Computational insights into the protonation states of catalytic dyad in BACE1–acyl guanidine based inhibitor complex

Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro

Here, we introduce the use of ANI-ML potentials as a rescoring function in the host-guest interaction in molecular docking. Our results show that the "docking power" of ANI potentials can compete with the current scoring functions at the same level of computational cost. Benchmarking studies on CASF-2016 dataset showed that ANI is ranked in the top 5 scoring functions among the other 34 tested. In particular, the ANI predicted interaction energies when used in conjunction with GOLD-PLP scoring function can boost the top ranked solution to be the closest to the x-ray structure. Rapid and accurate calculation of interaction energies between ligand and protein also enables screening of millions of drug candidates/docking poses. Using a unique protocol in which docking by GOLD-PLP, rescoring by ANI-ML potentials and extensive MD simulations along with end state free energy methods are combined, we have screened FDA approved drugs against the SARS-CoV-2 main protease (Mpro). The top six drug molecules suggested by the consensus of these free energy methods have already been in clinical trials or proposed as potential drug molecules in previous theoretical and experimental studies, approving the validity and the power of accuracy in our screening method.

Scaffold Morphing and In Silico Design of Potential BACE-1 (β-Secretase) Inhibitors: A Hope for a Newer Dawn in Anti-Alzheimer Therapeutics

Alzheimer's disease (AD) is the prime cause of 65-80% of dementia cases and is caused by plaque and tangle deposition in the brain neurons leading to brain cell degeneration. β-secretase (BACE-1) is a key enzyme responsible for depositing extracellular plaques made of β-amyloid protein. Therefore, efforts are being applied to develop novel BACE-1 enzyme inhibitors to halt plaque build-up. In our study, we analyzed some Elenbecestat analogues (a BACE-1 inhibitor currently in clinical trials) using a structure-based drug design and scaffold morphing approach to achieve a superior therapeutic profile, followed by in silico studies, including molecular docking and pharmacokinetics methodologies. Among all the designed compounds, SB306 and SB12 showed good interactions with the catalytic dyad motifs (Asp228 and Asp32) of the BACE-1 enzyme with drug-likeliness properties and a high degree of thermodynamic stability confirmed by the molecular dynamic and stability of the simulated system indicating the inhibitory nature of the SB306 and SB12 on BACE 1.

Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant

Here, we report the accuracy improvements of molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations by adoption of ANI-ML potentials in replacement of MM terms, the use of solvent-accessible surface area (SASA) and volume (SAV) values from the Monte Carlo sampling of the probe, and introducing two different interior dielectric constants for electrostatic interactions of protein-ligand (P-L) and polar solvation term in the MMPBSA calculations. Our results show that the Pearson correlation coefficients of MMPBSA-calculated values with respect to experimental binding free energies can be drastically improved from 0.48 to 0.90 by adoption of ANI-ML potentials in replacement of MM energy terms in the equation, referred to as ANI-PBSA. Moreover, we show that the SASA/SAV-combined equation in the scaled particle theory (SPT) can be a better choice to model nonpolar solvation term, reaching nearly the same accuracy by ANI-PBSA calculations. Finally, we introduce two different values of interior dielectric constants, which could be an alternative strategy between the single and variable constant definitions.

BACE-1 Inhibitors Targeting Alzheimer's Disease

The accumulation of amyloid-β (Aβ) is the main event related to Alzheimer's disease (AD) progression. Over the years, several disease-modulating approaches have been reported, but without clinical success. The amyloid cascade hypothesis evolved and proposed essential targets such as tau protein aggregation and modulation of β-secretase (β-site amyloid precursor protein cleaving enzyme 1 - BACE-1) and γ-secretase proteases. BACE-1 cuts the amyloid precursor protein (APP) to release the C99 fragment, giving rise to several Aβ peptide species during the subsequent γ-secretase cleavage. In this way, BACE-1 has emerged as a clinically validated and attractive target in medicinal chemistry, as it plays a crucial role in the rate of Aβ generation. In this review, we report the main results of candidates in clinical trials such as E2609, MK8931, and AZD-3293, in addition to highlighting the pharmacokinetic and pharmacodynamic-related effects of the inhibitors already reported. The current status of developing new peptidomimetic, non-peptidomimetic, naturally occurring, and other class inhibitors are demonstrated, considering their main limitations and lessons learned. The goal is to provide a broad and complete approach to the subject, exploring new chemical classes and perspectives.

pH Regulates Ligand Binding to an Enzyme Active Site by Modulating Intermediate Populations

Understanding the mechanism of ligands binding to their protein targets and the influence of various factors governing the binding thermodynamics is essential for rational drug design. The solution pH is one of the critical factors that can influence ligand binding to a protein cavity, especially in enzymes whose function is sensitive to the pH. Using computer simulations, we studied the pH effect on the binding of a guanidinium ion (Gdm⁺) to the active site of hen egg-white lysozyme (HEWL). HEWL serves as a model system for enzymes with two acidic residues in the active site and ligands with Gdm⁺ moieties, which can bind to the active sites of such enzymes and are present in several approved drugs treating various disorders. The computed free energy surface (FES) shows that Gdm⁺ binds to the HEWL active site using two dominant binding pathways populating multiple intermediates. We show that the residues close to the active site that can anchor the ligand could play a critical role in ligand binding. Using a Markov state model, we quantified the lifetimes and kinetic pathways connecting the different states in the FES. The protonation and deprotonation of the acidic residues in the active site in response to the pH change strongly influence the Gdm⁺ binding. There is a sharp jump in the ligand-binding rate constant when the pH approaches the largest pK_a of the acidic residue present in the active site. The simulations reveal that, at most, three Gdm⁺ can bind at the active site, with the Gdm⁺ bound in the cavity of the active site acting as a scaffold for the other two Gdm⁺ ions binding. These results can aid in providing greater insights into designing novel molecules containing Gdm⁺ moieties that can have high binding affinities to inhibit the function of enzymes with acidic residues in their active site.

Accurate Binding Free Energy Method from End-State MD Simulations

Herein, we introduce a new strategy to estimate binding free energies using end-state molecular dynamics simulation trajectories. The method is adopted from linear interaction energy (LIE) and ANI-2x neural network potentials (machine learning) for the atomic simulation environment (ASE). It predicts the single-point interaction energies between ligand–protein and ligand–solvent pairs at the accuracy of the wb97x/6-31G* level for the conformational space that is sampled by molecular dynamics (MD) simulations. Our results on 54 protein–ligand complexes show that the method can be accurate and have a correlation of R = 0.87–0.88 to the experimental binding free energies, outperforming current end-state methods with reduced computational cost. The method also allows us to compare BFEs of ligands with different scaffolds. The code is available free of charge (documentation and test files) at https://github.com/otayfuroglu/deepQM.

Dimethoxyindoles based thiosemicarbazones as multi-target agents; synthesis, crystal interactions, biological activity and molecular modeling

Alzheimer's disease (AD) is known as one of the most devastating neurodegenerative disease diagnosed for the old-aged people and cholinesterase inhibitors (ChEI) can be used as an effective palliative treatment for AD. A range of novel monomeric and dimeric indole based thiosemicarbazone derivatives 17-28 was synthesized in order to target cholinesterases (ChE). Biological importance of the targeted compounds 17-28 was investigated by employing the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes along with three different antioxidant property determination assays, namely DPPH free radical scavenging, ABTS cationic radical decolarization, and CUPRAC cupric reducing antioxidant capacity. The compounds 18 and 19 displayed the best inhibitor activity against BChE with IC₅₀ values of 7.42 and 1.95 μM, respectively. The antioxidant potentials were found to be moderate for DPPH and ABTS assays and the compounds 28 and 18 were the most potent candidates for both antioxidant assays. Cupric reducing capacity was the most promising assay and the compounds 25, 26 and 28 provided better inhibition values than all the standards. Further binding mode and affinity studies performed by molecular docking and molecular dynamics simulations. Accordingly, the compound 19 is the most plausible candidate that can compete with galantamine (GNT), a common pharmaceutics targeting both cholinesterase enzymes.

Impact of different protonation states on virtual screening performance against cruzain

The cysteine protease cruzain is a Chagas disease target, exploited in computational studies. However, there is no consensus on the protonation states of the active site residues Cys25, His162, and Glu208 at the enzyme's active pH range. We evaluated the impact of different protonation states of these residues on docking calculations. Through a retrospective study with cruzain inhibitors and decoys, we compared the performance of virtual screening using four grids, varying protonation states of Cys25, His162, and Glu208. Based on enrichment factors and ROC plots, docking with the four grids affected compound ranking and the overall charge of top-ranking compounds. Different grids can be complementary and synergistic, increasing the odds of finding different ligands with diverse chemical properties.

Molecular dynamics simulations reveal the plausible agonism/antagonism mechanism by steroids on androgen receptor mutations

Androgen receptors (AR) are the primary drug target in prostate cancer (PCa). There are several drugs developed against its activity for prostate cancer treatment, but cancer cells revive AR signaling against those drugs by using alternative steroids such as glucocorticoids. In addition, antagonists become agonists due to emergence of mutations in AR gene. The mechanism by which antagonists are converted into agonists and how AR signaling is recovered by other steroids has yet to be fully elucidated. In this study, we interrogated the role of bicalutamide conformation in its antagonist function and how glucocorticoids such as prednisolone and dexamethasone revive AR signaling at the molecular level by means of molecular dynamics. We found that the ''closed'' conformation of bicalutamide is essential for its antagonist function and W741 residue is forcing it into this conformation. Moreover, we show that prednisolone and dexamethasone behave like natural agonist DHT which confirm the experimental results that show their role in the reviving AR signaling in the case of AR^L701H mutation.

Screening Platform Based on Inductively Coupled Plasma Mass Spectrometry for β-Site Amyloid Protein Cleaving Enzyme 1 (BACE1) Inhibitors

β-Site amyloid protein cleaving enzyme 1 (BACE1) is a promising therapeutic target for developing inhibitors to alleviate Alzheimer's disease (AD). Herein, we established an inductively coupled plasma mass spectrometry (ICPMS)-based inhibitor screening platform. A biotin-labeled lanthanide-coded peptide probe (LCPP; biotin-PEG₂-EVNLDAEC-DOTA-Ln) was designed to determine the activity of BACE1 and evaluate the degree of inhibition of inhibitors. The platform was first validated with two commercially available inhibitors (BSI I and BSI IV) in terms of IC₅₀ values and then applied to two newly designed inhibitors (inhibitors II and III) based on the crystal structure of BACE1 interacting with inhibitor I, and each of them contained an acylguanidine core structure. We found that their inhibition effects were improved as evaluated by the sensitive and accurate LCPP-ICPMS platform, demonstrating its ability for new drug screening.

Computational modelling of potent β-secretase (BACE1) inhibitors towards Alzheimer's disease treatment

Researchers have identified the β-amyloid precursor protein cleaving enzyme 1 (BACE1) in the multifactorial pathway of Alzheimer's disease (AD) as a drug target. The design and development of molecules to inhibit BACE1 as a potential cure for AD thus remained significant. Herein, we simulated two potent BACE1 inhibitors (AM-6494 and CNP-520) to understand their binding affinity at the atomistic level. AM-6494 is a newly reported potent BACE1 inhibitor with an IC₅₀ value of 0.4 nM in vivo and now picked for preclinical considerations. Umibecestat (CNP-520), which was discontinued at human trials lately, was considered to enable a reasonable evaluation of our results. Using density functional theory (DFT) and Our Own N-layered Integrated molecular Orbital and Molecular Mechanics (ONIOM), we achieved the aim of this investigation. These computational approaches enabled the prediction of the electronic properties of AM-6494 and CNP-520 plus their binding energies when complexed with BACE1. For AM-6494 and CNP-520 interaction with protonated BACE1, the ONIOM calculation gave binding free energy of -62.849 and -33.463 kcal/mol, respectively. In the unprotonated model, we observed binding free energy of -59.758 kcal/mol in AM-6494. Taken together thermochemistry of the process and molecular interaction plot, AM-6494 is more favourable than CNP-520 towards the inhibition of BACE1. The protonated model gave slightly better binding energy than the unprotonated form. However, both models could sufficiently describe ligand binding to BACE1 at the atomistic level. Understanding the detailed molecular interaction of these inhibitors could serve as a basis for pharmacophore exploration towards improved inhibitor design.

User-Friendly Quantum Mechanics: Applications for Drug Discovery

Quantum mechanics (QM) methods provide a fine description of receptor-ligand interactions and of chemical reactions. Their use in drug design and drug discovery is increasing, especially for complex systems including metal ions in the binding sites, for the design of highly selective inhibitors, for the optimization of bi-specific compounds, to understand enzymatic reactions, and for the study of covalent ligands and prodrugs. They are also used for generating molecular descriptors for predictive QSAR/QSPR models and for the parameterization of force fields. Thanks to the continuous increase of computational power offered by GPUs and to the development of sophisticated algorithms, QM methods are becoming part of the standard tools used in computer-aided drug design (CADD). We present the most used QM methods and software packages, and we discuss recent representative applications in drug design and drug discovery.

BACE1 inhibitors: Current status and future directions in treating Alzheimer's disease

Alzheimer's disease (AD) is an irreversible, progressive neurodegenerative brain disorder with no current cure. One of the important therapeutic approaches of AD is the inhibition of β-site APP cleaving enzyme-1 (BACE1), which is involved in the rate-limiting step of the cleavage process of the amyloid precursor protein (APP) leading to the generation of the neurotoxic amyloid β (Aβ) protein after the γ-secretase completes its function. The produced insoluble Aβ aggregates lead to plaques deposition and neurodegeneration. BACE1 is, therefore, one of the attractive targets for the treatment of AD. This approach led to the development of potent BACE1 inhibitors, many of which were advanced to late stages in clinical trials. Nonetheless, the high failure rate of lead drug candidates targeting BACE1 brought to the forefront the need for finding new targets to uncover the mystery behind AD. In this review, we aim to discuss the most promising classes of BACE1 inhibitors with a description and analysis of their pharmacodynamic and pharmacokinetic parameters, with more focus on the lead drug candidates that reached late stages of clinical trials, such as MK8931, AZD-3293, JNJ-54861911, E2609, and CNP520. In addition, the manuscript discusses the safety concerns and insignificant physiological effects, which were highlighted for the most successful BACE1 inhibitors. Furthermore, the review demonstrates with increasing evidence that despite tremendous efforts and promising results conceived with BACE1 inhibitors, the latest studies suggest that their clinical use for treating Alzheimer's disease should be reconsidered. Finally, the review sheds light on alternative therapeutic options for targeting AD.

pH-dependent conformational dynamics of beta-secretase 1: A molecular dynamics study

Beta-secretase 1 (BACE-1) is an aspartyl protease implicated in the overproduction of β-amyloid fibrils responsible for Alzheimer disease. The process of β-amyloid genesis is known to be pH dependent, with an activity peak between solution pH of 3.5 and 5.5. We have studied the pH-dependent dynamics of BACE-1 to better understand the pH dependent mechanism. We have implemented support for graphics processor unit (GPU) accelerated constant pH molecular dynamics within the AMBER molecular dynamics software package and employed this to determine the relative population of different aspartyl dyad protonation states in the pH range of greatest β-amyloid production, followed by conventional molecular dynamics to explore the differences among the various aspartyl dyad protonation states. We observed a difference in dynamics between double-protonated, mono-protonated, and double-deprotonated states over the known pH range of higher activity. These differences include Tyr 71-aspartyl dyad proximity and active water lifetime. This work indicates that Tyr 71 stabilizes catalytic water in the aspartyl dyad active site, enabling BACE-1 activity.

Bennett acceptance ratio method to calculate the binding free energy of BACE1 inhibitors: Theoretical model and design of new ligands of the enzyme

In recent years, the design, development, and evaluation of several inhibitors of the BACE1 enzyme, as part of Alzheimer's treatment, have gathered the scientific community's interest. Here, a linear regression model was built using binding free energy calculations through the Bennett acceptance ratio method for 20 known inhibitors of the BACE1 enzyme, with a Pearson coefficient of R = 0.88 and R²  = 0.78. The validation of this model was verified employing eight additional random inhibitors, which also gave a linear correlation with R = 0.97 and R²  = 0.93. Furthermore, this linear regression model was also used for proposing the structure of four potential BACE1 inhibitors, and the most active of them gave a theoretical K_d  = 10 nM. However, these molecules have not been synthesized yet. Our team used a total time of more than 800 ns for the Molecular Dynamics to carry out this study, and all the software used were freely available.

Molecular Dynamics Studies of Histo-Blood Group Antigen Blocking Human Immunoglobulin A Antibody and Escape Mechanism in Noroviruses Upon Mutation

Norovirus is the causing agent of acute gastroenteritis disease globally. Efforts in developing therapeutics against virus infection mostly fail due to emergence of drug resistance that is a consequence of presence of high mutation rates in virus genome during virus' life cycle. In this study, we computationally analyzed the affinity of a drug target, wild type VP1 envelope protein and its three variants to a therapeutic antibody FAB5I2. We have found that mutations break important hydrogen bonds and cause high fluctuations in residues that form VP1-FAB5I2 complex interface. In addition to changes in dynamics, we also revealed that the affinity of FAB5I2 to VP1 protein drops significantly upon mutations in terms of relative binding free energy.

G-score: A function to solve the puzzle of modeling the protonation states of β-secretase binding pocket

The population density concept has emerged as a proposal for the analysis of molecular dynamics results, the key characteristic of population density is the evaluation of the simultaneous occurrence of a set of relevant parameters for a system. However, despite its statistical strength, selection of the tolerance level for the comparison of different models may appear as arbitrary. This work introduces the G-score, a function which summarizes and categorizes the results of population density analysis. Additionally, it incorporates parameters based on rmsd and dihedral angles, besides the protein-protein and protein-ligand interatomic distances conventionally used, which complement each other to provide a better description of the behavior of the system. These newly-proposed tools were applied to determine the most probable protonation state of the aspartic dyad of BACE1, Asp93 and Asp289, in the presence of three types of transition state inhibitors namely: reduced amides, tertiary carbinamines and hydroxyethylamines. The results show a full agreement between G-score values and population density charts, with the advantage of allowing a quick and direct comparison among all the considered models. We anticipate that the simplicity of calculating the parameters employed in this study will permit the extensive use of population density and the G-score for other molecular systems.

A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process

BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of better inhibitors.