsible for protein production in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiologic consequences. Here, we studied th...
Preprint
The proteasome is a large biomolecular complex responsible for protein degradation. It is under intense research due to its fundamental role in cellular homeostasis, and tremendous potential for medicinal applications. Recent data from X-ray crystallography and cryo-electron microscopy have suggested that there is a large-scale structural change up...
Article
Halogen bond (X‐bond) is a noncovalent interaction between a halogen atom and an electron donor. It is often rationalized by a region of the positive electrostatic potential on the halogen atom, so‐called σ‐hole. The X‐bond strength increases with the atomic number of the halogen involved; thus, for heavier halogens, relativistic effects become of...
Article
Targeting energy metabolism in Mycobacterium tuberculosis (Mtb) is a new paradigm in the search for innovative anti-TB drugs. NADH:menaquinone oxidoreductase is a non-proton translocating type II NADH dehydrogenase (NDH-2) that is an essential enzyme in the respiratory chain of Mtb and is not found in mammalian mitochondria. Phenothiazines (PTZs) r...
Preprint
Halogen bond (X-bond) is a noncovalent interaction between a halogen atom and an electron donor. It is often rationalized by a region of the positive electrostatic potential on the halogen atom, so-called $\sigma$-hole. The X-bond strength increases with the atomic number of the halogen involved, thus for heavier halogens, relativistic effects beco...
Article
Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes....
Article
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We emplo...
Article
In the field of noncovalent interactions a new paradigm has recently become popular. It stems from the analysis of molecular electrostatic potentials and introduces a label, which has recently attracted enormous attention. The label is σ-hole, and it was first used in connection with halogens. It initiated a renaissance of interest in halogenated c...
Article
Correction for 'The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole' by Michal Kolář et al., Phys. Chem. Chem. Phys., 2014, 16, 9987–9996.
Article
Full-text available
Human aldo-keto reductase 1B15 (AKR1B15) is a newly discovered enzyme which shares 92% amino acid sequence identity with AKR1B10. While AKR1B10 is a well characterized enzyme with high retinaldehyde reductase activity, involved in the development of several cancer types, the enzymatic activity and physiological role of AKR1B15 are still poorly know...
Article
The effect of halogen-to-hydrogen bond substitution on the binding energetics and biological activity of an aldose reductase inhibitor has been studied using X-ray crystallography, IC50 measurements, advanced binding free energy calculations and simulations. The replacement of Br or I atoms by an amine (NH2) group has not induced changes in the ori...
Article
The nature of halogen bonding in 128 complexes was investigated using advanced quantum mechanical calculations. First, isolated halogen donors were studied and their σ-holes were described in terms of size and magnitude. Later, both partners in the complex were considered and their interaction was described in terms of DFT-SAPT decomposition. The w...
Article
Full-text available
The σ-holes of halogen atoms on various aromatic scaffolds were described in terms of their size and magnitude. The electrostatic potential maps at the CAM-B3LYP-D3(bj)/def2-QZVP level were calculated and the σ-holes of more than 100 aromatic analogues were thoroughly analysed to relate the σ-holes to the binding preferences of the halogenated comp...
Article
This Minireview discusses the latest developments in modern quantum mechanics (QM)-based computer-aided drug design, especially using semiempirical QM (SQM) methods. It first tackles biochemical and biophysical quantities and the approaches to their measurements. Protein–ligand affinities are determined mostly by noncovalent interactions. The text...
Article
In this paper, we studied a designed series of aldose reductase (AR) inhibitors. The series had been derived from a known AR binder which had previously been shown to form a halogen bond between its bromine atom and the oxygen atom of the Thr-113 side chain of AR. In the series, the strength of the halogen bond was modulated by two factors, namely...
Article
The crystals of benzene and hexahalogenbenzenes have been studied by means of the density-functional theory augmented by an empirical dispersion correction term as well as by the symmetry-adapted perturbation theory. In order to elucidate the nature of noncovalent binding, pairwise interactions have been investigated. It has been demonstrated that...
Article
The accuracy and performance of implicit solvent methods for solvation free energy calculations were assessed on a set of 20 neutral drug molecules. Molecular dynamics (MD) provided ensembles of conformations in water and water-saturated octanol. The solvation free energies were calculated by popular implicit solvent models based on quantum mechani...
Article
Various cluster models of graphene and a periodic graphene with two organic electron acceptors (tetracyanoethylene and tetracyanoquinodimethane) were investigated by means of several quantum chemical and molecular mechanical approaches. The benchmark interaction energies of the coronene complexes were calculated at the MP2.5/CBS/6-31G*(0.25) level...
Article
A DNA dodecamer and the methyladenine···methylthymine (mA···mT) complex in aqueous environment have been studied by means of molecular dynamics simulation, with a modified force field accounting for the hypothetical absence of London dispersion forces. Under these conditions, the mA···mT complex is preserved, while the double-helical DNA oligomer p...
Article
In this study, an extensive sampling of the conformational space of nine HIV-1 protease inhibitors was performed to estimate the uncertainty with which a single-conformation scoring scheme approximates the ligand-protein binding free energy. The SMD implicit solvation/desolvation energy and gas-phase PM6-DH2 energy were calculated for a set of 1600...
Article
We investigated the intercalation of an antitumor drug ellipticine into four adenine-thymine (AT) rich DNA duplexes with the focus on the configurational entropy, by means of molecular dynamics (MD) simulations. Two possible binding orientations of ellipticine in a DNA double helix were studied, and the orientation with the pyrrole nitrogen exposed...
Article
The reliability of the AMBER force field is tested by comparing the total interaction energy and dispersion energy with the reference data obtained at the density functional theory-symmetry-adapted perturbation treatment (DFT-SAPT)/aug-cc-pVDZ level. The comparison is made for 194 different geometries of noncovalent complexes (H-bonded, stacked, mi...
Article
The structure of the phenol dimer and phenol...methanol complexes was determined by gradient optimization using the Hartree-Fock (HF), MP2, DFT, and RI-DFT-D methods with various basis sets. Theoretical rotational constants were compared with experimental values and the following conclusions were made: (1) HF and DFT methods fail to predict cluster...

Network

Cited By

Projects

Projects (2)
Project
To understand the theoretical aspects of halogen bonding, develop computational tools for its reliable description, and apply such tools for a variety of (bio)chemical applications.
Project
Ribosomes are cellular biomachines that synthesize proteins. The catalytic center is buried deep in the large subunit, so the nascent peptide chain has to leave the ribosome through an exit tunnel before it reaches cytoplasm or a membrane. We want to understand what happens with the peptide inside the tunnel, and with the tunnel itself. To this aim, we run large-scale molecular dynamics simulations at atomic resolution.