Identifying Substructures That Facilitate Compounds to Penetrate the Blood-Brain Barrier via Passive Transport Using Machine Learning Explainer Models.

The local interpretable model-agnostic explanation (LIME) method was used to interpret two machine learning models of compounds penetrating the blood-brain barrier. The classification models, Random Forest, ExtraTrees, and Deep Residual Network, were trained and validated using the blood-brain barrier penetration dataset, which shows the penetrability of compounds in the blood-brain barrier. LIME was able to create explanations for such penetrability, highlighting the most important substructures of molecules that affect drug penetration in the barrier. The simple and intuitive outputs prove the applicability of this explainable model to interpreting the permeability of compounds across the blood-brain barrier in terms of molecular features. LIME explanations were filtered with a weight equal to or greater than 0.1 to obtain only the most relevant explanations. The results showed several structures that are important for blood-brain barrier penetration. In general, it was found that some compounds with nitrogenous substructures are more likely to permeate the blood-brain barrier. The application of these structural explanations may help the pharmaceutical industry and potential drug synthesis research groups to synthesize active molecules more rationally.

Do Large Language Models Understand Chemistry? A Conversation with ChatGPT.

Large language models (LLMs) have promised a revolution in answering complex questions using the ChatGPT model. Its application in chemistry is still in its infancy. This viewpoint addresses the question of how well ChatGPT understands chemistry by posing five simple tasks in different subareas of chemistry.

The reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question.

The octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was investigated using atomistic molecular dynamics simulations via thermodynamic integration and multistate Bennett acceptance ratio methods. The GAFF and CHARMM36 force fields were used with six water models widely used in molecular dynamics simulations. The OPC4 water model provided the best agreement with the experimental octanol-water partition coefficient of DPPC using the two force fields. However, there is still plenty of room for improvement in water models with correct estimation of surface tension that uses better and suitable non-bonded interaction parameters between water-water and water-DPPC. The Gibbs free energy of transferring DPPC from octanol to water phase was calculated to be 19.8 ± 0.3 and 20.2 ± 0.3 kcal mol-1, giving a partition coefficient of 14.5 ± 0.4 and 14.8 ± 0.3 for the GAFF and CHARMM36 force fields, respectively. This study reinforces the importance of developing new water models that reproduce experimental surface tensions to reconcile the water-water and water-DPPC non-bonded interactions and the existing discrepancy between experimental measurements of amphiphilic molecules that are important in many areas of scientific applications and industry such as biophysics, surfactant, colloids, membranes, medicine, nanotechnology, and food and pharmaceutical industries, and so on. It raises two important open questions: Is the experimental octanol-water partition coefficient of DPPC reliable? Or is its calculation accurate using the OPC4 water model? With respect to the experimental measurements, there may be non-treated aspects such as the formation of aggregates in aqueous phase and limit of detection of the applied method. And, in the calculation, some effects are not possible to be considered in a correct way or viable time such as calculating quantum effects, sampling all conformations, considering phase transitions, and correctly evaluating the intermolecular forces to estimate an accurate surface tension.Communicated by Ramaswamy H. Sarma.

Absolute binding free energies of the antiviral peptide ATN-161 with protein targets of SARS-CoV-2.

The interactions of the antiviral pentapeptide ATN-161 with the closed and open conformations of the α5ß1 integrin, the SARS-CoV-2 major protease, and the omicron variant spike protein complexed with hACE2 were studied using molecular docking and molecular dynamics simulation. Molecular docking was performed to obtain ATN-161 binding poses with these studied protein targets. Subsequently, molecular dynamics simulations were performed to verify the ligand stability at the binding site of each protein target. Pulling simulations, umbrella sampling, and weighted histogram analysis method were used to obtain the potential of mean force of each system and calculate the Gibbs free energy of binding for the ATN-161 peptide in each binding site of these protein targets. The results showed that ATN-161 binds to α5ß1 integrin in its active and inactive form, binds weakly to the omicron variant spike protein complexed with hACE2, and strongly binds to the main protease target.Communicated by Ramaswamy H. Sarma.

Absolute binding free energies of mucroporin and its analog mucroporin-M1 with the heptad repeat 1 domain and RNA-dependent RNA polymerase of SARS-CoV-2.

The peptide Mucroporin and its analog Mucroporin-M1 were studied using the molecular docking and molecular dynamics simulation of their complexation with two protein targets, the Heptad Repeat 1 (HR1) domain and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. The molecular docking of the peptide-protein complexes was performed using the glowworm swarm optimization algorithm. The lowest energy poses were submitted to molecular dynamics simulation. Then, the binding free energies of Mucroporin and its analog Mucroporin-M1 with these two protein targets were calculated using the Multistate Bennett Acceptance Ratio (MBAR) method. It was verified that the peptides/HR1 domain complex showed stability in the interaction site determined by molecular docking. It was also found that Mucroporin-M1 has a much higher affinity than Mucroporin to the HR1 protein target. The peptides showed similar stability and affinity at the NTP binding site in the RdRp protein. Additional experimental studies are needed to confirm the antiviral activity of Mucroporin-M1 and a possible mechanism of action against SARS-CoV-2. However, here we indicate that Mucroporin-M1 may have potential antiviral activity against the HR1 domain with the possibility for further peptide optimization.Communicated by Ramaswamy H. Sarma.

Hydrophilic But Not Hydrophobic Surfactant Protein Genetic Variants Are Associated With Severe Acute Respiratory Syncytial Virus Infection in Children.

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection-related hospitalization in the first year of life. Surfactant dysfunction is central to pathophysiologic mechanisms of various pulmonary diseases including RSV. We hypothesized that RSV severity is associated with single nucleotide polymorphisms (SNPs) of surfactant proteins (SPs). We prospectively enrolled 405 RSV-positive children and divided them into moderate and severe RSV disease. DNA was extracted and genotyped for sixteen specific SP gene SNPs. SP-A1 and A2 haplotypes were assigned. The association of RSV severity with SP gene SNPs was investigated by multivariate logistic regression. A likelihood ratio test was used to test the goodness of fit between two models (one with clinical and demographic data alone and another that included genetic variants). p ≤ 0.05 denotes statistical significance. A molecular dynamics simulation was done to determine the impact of the SFTPA2 rs1965708 on the SP-A behavior under various conditions. Infants with severe disease were more likely to be younger, of lower weight, and exposed to household pets and smoking, as well as having co-infection on admission. A decreased risk of severe RSV was associated with the rs17886395_C of the SFTPA2 and rs2243639_A of the SFTPD, whereas an increased risk was associated with the rs1059047_C of the SFTPA1. RSV severity was not associated with SNPs of SFTPB and SFTPC. An increased risk of severe RSV was associated with the 1A0 genotype of SFTPA2 in its homozygous or heterozygous form with 1A3. A molecular dynamic simulation study of SP-A variants that differ in amino acid 223, an important amino acid change (Q223K) between 1A0 and 1A3, showed no major impact on the behavior of these two variants except for higher thermodynamic stability of the K223 variant. The likelihood ratio test showed that the model with multi-allelic variants along with clinical and demographic data was a better fit to predict RSV severity. In summary, RSV severity was associated with hydrophilic (but not with hydrophobic) SPs gene variants. Collectively, our findings show that SP gene variants may play a key role in RSV infection and have a potential role in prognostication.

Lung surfactant negatively affects the photodynamic inactivation of bacteria-in vitro and molecular dynamic simulation analyses.

In the context of the rapid increase of antibiotic-resistant infections, in particular of pneumonia, antimicrobial photodynamic therapy (aPDT), the microbiological application of photodynamic therapy (PDT), comes in as a promising treatment alternative since the induced damage and resultant death are not dependent on a specific biomolecule or cellular pathway. The applicability of aPDT using the photosensitizer indocyanine green with infrared light has been successfully demonstrated for different bacterial agents in vitro, and the combination of pulmonary delivery using nebulization and external light activation has been shown to be feasible. However, there has been little progress in obtaining sufficient in vivo efficacy results. This study reports the lung surfactant as a significant suppressor of aPDT in the lungs. In vitro, the clinical surfactant Survanta® reduced the aPDT effect of indocyanine green, Photodithazine®, bacteriochlorin-trizma, and protoporphyrin IX against Streptococcus pneumoniae. The absorbance and fluorescence spectra, as well as the photobleaching profile, suggested that the decrease in efficacy is not a result of singlet oxygen quenching, while a molecular dynamics simulation showed an affinity for the polar head groups of the surfactant phospholipids that likely impacts uptake of the photosensitizers by the bacteria. Methylene blue is the exception, likely because its high water solubility confers a higher mobility when interacting with the surfactant layer. We propose that the interaction between lung surfactant and photosensitizer must be taken into account when developing pulmonary aPDT protocols.

Structure and Thermotropic Behavior of Bovine- and Porcine-Derived Exogenous Lung Surfactants.

Two commercial exogenous pulmonary surfactants, Curosurf and Survanta, are investigated. Their thermotropic behavior and associated structural changes for the samples in bulk are characterized and described. For Survanta, the obtained results of differential scanning calorimetry showed a thermogram with three peaks on heating and only a single peak on cooling. Curosurf on the other hand, presents calorimetric thermograms with only one peak in both the heating and cooling scans. This distinct thermotropic behavior between the two pulmonary surfactants, a consequence of their particular compositions, is associated with structural changes that were evaluated by simultaneous small- and wide-angle X-ray scattering experiments with in situ temperature variation. Interestingly, for temperatures below ∼35 °C for Curosurf and ∼53 °C for Survanta, the scattering data indicated the coexistence of two lamellar phases with different carbon chain organizations. For temperatures above these limits, the coexistence of phases disappears, giving rise to a fluid phase in both pulmonary surfactants, with multilamelar vesicles for Curosurf and unilamellar vesicles for Survanta. This process is quasi-reversible under cooling, and advanced data analysis for the scattering data indicated differences in the structural and elastic properties of the pulmonary surfactants. The detailed and systematic investigation shown in this work expands on the knowledge of the structure and thermodynamic behavior of Curosurf and Survanta, being relevant from both physiological and biophysical perspectives and also providing a basis for further studies on other types of pulmonary surfactants.

Recent Open Issues in Coarse Grained Force Fields.

This viewpoint intends to show recent open issues of using coarse grained models in molecular dynamics simulation. It reviews the current knowledge of the comparison between experimental and simulation data of structural and physical chemical properties that depend on the hydrophilic and hydrophobic behavior of the molecule.

Molecular Modeling Study of Uncharged Oximes Compared to HI-6 and 2-PAM Inside Human AChE Sarin and VX Conjugates.

The deleterious effects of nerve agents over the enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) turned these compounds into the most dangerous chemical weapons known. Among the antidotes in use today against these agents, oximes in combination with other drugs are the only treatment with any action. HI-6 and 2-PAM are cationic oximes proved to be effective for the reactivation of AChE inhibited by the nerve agents VX and sarin (GB). However, when it comes to reactivation of AChE inside the central or peripheral nervous systems, charged molecules present low diffusion due to low penetration through the blood-brain barrier. Uncharged oximes appear as an interesting alternative to solve this problem, but the development and enhancement of more efficient uncharged oximes capable of reactivating human AChE is still necessary. Given the limitations for in vivo and in vitro experimental studies with nerve agents, modeling is an important tool that can contribute to a better understanding of factors that may affect the efficiency of uncharged oximes. In order to investigate the interaction and behavior of cationic and uncharged oximes, we performed here molecular docking, molecular dynamics simulations, and binding energies calculations of the known cationic oximes HI-6 and 2-PAM plus four uncharged oximes found in the literature, complexed with human AChE (HssACHE) conjugated with the nerve agents VX and GB. The uncharged oximes showed different behaviors, especially RS194B, which presented stability inside AChE-VX, but presented free binding energy lower than cationic oximes, suggesting that structural alterations could favor its interactions with these complexes. In contrast, HI-6 and 2-PAM showed higher affinities with more negative binding energy values and larger contribution of the amino acid Asp74, demonstrating the importance of the quaternary nitrogen to the affinity and interaction of oximes with AChE-GB and AChE-VX conjugates.

New insights into exogenous surfactant as a carrier of pulmonary therapeutics.

As an organ system, the lung has unique advantages and disadvantages for localized drug delivery. Its direct contact with the external environment allows for the upper airways to be easily accessible to intrapulmonary delivery. However, its complex branching structure makes direct delivery to the peripheral airways challenging. This review will discus the utility of exogenous surfactant, a lipoprotein complex currently used to treat neonatal respiratory distress syndrome, as a carrier for pulmonary therapeutics to enhance the delivery of these drugs to the deeper regions of the lung. The focus is to provide an update on the many tools available to develop new surfactant-based therapeutics using computer modeling, in vitro approaches, and in vivo testing, which may ultimately lead to clinical trials. Two clinical conditions, Acute Respiratory Distress Syndrome and Bacterial Pneumonia are utilized throughout as prototypical examples of pulmonary conditions in which surfactant drug combination may be beneficial. Consequently, the pharmaceuticals discussed are primarily those with antimicrobial or anti-inflammatory activities.

Mechanisms of histone lysine-modifying enzymes: A computational perspective on the role of the protein environment.

Epigenetic pathways are involved in a wide range of diseases, including cancer and neurological disorders. Specifically, histone modifying and reading processes are the most broadly studied and are targeted by several licensed drugs. Although there have been significant advances in understanding the mechanistic aspects underlying epigenetic regulation, the development of selective small-molecule inhibitors remains a challenge. Experimentally, it is generally difficult to elucidate the atomistic basis for substrate recognition, as well as the sequence of events involved in binding and the subsequent chemical processes. In this regard, computational modelling is particularly valuable, since it can provide structural features (including transition state structures along with kinetic and thermodynamic parameters) that enable both qualitative and quantitative evaluation of the mechanistic details involved. Here, we summarize knowledge gained from computational modelling studies elucidating the role of the protein environment in histone-lysine modifying and reading mechanisms. We give a perspective on the importance of calculations to aid and advance the understanding of these processes and for the future development of selective inhibitors for epigenetic regulators.

Structure-based de novo design, molecular docking and molecular dynamics of primaquine analogues acting as quinone reductase II inhibitors.

Primaquine is a traditional antimalarial drug with low parasitic resistance and generally good acceptance at higher doses, which has been used for over 60 years in malaria treatment. However, several limitations related to its hematotoxicity have been reported. It is believed that this toxicity comes from the hydroxylation of the C-5 and C-6 positions of its 8-aminoquinoline ring before binding to the molecular target: the quinone reductase II (NQO2) human protein. In this study we propose primaquine derivatives, with substitution at position C-6 of the 8-aminoquinoline ring, planned to have better binding to NQO2, compared to primaquine, but with a reduced toxicity related to the C-5 position being possible to be oxidized. On this sense the proposed analogues were suggested in order to reduce or inhibit hydroxylation and further oxidation to hemotoxic metabolites. Five C-6 substituted primaquine analogues were selected by de novo design and further submitted to docking and molecular dynamics simulations. Our results suggest that all analogues bind better to NQO2 than primaquine and may become better antimalarials. However, the analogues 3 and 4 are predicted to have a better activity/toxicity balance.

Antimalarial activity and mechanisms of action of two novel 4-aminoquinolines against chloroquine-resistant parasites.

Chloroquine (CQ) is a cost effective antimalarial drug with a relatively good safety profile (or therapeutic index). However, CQ is no longer used alone to treat patients with Plasmodium falciparum due to the emergence and spread of CQ-resistant strains, also reported for P. vivax. Despite CQ resistance, novel drug candidates based on the structure of CQ continue to be considered, as in the present work. One CQ analog was synthesized as monoquinoline (MAQ) and compared with a previously synthesized bisquinoline (BAQ), both tested against P. falciparum in vitro and against P. berghei in mice, then evaluated in vitro for their cytotoxicity and ability to inhibit hemozoin formation. Their interactions with residues present in the NADH binding site of P falciparum lactate dehydrogenase were evaluated using docking analysis software. Both compounds were active in the nanomolar range evaluated through the HRPII and hypoxanthine tests. MAQ and BAQ derivatives were not toxic, and both compounds significantly inhibited hemozoin formation, in a dose-dependent manner. MAQ had a higher selectivity index than BAQ and both compounds were weak PfLDH inhibitors, a result previously reported also for CQ. Taken together, the two CQ analogues represent promising molecules which seem to act in a crucial point for the parasite, inhibiting hemozoin formation.

New insights in the atmospheric HONO formation: new pathways for N2O4 isomerization and NO2 dimerization in the presence of water.

Isomerization of N(2)O(4) and dimerization of NO(2) in thin water films on surfaces are believed to be key steps in the hydrolysis of NO(2), which generates HONO, a significant precursor to the OH free radical in lower atmosphere and high-energy materials. Born-Oppenheimer molecular dynamics simulations using the density functional theory are carried out for NO(2)(H(2)O)(m), m ≤ 4, and N(2)O(4)(H(2)O)(n) clusters, n ≤ 7, used to mimic the surface reaction, to investigate the mechanism around room temperature. The results are (i) the NO(2) dimerization and N(2)O(4) isomerization reactions occur via two possible pathways, the non-water-assisted and water-assisted mechanisms; (ii) the NO(2) dimerization in the presence of water yields either ONONO(2)(H(2)O)(m) or NO(3)(-)NO(+)(H(2)O)(m) clusters, but it is also possible to form the HNO(3)(NO(2)(-))(H(3)O(+))(H(2)O)(m-2) transition state to form HONO and HNO(3), directly; (iii) the N(2)O(4) isomerization yields the NO(3)(-)NO(+)(H(2)O)(n) cluster, but it does not hydrolyze faster than the NO(2)(+)NO(2)(-)(H(2)O)(n) hydrolysis to directly form the HONO and HNO(3). New insights for hydrolysis of oxides of nitrogen in and on thin water films on surfaces in the atmosphere are discussed.

Born-Oppenheimer molecular dynamics on the H(2)S + NO(3) reaction in the presence and absence of water: the kinetic isotope effect.

The chemical mechanism of the H(2)S + NO(3) reaction in the absence and presence of water molecules was investigated using the Born-Oppenheimer molecular dynamics. These calculations were performed to gain insight into the underlying chemical mechanism and to evaluate the kinetic isotope effect in the H(2)S + NO(3) and D(2)S + NO(3) reactions. When H(2)O interacts with NO(3), the rate coefficient of the H(2)S + NO(3) reaction is smaller than that for H(2)O interacting with H(2)S. Deuterium generally decreases the rate when D(2)O interacts with D(2)S but has no effect when D(2)O interacting with NO(3). When H(2)O or D(2)O interacts with NO(3), the yields are larger compared to those for the reactions (H(2)O)H(2)S + NO(3) and (D(2)O)H(2)S + NO(3). Furthermore, the average reaction times of the reactions H(2)S + NO(3)(H(2)O) and H(2)S + NO(3)(D(2)O) are shorter than those when H(2)O or D(2)O interacts with H(2)S. The (H(2)O)H(2)S + NO(3) reaction may occur via two possible pathways: the non-water-assisted and water-assisted hydrogen abstraction mechanisms. However, the H(2)S + NO(3)(H(2)O) reaction only happens via the non-water-assisted mechanism.

Theoretical and experimental study of negative LiF clusters produced by fast ion impact on a polycrystalline 7LiF target.

The emission of negative cluster ions produced by the impact of approximately 60 MeV (252)Cf fission fragments on a (7)LiF polycrystalline target is analyzed. The negative ion mass spectrum is dominated by the ((7)LiF)(n)F(-) series, n = 1 to approximately 30. The desorption yield distribution of the ((7)LiF)(n)F(-) members has a maximum at n = 2 and then decreases as the sum of two exponentials whose decay parameters are k(Fast) = 0.9 and k(Slow) = 0.08. These k values are the same as those observed for the positive series and close to others obtained for condensed gas targets. Relative cluster ion stabilities, deduced from the experimental ion abundances for the (LiF)(n)F(-) series, are proposed to be correlated with theoretical structures according to their internal energy by using the deviation plot (D-plot) methodology. A pool of candidate cluster structures was generated using a genetic algorithm and further analyzed and optimized using density functional theory (DFT) with the hybrid functional B3LYP (DFT/B3LYP) and Moller-Plesset perturbation theory (MP2). For the small clusters (n = 1 to 2), the most stable structures are found to be linear, whereas the larger clusters (n = 4 to 6) present cubic or polyhedral structures. Fragmentation energies, ionization potentials, and relative stabilities are reported for the most abundant families of the (LiF)(n)F(-) and (LiF)(n)(-) series.