MM-GBSA Scoring Research Articles

Computational Insights into Enzyme‐Substrate Binding Interplay Exhibit Variable Binding Attributes: A Framework for Implementing Oxidoreductase‐Based Applications

AbstractLaccase (LAC) is a potent multicopper oxidase that relies on O2 for its catalytic activity. LAC has been affirmed as an environmentally friendly biocatalyst that often catalyzes a wide array of phenolic substrates. Bacterial‐derived LACs have been less investigated for non‐phenolic substrates in contrast to fungi‐derived LAC. To comprehend the substrates (3,4‐Dimethoxybenzyl alcohol, and Dimer (Guaiacyl 4‐O‐5 guaiacyl) binding interactions of LAC (Thermus thermophilus HB27) was carried out and contrasted with fungal‐derived Lignin peroxidase (LiP) (Trametes cervina) exploiting computational methods, including physicochemical properties, Sequence Annotated by Structure (SAS), Extra precision docking (Glide), and DESMOND‐directed MD‐ simulation. Protein structures exhibited by LAC, and LiP have diverse dissimilar component architects. The XP docking suggested LiP‐Dimer seems to have a comparatively lowest binding affinity (−8.413 kcal/mol), with an MMGBSA score of −33.249 kcal/mol. Further, docked complexes were validated leveraging 50 ns NPT system‐based MD‐simulation for structural and functional stability. The system achieved equilibrium and stability at the end of the simulation, with only the LiP‐3,4‐Dimethoxybenzyl alcohol complex maintained stability. The results of this study offer a framework for improving the binding ability of substrates by way of the use of in‐silico protein engineering, which might eventually result in more effective catalytic applications.

Leveraging shape screening and molecular dynamics simulations to optimize PARP1-Specific chemo/radio-potentiators for antitumor drug design

PARP1 plays a pivotal role in DNA repair within the base excision pathway, making it a promising therapeutic target for cancers involving BRCA mutations. Current study is focused on the discovery of PARP inhibitors with enhanced selectivity for PARP1. Concurrent inhibition of PARP1 with PARP2 and PARP3 affects cellular functions, potentially causing DNA damage accumulation and disrupting immune responses. In step 1, a virtual library of 593 million compounds has been screened using a shape-based screening approach to narrow down the promising scaffolds. In step 2, hierarchical docking approach embedded in Schrödinger suite was employed to select compounds with good dock score, drug-likeness and MMGBSA score. Analysis supplemented with decomposition energy, molecular dynamics (MD) simulations and hydrogen bond frequency analysis, pinpointed that active site residues; H862, G863, R878, M890, Y896 and F897 are crucial for specific binding of ZINC001258189808 and ZINC000092332196 with PARP1 as compared to PARP2 and PARP3. The binding of ZINC000656130962, ZINC000762230673, ZINC001332491123, and ZINC000579446675 also revealed interaction involving two additional active site residues of PARP1, namely N767 and E988. Weaker or no interaction was observed for these residues with PARP2 and PARP3. This approach advances our understanding of PARP-1 specific inhibitors and their mechanisms of action, facilitating the development of targeted therapeutics.

In-silico, Synthesis, Characterization, and In-vitro Studies on Benzylidene-based 2-chloroquinolin Derivatives as Free Radical Scavengers in Parkinson's Disease.

Parkinson's disease is the loss of dopaminergic neurons in the substantial nigra part of the brain leading to neurodegeneration. Whereas, reactive oxygen species and mitochondrial impairment are considered to be the major pathophysiology of neurodegeneration. The benzylidene-based 2-chloroquinolin derivatives were synthesized and characterized by FT-IR, NMR, and MS spectrometry which were screened using various in-silico approaches. The designed compounds were further assessed using in-vitro cytotoxicity assay by the MTT method, DPPH assay, and Glutathione measurements in the SHSY5Y neuroblastoma cell lines. The compounds JD-7 and JD-4 were found to have a binding affinity of - 7.941 and - 7.633 kcal/mol with an MMGBSA score of - 64.614 and - 62.817 kcal/mol. The compound JD-7 showed the highest % Cell viability of 87.64% at a minimal dose of 125 µg/mL by the MTT method. The neurotoxicity effects were observed at increasing concentrations from 0 to 125, 250, and 500 µg/mL. Further, free radical scavenging activity for the JD-7 was found to be 36.55 at lowest 125 µg/mL concentrations. At 125 µg/mL, GSH % and GSSG % were found to be increasing in rotenone treatment, whereas JD-7 and JD-4 were found in the downregulation of glutathione level in the pre-treated rotenone SHSY5Y neuroblastoma cell lines. The benzylidene-based chloroquinolin derivatives were synthesized, and among the compounds JD-1 to JD-13, the compounds JD-7, and JD-4 were found to have having highest % cell viability, free radical scavenging molecules, and glutathione levels in the SHSY5Y neuroblastoma cell lines and could be used as free radical scavengers in Parkinson's disease.

Molecular docking and dynamics simulations revealed the potential inhibitory activity of honey-iQfood ingredients against GSK-3β and CDK5 protein targets for brain health

Honey-iQfood is an herbal supplement made of a mixture of polyherbal extracts and wild honey. The mixture is traditionally claimed to improve various conditions related to brain cells and functions including dementia and Alzheimer’s disease. Glycogen synthase kinase-3 beta (GSK-3β) and cyclin-dependent kinase 5 (CDK5) have been identified as being involved in the pathological hyperphosphorylation of tau proteins, which leads to the formation of neurofibrillary tangles and causes Alzheimer’s disease. Therefore, this study was conducted to confirm the traditional claims by detection of active compounds, namely curcumin, gallic acid, catechin, rosmarinic acid, and andrographolide in the raw materials of Honey-iQfood through HPLC analysis, molecular docking, and dynamic simulations. Two potential compounds, andrographolide, and rosmarinic acid, produced the best binding affinities following the molecular docking of the active compounds against the GSK-3β and CDK5 targets. Andrographolide binds with GSK-3β at −8.2 kcal/mol, whereas rosmarinic acid binds to CDK5 targets at −8.6 kcal/mol. Molecular dynamics was further carried out to confirm the docking results and clarify their dynamic properties such as RMSD, RMSF, rGyr, SASA, PSA, and binding free energy. CDK5-andrographolide complexes had the best MM-GBSA score (−83.63 kcal/mol) compared to other complexes, indicating the better interaction profile and stability of the complex. These findings warrant further research into andrographolide and rosmarinic acid as efficient inhibitors of tau protein hyperphosphorylation to verify their therapeutic potential in brain-related illnesses. Communicated by Ramaswamy H. Sarma

Integrated gene expression profiling and functional enrichment analyses to discover biomarkers and pathways associated with Guillain-Barré syndrome and autism spectrum disorder to identify new therapeutic targets

Guillain-Barré syndrome (GBS) is one of the most prominent and acute immune-mediated peripheral neuropathy, while autism spectrum disorders (ASD) are a group of heterogeneous neurodevelopmental disorders. The complete mechanism regarding the neuropathophysiology of these disorders is still ambiguous. Even after recent breakthroughs in molecular biology, the link between GBS and ASD remains a mystery. Therefore, we have implemented well-established bioinformatic techniques to identify potential biomarkers and drug candidates for GBS and ASD. 17 common differentially expressed genes (DEGs) were identified for these two disorders, which later guided the rest of the research. Common genes identified the protein-protein interaction (PPI) network and pathways associated with both disorders. Based on the PPI network, the constructed hub gene and module analysis network determined two common DEGs, namely CXCL9 and CXCL10, which are vital in predicting the top drug candidates. Furthermore, coregulatory networks of TF-gene and TF-miRNA were built to detect the regulatory biomolecules. Among drug candidates, imatinib had the highest docking and MM-GBSA score with the well-known chemokine receptor CXCR3 and remained stable during the 100 ns molecular dynamics simulation validated by the principal component analysis and the dynamic cross-correlation map. This study predicted the gene-based disease network for GBS and ASD and suggested prospective drug candidates. However, more in-depth research is required for clinical validation. Communicated by Ramaswamy H. Sarma

Application of In-silico Methodologies in Exploring the Antagonistic Potential of Trigonella frenum-graecum on Cyclooxygenase-2 (Cox-2) in Cancer Treatment

Cancer is a disease in which abnormal cells divide uncontrollably and destroy body tissue. This research is dispensed utilizing in-silico drug design. Cyclooxygenase-2 (Cox-2) has been used as a target protein of the molecular docking study and fenugreek phytoconstituents obtained from PubChem were docked against Cox-2’s pocket (PDB ID: 5IKV). We used Maestro 12.8 and the Schrödinger Suite to conduct computer-based drug testing. To document compounds with the best inhibitory ability to act as cyclooxygenase antagonists in the treatment of cancer. Sixty (60) compounds described with fenugreek were docked to the active site of Cox-2 (5IKV). The results demonstrated that tricin to 2,5-dimethyl pyrazine, which are the best molecules docked at the active site of Cox-2, had -11.007 to -4.58 kcal/mol and an MM-GBSA score ranging from -31.06 to -24.52 respectively, which suggests the free binding energy posed competitive binding energy when compared to the co-crystallized ligand, 2-[[3-(Trifluoromethyl) Phenyl] Amino] Benzoic Acid. Numerous drugs have been made available, but due to their common side effects, researchers are now searching for novel herbal plants that can be utilized as long-term treatments with minimal adverse effects. Thus, utilizing computational studies such as molecular docking, MM-GBSA, pharmacophore modeling, and the lead compounds’ ADMETox characteristics were computed.

Inhibition of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) by microbially derived natural compounds: a computational study

The majority of the world population (around 25%) has latent Mycobacterium tuberculosis (Mtb) infection, among which only 5–10% of individuals develop active tuberculosis (TB), and 90–95% continue to have latent tuberculosis infection. This makes it the biggest global health concern. It has been reported that the resuscitation-promoting factor B (RpfB) is an exciting potential target for tuberculosis drug discovery due to its significant role in the reactivation of latent TB infection to an active infection. Several attempts have been made to investigate potential inhibitors against RpfB utilizing in-silico approaches. The present study also utilized a computational approach to investigate microbially derived natural compounds against the Mtb RpfB protein which is a very cost-effective This evaluation used structure-based virtual screening (SBVS), drug-likeness profiling, molecular docking, molecular dynamics simulation, and free-binding energy calculations. Six potential natural compounds, viz. Cyclizidine I, Boremexin C, Xenocoumacin 2, PM-94128, Cutinostatin B, and (+)1-O-demethylvariecolorquinone A were selected, which displayed a potential binding affinity between −52.39 and −60.87 Kcal/mol MMGBSA score and docking energy between −7.307 Kcal/mol to −6.972 Kcal/mol. All the complexes showed acceptable stability (<2.7 Å RMSD) during 100 ns MD simulation time except the RpfB protein-xenocoumacin 2 complex. This result exhibited that the selected compounds have high efficiency in inhibiting the Mtb RpfB and can be taken into account for additional in vitro and in vivo experimental validation. Communicated by Ramaswamy H. Sarma

Exploration of natural product database for the identification of potent inhibitor against IDH2 mutational variants for glioma therapy

Mutation in isocitrate dehydrogenase 2 (mIDH2) is an oncogenic driver prevalently reported in various cancer types including gliomas. To date, enasidenib is the only FDA-approved drug widely used as a mIDH2 (R140Q) inhibitor. However, dose-limiting toxicity and modest brain penetrating capability restrict its use as a plausible mIDH2 inhibitor. Furthermore, secondary site mutations (Q316E and I319M) were identified in patients with enasidenib treatments resulting in acquired therapeutic resistance. Hence, in the present investigation, we aimed to identify novel and potent drug-like compounds to overcome the existing drawbacks using an integrated in-silico strategy. A sum of 1574 natural compounds from the naturally occurring plant-based anti-cancerous compound activity target (NPACT) database was proclaimed and subjected to molecular docking. The binding affinities of the resultant natural compounds were rescored using MM-GBSA scoring functions. The resultant lead molecules were subjected to anticancer activity prediction using the machine-learning model. Furthermore, the toxicity and drug-likeliness of the lead compounds were investigated using ADMET properties. Eventually, the integrated in silico approach resulted in a lead molecule, namely squalene (NPACT00954) against mIDH2 protein. The screened compound was subjected to mutational analysis accomplishing second-site mutations. Interestingly, squalene exhibited appreciable binding affinity alongside good brain penetrating potential than enasidenib. Indeed, the reproducibility and significance of our results are examined by running 3 replicas of 100-ns simulations per system using the random initial velocities of the atoms generated by Maxwell distribution at a given temperature. Thus, we hypothesize from our results that further optimization of squalene could be beneficial for the treatment and management of glioma in the near future.

Chemoprofiling and insilico prioritization of bioactive compounds from Laetiporus versisporus (Lloyd) Imazeki reveals potential Bcl-2 inhibitor

Laetiporus versisporus (Lloyd) Imazeki is an edible mushroom that grows abundantly in kodaikanal hills (India) during rainy season. Till now, there is a dearth of reports on chemoprofile and anticancer potential of this mushroom. In our recent study, L.versisporus ethanolic extract was reported to confer hepato-protective activity against DEN-induced HCC rats and also found to downregulate Bcl-2 activity. Moreover, the phytocompounds of a related species namely, L. sulphurous is also reported to potentially modulate Bcl-2 in glioblastoma. Hence, by this study, the bioactive compounds from L. versisporus ethanolic extract were profiled using LC-MS analysis and were virtually screened against ligand binding site of Bcl-2 in order to predict potential moieties with anticancer efficacies. Further, the top 3 potential hits were shortlisted based on MMGBSA score, ADME properties and stable complex formation during MD simulation. Amongst these hits, (6S)-1alpha, 25-dihydroxy vitaminD36,19-sulfurdioxide adduct was found to be highly promising in terms of binding affinity and ADME features comparable to the known inhibitor (DRO), thus shall be further probed for therapeutic efficacy using experimental validations for effective and natural mode of combating Bcl-2 mediated cancers. Communicated by Ramaswamy H. Sarma

Polyphenolic Phytochemicals Exhibit Promising SARS-COV-2 Papain Like Protease (PLpro) Inhibition Validated through a Computational Approach

In the present study, in silico PLpro inhibitory potential of 28 polyphenolic compounds was validated, which possesses in vivo inhibitory potential against different SARS-CoV-2 replication enzymes. Among 28 polyphenolic compounds amentoflavone, tiliroside, papyriflavanol A and indinavir exhibited good binding affinity of toward PLpro has been considered for further virtual screening processes. Comprehensive analysis indicates that amentoflavone, tiliroside, and papyriflavanol A phenolic compounds demonstrate very high stability and higher inhibiting potential to bind with the Thr158 and Leu162 dyad of PLpro among 28 phenolic compounds. Further ADME and DFT analysis of amentoflavone, and papyrifalvanol A reveal that possess excellent pharmacokinetic and molecular electrostatic potentials. MD simulation and MM-GBSA analysis of amentoflavone, tiliroside, and one anti-viral drug indinavir toward PLpro (PDB ID 6W9C) result revealed that phenolic compounds amentoflavone, tiliroside possess excellent simulation trajectories toward the binding pocket of PLpro essential to inhibit SARS-CoV-2 multiplication. Further MM-GBSA analysis affirm that PLpro-amentoflavone complex exhibit high MMGBSA score of −106.56Kcal/mol. However, further human clinical trials are essential to justify their clinical pertinence.

In Silico Analysis Using SARS-CoV-2 Main Protease and a Set of Phytocompounds to Accelerate the Development of Therapeutic Components against COVID-19

SARS-CoV-2, the virus that caused the widespread COVID-19 pandemic, is homologous to SARS-CoV. It would be ideal to develop antivirals effective against SARS-CoV-2. In this study, we chose one therapeutic target known as the main protease (Mpro) of SARS-CoV-2. A crystal structure (Id: 6LU7) from the protein data bank (PDB) was used to accomplish the screening and docking studies. A set of phytocompounds was used for the docking investigation. The nature of the interaction and the interacting residues indicated the molecular properties that are essential for significant affinity. Six compounds were selected, based on the docking as well as the MM-GBSA score. Pentagalloylglucose, Shephagenin, Isoacteoside, Isoquercitrin, Kappa-Carrageenan, and Dolabellin are the six compounds with the lowest binding energies (−12 to −8 kcal/mol) and show significant interactions with the target Mpro protein. The MMGBSA scores of these compounds are highly promising, and they should be investigated to determine their potential as Mpro inhibitors, beneficial for COVID-19 treatment. In this study, we highlight the crucial role of in silico technologies in the search for novel therapeutic components. Computational biology, combined with structural biology, makes drug discovery studies more rigorous and reliable, and it creates a scenario where researchers can use existing drug components to discover new roles as modulators or inhibitors for various therapeutic targets. This study demonstrated that computational analyses can yield promising findings in the search for potential drug components. This work demonstrated the significance of increasing in silico and wetlab research to generate improved structure-based medicines.

In Silico Docking Studies of Vascular Endothelial Growth Factor-A (VEGFA): Possible Implications in Chronic Myeloid Leukemia (CML) Therapy

Background: Dysregulated angiogenesis resulting in neovascularization is a critical event in the expansion and progression of Chronic Myeloid Leukemia (CML), hematopoietic cancer. Vascular Endothelial Growth Factor- A (VEGFA), an important angiogenesis mediator, has been a target for treating cancer. Although several anti-VEGFA drugs are available, they are associated with adverse side effects, promoting the need to identify better drugs that may be less toxic. Objective: Our aim was to investigate whether Tyrosine Kinase Inhibitors (TKIs) could be repurposed for use as VEGFA inhibitors via in silico docking software. We also investigated the potential of phytochemicals as VEGFA inhibitors. Methods: We performed molecular docking using Schrödinger Maestro software suite 2014-3 to determine the most potent phytochemical and TKI VEGFA antagonists. Results: Among the TKIs investigated, Bosutinib had the best binding affinity and may be the most potent TKI against VEGFA. The order of binding affinities for the top ten docked ligands was: Ginsenoside Rg3&gt; Bosutinib&gt; Vitamin D&gt; Paclitaxel&gt; Dasatinib&gt; Saponins&gt; Ponatinib&gt; Squalamine&gt; Imatinib&gt; Nilotinib. We found that Ginsenoside Rg3 had the highest binding affinity (MMGBSA score= -99.4 kcal/mol, glide Gscore = -9.16 kcal/mol) to VEGFA. Conclusion: Our study has shown for the first time the binding poses of these TKIs and phytochemicals to VEGFA, using computational methods. We propose that the use of the top scoring ligands, in isolation or a combination of phytochemicals plus TKI, could serve as potent angiogenesis inhibitors via their binding to and inhibiting VEGFA expression to prevent CML progression. We have also profiled the ligand binding residues, which may be explored in designing pharmacophores.

Receptor based virtual screening of potential novel inhibitors of tigar [TP53 (tumour protein 53)-induced glycolysis and apoptosis regulator

TP53 (tumor protein 53)-induced glycolysis and apoptosis regulator (TIGAR) belongs to the phosphatases family of proteins that modulates the level of reactive oxygen species in tumor cells. This protein plays a vital role as a negative regulator of glycolysis, thus lowering ROS levels in the cells, which helps the cancerous cells to resist programmed cell death. Besides, TIGAR also mediates the DNA damage repair in cancer cells by increasing tumor cell survival. In the current study, we have screened natural products that compete with the substrate to bind to the active site of TIGAR. Extra precision and MMGBSA scoring function were used to screen the lead molecules. Five compounds were considered as lead molecules with 2-(2-(3,4-dihydroxy phenyl)-3,5-dihydroxy-8-(4-hydroxyphenyl)-4-oxo-4H-furo[2,3-h]chromen-9-yl) acetic acid(DDFA) as a top lead with a docking score of −9.428, and −53.16 MMGBSA, bind to the positively charged amino acids present in the active site. Further, the molecular dynamics simulation studies indicated the structural stability attained by TIGAR protein upon the binding of DDFA, suggesting it to be a potent inhibitor of TIGAR, and could be employed as an anticancer drug during combinational therapy.

In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease

In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone have comparable inhibition activity to SARS CoV-2 main protease in comparison to Remdesivir. 5-hydroxy7,8,2’,3’-tetramethoxyflavone has the lowest docking score, which was further validated by protein ligand contact fraction examination, although MMGBSA score is lowest for Remdesivir.

Computer-aided approaches reveal trihydroxychroman and pyrazolone derivatives as potential inhibitors of SARS-CoV-2 virus main protease.

COVID-19 was declared a pandemic by the World Health Organization (WHO) in March 2020. The disease is caused by severe acute respiratory syndrome coronavirus 2 (SARSCoV-2). The aim of this study is to target the SARS-CoV-2 virus main protease (Mpro) via structure-based virtual screening. Consequently, > 580,000 ligands were processed via several filtration and docking steps, then the top 21 compounds were analysed extensively via MM-GBSA scoring and molecular dynamic simulations. Interestingly, the top compounds showed favorable binding energies and binding patterns to the protease enzyme, forming interactions with several key residues. Trihydroxychroman and pyrazolone derivatives, SN02 and SN18 ligands, exhibited very promising binding modes along with the best MM-GBSA scoring of -40.9 and -41.2 kcal mol-1, resp. MD simulations of 300 ns for the ligand-protein complexes of SN02 and SN18 affirmed the previously attained results of the potential inhibition activity of these two ligands. These potential inhibitors can be the starting point for further studies to pave way for the discovery of new antiviral drugs for SARS-CoV-2.

Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach

The pandemic caused by novel coronavirus disease 2019 (COVID-19) infecting millions of populations worldwide and counting, has demanded quick and potential therapeutic strategies. Current approved drugs or molecules under clinical trials can be a good pool for repurposing through in-silico techniques to quickly identify promising drug candidates. The structural information of recently released crystal structures of main protease (Mpro) in APO and complex with inhibitors, N3, and 13b molecules was utilized to explore the binding site architecture through Molecular dynamics (MD) simulations. The stable state of Mpro was used to conduct extensive virtual screening of the aforementioned drug pool. Considering the recent success of HIV protease molecules, we also used anti-protease molecules for drug repurposing purposes. The identified top hits were further evaluated through MD simulations followed by the binding free energy calculations using MM-GBSA. Interestingly, in our screening, several promising drugs stand out as potential inhibitors of Mpro. However, based on control (N3 and 13b), we have identified six potential molecules, Leupeptin Hemisulphate, Pepstatin A, Nelfinavir, Birinapant, Lypression and Octreotide which have shown the reasonably significant MM-GBSA score. Further insight shows that the molecules form stable interactions with hot-spot residues, that are mainly conserved and can be targeted for structure- and pharmacophore-based designing. The pharmacokinetic annotations and therapeutic importance have suggested that these molecules possess drug-like properties and pave their way for in-vitro studies. Communicated by Ramaswamy H. Sarma

Pharmacophore-based designing of putative ROS-1 targeting agents for NSCLC

Non-small cell lung cancer (NSCLC) is a fatal non-immunogenic malignancy, and proto-oncogene receptor tyrosine kinase (ROS-1) is one of its clinically relevant biomarkers. In this context, herein, we report a series of benzimidazol-2-amine derivatives which were synthesized on the basis of the pharmacophore of ROS-1 and evaluated for anti-proliferative activity. For this, the in silico receptor-ligand pharmacophore model of ROS-1, previously published by our own group, was utilized to screen out an in-house database of small molecule heterocycles. Docking analysis of the selected compounds was carried out within the active site of wild-type (WT) ROS-1 as well as Gly2032Arg mutant ROS-1 protein, which confirmed the retention of conserved interaction between selected molecules and hinge region amino acids Glu2027 and Met2029. Docking was followed by molecular dynamics simulations for the stability of the complexes and calculation of the MM-GBSA score for binding affinity. Finally, compounds were synthesized and the anti-proliferative potential of compounds was evaluated using the A549 cell line. Compounds 3a and 3b presented significant GI50 values between 23.0 and 25.4μM, among all the tested compounds.

Moleculer dynamics simulaiton revealed reciever domain of Acinetobacter baumannii BfmR enzyme as the hot spot for future antibiotics designing

Acinetobacter baumannii is an alarming nosocomial pathogen that is resistant to multiple drugs. The pathogen is forefront of scientific attention because of high mortality and morbidity found for its complications in the past decade. As a consequence, identification of novel drug candidates and subsequent designing of novel chemical scaffolds is an imperative need of time. In the present study, we used a recently reported structure of BfmR enzyme and performed structure based virtual screening, MD simulation and binding free energies calculations. MD simulation revealed a profound movement of the best-characterized inhibitor towards the α4-β5-α5 face of the enzyme receiver domain, thus indicating its high affinity for this site compared to phosphorylation. Furthermore, it was observed that the enzyme and enzyme-inhibitor complex have high structure stability with mean RMSD of 1.2 and 1.1 Å, respectively. Binding free energy calculations for the complex unraveled high stability with MMGBSA score of −26.21 kcal/mol and MMPBSA score of −1.47 kcal/mol. Van der Waal energy was found highly favorable with value of −30.25 kcal/mol and dominated significantly the overall binding energy. Furthermore, a novel WaterSwap assay was used to circumvent the limitations of MMGB/PBSA that complements the inhibitor affinity for enzyme active pocket as depicted by the low convergence of Bennett, TI and FEP algorithms. Results yielded from this study will not only give insight into the phenomena of inhibitor movement towards the enzyme receiver domain, but will also provide a useful baseline for designing derivatives with improved biological and pharmacokinetics profiles.Communicated by Ramaswamy H. Sarma

Toxicodynamics of Organophosphates with Human Acetylcholinesterase Interaction at Novel Site Trp-86 for Antidote Action

Molecular Docking, site directed mutagenesis and molecular dynamic (MD) simulation approaches were used to explore mode of binding and inhibition for human acetylcholinesterase (hAChE) and organophosphates (OPs). More than 200 OPs molecules were investigated using Glide docking module of Schrodinger suite as co-crystal structure between two are not available in protein data bank. In initial screening Trp86 was found to be involved in maximum π-cation interaction on anionic subsite of hAChE other than Ser203 (catalytic site). With extra precision glide docking phoxim ethyl phosphonate (PEP) tops among 200 OPs based on glide docking score while interacted with Trp86, Gly121 and Ser203 whereas MMGBSA score shows less binding affinity than heptenophos and dichlorovos. Trp86 preferred π interaction with ring bearing OPs and hydrophobic interactions with smaller OPs without ring bearing structures. Site directed mutagenesis at Trp86 (Trp86 to Ala86) shown the deterioration of the binding site in terms of size reduction, loss of electrostatic and geometric stabilization in binding cavity and significant reduction in binding of OPs in preferred orientation. Dock score of both wild and mutated hAChE shows a perfect qualitative agreement (R 2 =64.1%) towards the study. Molecular dynamic simulation (GROMACS 4.5.5) of hAChE-PEP complex for 4×10 4 pico-second with SPC16 water system at 310K temperature explained the evident role of Trp86 in stabilizing the ligand at P-site of the enzyme. Asp74 and Tyr 124 were noticed in conveying H-bonds. Trp86 have shown consistent and stable distance between residues and ligand. Asp74 and Tyr124 appeared as important residues which contributed H bonds and Ser203 was expected to be closer for interaction to happen as it disappeared during simulation. Study suggests role of Trp86 on binding site is equally important to take consideration. As residue Trp86 plays significant role, it can be taken into consideration for the studies on development of more efficient antidotes to overcome the case of human poisoning.

Identification of non-resistant ROS-1 inhibitors using structure based pharmacophore analysis

Proto-oncogene receptor tyrosine kinase ROS-1 plays a key role in regulating a variety of cancers mainly non-small cell lung cancer (NSCLC). The marketed ROS-1 inhibitors such as Crizotinib suffer from the tribulations of growing resistance due to mutations primarily Gly2032Arg in the ROS-1 protein. To curb the problem of resistance, researchers have developed inhibitors such as Lorlatinib against the mutant protein. The present study was designed to identify inhibitors against wild type (WT) as well as mutant ROS-1 protein that will offer a broader spectrum of activity. Exploring crystal structure of ROS-1 complexed with Lorlatinib, receptor-ligand pharmacophore model was developed using Discovery Studio (DS) software. The developed pharmacophore model consisted of one hydrogen bond acceptor (HBA), one hydrogen bond donor (HBD) and two hydrophobic features (HY), subsequently utilized for virtual screening of commercially available databases and the retrieved hits were further subjected to fitness score and Lipinski’s filter. Thereafter, the retrieved hits were docked in WT and mutated (Gly2032Arg) proteins of ROS-1. Total five molecules were retrieved with good docking scores and good binding interactions within the active site of WT and mutated ROS-1. The binding energies of the ligand-receptor complexes were predicted via calculation of MM-GBSA score. To predict the stability of the ligand receptor complexes with mutant and wild type proteins, molecular dynamic simulation was performed. Thus, these identified hits show good binding affinities with WT and mutant ROS-1 proteins that may be further evaluated for their in-vitro/in-vivo activity.