Assessing the Interactions between Snake Venom Metalloproteinases and Hydroxamate Inhibitors Using Kinetic and ITC Assays, Molecular Dynamics Simulations and MM/PBSA-Based Scoring Functions.

species are the main cause of snake bites in rural communities of tropical developing countries of Central and South America. Envenomation by snakes is characterized by prominent local inflammation, hemorrhage and necrosis as well as systemic hemostatic disturbances. These pathological effects are mainly caused by the major toxins of the viperidae venoms, the snake venom metalloproteinases (SVMPs).

Pyrolytic conversion of glucose into hydroxymethylfurfural and furfural: Benchmark quantum-chemical calculations.

Quantum chemical methods have been intensively applied to study the pyrolytic conversion of glucose into hydroxymethylfurfural (HMF) and furfural (FF). Herein, we collect the most relevant mechanistic proposals from the recent literature and organize them into a single reaction network. All the transition structures (TSs) and intermediates are characterized using highly accurate ab initio methods and the possible reaction pathways are assessed in terms of the Gibbs energies of the TSs and intermediates with respect to β-glucopyranose, selecting a 2D ideal-gas standard state at 773 K to represent the pyrolysis conditions.

Atoms in molecules in real space: a fertile field for chemical bonding.

In this perspective, we review some recent advances in the concept of atoms-in-molecules from a real space perspective. We first introduce the general formalism of atomic weight factors that allows unifying the treatment of fuzzy and non-fuzzy decompositions under a common algebraic umbrella. We then show how the use of reduced density matrices and their cumulants allows partitioning any quantum mechanical observable into atomic or group contributions.

Toward Reliable and Insightful Entropy Calculations on Flexible Molecules.

The absolute entropy of a flexible molecule can be approximated by the sum of a rigid-rotor-harmonic-oscillator (RRHO) entropy and a Gibbs-Shannon entropy associated to the Boltzmann distribution for the occupation of the conformational energy levels. Herein, we show that such partitioning, which has received renewed interest, leads to accurate entropies of single molecules of increasing size provided that the conformational part is estimated by means of a set of discretization and expansion techniques that are able to capture the significant correlation effects among the torsional motions. To ensure a reliable entropy estimation, we rely on extensive sampling as that produced by classical molecular dynamics simulations on the microsecond time scale, which is currently affordable for small- and medium-sized molecules.

QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach.

The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters.

A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy.

Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy.

Aptamers targeting protein-specific glycosylation in tumor biomarkers: general selection, characterization and structural modeling.

Detecting specific protein glycoforms is attracting particular attention due to its potential to improve the performance of current cancer biomarkers. Although natural receptors such as lectins and antibodies have served as powerful tools for the detection of protein-bound glycans, the development of effective receptors able to integrate in the recognition both the glycan and peptide moieties is still challenging. Here we report a method for selecting aptamers toward the glycosylation site of a protein.

Influence of charge configuration on substrate binding to SARS-CoV-2 main protease.

While the state-of-the-art computational simulations support the neutral state for the catalytic dyad of the SARS-CoV-2 main protease, the recently-reported neutron structure exhibits a zwitterionic form. To better compare the structural and dynamical features of the two charge configurations, we perform a Molecular Dynamics study of the dimeric enzyme in complex with a peptide substrate. The simulations show that the enzyme charge configuration from the neutron structure is not compatible with a catalytically-competent binding mode for peptide substrates.

Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A.

In this work, we investigate the conformational properties of unguisin A, a natural macrocyclic heptapeptide that incorporates a γ-aminobutyric acid (Gaba), and four of its difluorinated stereoisomers at the Gaba residue. According to nuclear magnetic resonance (NMR) experiments, their secondary structure depends dramatically on the stereochemistry of the fluorinated carbon atoms. However, many molecular details of the structure and flexibility of these systems remain unknown, so that a rationale of the conformational changes induced by the fluorine atoms in the macrocycle is still missing.

SARS-CoV-2 Main Protease: A Molecular Dynamics Study.

Herein, we investigate the structure and flexibility of the hydrated SARS-CoV-2 main protease by means of 2.0 μs molecular dynamics (MD) simulations in explicit solvent. After having performed electrostatic p calculations on several X-ray structures, we consider both the native (unbound) configuration of the enzyme and its noncovalent complex with a model peptide, Ace-Ala-Val-Leu-Gln∼Ser-Nme, which mimics the polyprotein sequence recognized at the active site.

Fluorine conformational effects characterized by energy decomposition analysis.

Electrostatic and stereoelectronic effects associated with fluorine atoms can be exploited as conformational tools for the design of shape-controlled functional molecules. To gain further insight into the nature and strength of these effects, we use the Interacting Quantum Atoms (IQA) method augmented with the semiclassical pairwise dispersion potential to decompose the conformational energies of fluoro-substituted molecules into fragment-based energy contributions, which include deformation/distortion terms and the electrostatic, exchange-correlation and dispersion interactions. The studied molecules comprise various F-CH-CH-X and F-CH-CO-X systems, as well as selected conformers of an α,β-difluoro-γ-amino-acid derivative that is potentially useful for the design of shape-controlled bioactive amino acids and peptides.

Alkali and Alkaline-Earth Cations in Complexes with Small Bioorganic Ligands: Ab Initio Benchmark Calculations and Bond Energy Decomposition.

Herein, we report a computational database for the complexes of alkali [Li(I), Na(I), K(I)] and alkaline-earth [Be(II), Mg(II) and Ca(II)] cations with 25 small ligands with varying charge and donor atoms ("O", "N", and "S") that provides geometries and accurate bond energies useful to analyze metal-ligand interactions in proteins and nucleic acids. The role of the ligand→metal charge transfer, the equilibrium bond distance, the electronegativity of the donor atom, the ligand polarizability, and the relative stability of the complexes are discussed in detail. The interacting quantum atoms (IQA) method is used to decompose the binding energy into electrostatic and quantum mechanical contributions.

Affinity Calculations of Cyclodextrin Host-Guest Complexes: Assessment of Strengths and Weaknesses of End-Point Free Energy Methods.

The end-point methods like MM/PBSA or MM/GBSA estimate the free energy of a biomolecule by combining its molecular mechanics energy with solvation free energy and entropy terms. On the one hand, their performance largely depends on the particular system of interest, and despite numerous attempts to improve their reliability that have resulted in many variants, there is still no clear alternative to improve their accuracy. On the other hand, the relatively small cyclodextrin host-guest complexes, for which high-quality binding calorimetric data are usually available, are becoming reference models for testing the accuracy of free energy methods.

Interacting Quantum Atoms Approach and Electrostatic Solvation Energy: Assessing Atomic and Group Solvation Contributions.

The interacting quantum atoms (IQA) method decomposes the total energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here we incorporate electrostatic continuum solvent effects into the IQA energy decomposition. To this end, the interaction between the solute electrostatic potential and the solvent screening charges as defined within the COSMO solvation model is now included in a new version of the PROMOLDEN code, allowing thus to apply IQA in combination with COSMO-quantum chemical methods as well as to partition the electrostatic solvation energy into effective atomic and group contributions.

Application of the Interacting Quantum Atoms Approach to the S66 and Ionic-Hydrogen-Bond Datasets for Noncovalent Interactions.

The interacting quantum atoms (IQA) method can assess, systematically and in great detail, the strength and physics of both covalent and noncovalent interactions. The lack of a pair density in density functional theory (DFT), which precludes the direct IQA decomposition of the characteristic exchange-correlation energy, has been recently overcome by means of a scaling technique, which can largely expand the applicability of the method. To better assess the utility of the augmented IQA methodology to derive quantum chemical decompositions at the atomic and molecular levels, we report the results of Hartree-Fock (HF) and DFT calculations on the complexes included in the S66 and the ionic H-bond databases of benchmark geometry and binding energies.

Ligand Strain and Entropic Effects on the Binding of Macrocyclic and Linear Inhibitors: Molecular Modeling of Penicillopepsin Complexes.

Using extensive molecular dynamics simulations, we investigate the structure and dynamics of the complexes formed between penicillopepsin and two peptidomimetic inhibitors: a linear compound, isovaleryl(P)-valine(P)-asparagine(P)-leucine(P)-phosphonate-phenylalanine(P'), and its macrocylic analog that includes a methylene bridge between the Asn(P) and Phe(P') side chains. The macrocyclic inhibitor, which has a 420-fold stronger affinity than that of the acyclic one, has been considered to lower the entropic penalty for binding. To better understand this binding preference, the solution structure of the inhibitors is studied by molecular dynamics simulations.

Molecular Dynamics Studies of Matrix Metalloproteases.

Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP.

Conformational and entropy analyses of extended molecular dynamics simulations of α-, β- and γ-cyclodextrins and of the β-cyclodextrin/nabumetone complex.

Herein, we report the results of 5.0 μs molecular dynamics simulations of native α-, β- and γ-cyclodextrins (CDs) in explicit water solvent that are useful to describe, in a comparative manner, the distorted geometry of the CD molecules in aqueous solution, the width and fluctuations of their cavities, and the number of cavity waters. By discretizing the time evolution of the dihedral angles, the rate of conformational change of the torsional motions and the conformational entropy are calculated for the three CDs, thus allowing the analysis of the extent of the MD sampling and the entropic significance of the CD flexibility.

Role of the Protonation State on the Structure and Dynamics of Albumin.

Human serum albumin undergoes reversible conformational transitions associated with ligand binding or pH changes. Among them, the neutral to base (N → B) transition occurring between pH 7 and pH 9 seems to be relevant for its function as a carrier. Unfortunately, a detailed atomic model for the B-form is still lacking, and several open questions remain concerning the charge distribution of the N-form.

Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations.

Snake venom metalloproteinases are important toxins that play fundamental roles during envenomation. They share a structurally similar catalytic domain, but with diverse hemorrhagic capabilities. To understand the structural basis for this difference, we build and compare two dynamical models, one for the hemorrhagic atroxlysin-I from Bothrops atrox and the other for the non-hemorraghic leucurolysin-a from Bothrops leucurus.

Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations.

The extent and significance of conformational sampling is a major factor determining the reliability of long-scale molecular simulations of large and flexible biomolecules. Although several methods have been proposed to quantify the effective sample size of molecular simulations by transforming root mean squared distances between pairs of configurations into statistical/probabilistic quantities, there is still no standard technique for measuring the size of sampling. In this work, we study conformational entropy (Sconform) as a purely informational and probabilistic measure of sampling that does not require the adoption of any clustering protocol or distance metric between configurations.

Molecular modeling of bioorganometallic compounds: thermodynamic properties of molybdocene-glutathione complexes and mechanism of Peptide hydrolysis.

The computational study of bioinorganic complexes between transition metals and flexible ligands is still challenging, given that, besides requiring extensive conformational searches, the treatment of metal-ligand bonds demands the application of quantum chemical methods. Herein, the adducts formed between molybdocene, which exhibits antitumor activity and reacts with thiol groups to give stable water-soluble complexes, and the tripeptide glutathione, which is a major source of biological thiols, are studied. Conformational searches are performed using the semiempirical PM6 method followed by geometry optimizations and single-point calculations using density functional theory methods.

Extensive simulations of the full-length matrix metalloproteinase-2 enzyme in a prereactive complex with a collagen triple-helical peptide.

Collagen hydrolysis catalyzed by matrix metalloproteinases is an important and complex process involved in a variety of physiological and pathological conditions. To contribute to its characterization at the molecular level, herein we analyze three different models for the complex formed between the full-length matrix metalloproteinase-2 (MMP-2) enzyme and a synthetic triple-helical peptide (fTHP-5). The considered MMP-2/fTHP-5 complexes mainly differ in the location of the C-terminal hemopexin-like domain, but in all of them, the middle α-chain of the substrate (B-chain) is placed within the active site groove.

An integrated computational and experimental approach to gaining selectivity for MMP-2 within the gelatinase subfamily.

Looking for water-soluble inhibitors of matrix metalloproteinase-2 (MMP-2 or gelatinase A), we have previously reported compound 1, a potent MMP-2 inhibitor with a promising selectivity over the structurally homologous MMP-9 (gelatinase B). Here we report the results of Molecular Dynamics (MD) simulations for both gelatinases (MMP-2 and MMP-9), and for the corresponding MMP/1 complexes, in an attempt to shed light on the observed selectivity between the two enzymes. These studies indicated a higher plasticity of MMP-2 at the S1' pocket and suggested an induced-fit effect at the "back door" of this pocket.

A combined semiempirical and DFT computational protocol for studying bioorganometallic complexes: application to molybdocene-cysteine complexes.

Computational methods can help in the design of new bioorganometallic compounds. However, the presence of multihapto or σ/π metal-ligand bonding still precludes the direct application of either pure molecular mechanics (MM) or hybrid quantum mechanics-MM methods to study the flexibility of biomolecules in complex with organometallics. Herein, we present a computational protocol aimed to the evaluation of the relative free energies of bioorganometallic compounds, which explores the conformational space by means of Molecular Dynamics simulations using the semiempirical PM6 method coupled with the COnductor-like Screening MOdel solvation model followed by density functional theory (DFT) calculations including the DFT-D3 dispersion energy correction on the most stable conformers.