Binding ΔG Research Articles

Synthesis and biological studies of acetophenone-based novel chalcone, semicarbazone, thiosemicarbazone and indolone derivatives: Structure-Activity relationship, molecular docking, molecular dynamics, and kinetic studies

This study presents the synthesis and evaluation of nine acetophenone derivatives (1–9), with compounds 2, 4, 5, 6, 7, and 9 being novel and synthesized for the first time. These derivatives encompass diverse structural motifs including chalcone, thiosemicarbazone, semicarbazone, and indolone derivatives. The structures of synthesized compound were confirmed by NMR analysis. The synthesized compounds were assessed for their in vitro enzyme inhibition against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and α-Glycosidase enzymes, as well as their antioxidant capacities using the DPPH radical scavenging assay. With Ki values ranging from 8.96±0.40 to 44.16±4.25 nM, these showed effective inhibition of AChE. However, the inhibitory characteristics of all drugs were almost the same. The Ki values of the two most active compounds, (3) and (4), were 8.96±0.40 and 11.33±0.58 nM, respectively. Regarding α-Glycosidase, they demonstrate that all novel compounds (1–9) have IC50 values between 30.16 and 133.98 µM, whereas the Ki values vary from 42.71±5.90 to 128.78±8.03 µM. Compound 4 emerged as a notable inhibitor, displaying significant inhibition against all used enzymes. Molecular docking studies revealed its exceptional binding affinities, corroborated by MM-GBSA ΔG binding free energies, and Glide Emodel scores. Compound 7 also exhibited promising inhibitory potential against α-Glycosidase. Docking scores for hAChE -12.207, for hBChE -10.140 and for α-Glycosidase -10.590 kcal/mol. The 250 ns molecular dynamics simulations confirmed the stability of the ligand-protein complexes, particularly with compound 4. The ligand-protein complexes were found extremely stable according to the MD simulations. Additionally, ADME predictions indicated favorable pharmacokinetic properties and drug-likeness for all compounds, further supporting their potential as orally active agents. Compound 4, in particular, stands out as a multitarget drug candidate, with strong inhibition against key enzymes implicated in neurodegenerative diseases and diabetes, suggesting its therapeutic potential in these conditions.

Chemical Compositions and Antimicrobial and Mosquito Larvicidal Activities of the Leaf Essential Oils of Goniothalamus yunnanensis W.T.Wang and G. touranensis Ast: Experimental and In Silico Approaches.

The current research describes a phytochemical analysis and antimicrobial activity of essential oils extracted from the leaves of two Vietnamese Annonaceae species Goniothalamus yunnanensis W.T.Wang and G. touranensis Ast. By the GC-FID/MS (gas chromatography-flame ionization detection/mass spectrometry) analyses, sesquiterpene hydrocarbons accounted for the highest percentage of 68.22 % in G. yunnanensis leaf essential oil with bicyclogermacrene (31.03 %) and (E)-caryophyllene (21.12 %) being the main compounds. G. touranensis leaf essential oil was dominated by monoterpene hydrocarbons (57.08 %) with p-cymene (19.95 %) and α-pinene (16.82 %) being the major compounds. By the microdilution broth susceptibility assay, two oil samples showed strong antibacterial effects on the Gram-positive bacteria Enterococcus faecalis ATCC51299, Staphylococcus aureus ATCC29213, and Bacillus cereus ATCC11778 with the MIC values of 16-64 μg/mL. They also inhibited the growth of the yeast Candida albicans ATCC 60193 with the same MIC value of 128 μg/mL. From the vector-based intervention approach, both oil samples showed strong mosquito larvicidal activity against four-instar larvae of Aedes aegypti and Ae. albopictus with the 24 h LC50 values of 16.75-27.60 μg/mL and 24 h LC90 values of 24.31-46.18 μg/mL. Docking results indicated that bicyclogermacrene and p-cymene exhibited the highest ΔG (binding affinity) values of -8.208 and -6.799 kcal/mol with the olfactory binding proteins (OBPs) of Ae. aegypti and Ae. albopictus, respectively.

Specialized compounds of four Cameroonian spices: Isolation, characterization, and in silico evaluation as prospective SARS-CoV-2 inhibitors

Abstract Since the emergency of coronavirus disease 2019, no specific drug has been developed within the fighting program against its spread. In Cameroon, it has been reported that the dish “yellow soup” can significantly curb the progress of the disease, while no chemical investigations have been done so far to support that conclusion. Chemical investigations of four selected spices of that dish led to the isolation of a total of 44 distinct pure compounds, which were identified using spectroscopic data. Furthermore, the docking scores of the isolated compounds were inspected by AutoDock4.2.6 software toward SARS-CoV-2 multi-targets involving main protease (Mpro), helicase, papain-like protease (PLpro), and human angiotensin‐converting enzyme 2 (ACE2). The most potent isolated compounds underwent molecular dynamics (MD) simulations over 100 ns. Stigmasterol demonstrated outstanding potency toward Mpro and PLpro with ΔG binding values of −35.6 and −36.6 kcal/mol, respectively, compared to nirmatrelvir. Nevertheless, 3β-taraxeryl acetate revealed good binding affinity against helicase and lupeol unveiled superior binding energy toward ACE2 compared to nirmatrelvir. Post-MD analyses manifested great steadiness of the isolated compounds within the binding pockets of SARS-CoV-2 targets throughout 100 ns MD simulations. Stigmasterol, 3β-taraxeryl acetate, and lupeol are recommended for further in vivo/in vitro tests toward SARS-CoV-2 multi-targets.

New tetrahydro-isoquinoline derivatives as cholinesterase and α-glycosidase inhibitors: Synthesis, characterization, molecular docking & dynamics, ADME prediction, in vitro cytotoxicity and enzyme inhibition studies

In the presented work, it was reported about the synthesis procedure of new isoquinoline derivatives starting from chalcones and acetoacetanilide, a multi-step synthesis pathway yielded four isoquinoline derivatives (5a-d). At the first stage of our research, corresponding cyclohexanone derivatives are synthesized from the Michael addition reaction of chalcones with acetoacetanilide. After that, on the based cyclohexanone derivative was obtained novel isoquinoline derivatives. According to the structures, a plausible reaction mechanism was suggested. The structure of the synthesized compounds was confirmed by NMR spectroscopy method and X-Ray analysis. Additionally, to determine cholinesterase and α-glycosidase inhibition activity compounds 5(a-d) were tested against AChE, BChE and α-Gly as in vitro. In this work, the novel isoquinoline derivatives 5(a-d) demonstrated encouraging inhibitory action against α-glucosidase, as seen by their IC50 values ranging from 9.95 to 19.25 nM. This indicates that they were approximately 1–3 times more active than acarbose (IC50 = 23.07 nM). Also, the molecular docking IFD XP Gscores, dynamics simulations and MM-GBSA ΔG binding free energies of the isoquinoline derivatives on hAChE, hBChE and α-Gly are determined. The molecular dynamics (MD) simulations conducted in this study provided valuable insights into the dynamic behaviors, stabilities, and interaction profiles of ligand–protein complexes involving the R and S isomers of compounds 5c-hAChE, 5c-hBChE, and 5a-αGly. The MD simulations were crucial for understanding the complex stabilities and dynamic mechanisms of the ligand–protein interactions, shedding light on the potential inhibitory roles of these compounds..

In silico study: molecular docking of SARS-Cov-2 endoribonuclease on active compounds of Gmelina arborea Roxb. bark

Infection by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) triggers COVID-19 disease of the respiratory tract similar to pneumonia. The virus encodes four structural proteins and 16 non-structural proteins (nsp), one of which includes nsp15 or endoribonuclease (NendoU). NendoU plays an important role in viral replication and transcription and reduces the stimulation of immune cell responses. Active compounds in Gmelina arborea Roxb. bark have antioxidant properties that can inhibit the NendoU activity of SARS-CoV-2. This study aims to analyze the potential of compounds from Gmelina arborea Roxb. bark in inhibiting SARS-CoV-2 NendoU within in silico using the YASARA structure application. Balnophonin is the best test ligand based on binding ΔG value, dissociation constant (Kd), prediction of physicochemical characteristics, pharmacokinetics, and toxicity. Therefore, balanophonin can be developed as an effective alternative drug to inhibit SARS CoV-2 NendoU.

Identification of potential focal adhesion kinase (FAK) inhibitors: a molecular modeling approach

Focal adhesion kinase (FAK) is an enzyme of paramount importance as it is involved in several critical roles, which are linked to proliferation of cancer cells. FAK is quintessential for cancer cell mitigation, adhesion and survival, downregulation of which interferes with the growth of cancer cells. The expression of FAK is elevated in breast cancer, hepatocellular carcinomas, neuroblastoma cells, demonstrating the need for FAK inhibitors as a potential treatment. Based on an in silico drug screen, the study aimed to identify potential FAK inhibitors. 3180 molecules retrieved from the Zinc database comprising biogenic molecules, FDA-approved drugs and compounds in clinical trials were screened against the FAK enzyme (PDB:2ETM). The XP docking study of the best 51 ligands revealed that ZINC02033589 (Silymarin) showed good binding to FAK with −10.97 kcal/mol dock score followed by ZINC00518397 with −8.23 kcal/mol and ZINC03831112 − 8.07 kcal/mol. The interactions of the top three ligands with FAK were further validated by molecular dynamic simulation study of 100 ns and MM-GBSA calculations. The ΔG of binding of ZINC02033589, ZINC00518397 and ZINC03831112 was found to be −59.09, −45.08 and −48.53 kcal/mol respectively. The study established the fact that among the three molecules, ZINC02033589 showed good stability and binding towards FAK. These results could usher in the development of potential FAK inhibitor entities, that could be persuaded and substantiated by the molecules identified in this study for subsequent synthetic and bioactivity research studies. Communicated by Ramaswamy H. Sarma

Functionalized 2-Amino-4H-1-Benzopyran-4-yl Phosphonate Scaffolds: Synthesis, Anticancer Evaluation and Computational Studies

Prostate, breast, and lung cancers are various human cancers that have been associated with SRC kinase mutations. Therefore, the development of potent and selective SRC kinase inhibitors is an exciting area of interest for researchers. In this study, we synthesized a series of 2-amino-4H-1-benzopyran-4-yl phosphonate derivatives through a one-pot reaction involving appropriately substituted salicylaldehydes, malononitrile, and diethyl phosphite, with meglumine as the catalyst. We conducted in vitro screening of these compounds for their anticancer activity against human prostate cancer (DU-145), breast cancer (MCF-7), and lung cancer (A549) cell lines using the MTT assay. Notably, compounds 4a, 4j, 4k, and 4l exhibited promising anticancer activity. Molecular docking studies of these compounds supported their potential as therapeutic agents for SRC kinase inhibition. Specifically, compounds 4a, 4b, 4c, 4d, and 4e demonstrated strong ΔG binding affinities ranging from −7.9 to −7.4 kcal/mol. These findings suggest that these molecules hold promise for cancer treatment.

Molecular docking, simulations of animal peptides against the envelope protein of Dengue virus

Peptides are biologically active, small molecules with high specificity in its mode of action that can be effective at nanomolar concentrations. Peptide-based antiviral medicines have already been licensed and used to treat human immunodeficiency virus (HIV), influenza virus and hepatitis C virus. So far, no peptide drug has been approved for antiviral treatment against Dengue virus, and many are under clinical trials. Therefore, developing a reasonable peptide against the Dengue virus Envelope protein structure will be a successful strategy for treating Dengue. Hence, we investigated protein-protein docking interactions between 215 peptides retrieved from the AVP database against the envelope protein using Cluspro and HADDOCK followed by the evaluation of their allegenicity, toxicity and physicochemical characteristics investigation. Further validation of the protein–peptide complexes was performed with Molecular dynamics simulations and Molecular Mechanics Poisson–Boltzmann surface area (MMPBSA) analysis on the hit inhibitors. This study revealed that Indolicidin (−75.026 ± 1.54 KJ/mol) and Human Neutrophil peptide-1 (−71.6551 ± 2.112 KJ/mol) shows higher negative ΔG binding implicating their relative stabilization in the protein–peptide interactions during 100 ns of dynamic simulations. Also, both the peptides exhibited desirable physicochemical properties and were nonallergenic. Hence, we further aim to test these peptides by in vitro and in vivo studies to confirm their efficacy against Dengue virus. Communicated by Ramaswamy H. Sarma

Potential Effect of Baobab's Polyphenols as Antihyperlipidemic Agents: In Silico Study.

Adansonia digitata L. is an African tree commonly called baobab. This tree is effectively used in traditional medicine to treat cardiovascular disorders. Hyperlipidemia is a well-known cardiovascular risk factor associated with the increased incidence of mortality worldwide. This study aimed to demonstrate the mechanism of baobab polyphenols in the activities of hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase and pancreatic lipase as lipid metabolic enzymes. Molecular docking and an incentive for drug design showed that all the polyphenols in baobab bound to the proteins with higher affinity and a lower binding energy compared with simvastatin as the positive control (ΔG: from -5.5 kcal/mol to -6.5 kcal/mol). The same polyphenols exhibited a considerable binding affinity to pancreatic lipase (ΔG: from -7.5 kcal/mol to -9.8 kcal/mol) in comparison with the control and HMG-CoA reductase. Quercetin showed the best docking score from the selected Baobab polyphenols (ΔG = -9.8 kcal/mol). The root mean square deviation (RMSD) results indicated that stable epicatechin and quercetin complexes were demonstrated with HMG-CoA reductase, and other less stable complexes were developed using rutin and chlorogenic acid. Moreover, the analysis of the root mean square fluctuation (RMSF) simulation results was consistent with that of the RMSD. The RMSF value for all the baobab polyphenols, including the crystal control ligand, was kept between 0.80 and 8.00 Å, similarly to simvastatin, and less than 4.8 Å for pancreatic lipase. Chlorogenic acid, quercetin, epicatechin, and rutin had negative ΔG binding scores from highest to lowest. The same ligands displayed more negative ΔG binding scores than those observed in HMG-CoA reductase and crystal control ligand (methoxyundecyl phosphinic acid) in their simulation with pancreatic lipase. In conclusion, baobab polyphenols interact with HMG-CoA reductase and pancreatic lipase to inhibit their substrate binding and block their activity.

Cheminformatics Strategies Unlock Marburg Virus VP35 Inhibitors from Natural Compound Library.

The Ebola virus and its close relative, the Marburg virus, both belong to the family Filoviridae and are highly hazardous and contagious viruses. With a mortality rate ranging from 23% to 90%, depending on the specific outbreak, the development of effective antiviral interventions is crucial for reducing fatalities and mitigating the impact of Marburg virus outbreaks. In this investigation, a virtual screening approach was employed to evaluate 2042 natural compounds for their potential interactions with the VP35 protein of the Marburg virus. Average and worst binding energies were calculated for all 20 poses, and compounds that exhibited binding energies <-6 kcal/mol in both criteria were selected for further analysis. Based on binding energies, only six compounds (Estradiol benzoate, INVEGA (paliperidone), Isosilybin, Protopanaxadiol, Permethrin, and Bufalin) were selected for subsequent investigations, focusing on interaction analysis. Among these selected compounds, Estradiol benzoate, INVEGA (paliperidone), and Isosilybin showed strong hydrogen bonds, while the others did not. In this study, the compounds Myricetin, Isosilybin, and Estradiol benzoate were subjected to a molecular dynamics (MD) simulation and free binding energy calculation using MM/GBSA analysis. The reference component Myricetin served as a control. Estradiol benzoate exhibited the most stable and consistent root-mean-square deviation (RMSD) values, whereas Isosilybin showed significant fluctuations in RMSD. The compound Estradiol benzoate exhibited the lowest ΔG binding free energy (-22.89 kcal/mol), surpassing the control compound's binding energy (-9.29 kcal/mol). Overall, this investigation suggested that Estradiol benzoate possesses favorable binding free energies, indicating a potential inhibitory mechanism against the VP35 protein of the Marburg virus. The study proposes that these natural compounds could serve as a therapeutic option for preventing Marburg virus infection. However, experimental validation is required to further corroborate these findings.

Unraveling effective extracellular signal-regulated kinase 2 inhibitors: a de novo drug design strategy enhanced by in-depth in silico analyses

Extracellular signal-regulated kinase 2 (ERK-2) is a serine/threonine protein kinase in eukaryotic cells and belongs to the mitogen-activated protein kinase (MAPK) family. An activated form of ERK-2 phosphorylates substrates in the nucleus or cytoplasm and causes specific proteins to be expressed or activated, regulating cell proliferation, differentiation and other functions. Caffeic acid (3,4 − dihydroxy cinnamic acid), as previously reported, directly interacts with ERK-2 and reduces its effects in vitro. It is also reported to have a variety of pharmacological effects, including anti-inflammatory, immunomodulatory, antioxidant and anticancer activities. In the current study, a deep-learning protocol was employed to develop effective 100 compounds by modifying the chemical structure of DHC to improve its inhibitory performance against ERK-2. Calculations of physicochemical properties for those compounds revealed that 20 compounds had drug scores better than DHC (≥ 80%). Following that, molecular docking calculations were performed on the selected compounds and DHC. The obtained data revealed that five compounds had docking scores better than DHC (≥ −5.9 kcal/mol). Moreover, data from molecular mechanics and the Poisson − Boltzmann surface area (MM/PBSA) binding energy over 200 ns MD simulation confirmed that Cmd-1 and Cmd-4 exhibited higher stability with ΔG binding of −40.8 and −49.1 kcal/mol, respectively, which is better than DHC (−35.1 kcal/mol). Finally, various energetic and structural studies showed the high stability of the two generated compounds within the active site of ERK-2. This study highlights the potential use of Cmd-1 and Cmd-4 as promising anti-ERK-2 drug candidates. Communicated by Ramaswamy H. Sarma

Identification of Potential Inhibitors for Beta-Lactamase in Methicillin- Resistant Staphylococcus aureus from Flavonoids Using a Computational Drug Discovery Approach

Background: Staphylococcus aureus (S. aureus) is a Gram-positive bacterium causing a wide range of human infections, leading to life-threatening invasive disorders, hospitalization, and mortality. Producing β-lactamase enzymes in S. aureus is one of the main mechanisms of the pathogen that makes the bacteria resistant to beta-lactam antibiotics, resulting in methicillin-resistant S. aureus (MRSA) strains. Therefore, it is crucial to identify novel β-lactamase inhibitors to combat infections caused by MRSA strains. Methods: In silico virtual screening approach was executed to evaluate the binding affinity of several natural flavonoids to the MRSA β-lactamase active site. After that, the stability of interactions between top inhibitors and the residues incorporated inside the β-lactamase was examined by molecular dynamics (MD) simulation. Moreover, the most connected amino acid within the catalytic domain of the enzyme was determined. Results: Rutin, isoquercitrin, nicotiflorin, quercetin-3-rhamnoside, vicenin-2, quercitrin, and orientin demonstrated a salient binding affinity with the β-lactamase active site (ΔG binding &lt; −10 kcal/mol). Interestingly, the inhibition constant value (Ki) for rutin was estimated at the picomolar scale. The docked poses of these compounds were demonstrated to be stable. Moreover, Gln237 was revealed to be the most crucial residue involved in ligand binding. Conclusion: Rutin, isoquercitrin, nicotiflorin, quercetin-3-rhamnoside, vicenin-2, quercitrin, and orientin may be potent inhibitors of β-lactamase and may be helpful for the treatment of several invasive infections caused by MRSA strains. However, experimental studies are needed in the future to validate our findings.

Exploring the therapeutic potential of galidesivir analogs against Zaire ebolavirus protein 24 (V24): database screening, molecular docking, drug-relevant property evaluation and molecular dynamics simulations

The recent outbreak of the Ebola virus (EBOV) has marked it as one of the most severe health threats globally. Among various anti-EBOV inhibitors studied, galidesivir (BCX4430) has shown remarkable efficacy. This study aims to identify novel potential anti-EBOV drugs among galidesivir analogs, focusing on the Zaire ebolavirus (Z-EBOV), which exhibits a mortality rate of 90%. We subjected 200 candidate compounds to molecular docking calculations, followed by an evaluation of the bioactivity of the top 25 compounds using the OSIRIS Property Explorer. Initial 50 ns molecular dynamics (MD) simulations were then performed. According to our findings, only six compounds exhibited positive drug scores. We further performed molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations of binding energy over 50 ns, selecting the two top-performing compounds for extended 150 ns MD simulations. CID 117698807 and CID 117712809 showed higher binding stability compared to galidesivir, with ΔG binding values of −36.7 and −53.4 kcal/mol, respectively. Both compounds demonstrated high stability within the Z-EBOV-V24 active site over the 150 ns MD simulations. Hence, our study proposes CID 117698807 and CID 117712809 as potential anti-Z-EBOV-V24 drug candidates, warranting further investigation. Communicated by Ramaswamy H. Sarma

Cinnamic acids as promising bioactive compounds for cancer therapy by targeting MAPK3: a computational simulation study.

Mitogen-activated protein kinase-3 (MAPK3) is the upstream regulator in the MAPK cascade and is involved in many critical signaling pathways and biological processes, such as cell proliferation, survival, and apoptosis. MAPK3 overexpression is linked to onset, development, metastasis, and drug resistance in several human cancers. Thus, identifying novel and effective MAPK3 inhibitors is highly demanded. Herein, we aimed to discover organic compounds from cinnamic acid derivatives as potential MAPK3 inhibitors. The binding affinity of 20 cinnamic acids to the MAPK3 active site was tested using the AutoDock 4.0 software. Top-ranked cinnamic acids were ranked based on the ΔG binding values between the ligands and the receptor's active site. Interaction modes between top-ranked cinnamic acids and MAPK3 catalytic site were indicated using the Discovery Studio Visualizer tool. Molecular dynamics (MD) simulation was carried out to study the stability of the docked pose for the most potent MAPK3 inhibitor in this study. Cynarin, chlorogenic acid, rosmarinic acid, caffeic acid 3-glucoside, and cinnamyl caffeate exhibited a salient binding affinity to the MAPK3 active site with the criteria of ΔG binding <-10 k cal/mol. Further, the inhibition constant value for cynarin was calculated at the picomolar concentration. The docked pose of cynarin within the MAPK3 catalytic domain was stable in 100 ns simulation. Cynarin, chlorogenic acid, rosmarinic acid, caffeic acid 3-glucoside, and cinnamyl caffeate might be helpful in cancer therapy by inhibiting MAPK3.

Design and development of novel potential inhibitors of the human USP21 enzyme using a pharmacophore-based virtual screening technique.

An overexpression and increase have been observed in the concentration and activity of the USP21 enzyme in many cancers, necessitating the need for the development of new inhibitor drugs against the same. The current study attempts to discover one such novel potential inhibitor of USP21 by the application of various bioinformatics techniques which include molecular modelling, pharmacophore mapping, and pharmacophore-based virtual screening, molecular docking, and ADMET prediction followed by molecular dynamics simulations. Following this inverted-funnel-like approach, we finally ended up with one ligand- ZINC02422616 which displays a very high binding affinity towards the USP21 domain. This ligand contains all the pharmacophoric features displayed by the compounds that are potential inhibitors of the USP21 domain. Moreover, it shows a favourable pharmacokinetic, pharmacodynamic, and ADMET profile along with strong hydrophobic interaction and hydrogen bonding with the domain. Simulation studies showed that the complex remains stable over time, with the bound protein displaying a more constrained motion in the conformational space compared to the unbound form. The ligand showed a highly favourable free energy landscape/surface, forming several energy minimas in contrast to the unbound domain in which most conformations occupied a relatively higher energy state. Moreover, the ligand also displayed a Kd of 422.8nM and a free energy of binding ΔG of -8.6kcal/mol, both of which indicate a very high affinity towards the target domain.This potential drug candidate can then be used as a viable treatment method for many types of cancers caused by USP21. his article is protected by copyright. All rights reserved.

Golgi α-mannosidase: opposing structures of Drosophila melanogaster and novel human model using molecular dynamics simulations and docking at different pHs

The search for Golgi α-mannosidase II (GMII) potent and specific inhibitors has been a focus of many studies for the past three decades since this enzyme is a key target for cancer treatment. α-Mannosidases, such as those from Drosophila melanogaster or Jack bean, have been used as functional models of the human Golgi α-mannosidase II (hGMII) because mammalian mannosidases are difficult to purify and characterize experimentally. Meanwhile, computational studies have been seen as privileged tools able to explore assertive solutions to specific enzymes, providing molecular details of these macromolecules, their protonation states and their interactions. Thus, modelling techniques can successfully predict hGMII 3D structure with high confidence, speeding up the development of new hits. In this study, Drosophila melanogaster Golgi mannosidase II (dGMII) and a novel human model, developed in silico and equilibrated via molecular dynamics simulations, were both opposed for docking. Our findings highlight that the design of novel inhibitors should be carried out considering the human model’s characteristics and the enzyme operating pH. A reliable model is evidenced, showing a good correlation between K i /IC50 experimental data and theoretical ΔG binding estimations in GMII, opening the possibility of optimizing the rational drug design of new derivatives. Communicated by Ramaswamy H. Sarma

Elucidation of bezlotoxumab binding specificity to toxin B in Clostridioides difficile

C. difficile or Clostridioides difficile infection (CDI) is currently one of the major causes of epidemics worldwide. Toxin B from Clostridioides difficile toxin B (TcdB) infection is the main target protein inhibiting CDI recurrence. Clinical research suggested that bezlotoxumab’s (Bez) efficiency is significantly reduced in neutralizing the B2 strain compared to the B1 strain. The monoclonal antibody (mAb) functions by binding to the epitope 1 and 2 regions in the combined repetitive oligopeptide (CROP) domain. Some binding residues are distinctively different between B1 and B2 strains. In this work, we aimed to elucidate and compare insights into the interaction of toxins B1 and B2 in complex with Bez by using all-atom molecular dynamics (MD) simulations and binding free energy calculations. The predicted ΔG binding values suggested that the antibody (Ab) could bind to toxin B1 significantly better than B2, supported by higher salt bridge and hydrogen bonding (H-bonding) interactions, as well as the number of contact residues between the two focused proteins. The toxin B1 residues important for binding with Bez were E1878, T1901, E1902, F1905, N1941, V1946, N2031, T2032, E2033, V2076, V2077, and E2092. The lower susceptibility of Bez towards toxin B2 was primarily due to a change of residue E2033 from glutamate to alanine (A2033) and the loss of E1878 and E1902 contributions, as determined by the intermolecular interaction changes from the dynamic residue interaction network (dRIN) analysis. The obtained data strengthen our understanding of Bez/toxin B binding.

Identification of Four New Chemical Series of Small Drug-Like Natural Products as Potential Neuropilin-1 Inhibitors by Structure-Based Virtual Screening: Pharmacophore-Based Molecular Docking and Dynamics Simulation.

Neuropilin-1 (NRP-1), a surface transmembrane glycoprotein, is one of the most important co-receptors of VEGF-A165 (vascular endothelial growth factor) responsible for pathological angiogenesis. In general, NRP-1 overexpression in cancer correlates with poor prognosis and more tumor aggressiveness. NRP-1 role in cancer has been mainly explained by mediating VEGF-A165-induced effects on tumor angiogenesis. NRP-1 was recently identified as a co-receptor and an independent gateway for SARS-CoV-2 through binding subunit S2 of Spike protein in the same way as VEGF-A165. Thus, NRP-1 is of particular value as a target for cancer therapy and other angiogenesis-dependent diseases as well as for SARS-CoV-2 antiviral intervention. Herein, The Super Natural II, the largest available database of natural products (∼0.33 M), pre-filtered with drug-likeness criteria (absorption, distribution, metabolism and excretion/toxicity), was screened against NRP-1. NRP-1/VEGF-A165 interaction is one of protein-protein interfaces (PPIs) known to be challenging when approached in-silico. Thus, a PPI-suited multi-step virtual screening protocol, incorporating a derived pharmacophore with molecular docking and followed by MD (molecular dynamics) simulation, was designed. Two stages of pharmacophorically constrained molecular docking (standard and extra precisions), a mixed Torsional/Low-mode conformational search and MM-GBSA ΔG binding affinities calculation, resulted in the selection of 100 hits. These 100 hits were subjected to 20 ns MD simulation, that was extended to 100 ns for top hits (20) and followed by post-dynamics analysis (atomic ligand-protein contacts, RMSD, RMSF, MM-GBSA ΔG, Rg, SASA and H-bonds). Post-MD analysis showed that 19 small drug-like nonpeptide natural molecules, grouped in four chemical scaffolds (purine, thiazole, tetrahydropyrimidine and dihydroxyphenyl), well verified the derived pharmacophore and formed stable and compact complexes with NRP-1. The discovered molecules are promising and can serve as a base for further development of new NRP-1 inhibitors.

In-silico natural product database mining for novel neuropilin-1 inhibitors: molecular docking, molecular dynamics and binding energy computations

In the search for new metabolite inhibitors, a natural product activity and species source (NPASS) database was virtually screened using AutoDock software to identify potential NRP1 inhibitors. NPASS compounds complexed with NRP1 were subjected to molecular dynamics (MD) simulations. Furthermore, NPASS-NRP1 binding affinities were calculated using the MM-GBSA approach. Based on calculated binding energies, kamolonol (NPC146388) demonstrated lower NRP1 binding affinity than the co-crystallized HRG/Arg-1 ligand with binding energy (ΔG binding) values of –34.5 and –32.0 kcal/mol, respectively. Structural and energetic analysis showed high stability for kamolonol and HRG/Arg-1 with NRP1 over the 200 ns MD simulations. The studied physicochemical properties of kamolonol and HRG/Arg-1 revealed that these compounds obey Lipinski's rule of five. ADMET characteristics of kamolonol and HRG/Arg-1 were predicted, and kamolonol showed better ADMET properties compared to HRG/Arg-1. Based on these results, kamolonol is a promising NRP1 inhibitor worthy of further experimental assays as anti-carcinoma remediation.

Venetoclax analogs as promising anticancer therapeutics via targeting Bcl-2 protein: in-silico drug discovery study

B-cell lymphoma 2 (Bcl-2) protein plays a vital role in enhancing malignant cell survival by alleviating programmed cell death. Therefore, Bcl-2 protein has been identified as a charming druggable target for cancer treatment. Venetoclax has enticed considerable attention as a potential Bcl-2 inhibitor. Herein, in-silico computations were executed to search for new venetoclax analogs against the Bcl-2 protein. A library involving 4112 was collected, prepared, and virtually screened against Bcl-2 protein using AutoDock Vina1.1.2 software. Promising analogs in complex with Bcl-2 protein were further submitted to molecular dynamics (MD) simulations, pursued by binding energy computations using the MM-GBSA approach. Compared to venetoclax (ΔGbinding = −51.2 kcal/mol), PubChem-873-158-83 and PubChem-148-422-478 demonstrated greater binding affinities with Bcl-2 protein throughout 100 ns MD simulations with ΔGbinding values of −69.1 and −62.4 kcal/mol, respectively. Structural and energetical analyses unveiled good stabilization of the identified analogs complexed with Bcl-2 protein over the MD course. The pharmacokinetic features of the two identified analogs were anticipated and unveiled the oral bioavailability of these compounds. Further in-vitro/in-vivo biological evaluations around these compounds could assist in identifying anticancer leads towards Bcl-2 protein.Communicated by Ramaswamy H. Sarma