AMBER force field implementation of the boronate function to simulate the inhibition of beta-lactamases by alkyl and aryl boronic acids

An improved dataset of force fields, electronic and physicochemical descriptors of metabolic substrates

In silico prediction of xenobiotic metabolism is an important strategy to accelerate the drug discovery process, as candidate compounds often fail in clinical phases due to their poor pharmacokinetic profiles. Here we present MetaQM, a dataset of quantum-mechanical (QM) optimized metabolic substrates, including force field parameters, electronic and physicochemical properties. MetaQM comprises 2054 metabolic substrates extracted from the MetaQSAR database. We provide QM-optimized geometries, General Amber Force Field (FF) parameters for all studied molecules, and an extended set of structural and physicochemical descriptors as calculated by DFT and PM7 methods. The generated data can be used in different types of analysis. FF parameters can be applied to perform classical molecular mechanics calculations as exemplified by the validating molecular dynamics simulations reported here. The calculated descriptors can represent input features for developing improved predictive models for metabolism and drug design, as exemplified in this work. Finally, the QM-optimized molecular structures are valuable starting points for both ligand- and structure-based analyses such as pharmacophore mapping and docking simulations.

Development of AMBER Parameters for Molecular Simulations of Selected Boron-Based Covalent Ligands

Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies is crucial. Nevertheless, the suitable molecular mechanics parameterization and the force fields needed to perform these simulations are not completely available for this class of molecules. In this paper, Amber force field parameters for phenyl-, benzyl-, benzylamino-, and methylamino-boronates, a group of boron-containing compounds involved in different branches of the medicinal chemistry, were created. The robustness of the obtained data was confirmed through molecular dynamics simulations on ligand/β-lactamases covalent complexes. The ligand torsional angles, populated over the trajectory frames, were confirmed by values found in the ligand geometries, located through optimizations at the DFT/B3LYP/6-31g(d) level, using water as a solvent. In summary, this study successfully provided a library of parameters, opening the possibility to perform molecular dynamics simulations of this class of boron-containing compounds.

Molecular Basis of Bicyclic Boronate β-Lactamase Inhibitors of Ultrabroad Efficacy - Insights From Molecular Dynamics Simulation Studies

β-Lactam antibiotics represent about 70% of all antibacterial agents in clinical use. They are safe and highly effective drugs that have been used for more than 50 years, and, in general, well tolerated by most patients. However, its usefulness has been dramatically reduced with the spread and dissemination worldwide of multi-drug resistant bacteria. These pathogens elude the therapeutic action of these antibiotics by expressing β-lactamase enzymes that catalyze the hydrolysis of their β-lactam ring to give inactive products, which is one of the most relevant resistance mechanisms in deadly pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacteriaceae. From the drug development point of view, the design of an efficient β-lactamase inhibitor able to block this antibiotic resistance mechanism and restore β-lactam antibiotics efficacy is challenging. This is due to: (1) the huge structural diversity of these enzymes in both the amino acid sequence and architecture of the active site; (2) the distinct hydrolytic capability against different types of substrates; (3) the variety of enzyme mechanisms of action employed, either involving covalent catalyzed processes (serine hydrolases) or non-covalent catalysis (zinc-dependent hydrolases); and (4) the increasing emergence and spread of bacterial pathogens capable of simultaneously producing diverse β-lactamases. Hence, a long-pursued goal has been the development of ultrabroad-spectrum inhibitors able to inhibit both serine- and metallo-β-lactamases. The recent development of taniborbactam (formerly VNRX-5133) and QPX7728, which are bicyclic boronate inhibitors currently under clinical development, represents a huge step forward in this goal. In this article, the molecular basis of the ultrabroad-spectrum of activity of these boron-based inhibitors is analyzed by molecular dynamics simulation studies using the available crystal structures in complex with both inhibitors, or the models constructed from wild-type forms. The efficacy of taniborbactam and QPX7728 is compared with the cyclic boronate inhibitor vaborbactam, which is the first boron-based β-lactamase inhibitor approved by the FDA in combination with meropenem for the treatment of complicated urinary tract infections.

Systematic Parameterization and Simulation of Boronic Acid-β-Lactamase Aqueous Solution in Developing the ABEEMσπ Polarizable Force Field

Boronic acid, an inhibitor of β-lactamase, has begun to be applied to the treatment of biological infections and tumors. Scientists are working to develop new and more effective boronic acid. Molecular dynamics (MD) simulation provides a powerful auxiliary tool for drug design. However, the current force fields have no boron-related parameters. In this work, an atom-bond electronegativity equalization method at the σπ level (ABEEMσπ) polarizable force field (ABEEMσπ PFF) of boronic acid and β-lactamase has been developed to determine the potential functions and parameters. The interaction between boron and serine in β-lactamase is regarded as a bonded mode. The interaction between them is simulated by the Morse potential energy function, which is close to the experimental change of the stretching potential energy in a large range. The potential energy surfaces of the bond length, bond angle, and dihedral angle of boronic acid-β-lactamase have the same stability point and change trend as M06-2X/6-311G**. For 47 boronic acid-β-lactamase training molecules, the linear correlation coefficient (R) of the charge distribution between the ABEEMσπ PFF and HF/STO-3G is greater than 0.96. Attributed to the fact that the charge distribution of the ABEEMσπ PFF can fluctuate with the change of geometry and environment, the polarization effect and charge-transfer effect are well reflected. The binding ability of different boronic acids with the same β-lactamase is different. A total of 10 boronic acid-β-lactamase model molecules and 10 boronic acid-β-lactamase and water complexes are simulated. The order of binding energy of five large model molecules calculated by the ABEEMσπ PFF is consistent with that of the MP2 method. The binding energies of boronic acid-β-lactamase and water complexes are close to those of the MP2 method. The results of MD simulation of five aqueous boronic acid-β-lactamase complexes in the NVT ensemble verify the rationality of boron-related parameters of the ABEEMσπ PFF, which have a good application prospect. This study lays a solid theoretical foundation for further study of the inhibition of boronic acid on β-lactamase.

Sequential pore wall functionalization in covalent organic frameworks and application to stable camptothecin delivery systems

Post-synthetic modification of covalent organic frameworks (COFs) is strongly demanded in order to provide additional functionalities to their structures. However, the introduction of functional groups during the synthesis of two dimensional COFs (2D COFs) is highly discouraged, as they can interfere with the π-π stacking forces, compromising framework integrity. Here, we show that direct incorporation of nucleophyllic groups (e.g., primary amines) on pore wall during the synthesis of a 2D-COF (COF-5) is possible by sequential substitution of original monomers. Subsequent bonding of the antitumor drug camptothecin results in a stable hydrophobic drug delivery system. Water adsorption isotherms modelling indicates that the insertion of CPT ligand in the framework promotes a hydrophobic effect that protects a region of COF chain from boronate ester hydrolysis and resulting degradation, which is also proven by stability testing in physiological conditions. Furthermore, this hydrophobic nature favors cell internalization kinetics by promoting interactions with the lipophilic cell membrane. To the best of our knowledge, this is the first case of a stable drug delivery system based on covalently conjugated COFs.

Iron's Wake: The Performance of Quantum Mechanical-Derived Versus General-Purpose Force Fields Tested on a Luminescent Iron Complex

Recently synthetized iron complexes have achieved long-lived excited states and stabilities which are comparable, or even superior, to their ruthenium analogues, thus representing an eco-friendly and cheaper alternative to those materials based on rare metals. Most of computational tools which could help unravel the origin of this large efficiency rely on ab-initio methods which are not able, however, to capture the nanosecond time scale underlying these photophysical processes and the influence of their realistic environment. Therefore, it exists an urgent need of developing new low-cost, but still accurate enough, computational methodologies capable to deal with the steady-state and transient spectroscopy of transition metal complexes in solution. Following this idea, here we focus on the comparison between general-purpose transferable force-fields (FFs), directly available from existing databases, and specific quantum mechanical derived FFs (QMD-FFs), obtained in this work through the Joyce procedure. We have chosen a recently reported Fe^III complex with nanosecond excited-state lifetime as a representative case. Our molecular dynamics (MD) simulations demonstrated that the QMD-FF nicely reproduces the structure and the dynamics of the complex and its chemical environment within the same precision as higher cost QM methods, whereas general-purpose FFs failed in this purpose. Although in this particular case the chemical environment plays a minor role on the photo physics of this system, these results highlight the potential of QMD-FFs to rationalize photophysical phenomena provided an accurate QM method to derive its parameters is chosen.

Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation

Boric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program containing the Seminario method. The minimized structure, after obtaining novel parameters and using the sander program, was compared with the experimental crystallographic structures, and it was observed that the root-mean-square deviation (RMSD) value between the experimental structure and minimized structure agreed reasonably well. In addition, the molecule was heated, and the molecular dynamics simulation was successfully obtained with the novel parameters.

Design, synthesis and in vitro evaluation of a Dopa-organoboron compound that acts as a bladder relaxant through non-catecholamine receptors

Bladder relaxation through drug administration is an interesting topic in medicinal and combinatorial chemistry. In fact, compounds targeting catecholamine receptors [dopamine receptors and beta-adrenergic receptors (βAR) expressed in the bladder] are among the compounds commonly employed for this purpose. In particular, recent investigations have tended to focus on the β₃-adrenoceptor (β₃AR) as a target in the treatment of urinary incontinence and other disorders. However, organoboron compounds have been suggested as potent and efficient agents on these drug targets. In this work, through a docking study, we identified the parameters that induce a theoretical improvement in the affinity and activity of the organoboron compounds on the catecholamine receptors expressed in the bladder. Then, the identified potential drug, a boron-containing dopa-derivative named DPBX-L-Dopa, was synthesized and characterized. This compound induces a relaxation on the smooth muscle of the rat bladder, behaving as a weak relaxant compared to isoproterenol but with similar efficacy to BRL377, a selective β₃AR agonist. However, unexpectedly, this effect was not blocked by propranolol or haloperidol at the concentrations at which they are able to block the catecholamine receptors in bladder tissue. In view of these results, the effect of DPBX-L-Dopa compound on the alpha 1 adrenergic receptors (α₁AR) of aorta of the rats was also explored; however, no response of the tissue to this compound was obtained. The possible mechanisms of the action of this compound were explored and are discussed further.

Theoretical Coupling and Stability of Boronic Acid Adducts with Catecholamines

Background:

Catecholamines combined with boric/boronic acids are attractive chemical agents in drug design because some of their adducts have shown interesting biological activity. Scant information exists about their stability.

Objective:

The aim of the present theoretical study was to explore the role of boron in molecules that combine catecholamines and boric/boronic acids, with a particular interest in examining stability.

Method:

The methodology was based on the US GAMESS program using DFT with the B3LYP exchange-correlation functional and the 6-31G (d,p) split-valence basis set.

Results:

According to the current findings, the boron-containing compounds (BCCs) exhibit weaker bonding to the hydroxyls on the ethylamine moiety than to those in the aromatic ring. The strongest binding site of a hydroxyl group was often found to be in meta-position (relative to ethylamine moiety) for boron-free compounds and in para-position for BCCs. Nonetheless, the methyl substituent in the amino group was able to induce changes in this pattern. We analyzed feasible boronsubstituted structures and assessed the relative strength of the respective C-B bonds, which allowed for the identification of the favorable points for reaction and stability.

Conclusion:

It is feasible to form adducts by bonding on the amine and catechol sides of catecholamines. The presence of boron stabilizes the adducts in para-position. Since some of these BCCs are promising therapeutic agents, understanding the mechanisms of reaction is relevant for drug design.

Design, synthesis and in vitro evaluation of a Dopa-organoboron compound that acts as a bladder relaxant through non-catecholamine receptors

Bladder relaxation through drug administration is an interesting topic in medicinal and combinatorial chemistry. In fact, compounds targeting catecholamine receptors [dopamine receptors and beta-adrenergic receptors (βAR) expressed in the bladder] are among the compounds commonly employed for this purpose. In particular, recent investigations have tended to focus on the β₃-adrenoceptor (β₃AR) as a target in the treatment of urinary incontinence and other disorders. However, organoboron compounds have been suggested as potent and efficient agents on these drug targets. In this work, through a docking study, we identified the parameters that induce a theoretical improvement in the affinity and activity of the organoboron compounds on the catecholamine receptors expressed in the bladder. Then, the identified potential drug, a boron-containing dopa-derivative named DPBX-L-Dopa, was synthesized and characterized. This compound induces a relaxation on the smooth muscle of the rat bladder, behaving as a weak relaxant compared to isoproterenol but with similar efficacy to BRL377, a selective β₃AR agonist. However, unexpectedly, this effect was not blocked by propranolol or haloperidol at the concentrations at which they are able to block the catecholamine receptors in bladder tissue. In view of these results, the effect of DPBX-L-Dopa compound on the alpha 1 adrenergic receptors (α₁AR) of aorta of the rats was also explored; however, no response of the tissue to this compound was obtained. The possible mechanisms of the action of this compound were explored and are discussed further.

Synthesis of BODIPY-Peptide Conjugates for Fluorescence Labeling of EGFR Overexpressing Cells

Regioselective functionalization of 2,3,5,6,8-pentachloro-BODIPY 1 produced unsymmetric BODIPY 5, bearing an isothiocyanate group suitable for conjugation, in only four steps. The X-ray structure of 5 reveals a nearly planar BODIPY core with aryl dihedral angles in the range 47.4-62.9°. Conjugation of 5 to two EGFR-targeting pegylated peptides, 3PEG-LARLLT (6) and 3PEG-GYHWYGYTPQNVI (7), under mild conditions (30 min at room temperature), afforded BODIPY conjugates 8 and 9 in 50-80% isolated yields. These conjugates showed red-shifted absorption and emission spectra compared with 5, in the near-IR region, and were evaluated as potential fluorescence imaging agents for EGFR overexpressing cells. SPR and docking investigations suggested that conjugate 8 bearing the LARLLT sequence binds to EGFR more effectively than 9 bearing the GYHWYGYTPQNVI peptide, in part due to the lower solubility of 9, and its tendency for aggregation at concentrations above 10 μM. Studies in human carcinoma HEp2 cells overexpressing EGFR demonstrated low dark and photo cytotoxicities for BODIPY 5 and the two peptide conjugates, and remarkably high cellular uptake for both conjugates 8 and 9, up to 90-fold compared with BODIPY 5 after 1 h. Fluorescence imaging studies in HEp2 cells revealed subcellular localization of the BODIPY-peptide conjugates mainly in the Golgi apparatus and the cell lysosomes. The low cytotoxicity of the new conjugates and their remarkably high uptake into EGFR overexpressing cells renders them promising imaging agents for cancers overexpressing EGFR.

Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule

The thrombin‐binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G‐quadruplex‐forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three‐carbon spacer (spacer‐C₃), unlocked nucleic acid (UNA) and 3′‐amino‐modified UNA (amino‐UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G‐quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer‐C₃ introduction at the T7 loop position (TBA‐SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA‐SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties.

Co-pyrolysis mechanism of seaweed polysaccharides and cellulose based on macroscopic experiments and molecular simulations

Co-pyrolysis conversion of seaweed (Enteromorpha clathrat and Sargassum fusiforme) polysaccharides and cellulose has been investigated. From the Py-GC/MS results, Enteromorpha clathrata (EN) polysaccharides pyrolysis mainly forms furans; while the products of Sargassum fusiforme (SA) polysaccharides pyrolysis are mainly acid esters. The formation mechanisms of H2O, CO2, and SO2 during the pyrolysis of seaweed polysaccharides were analyzed using the thermogravimetric-mass spectrometry. Meanwhile the pyrolysis of seaweed polysaccharide based on the Amber and the ReaxFF force fields, has also been proposed and simulated respectively. The simulation results coincided with the experimental results. During the fast pyrolysis, strong synergistic effects among cellulose and seaweed polysaccharide molecules have been simulated. By comparing the experimental and simulation value, it has been found that co-pyrolysis could increase the number of molecular fragments, increase the pyrolysis conversion rate, and increase gas production rate at the middle temperature range.

Utilization of Boron Compounds for the Modification of Suberoyl Anilide Hydroxamic Acid as Inhibitor of Histone Deacetylase Class II Homo sapiens

Histone deacetylase (HDAC) has a critical function in regulating gene expression. The inhibition of HDAC has developed as an interesting anticancer research area that targets biological processes such as cell cycle, apoptosis, and cell differentiation. In this study, an HDAC inhibitor that is available commercially, suberoyl anilide hydroxamic acid (SAHA), has been modified to improve its efficacy and reduce the side effects of the compound. Hydrophobic cap and zinc-binding group of these compounds were substituted with boron-based compounds, whereas the linker region was substituted with p-aminobenzoic acid. The molecular docking analysis resulted in 8 ligands with ΔG_binding value more negative than the standards, SAHA and trichostatin A (TSA). That ligands were analyzed based on the nature of QSAR, pharmacological properties, and ADME-Tox. It is conducted to obtain a potent inhibitor of HDAC class II Homo sapiens. The screening process result gave one best ligand, Nova2 (513246-99-6), which was then further studied by molecular dynamics simulations.

Cell-based and in-silico studies on the high intrinsic activity of two boron-containing salbutamol derivatives at the human β₂-adrenoceptor

Salbutamol is a well-known β(2) adrenoceptor (β(2)AR) partial agonist. We synthesized two boron-containing salbutamol derivatives (BCSDs) with greater potency and efficacy, compared to salbutamol, for inducing β(2)AR-mediated smooth-muscle relaxation in guinea-pig tracheal rings. However, the mechanism involved in this pharmacological effect remains unclear. In order to gain insight, we carried out binding and functional assays for BCSDs in HEK-293T cells transfected with the human β(2)AR (hβ(2)AR). The transfected hβ(2)AR showed similar affinity for BCSDs and salbutamol, but adenosine 3',5'-cyclic phosphate (cAMP) accumulation induced by both BCSDs was similar to that elicited by isoproterenol and greater than that induced by salbutamol. The boron-containing precursors (boric and phenylboronic acids, 100 μM) had no significant effect on salbutamol binding or salbutamol-induced cAMP accumulation. These experimental results are in agreement with theoretical docking simulations on lipid bilayer membrane-embedded hβ(2)AR structures. These receptors showed slightly higher affinity for BCSDs than for salbutamol. An essential change between putative active and inactive conformational states depended on the interaction of the tested ligands with the fifth, sixth and seventh transmembrane domains. Overall, these data suggest that BCSDs induce and stabilize conformational states of the hβ(2)AR that are highly capable of stimulating cAMP production.

Effects of the Val211Gly substitution on molecular dynamics of the CMY-2 cephalosporinase: implications on hydrolysis of expanded-spectrum cephalosporins

CMY-30, a naturally occurring class C β-lactamase differing from the Citrobacter freundii-derived CMY-2 by a Val211Gly substitution in the Ω-loop, exhibits increased hydrolytic efficiency against ceftazidime and cefotaxime. Kinetic constants of CMY-2 and CMY-30 against the latter substrates suggested that the improved efficiency of the Gly211 variant was due to an increase in k(cat). The structural basis of the increased turn-over rates of oxyimino-cephalosporins caused by Val211Gly was studied using 5 ns molecular dynamics simulations of CMY-2 and CMY-30 in their free forms and in covalent complexes with ceftazidime (acyl-enzyme) as well as a boronic acid analogue of ceftazidime (deacylation transition state). Analysis of thermal factors indicated that Val211Gly increased the flexibility of the Ω-loop/H7-helix and the Q120-loop formed by amino acids 112-125, and also altered the vibrations of the H10-helix/R2-loop. Structural elements containing the catalytic residues remained relatively rigid except Tyr150 in acyl-enzyme species. Regions exhibiting altered flexibility due to the substitution appear to move in a concerted manner in both enzymes. This movement was more intense in CMY-30 and also at directions different to those observed for CMY-2. Additionally, it appeared that the Val211Gly increased the available space for the accommodation of the R1 side chain of ceftazidime. These findings are likely associated with the significantly increased vibrations of the bound compounds observed in CMY-30 complexes. Therefore, the extended spectrum properties of CMY-30 seem to arise through a complex process implicating changes in protein movement and in the mode of substrate accommodation.

Permeation through the cell membrane of a boron-based β-lactamase inhibitor

Bacteria express beta-lactamases to counteract the beneficial action of antibiotics. Benzo[b]-thiophene-2-boronic acid (BZB) derivatives are β-lactamase inhibitors and, as such, promising compounds to be associated with β-lactam antibacterial therapies. The uncharged form of BZB, in particular, is suggested to diffuse through the outer membrane of gram negative bacteria. In this study, through the combination of electrophysiological experiments across reconstituted PC/n-decane bilayers and metadynamics-based free energy calculations, we investigate the permeation mechanism of boronic compounds. Our experimental data establish that BZB passes through the membrane, while computer simulations provide hints for the existence of an aqueous, water-filled monomolecular channel. These findings provide new perspectives for the design of boronic acid derivatives with high membrane permeability.

Design, synthesis and in vitro evaluation of (R)-4-(2-(tert-butylamino)-1-hydroxyethyl)-2-(hydroxymethyl)phenyl hydrogen phenylboronate: a novel salbutamol derivative with high intrinsic efficacy on the β2 adrenoceptor

We tested a set of boron containing arylethanolamine derivatives on the human and guinea pig β(2) adrenoceptor (β(2)AR) 3-D structures by docking methodology. The compound with the highest affinity based on docking analysis, (R)-4-(2-(tert-butylamino)-1-hydroxyethyl)-2-(hydroxymethyl)phenyl hydrogen phenylboronate (boronterol) was synthesized, characterized and tested in guinea pig tracheal rings at basal tone and with histamine-induced contractions. Boronterol was at least eightfold more potent than salbutamol as a smooth muscle relaxant drug (judged by the EC(50) values) and showed a similar maximal relaxant effect as isoproterenol. ICI118,551 showed competitive antagonism on the relaxing effect of boronterol. These results suggest the β(2)AR agonist action of boronterol.

Pharmacokinetic parameters and a theoretical study about metabolism of BR-AEA (a salbutamol derivative) in rabbit

In this study, we report the pharmacokinetics of 1-(4-di-hydroxy-3,5-dioxa-4-borabicyclo[4.4.0]deca-7,9,11- trien-9-yl)-2-(tert-butylamino)ethanol (BR-AEA). This compound was identified as a more potent beta(2) adrenoceptor (beta(2)AR) agonist than salbutamol. A sensitive and reproducible high-performance liquid chromatography (HPLC) method was used for determining the time-dependent BR-AEA concentration in healthy rabbit plasma. The pharmacokinetic parameters obtained are explained in relation to the compound's metabolism by sulfotransferases. For this purpose, docking simulations were carried out on SULT1A3, SULT1C1, and SULT1A1 3-D models using the Autodock 3.0.5 program. According to the HPLC results, t(1/2) = 2.36 +/- 0.18 h and K(e) = 0.32 +/- 0.02 h(-1) for BR-AEA in rabbit plasma. Thus, BR-AEA has a greater half-life compared with salbutamol (t(1/2) = 0.66 +/- 0.08 h). This could be due to the protection that the boronic acid moiety of BR-AEA offers to the hydroxyl groups that would otherwise be susceptible to sulfation when exposed inside the active site of the sulfotransferase. This could be due to the fact that BR-AEA has a high affinity for the side-chain hydroxyl groups of Ser and Tyr residues of the enzymes, which are located outside the active site.

Carborane clusters in computational drug design: a comparative docking evaluation using AutoDock, FlexX, Glide, and Surflex

Compounds containing boron atoms play increasingly important roles in the therapy and diagnosis of various diseases, particularly cancer. However, computational drug design of boron-containing therapeutics and diagnostics is hampered by the fact that many software packages used for this purpose lack parameters for all or part of the various types of boron atoms. In the present paper, we describe simple and efficient strategies to overcome this problem, which are based on the replacement of boron atom types with carbon atom types. The developed methods were validated by docking closo- and nido-carboranyl antifolates into the active site of a human dihydrofolate reductase (hDHFR) using AutoDock, Glide, FlexX, and Surflex and comparing the obtained docking poses with the poses of their counterparts in the original hDHFR-carboranyl antifolate crystal structures. Under optimized conditions, AutoDock and Glide were equally good in docking of the closo-carboranyl antifolates followed by Surflex and FlexX, whereas Autodock, Glide, and Surflex proved to be comparably efficient in the docking of nido-carboranyl antifolates followed by FlexX. Differences in geometries and partial atom charges in the structures of the carboranyl antifolates resulting from different data sources and/or optimization methods did not impact the docking performances of AutoDock or Glide significantly. Binding energies predicted by all four programs were in accordance with experimental data.