Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins

Aim

Structure-based identification of natural compounds against SARS-CoV-2, Delta and Omicron target proteins.

Materials & methods

Several known antiviral natural compounds were subjected to molecular docking and MD simulation against SARS-CoV-2 Mpro, Helicase and Spike, including Delta and Omicron Spikes.

Results

Of the docked ligands, 20 selected for each complex exhibited overall good binding affinities (-7.79 to -5.06 kcal/mol) with acceptable physiochemistry following Lipinski's rule. Finally, two best ligands from each complex upon simulation showed structural stability and compactness.

Conclusion

Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A were identified as potential inhibitors of SARS-CoV-2 Mpro, Helicase and Spike, while Orientin and Obetrioside also showed good binding affinities with Omicron Spike. Catechin and Neridienone A formed stable complexes with Delta Spike.

Investigation of antioxidant and antibacterial effects of citrus fruits peels extracts using different extracting agents: Phytochemical analysis with in silico studies

The peels extracted from various citrus species are major source of phenols, flavonoids and anti-microbial agents. The purpose of this study was a detailed investigation of the phytochemical and pharmacological character of the ethanolic (80%), methanolic and acetone extracts of the peel of local variants of orange (lemon, grape fruit, mousami, fruiter, and shikri malta). The extracts were studied to find out the total phenolic contents (TPC), and total flavonoids (TF) present. The antioxidant activities were assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging effect, and the reducing power was determined through free radical scavenging activity (FRAP) assays. The sensitivity of four bacterial strains to peels extracts was examined by applying the diffusion disc on agar medium method. It was found that ethanol was the best extracting agent for TPC and TF in fruit peels under study. The highest TPC (21.33 ± 0.06 mg GAE/g) was quantified in orange peels, whereas fruiter contained the lowest TPC (20.40 ± 0.03 mg GAE/g) in ethanolic extract. The highest amount of TF (2.02 ± 0.08 mg QE/g) was quantified in lemon peels, whereas shikri malta contained lowest quantity of TF (1.04 ± 0.02 mg QE/g). The highest free radical scavenging activity (93.1%) of DPPH was exhibited by lemon peels, whereas the least activity (78.6%) was shown by mousami peels. Ethanolic extract of orange peels demonstrated more reducing power while showing an absorption of 1.98, followed by methanolic (1.11) and acetone (0.81) extracts. The inhibition effect of methanolic extract of lemon peels (inhibition zone = 18 mm) against B. subtilis was considerable and comparable to that of ciprofloxacin. Gas chromatography/mass spectrometry (GC/MS) was used to detect the compounds in ethanolic extract and up to 14 compounds were detected. These compounds were also assessed for their docking scores. Plausible binding modes with polyphenol oxidase and four best compounds were selected for molecular dynamics (MD) simulation to analyze their structural stability with receptor.

Exploiting the co-crystal ligands shape, features and structure-based approaches for identification of SARS-CoV-2 Mpro inhibitors

SARS-CoV-2 enters the host cell through the ACE2 receptor and replicates its genome using an RNA-Dependent RNA Polymerase (RDRP). The functional RDRP is released from pro-protein pp1ab by the proteolytic activity of Main protease (Mpro) which is encoded within the viral genome. Due to its vital role in proteolysis of viral polyprotein chains, it has become an attractive potential drug target. We employed a hierarchical virtual screening approach to identify small synthetic protease inhibitors. Statistically optimized molecular shape and color-based features (various functional groups) from co-crystal ligands were used to screen different databases through various scoring schemes. Then, the electrostatic complementarity of screened compounds was matched with the most active molecule to further reduce the hit molecules' size. Finally, five hundred eighty-seven molecules were docked in Mpro catalytic binding site, out of which 29 common best hits were selected based on Glide and FRED scores. Five best-fitting compounds in complex with Mpro were subjected to MD simulations to analyze their structural stability and binding affinities with Mpro using MM/GB(PB)SA models. Modeling results suggest that identified hits can act as the lead compounds for designing better active Mpro inhibitors to enhance the chemical space to combat COVID-19.Communicated by Ramaswamy H. Sarma.

Development of a Covalent Inhibitor of c-Jun N-Terminal Protein Kinase (JNK) 2/3 with Selectivity over JNK1

The c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family, which includes JNK1-JNK3. Interestingly, JNK1 and JNK2 show opposing functions, with JNK2 activity favoring cell survival and JNK1 stimulating apoptosis. Isoform-selective small molecule inhibitors of JNK1 or JNK2 would be useful as pharmacological probes but have been difficult to develop due to the similarity of their ATP binding pockets. Here, we describe the discovery of a covalent inhibitor YL5084, the first such inhibitor that displays selectivity for JNK2 over JNK1. We demonstrated that YL5084 forms a covalent bond with Cys116 of JNK2, exhibits a 20-fold higher Kinact/KI compared to that of JNK1, and engages JNK2 in cells. However, YL5084 exhibited JNK2-independent antiproliferative effects in multiple myeloma cells, suggesting the existence of additional targets relevant in this context. Thus, although not fully optimized, YL5084 represents a useful chemical starting point for the future development of JNK2-selective chemical probes.

Allosteric modulation of a human odorant receptor

Odor perception is first determined by how the myriad of environmental volatiles are detected at the periphery of the olfactory system. The combinatorial activation of dedicated odorant receptors generates enough encoding power for the discrimination of tens of thousands of odorants. Recent studies have revealed that odorant receptors undergo widespread inhibitory modulation of their activity when presented with mixtures of odorants, a property likely required to maintain discrimination and ensure sparsity of the code for complex mixtures. Here, we establish the role of human OR5AN1 in the detection of musks and identify distinct odorants capable of enhancing its activity in binary mixtures. Chemical and pharmacological characterization indicate that specific α-β unsaturated aliphatic aldehydes act as positive allosteric modulators. Sensory experiments show decreased odor detection threshold in humans, suggesting that allosteric modulation of odorant receptors is perceptually relevant and likely adds another layer of complexity to how odors are encoded in the peripheral olfactory system.

Mechanistic Insight into the Inhibition of Choline Acetyltransferase by Proton Pump Inhibitors

Various pharmacoepidemiological investigational studies have indicated that Proton Pump Inhibitors (PPIs) may increase the likelihood of developing Alzheimer's disease (AD) and non-AD related dementias. Previously, we have reported the inhibition of the acetylcholine biosynthesizing enzyme choline acetyltransferase (ChAT) by PPIs, for which omeprazole, lansoprazole, and pantoprazole exhibited IC₅₀ values of 0.1, 1.5, and 5.3 μM, respectively. In this study we utilize a battery of computational tools to perceive a mechanistic insight into the molecular interaction of PPIs with the ChAT binding pocket that may further help in designing novel ChAT ligands. Various in-silico tools make it possible for us to elucidate the binding interaction, conformational stability, and dynamics of the protein-ligand complexes within a 200 ns time frame. Further, the binding free energies for the PPI-ChAT complexes were explored. The results suggest that the PPIs exhibit equal or higher binding affinity toward the ChAT catalytic tunnel and are stable throughout the simulated time and that the pyridine ring of the PPIs interacts primarily with the catalytic residue His₃₂₄. A free energy landscape analysis showed that the folding process was linear, and the residue interaction network analysis can provide insight into the roles of various amino acid residues in stabilization of the PPIs in the ChAT binding pocket. As a major factor for the onset of Alzheimer's disease is linked to cholinergic dysfunction, our previous and the present findings give clear insight into the PPI interaction with ChAT. The scaffold can be further simplified to develop novel ChAT ligands, which can also be used as ChAT tracer probes for the diagnosis of cholinergic dysfunction and to initiate timely therapeutic interventions to prevent or delay the progression of AD.

Discovery of potential FGFR3 inhibitors via QSAR, pharmacophore modeling, virtual screening and molecular docking studies against bladder cancer

BACKGROUND

Fibroblast growth factor receptor 3 is known as a favorable aim in vast range of cancers, particularly in bladder cancer treatment. Pharmacophore and QSAR modeling approaches are broadly utilized for developing novel compounds for the determination of inhibitory activity versus the biological target. In this study, these methods employed to identify FGFR3 potential inhibitors.

METHODS

To find the potential compounds for bladder cancer targeting, ZINC and NCI databases were screened. Pharmacophore and QSAR modeling of FGFR3 inhibitors were utilized for dataset screening. Then, with regard to several factors such as Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties and Lipinski's Rule of Five, the recognized compounds were filtered. In further step, utilizing the flexible docking technique, the obtained compounds interactions with FGFR3 were analyzed.

RESULTS

The best five compounds, namely ZINC09045651, ZINC08433190, ZINC00702764, ZINC00710252 and ZINC00668789 were selected for Molecular Dynamics (MD) studies. Off-targeting of screened compounds was also investigated through CDD search and molecular docking. MD outcomes confirmed docking investigations and revealed that five selected compounds could make steady interactions with the FGFR3 and might have effective inhibitory potencies on FGFR3.

CONCLUSION

These compounds can be considered as candidates for bladder cancer therapy with improved therapeutic properties and less adverse effects.

Molecular basis of ligand selectivity for melatonin receptors

Sleep disorders in adults are related to adverse health effects such as reduced quality of life and increased mortality. About 30-40% of adults are suffering from different sleep disorders. The human melatonin receptors (MT1 and MT2) are family A G protein-coupled receptors that respond to the neurohormone melatonin MEL which regulates circadian rhythm and sleep. Many efforts have been made to develop drugs targeting melatonin receptors to treat insomnia, circadian rhythm disorders, and even cancer. However, designing subtype-selective melatonergic drugs remains challenging due to their high similarities in both sequences and structures. MEL (a function-selective compound with a bulky β-naphthyl group) behaves as an MT2-selective antagonist, whereas it is an agonist of MT1. Here, molecular dynamics simulations were used to investigate the ligand selectivity of MT receptors at the atomic level. We found that the binding conformation of MEL differs in different melatonin receptors. In MT1, the naphthalene ring of MEL forms a structure perpendicular to the membrane surface. In contrast, there is a 130° angle between the naphthalene ring of MEL and the membrane surface in MT2. Because of this conformational difference, the MEL leads to a constant water channel in MT1 which activates the receptor. However, MEL hinders the formation of continuous water channels, resulting in an inactive state of MT2. Furthermore, we found that A117^3.29 in MT2 is a crucial amino acid capable of hindering the conformational flip of the MEL molecule. These results, coupled with previous functional data, reveal that although MT1 and MT2 share highly similar orthosteric ligand-binding pockets, they also display distinctive features that could be used to design selective compounds. Our findings provide new insights into functionally selective melatonergic drug development for sleep disorders.

Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism

The receptor-binding domains (RBDs) of the SARS-CoV-2 spike trimer exhibit "up" and "down" conformations often targeted by neutralizing antibodies. Only in the "up" configuration can RBDs bind to the ACE2 receptor of the host cell and initiate the process of viral multiplication. Here, we identify a lead compound (3-oxo-valproate-coenzyme A conjugate or Val-CoA) that stabilizes the spike trimer with RBDs in the down conformation. Val-CoA interacts with three R408 residues, one from each RBD, which significantly reduces the inter-subunit R408-R408 distance by ∼ 13 Å and closes the central pore formed by the three RBDs. Experimental evidence is presented that R408 is part of a triggering mechanism that controls the prefusion to postfusion state transition of the spike trimer. By stabilizing the RBDs in the down configuration, this and other related compounds can likely attenuate viral transmission. The reported findings for binding of Val-CoA to the spike trimer suggest a new approach for the design of allosteric antiviral drugs that do not have to compete for specific virus-receptor interactions but instead hinder the conformational motion of viral membrane proteins essential for interaction with the host cell. Here, we introduce an approach to target the spike protein by identifying lead compounds that stabilize the RBDs in the trimeric "down" configuration. When these compounds trimerize monomeric RBD immunogens as co-immunogens, they could also induce new types of non-ACE2 blocking antibodies that prevent local cell-to-cell transmission of the virus, providing a novel approach for inhibition of SARS-CoV-2.

Structural analysis and molecular dynamics simulation studies of HIV-1 antisense protein predict its potential role in HIV replication and pathogenesis

The functional significance of the HIV-1 Antisense Protein (ASP) has been a paradox since its discovery. The expression of this protein in HIV-1-infected cells and its involvement in autophagy, transcriptional regulation, and viral latency have sporadically been reported in various studies. Yet, the definite role of this protein in HIV-1 infection remains unclear. Deciphering the 3D structure of HIV-1 ASP would throw light on its potential role in HIV lifecycle and host-virus interaction. Hence, using extensive molecular modeling and dynamics simulation for 200 ns, we predicted the plausible 3D-structures of ASP from two reference strains of HIV-1 namely, Indie-C1 (subtype-C) and NL4-3 (subtype-B) so as to derive its functional implication through structural domain analysis. In spite of sequence and structural differences in subtype B and C ASP, both structures appear to share common domains like the Von Willebrand Factor Domain-A (VWFA), Integrin subunit alpha-X (ITGSX), and ETV6-Transcriptional repressor, thereby reiterating the potential role of HIV-1 ASP in transcriptional repression and autophagy, as reported in earlier studies. Gromos-based cluster analysis of the centroid structures also reassured the accuracy of the prediction. This is the first study to elucidate a highly plausible structure for HIV-1 ASP which could serve as a feeder for further experimental validation studies.

An in-silico investigation of fluoride ions impact on pancreatic lipase

Fluorine is a halogen beneficial to teeth and bones at a lower concentration. But in excess, it is a toxin and causes adverse effects. Fluoride is toxic to enzymes generally when it inhibits the enzyme activity involved in metabolic pathways. Here we study invitro and invivo findings on the interaction of fluoride on the enzymes Aconitase, Adenylyl cyclase, Arginase, Cytochrome-c-oxidase, Glucose-6-phosphatase, Protein phosphatase, Succinate dehydrogenase from liver and lipase from pancreas by using molecular docking and simulations to gain insights into the mechanism by which fluoride modifies the activity of pancreatic lipase. our molecular modeling and docking studies identified that lipase is the most strongly inhibited enzyme compared to other enzymes mentioned above with -0.42 Kcal/mol binding energy and 495.78 milli molar of predicted IC50 value with interaction with Phe227 residue. To further validate this, we have taken the lipase enzyme in presence of fluoride ions for molecular dynamic simulations of 100 ns. To analyze the impact of fluoride ions on the lipase dynamics, two different simulations of 100 ns each were performed. In one simulation, we have simulated lipase in its apo form in the aqueous environment without any fluoride ions and in another simulation lipase in its apo form was kept in the presence of randomly placed fluoride ions countered with sodium ions to maintain the pH as neutral. The simulation analysis revealed that major fluctuations in lipase was observed between 230 and 300 residues in presence of fluoride ions. Interestingly, this is the exact location of the "lid" like acting loop of residues responsible for the inward/outward movement of the substrate to lipase catalytically active site containing catalytic triad of residues Leu153, His263, and Pro177. His263 residue random flip is believed to be the critical incident that causes the substrate's inward/outward movement at the catalytically active site coordinated by "lid" opening, providing enough space for the substrate.

Suramin, penciclovir, and anidulafungin exhibit potential in the treatment of COVID-19 via binding to nsp12 of SARS-CoV-2

COVID-19, for which no confirmed therapeutic agents are available, has claimed over 48,14,000 lives globally. A feasible and quicker method to resolve this problem may be 'drug repositioning'. We investigated selected FDA and WHO-EML approved drugs based on their previously promising potential as antivirals, antibacterials or antifungals. These drugs were docked onto the nsp12 protein, which reigns the RNA-dependent RNA polymerase activity of SARS-CoV-2, a key therapeutic target for coronaviruses. Docked complexes were reevaluated using MM-GBSA analysis and the top three inhibitor-protein complexes were subjected to 100 ns long molecular dynamics simulation followed by another round of MM-GBSA analysis. The RMSF plots, binding energies and the mode of physicochemical interaction of the active site of the protein with the drugs were evaluated. Suramin, Penciclovir, and Anidulafungin were found to bind to nsp12 with similar binding energies as that of Remdesivir, which has been used as a therapy for COVID-19. In addition, recent experimental evidences indicate that these drugs exhibit antiviral efficacy against SARS-CoV-2. Such evidence, along with the significant and varied physical interactions of these drugs with the key viral enzyme outlined in this investigation, indicates that they might have a prospective therapeutic potential in the treatment of COVID-19 as monotherapy or combination therapy with Remdesivir.

Virtual Screening Identifies Novel and Potent Inhibitors of Mycobacterium tuberculosis PknB with Antibacterial Activity

Mycobacterium tuberculosis protein kinase B (PknB) is essential to mycobacterial growth and has received considerable attention as an attractive target for novel anti-tuberculosis drug development. Here, virtual screening, validated by biological assays, was applied to select candidate inhibitors of M. tuberculosis PknB from the Specs compound library (www.specs.net). Fifteen compounds were identified as hits and selected for in vitro biological assays, of which three indoles (2, AE-848/42799159; 4, AH-262/34335013; 10, AP-124/40904362) inhibited growth of M. tuberculosis H37Rv with minimal inhibitory concentrations of 6.2, 12.5, and 6.2 μg/mL, respectively. Two compounds, 2 and 10, inhibited M. tuberculosis PknB activity in vitro, with IC₅₀ values of 14.4 and 12.1 μM, respectively, suggesting this to be the likely basis of their anti-tubercular activity. In contrast, compound 4 displayed anti-tuberculosis activity against M. tuberculosis H37Rv but showed no inhibition of PknB activity (IC₅₀ > 128 μM). We hypothesize that hydrolysis of its ethyl ester to a carboxylate moiety generates an active species that inhibits other M. tuberculosis enzymes. Molecular dynamics simulations of modeled complexes of compounds 2, 4, and 10 bound to M. tuberculosis PknB indicated that compound 4 has a lower affinity for M. tuberculosis PknB than compounds 2 and 10, as evidenced by higher calculated binding free energies, consistent with experiment. Compounds 2 and 10 therefore represent candidate inhibitors of M. tuberculosis PknB that provide attractive starting templates for optimization as anti-tubercular agents.

In Silico and In Vivo Evaluation of Synthesized SCP-2 Inhibiting Compounds on Life Table Parameters of Helicoverpa armigera (Hübner)

For environment-friendly, safe and nonpersistent chemical control of a significant polyphagous insect pest, Helicoverpa armigera, discovery of growth-regulating xenobiotics can offer a sustainable alternative to conventional insecticides. For this purpose, chemically synthesized compounds to inhibit sterol carrier protein (SCP-2) function using in silico and in vivo assays were evaluated to estimate their impact on the survivals and lifetable indices of H. armigera. From nine chemically synthesized compounds, OA-02, OA-06 and OA-09 were selected for this study based on binding poses mimicking cholesterol, a natural substrate of sterol carrier protein and molecular dynamics simulations. In vivo bioassays revealed that all compounds significantly reduced the larval and pupal weight accumulations and stadia lengths. Subsequently, the pupal periods were prolonged upon treatment with higher doses of the selected compounds. Moreover, OA-09 significantly reduced pupation and adult emergence rates as well as the fertility of female moths; however, fecundity remained unaffected, in general. The life table parameters of H. armigera were significantly reduced when treated with OA-09 at higher doses. The population treated with 450 μM of OA-09 had the least net reproductive rates (Ro) and gross reproductive rate (GRR) compared to the control population. The same compound resulted in a declining survival during the early stages of development coupled with reduced larval and pupal durations, and fertility. These results have a significant implication for developing an effective and sustainable chemical treatment against H. armigera infestation.

Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations

RNA dependent RNA polymerase (RdRp), is an essential in the RNA replication within the life cycle of the severely acute respiratory coronavirus-2 (SARS-CoV-2), causing the deadly respiratory induced sickness COVID-19. Remdesivir is a prodrug that has seen some success in inhibiting this enzyme, however there is still the pressing need for effective alternatives. In this study, we present the discovery of four non-nucleoside small molecules that bind favorably to SARS-CoV-2 RdRp over the active form of the popular drug remdesivir (RTP) and adenosine triphosphate (ATP) by utilizing high-throughput virtual screening (HTVS) against the vast ZINC compound database coupled with extensive molecular dynamics (MD) simulations. After post-trajectory analysis, we found that the simulations of complexes containing both ATP and RTP remained stable for the duration of their trajectories. Additionally, it was revealed that the phosphate tail of RTP was stabilized by both the positive amino acid pocket and magnesium ions near the entry channel of RdRp which includes residues K551, R553, R555 and K621. It was also found that residues D623, D760, and N691 further stabilized the ribose portion of RTP with U10 on the template RNA strand forming hydrogen pairs with the adenosine motif. Using these models of RdRp, we employed them to screen the ZINC database of ~ 17 million molecules. Using docking and drug properties scoring, we narrowed down our selection to fourteen candidates. These were subjected to 200 ns simulations each underwent free energy calculations. We identified four hit compounds from the ZINC database that have similar binding poses to RTP while possessing lower overall binding free energies, with ZINC097971592 having a binding free energy two times lower than RTP.

Mechanism of the distinct toxicity level of imidacloprid and thiacloprid against honey bees: An in silico study based on cytochrome P450 9Q3

The honey bee, Apis mellifera, shows variation in sensitivity to imidacloprid and thiacloprid, which does not reside at the target site but rather in the rapidly oxidative metabolism mediated by P450s (such as a single P450, CYP9Q3). An in silico study was conducted to investigate the various metabolism of imidacloprid and thiacloprid. The binding potency of thiacloprid was stronger and a stable π-π interaction with Phe121 and the N-H⋯N hydrogen bond with Asn214 are found in the CYP9Q3-thiacloprid system but absent in imidacloprid, which might affect the potential metabolic activity. Moreover, the values of highest occupied molecular orbit (HOMO) energy and the vertical ionization potential (IP) of two compounds demonstrated that thiacloprid is more likely to oxidation. The findings revealed the probable binding modes of imidacloprid and thiacloprid with CYP9Q3 and might facilitate future design of the low bee toxicity neonicotinoid insecticides.

BAY-069, a Novel (Trifluoromethyl)pyrimidinedione-Based BCAT1/2 Inhibitor and Chemical Probe

The branched-chain amino acid transaminases (BCATs) are enzymes that catalyze the first reaction of catabolism of the essential branched-chain amino acids to branched-chain keto acids to form glutamate. They are known to play a key role in different cancer types. Here, we report a new structural class of BCAT1/2 inhibitors, (trifluoromethyl)pyrimidinediones, identified by a high-throughput screening campaign and subsequent optimization guided by a series of X-ray crystal structures. Our potent dual BCAT1/2 inhibitor BAY-069 displays high cellular activity and very good selectivity. Along with a negative control (BAY-771), BAY-069 was donated as a chemical probe to the Structural Genomics Consortium.

The New Microtubule-Targeting Agent SIX2G Induces Immunogenic Cell Death in Multiple Myeloma

Microtubule-targeting agents (MTAs) are effective drugs for cancer treatment. A novel diaryl [1,2]oxazole class of compounds binding the colchicine site was synthesized as cis-restricted-combretastatin-A-4-analogue and then chemically modified to have improved solubility and a wider therapeutic index as compared to vinca alkaloids and taxanes. On these bases, a new class of tricyclic compounds, containing the [1,2]oxazole ring and an isoindole moiety, has been synthetized, among which SIX2G emerged as improved MTA. Several findings highlighted the ability of some chemotherapeutics to induce immunogenic cell death (ICD), which is defined by the cell surface translocation of Calreticulin (CALR) via dissociation of the PP1/GADD34 complex. In this regard, we computationally predicted the ability of SIX2G to induce CALR exposure by interacting with the PP1 RVxF domain. We then assessed both the potential cytotoxic and immunogenic activity of SIX2G on in vitro models of multiple myeloma (MM), which is an incurable hematological malignancy characterized by an immunosuppressive milieu. We found that the treatment with SIX2G inhibited cell viability by inducing G2/M phase cell cycle arrest and apoptosis. Moreover, we observed the increase of hallmarks of ICD such as CALR exposure, ATP release and phospho-eIF2α protein level. Through co-culture experiments with immune cells, we demonstrated the increase of (i) CD86 maturation marker on dendritic cells, (ii) CD69 activation marker on cytotoxic T cells, and (iii) phagocytosis of tumor cells following treatment with SIX2G, confirming the onset of an immunogenic cascade. In conclusion, our findings provide a framework for further development of SIX2G as a new potential anti-MM agent.

Antimicrobial abietane-type diterpenoids from Torreya grandis

Twelve undescribed abietane-type diterpenoids, along with ten known analogues were isolated from the twigs and leaves of Torreya grandis var. merrillii Hu. Their structures were characterized by spectroscopic data analyses, single-crystal X-ray diffraction, and ECD spectra. Torgranols A-C possess three different architectures shaped via a common 6,7-seco-procedure and subsequent ring formations. In particular, torgranol A represents the first example of a 6,7-seco-abietane diterpenoid featuring a unique oxygen bridge between C-3 and C-6. The biosynthetic pathways for torgranols A-C were proposed. Some compounds displayed antimicrobial activities against Mycobacterium tuberculosis and/or Staphylococcus aureus.

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

Better force fields start with better data: A data set of cation dipeptide interactions

We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids - including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology.

Diterpenoids from Sauropus spatulifolius Leaves with Antimicrobial Activities

As a plant used in both food and medicine, Sauropus spatulifolius is consumed widely as a natural herbal tea, food source, and Chinese medicine. Inspired by its extensive applications, we conducted a systematic phytochemical study of the leaves of S. spatulifolius. Thirteen new diterpenoids, sauspatulifols A-M (1-13), including four ent-cleistanthane-type diterpenoids (1-4), eight 15,16-di-nor-ent-cleistanthane-type diterpenoids (5-12), and one 17-nor-ent-pimarane-type diterpenoid (13) as well as one known diterpenoid, cleistanthol (14), were isolated. All of these diterpenoids feature a 2α,3α-dihydroxy unit within the A ring, and their structures were elucidated by spectroscopic data analysis, electronic circular dichroism calculations, and single-crystal X-ray diffraction analysis. Compound 14 displayed moderate inhibitory activity against Staphylococcus aureus, Staphylococcus epidermidis, Bacillus subtilis, and Shigella flexneri with the same minimum inhibitory concentration value of 12 μg/mL as well as activity against vesicular stomatitis virus and influenza A virus.

Synthesis of 2H-Imidazo[2',1':2,3] [1,3]thiazolo[4,5-e]isoindol-8-yl-phenylureas with promising therapeutic features for the treatment of acute myeloid leukemia (AML) with FLT3/ITD mutations

Despite progressive advances in understanding the molecular biology of acute myeloid leukemia (AML), the conventional therapeutic approach has not changed substantially, and the outcome for most patients is poor. Thus, continuous efforts on the discovery of new compounds with improved features are required. Following a multistep sequence, we have identified a new tetracyclic ring system with strong antiproliferative activity towards several haematological cell lines. The new compounds possess structural properties typical of inactive-state-binding kinase inhibitors and are structurally related to quizartinib which is known as type-II tyrosine kinase inhibitor. In particular, the high activity found in two cell lines MOLM-13 and MV4-11, expressing the constitutively activated mutant FLT3/ITD, indicates inhibition of FLT3 kinase and on the basis of structure-activity relationship (SAR) the presence of an ureido moiety demonstrates to play a key role in driving the antiproliferative activity towards these cell lines. Molecular modelling studies supported the mechanism of recognition of the most active compounds within the FLT3 pocket where quizartinib binds. Moreover, Molecular Dynamics simulation (MDs) revealed the formation of a recurrent H-bond with Asp829, which more stabilizes the complex of 9c and the FLT3 inactive state. In MV4-11 cell line compound 9c reduces the phosphorylation of FLT3 (Y591) and some of its downstream targets leading to cell cycle arrest at G1 phase and induction of apoptosis. In an MV4-11 xenograft mouse model, 9c significantly reduces the tumor growth at the dose of 1-3 mg/kg without apparent toxicity.

Structure and activity of the DHNA Coenzyme-A Thioesterase from Staphylococcus aureus providing insights for innovative drug development

Humanity is facing an increasing health threat caused by a variety of multidrug resistant bacteria. Within this scenario, Staphylococcus aureus, in particular methicillin resistant S. aureus (MRSA), is responsible for a number of hospital-acquired bacterial infections. The emergence of microbial antibiotic resistance urgently requires the identification of new and innovative strategies to treat antibiotic resistant microorganisms. In this context, structure and function analysis of potential drug targets in metabolic pathways vital for bacteria endurance, such as the vitamin K₂ synthesis pathway, becomes interesting. We have solved and refined the crystal structure of the S. aureus DHNA thioesterase (SaDHNA), a key enzyme in the vitamin K₂ pathway. The crystallographic structure in combination with small angle X-ray solution scattering data revealed a functional tetramer of SaDHNA. Complementary activity assays of SaDHNA indicated a preference for hydrolysing long acyl chains. Site-directed mutagenesis of SaDHNA confirmed the functional importance of Asp16 and Glu31 for thioesterase activity and substrate binding at the putative active site, respectively. Docking studies were performed and rational designed peptides were synthesized and tested for SaDHNA inhibition activity. The high-resolution structure of SaDHNA and complementary information about substrate binding will support future drug discovery and design investigations to inhibit the vitamin K₂ synthesis pathway.

Discovery of Tyrosinase Inhibitors: Structure-Based Virtual Screening and Biological Evaluation

Tyrosinase (EC 1.14.18.1) plays an indispensable role in the rate-limiting steps of melanin biosynthesis, and its uncontrolled activity may result in various diseases, such as albinism, melanoma, freckles, etc. The inhibition of tyrosinase activity may provide a useful and efficient strategy to treat hyperpigmentation disorders. However, the widely used tyrosinase inhibitors, like α-arbutin, hydroquinone, and kojic acid, have many shortcomings, such as lower efficacy and much more side effects. Herein, we reported the use of homology modeling and multistep structure-based virtual screening for the discovery of novel tyrosinase inhibitors. In this study, 10 initial potential hits (compounds T1–T10) were evaluated for enzyme inhibition and kinetic study, with kojic acid being used as a control. Among them, the IC50 values of both T1 (11.56 ± 0.98 μmol/L) and T5 (18.36 ± 0.82 μmol/L) were superior to that of kojic acid (23.12 ± 1.26 μmol/L). Moreover, T1 and T5 were also identified as the effective noncompetitive tyrosinase inhibitors by the subsequent kinetic study. Above all, T1 and T5 may represent the promising drug candidates for hyperpigmentation therapy in pharmaceutical fields, as well as the effective whitening agents in cosmetic applications.

Development of 11C-Labeled ASEM Analogues for the Detection of Neuronal Nicotinic Acetylcholine Receptors (α7-nAChR)

The homo-pentameric alpha 7 receptor is one of the major types of neuronal nicotinic acetylcholine receptors (α7-nAChRs) related to cognition, memory formation, and attention processing. The mapping of α7-nAChRs by PET pulls a lot of attention to realize the mechanism and development of CNS diseases such as AD, PD, and schizophrenia. Several PET radioligands have been explored for the detection of the α7-nAChR. 18F-ASEM is the most functional for in vivo quantification of α7-nAChRs in the human brain. The first aim of this study was to initially use results from in silico and machine learning techniques to prescreen and predict the binding energy and other properties of ASEM analogues and to interpret these properties in terms of atomic structures using 18F-ASEM as a lead structure, and second, to label some selected candidates with carbon-11/hydrogen-3 (11C/3H) and to evaluate the binding properties in vitro and in vivo using the labeled candidates. In silico predictions are obtained from perturbation free-energy calculations preceded by molecular docking, molecular dynamics, and metadynamics simulations. Machine learning techniques have been applied for the BBB and P-gp-binding properties. Six analogues of ASEM were labeled with 11C, and three of them were additionally labeled with 3H. Binding properties were further evaluated using autoradiography (ARG) and PET measurements in non-human primates (NHPs). Radiometabolites were measured in NHP plasma. All six compounds were successfully synthesized. Evaluation with ARG showed that 11C-Kln83 was preferably binding to the α7-nAChR. Competition studies showed that 80% of the total binding was displaced. Further ARG studies using 3H-KIn-83 replicated the preliminary results. In the NHP PET study, the distribution pattern of 11C-KIn-83 was similar to other α7 nAChR PET tracers. The brain uptake was relatively low and increased by the administration of tariquidar, indicating a substrate of P-gp. The ASEM blocking study showed that 11C-KIn-83 specifically binds to α7 nAChRs. Preliminary in vitro evaluation of KIn-83 by ARG with both 11C and 3H and in vivo evaluation in NHP showed favorable properties for selectively imaging α7-nAChRs, despite a relatively low brain uptake.

Bioinformatics approaches identified dasatinib and bortezomib inhibit the activity of MCM7 protein as a potential treatment against human cancer

Minichromosome Maintenance Complex Component 7 (MCM7) is a key component of the DNA replication licensing factor and hexamer MCM (MCM2-7) complex that regulates the DNA replication process. The MCM7 protein is associated with tumor cell proliferation that plays an important role in different human cancer progression. As the protein is highly expressed during the cancer development process, therefore, inhibition of the protein can be utilized as a treatment option for different human cancer. However, the study aimed to identify potential small molecular drug candidates against the MCM7 protein that can utilize treatment options for human cancer. Initially, the compounds identified from protein-drugs network analysis have been retrieved from NetworkAnalyst v3.0 server and screened through molecular docking, MM-GBSA, DFT, pharmacokinetics, toxicity, and molecular dynamics (MD) simulation approach. Two compounds namely Dasatinib (CID_3062316) and Bortezomib (CID_387447) have been identified throughout the screening process, which have the highest negative binding affinity (Kcal/mol) and binding free energy (Kcal/mol). The pharmacokinetics and toxicity analysis identified drug-like properties and no toxicity properties of the compounds, where 500 ns MD simulation confirmed structural stability of the two compounds to the targeted proteins. Therefore, we can conclude that the compounds dasatinib and bortezomib can inhibit the activity of the MCM7 and can be developed as a treatment option against human cancer.

Calculation of Crystal-Solution Dissociation Constants

The calculation of dissociation constants is an important problem in molecular biophysics. For such a calculation, it is important to correctly calculate both terms of the binding free energy; that is, the enthalpy and entropy of binding. Both these terms can be computed using molecular dynamics simulations, but this approach is very computationally expensive, and entropy calculations are especially slow. We develop an alternative very fast method of calculating the binding entropy and dissociation constants. The main part of our approach is based on the evaluation of movement ranges of molecules in the bound state. Then, the range of molecular movements in the bound state (here, in molecular crystals) is used for the calculation of the binding entropies and, then (using, in addition, the experimentally measured sublimation enthalpies), the crystal-to-vapor dissociation constants. Previously, we considered the process of the reversible sublimation of small organic molecules from crystals to vapor. In this work, we extend our approach by considering the dissolution of molecules, in addition to their sublimation. Similar to the sublimation case, our method shows a good correlation with experimentally measured dissociation constants at the dissolution of crystals.

Comparative Immunogenicity of the Recombinant Receptor-Binding Domain of Protein S SARS-CoV-2 Obtained in Prokaryotic and Mammalian Expression Systems

The receptor-binding domain (RBD) of the protein S SARS-CoV-2 is considered to be one of the appealing targets for developing a vaccine against COVID-19. The choice of an expression system is essential when developing subunit vaccines, as it ensures the effective synthesis of the correctly folded target protein, and maintains its antigenic and immunogenic properties. Here, we describe the production of a recombinant RBD protein using prokaryotic (pRBD) and mammalian (mRBD) expression systems, and compare the immunogenicity of prokaryotic and mammalian-expressed RBD using a BALB/c mice model. An analysis of the sera from mice immunized with both variants of the protein revealed that the mRBD expressed in CHO cells provides a significantly stronger humoral immune response compared with the RBD expressed in E.coli cells. A specific antibody titer of sera from mice immunized with mRBD was ten-fold higher than the sera from the mice that received pRBD in ELISA, and about 100-fold higher in a neutralization test. The data obtained suggests that mRBD is capable of inducing neutralizing antibodies against SARS-CoV-2.

Molecular Simulation of Stapled Peptides

Constrained peptides represent a relatively new class of biologic therapeutics, which have the potential to overcome several limitations of small-molecule drugs, and of designed antibodies. Because of their modest size, the rational design of such peptides is becoming increasingly amenable to computer simulation; multi-microsecond molecular dynamic (MD) simulations are now routinely possible on consumer-grade graphical processors (GPUs). Here, we describe the procedures for performing and analyzing MD simulations of hydrocarbon-stapled peptides using the CHARMM energy function, in isolation and in complex with a binding partner, to investigate their conformational properties and to compute changes in their binding affinity upon mutation.

Mechanistic Studies on the Base-Promoted Ring Opening of Glycal-Derived gem-Dibromocyclopropanes

In the presence of a nucleophilic base, ring-fused gem-dibromocyclopropanes derived from d-glycals undergo ring opening to give 2-deoxy-2-(E-bromomethylene)glycosides. Such cleavage of an exocyclic cyclopropane bond contrasts with the more usual silver-promoted ring-expansion reactions in which endocyclic bond cleavage occurs. Experimental and theoretical studies are reported which provide insights into the reaction mechanism and the origin of its kinetic selectivity for E-configured bromoalkene products. Density functional theory computations (M06-2X) predict that the reaction commences with alkoxide-induced HBr elimination from the dibromocyclopropane to form a bromocyclopropene. Ring opening then gives a configurationally stable zwitterionic (oxocarbenium cation/vinyl carbanion) intermediate, which undergoes nucleophilic addition and protonation to give the bromoalkene. There are two competing sources of the proton in the final step: One is the alcohol (co)solvent, and the other is the molecule of alcohol produced during the initial deprotonation step. The roles of the formed alcohol molecule and the bulk (co)solvent are demonstrated by isotope-labeling studies performed with deuterated solvents. The acid-promoted isomerization of the E-bromoalkene product into the corresponding Z-bromoalkene is also described. The mechanistic knowledge gained in this investigation sheds light on the unusual chemistry of this system and facilitates its future application in new settings.

Monoterpene-Containing Substituted Coumarins as Inhibitors of Respiratory Syncytial Virus (RSV) Replication

Respiratory syncytial virus (RSV) is a critical cause of infant mortality. However, there are no vaccines and adequate drugs for its treatment. We showed, for the first time, that O-linked coumarin-monoterpene conjugates are effective RSV inhibitors. The most potent compounds are active against both RSV serotypes, A and B. According to the results of the time-of-addition experiment, the conjugates act at the early stages of virus cycle. Based on molecular modelling data, RSV F protein may be considered as a possible target.

Graphical Gaussian process regression model for aqueous solvation free energy prediction of organic molecules in redox flow batteries

The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, pK_a and redox potentials in an organic redox flow battery. In this work, we present a machine learning (ML) model that can learn and predict the aqueous solvation free energy of an organic molecule using the Gaussian process regression method based on a new molecular graph kernel. To investigate the performance of the ML model for electrostatic interaction, the nonpolar interaction contribution of the solvent and the conformational entropy of the solute in the solvation free energy, three data sets with implicit or explicit water solvent models, and contribution of the conformational entropy of the solute are tested. We demonstrate that our ML model can predict the solvation free energy of molecules at chemical accuracy with a mean absolute error of less than 1 kcal mol^-1 for subsets of the QM9 dataset and the Freesolv database. To solve the general data scarcity problem for a graph-based ML model, we propose a dimension reduction algorithm based on the distance between molecular graphs, which can be used to examine the diversity of the molecular data set. It provides a promising way to build a minimum training set to improve prediction for certain test sets where the space of molecular structures is predetermined.

Topology Automated Force-Field Interactions (TAFFI): A Framework for Developing Transferable Force Fields

Force-field development has undergone a revolution in the past decade with the proliferation of quantum chemistry based parametrizations and the introduction of machine learning approximations of the atomistic potential energy surface. Nevertheless, transferable force fields with broad coverage of organic chemical space remain necessary for applications in materials and chemical discovery where throughput, consistency, and computational cost are paramount. Here, we introduce a force-field development framework called Topology Automated Force-Field Interactions (TAFFI) for developing transferable force fields of varying complexity against an extensible database of quantum chemistry calculations. TAFFI formalizes the concept of atom typing and makes it the basis for generating systematic training data that maintains a one-to-one correspondence with force-field terms. This feature makes TAFFI arbitrarily extensible to new chemistries while maintaining internal consistency and transferability. As a demonstration of TAFFI, we have developed a fixed-charge force-field, TAFFI-gen, from scratch that includes coverage for common organic functional groups that is comparable to established transferable force fields. The performance of TAFFI-gen was benchmarked against OPLS and GAFF for reproducing several experimental properties of 87 organic liquids. The consistent performance of these force fields, despite their distinct origins, validates the TAFFI framework while also providing evidence of the representability limitations of fixed-charge force fields.

Investigating single amino acid substitutions in PIM1 kinase: A structural genomics approach

PIM1, is a serine/threonine proto-oncogene kinase, involved in many biological functions, including cell survival, proliferation, and differentiation, thus play a key role in oncogenesis. It plays a crucial role in the onset and progression of various hematopoietic and non-hematopoietic malignancies, including acute myeloid leukemia and prostate cancer. Mutations in PIM1, especially in its kinase domain, can induce abnormal structural changes and thus alter functionalities that can lead to disease progression and other complexities. Herein, we have performed an extensive analysis of the PIM1 mutations at sequence and structure level while utilizing state-of-the-art computational approaches. Based on the impact on PIM1, numerous pathogenic and destabilizing mutations were identified and subsequently analyzed in detail. Finally, two amino acid substitutions (W109C and F147C) in the kinase domain of PIM1 were selected to explore their impact on the PIM1 structure in a time evolution manner using all-atom molecular dynamics (MD) simulations for 200 ns. MD results indicate significant conformational altercations in the structure of PIM1, especially upon F147C mutation. This study provides a significant insight into the PIM1 dysfunction upon single amino acid substitutions, which can be utilized to get insights into the molecular basis of PIM1-associated disease progression.

A Novel Phenylpyrrolidine Derivative: Synthesis and Effect on Cognitive Functions in Rats with Experimental Ishemic Stroke

We performed an in silico, in vitro, and in vivo assessment of a potassium 2-[2-(2-oxo-4-phenylpyrrolidin-1-yl) acetamido]ethanesulfonate (compound 1) as a potential prodrug for cognitive function improvement in ischemic brain injury. Using in silico methods, we predicted the pharmacological efficacy and possible safety in rat models. In addition, in silico data showed neuroprotective features of compound 1, which were further supported by in vitro experiments in a glutamate excitotoxicity-induced model in newborn rat cortical neuron cultures. Next, we checked whether compound 1 is capable of crossing the blood-brain barrier in intact and ischemic animals. Compound 1 improved animal behavior both in intact and ischemic rats and, even though the concentration in intact brains was low, we still observed a significant anxiety reduction and activity escalation. We used molecular docking and molecular dynamics to support our hypothesis that compound 1 could affect the AMPA receptor function. In a rat model of acute focal cerebral ischemia, we studied the effects of compound 1 on the behavior and neurological deficit. An in vivo experiment demonstrated that compound 1 significantly reduced the neurological deficit and improved neurological symptom regression, exploratory behavior, and anxiety. Thus, here, for the first time, we show that compound 1 can be considered as an agent for restoring cognitive functions.

Novel propargylamine-based inhibitors of cholinesterases and monoamine oxidases: Synthesis, biological evaluation and docking study

A combination of several pharmacophores in one molecule has been successfully used for multi-target-directed ligands (MTDL) design. New propargylamine substituted derivatives combined with salicylic and cinnamic scaffolds were designed and synthesized as potential cholinesterases and monoamine oxidases (MAOs) inhibitors. They were evaluated invitro for inhibition of acetyl- (AChE) and butyrylcholinesterase (BuChE) using Ellman's method. All the compounds act as dual inhibitors. Most of the derivatives are stronger inhibitors of AChE, the best activity showed 5-bromo-N-(prop-2-yn-1-yl)salicylamide 1e (IC₅₀ = 8.05 µM). Carbamates (4-bromo-2-[(prop-2-yn-1-yl)carbamoyl]phenyl ethyl(methyl)carbamate 2d and 2,4-dibromo-6-[(prop-2-yn-1-yl)carbamoyl]phenyl ethyl(methyl)carbamate 2e were selective and the most active for BuChE (25.10 and 26.09 µM). 4-Bromo-2-[(prop-2-yn-1-ylimino)methyl]phenol 4a was the most potent inhibitor of MAOs (IC₅₀ of 3.95 and ≈10 µM for MAO-B and MAO-A, respectively) along with a balanced inhibition of both cholinesterases being a real MTDL. The mechanism of action was proposed, and binding modes of the hits were studied by molecular docking on human enzymes. Some of the derivatives also exhibited antioxidant properties. Insilico prediction of physicochemical parameters affirm that the molecules would be active after oral administration and able to reach brain tissue.

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model

Molecular dynamics (MD) simulations performed with force fields that include explicit electronic polarization are becoming more prevalent in the field. The increasing emergence of these simulations is a result of continual refinement against a range of theoretical and empirical target data, optimization of software algorithms for higher performance, and availability of graphical processing unit hardware to further accelerate the simulations. Polarizable MD simulations are likely to be most impactful in biomolecular systems in which heterogeneous environments or unique microenvironments exist that would lead to inaccuracies in simulations performed with fixed-charge, nonpolarizable force fields. The further adoption of polarizable MD simulations will benefit from tutorial material that specifically addresses preparing and analyzing their unique features. In this chapter, we introduce common protocols for preparing routine biomolecular systems containing proteins, including both a globular protein in aqueous solvent and a transmembrane model peptide in a phospholipid bilayer. Details and example input files are provided for preparation of the simulation system using CHARMM, performing the simulations with OpenMM, and analyzing interesting dipole moment properties in CHARMM.

Ensemble completeness in conformer sampling: the case of small macrocycles

In this study we compare the three algorithms for the generation of conformer ensembles Biovia BEST, Schrödinger Prime macrocycle sampling (PMM) and Conformator (CONF) form the University of Hamburg, with ensembles derived for exhaustive molecular dynamics simulations applied to a dataset of 7 small macrocycles in two charge states and three solvents. Ensemble completeness is a prerequisite to allow for the selection of relevant diverse conformers for many applications in computational chemistry. We apply conformation maps using principal component analysis based on ring torsions. Our major finding critical for all applications of conformer ensembles in any computational study is that maps derived from MD with explicit solvent are significantly distinct between macrocycles, charge states and solvents, whereas the maps for post-optimized conformers using implicit solvent models from all generator algorithms are very similar independent of the solvent. We apply three metrics for the quantification of the relative covered ensemble space, namely cluster overlap, variance statistics, and a novel metric, Mahalanobis distance, showing that post-optimized MD ensembles cover a significantly larger conformational space than the generator ensembles, with the ranking PMM > BEST >> CONF. Furthermore, we find that the distributions of 3D polar surface areas are very similar for all macrocycles independent of charge state and solvent, except for the smaller and more strained compound 7, and that there is also no obvious correlation between 3D PSA and intramolecular hydrogen bond count distributions.

Antifungal Azoles as Tetracycline Resistance Modifiers in Staphylococcus aureus

Staphylococcus aureus has developed resistance to antimicrobials since their first use. The S. aureus major facilitator superfamily (MFS) efflux pump Tet(K) contributes to resistance to tetracyclines. The efflux pump diminishes antibiotic accumulation, and biofilm hampers the diffusion of antibiotics. None of the currently known compounds have been approved as efflux pump inhibitors (EPIs) for clinical use. In the current study, we screened clinically approved drugs for possible Tet(K) efflux pump inhibition. By performing in silico docking followed by in vitro checkerboard assays, we identified five azoles (the fungal ergosterol synthesis inhibitors) showing putative EPI-like potential with a fractional inhibitory concentration index of ≤0.5, indicating synergism. The functionality of the azoles was confirmed using ethidium bromide (EtBr) accumulation and efflux inhibition assays. In time-kill kinetics, the combination treatment with butoconazole engendered a marked increase in the bactericidal capacity of tetracycline. When assessing the off-target effects of the azoles, we observed no disruption of bacterial membrane permeability and polarization. Finally, the combination of azoles with tetracycline led to a significant eradication of preformed mature biofilms. This study demonstrates that azoles can be repurposed as putative Tet(K) EPIs and to reduce biofilm formation at clinically relevant concentrations. IMPORTANCE Staphylococcus aureus uses efflux pumps to transport antibiotics out of the cell and thus increases the dosage at which it endures antibiotics. Also, efflux pumps play a role in biofilm formation by the excretion of extracellular matrix molecules. One way to combat these pathogens may be to reduce the activity of efflux pumps and thereby increase pathogen sensitivity to existing antibiotics. We describe the in silico-based screen of clinically approved drugs that identified antifungal azoles inhibiting Tet(K), a pump that belongs to the major facilitator superfamily, and showed that these compounds bind to and block the activity of the Tet(K) pump. Azoles enhanced the susceptibility of tetracycline against S. aureus and its methicillin-resistant strains. The combination of azoles with tetracycline led to a significant reduction in preformed biofilms. Repurposing approved drugs may help solve the classical toxicity issues related to efflux pump inhibitors.

17β-Estradiol-Induced Conformational Changes of Human Microsomal Triglyceride Transfer Protein: A Computational Molecular Modelling Study

Human microsomal triglyceride transfer protein (hMTP) plays an essential role in the assembly of apoB-containing lipoproteins, and has become an important drug target for the treatment of several disease states, such as abetalipoproteinemia, fat malabsorption and familial hypercholesterolemia. hMTP is a heterodimer composed of a larger hMTPα subunit and a smaller hMTPβ subunit (namely, protein disulfide isomerase, hPDI). hPDI can interact with 17β-estradiol (E₂), an endogenous female sex hormone. It has been reported that E₂ can significantly reduce the blood levels of low-density lipoprotein, cholesterol and triglyceride, and modulate liver lipid metabolism in vivo. However, some of the estrogen’s actions on lipid metabolism are not associated with estrogen receptors (ER), and the exact mechanism underlying estrogen’s ER-independent lipid-modulating action is still not clear at present. In this study, the potential influence of E₂ on the stability of the hMTP complex is investigated by jointly using multiple molecular dynamics analyses based on available experimental structures. The molecular dynamics analyses indicate that the hMTP complex in the presence of E₂ has reduced interface contacts and surface areas. A steered molecular dynamics analysis shows that the forces required to separate the two subunits (namely, hPDI and hMTPα subunit) of the hMTP complex in the absence of E₂ are significantly higher than the forces required to separate the complex in which its hPDI is already bound with E₂. E₂ makes the interface between hMTPα and hPDI subunits more flexible and less stable. The results of this study suggest that E₂-induced conformational changes of the hMTP complex might be a novel mechanism partly accounting for the ER-independent lipid-modulating effect of E₂.

Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free energies

Experimental solvation free energies are nowadays commonly included as target properties in the validation of condensed-phase force fields, sometimes even in their calibration. In a previous article [Kashefolgheta et al., J. Chem. Theory. Comput., 2020, 16, 7556-7580], we showed how the involved comparison between experimental and simulation results could be made more systematic by considering a full matrix of cross-solvation free energies . For a set of N molecules that are all in the liquid state under ambient conditions, such a matrix encompasses N×N entries for considering each of the N molecules either as solute (A) or as solvent (B). In the quoted study, a cross-solvation matrix of 25 × 25 experimental value was introduced, considering 25 small molecules representative for alkanes, chloroalkanes, ethers, ketones, esters, alcohols, amines, and amides. This experimental data was used to compare the relative accuracies of four popular condensed-phase force fields, namely GROMOS-2016H66, OPLS-AA, AMBER-GAFF, and CHARMM-CGenFF. In the present work, the comparison is extended to five additional force fields, namely GROMOS-54A7, GROMOS-ATB, OPLS-LBCC, AMBER-GAFF2, and OpenFF. Considering these nine force fields, the correlation coefficients between experimental values and simulation results range from 0.76 to 0.88, the root-mean-square errors (RMSEs) from 2.9 to 4.8 kJ mol-1, and average errors (AVEEs) from -1.5 to +1.0 kJ mol-1. In terms of RMSEs, GROMOS-2016H66 and OPLS-AA present the best accuracy (2.9 kJ mol-1), followed by OPLS-LBCC, AMBER-GAFF2, AMBER-GAFF, and OpenFF (3.3 to 3.6 kJ mol-1), and then by GROMOS-54A7, CHARM-CGenFF, and GROMOS-ATB (4.0 to 4.8 kJ mol-1). These differences are statistically significant but not very pronounced, and are distributed rather heterogeneously over the set of compounds within the different force fields.

Evidence for a credit-card-swipe mechanism in the human PC floppase ABCB4

ABCB4 is described as an ATP-binding cassette (ABC) transporter that primarily transports lipids of the phosphatidylcholine (PC) family but is also capable of translocating a subset of typical multidrug-resistance-associated drugs. The high degree of amino acid identity of 76% for ABCB4 and ABCB1, which is a prototype multidrug-resistance-mediating protein, results in ABCB4's second subset of substrates, which overlap with ABCB1's substrates. This often leads to incomplete annotations of ABCB4, in which it was described as exclusively PC-lipid specific. When the hydrophilic amino acids from ABCB4 are changed to the analogous but hydrophobic ones from ABCB1, the stimulation of ATPase activity by 1,2-dioleoyl-sn-glycero-3-phosphocholine, as a prime example of PC lipids, is strongly diminished, whereas the modulation capability of ABCB1 substrates remains unchanged. This indicates two distinct and autonomous substrate binding sites in ABCB4.