Molecular dynamics and combined docking studies for the identification of Zaire ebola virus inhibitors

Molecular activity of bioactive phytocompounds for inhibiting host cell attachment and membrane fusion interacting with West Nile Virus envelope glycoprotein

West Nile virus is an arbovirus primarily spread by mosquitoes, which are the principal carriers and belong to the Flaviviridae category. This widespread disease lacks specific treatments despite its potential lethality, urgently demanding novel pharmaceutical research and development aims to prevent severe or long-term complications and improve overall outcomes. Pandemic awareness, increasing global incidence, fatal illness effects, expenses associated with outbreaks, reducing suffering, and other broader implications highlight the study's wider significance. Drug design as a novel treatment approach to reduce the risk of resistance to the virus resulting from overuse of broad-spectrum antiviral therapies for unrelated viral diseases has been evaluated using computational techniques. Initially, molecular docking targeted the envelope glycoprotein of the WNV, utilizing a set of 5375 phytochemicals found in the IMPPAT database. Their binding affinities were -7.464, -5.802, -5.617, and -4.92, kcal/mol for CID: 359 (Phloroglucinol), 9064 (Cianidanol), 25310 (L-Rhamnose), and 492405 (Favipiravir), respectively. The lead compounds and the control ligand both bind at the common active site of the macro-molecule, as evidenced by their interactions with the same amino acid residues at LEU281, ASN47, THR282, SER29, MET48, MET46, and MET45, correspondingly. In post-docking MM-GBSA the negative binding energy of the P-L complex for the compounds CIDs: 359, 9064, 25310, and 492405 (control) were -29.16, -33.45, -32.02, and -3.16 kcal/mol, correspondingly. The selected compounds are secure and efficient since they demonstrate excellent toxicological and Pk characteristics. The compounds were further evaluated to confirm their stability and binding affinity to the target protein by molecular dynamics simulation (RMSD, RMSF, Rg, SASA, H-bond, P-L, and L-P contact). Following this, principal component analysis (PCA) and dynamic cross-correlation matrix (DCCM) studies were conducted using the MD trajectory data. The ligands evaluated in this study demonstrated considerable stability of the proteins' binding site when complexed with CID: 9064 and CID: 25310, respectively, in the MD simulation, which also revealed a high negative binding free energy value, indicating a robust interaction between the target and lead compounds. The three principal components (PC1, PC2, PC3) for the lead compounds corresponding to CID: 9064 (40.37%, 23.02%, and 8.82%) and CID: 25310 (73.04%, 10.06%, and 3.77%), respectively, indicate that their complexes are more stable than the other L-P complexes. Consequently, both the compounds derived from the plants Tamarindus indica and Plantago ovate, respectively, may potentially impede the viral activity of the WNV envelope glycoprotein, indicating the possibility of these compounds as prospective phytochemical therapeutic candidates. This preclinical study can be used in further drug development processes, including in vivo studies and animal trials.

Elucidating the antioxidant potential of some flavanones as MAO-B inhibitors through DAM, in silico molecular docking and computational analysis

Seven flavanones underwent computational evaluation to determine their effectiveness in filtering UV radiation and scavenging free radicals. The investigated flavanones exhibited enhanced radical scavenging capabilities relative to the parent flavanone, with Hesperidin demonstrating the highest EA and Qmax values, consistent with its antireductant activity. The remaining flavanones displayed lower IE values, suggesting their antioxidant efficacy. Spectroscopic analysis revealed that the HOMO-LUMO and HOMO-1-LUMO transitions are the primary electronic transitions in the UV-Visible spectra of the studied flavanones. Their absorption within the UV-A and UV-B range (260-345 nm) indicates potential utility as UV filters. Theoretical calculations demonstrate that the reactivity of flavanones is concentrated in ring [B], with a reactivity order of 3' > 4' > 2' > 6 > 7 > 5. The BDE values reveal that the 3'-OH group has the lowest value, followed by the 4' position, while hydrogen bonding is responsible for the increased BDE value at position 5. The values of ΔBDE and ΔAIP, relative to phenol, provide a framework for elucidating the preferred mechanism, HAT or SET, underlying the antioxidant behavior. Molecular docking simulations identified hesperetin, 2'-Hydroxyflavanone, 4'-Hydroxyflavanone, Eriodictyol, and Naringenin as potential MAO-B inhibitors, outperforming their synthetic counterparts in this regard.

DFT, Molecular Docking, Bioactivity and ADME Analyses of Vic-dioxim Ligand Containing Hydrazone Group and its Zn(II) Complex

BACKGROUND

Cancer is one of the diseases affecting a large population worldwide and resulting in death. Finding new anti-cancer drugs that are target-focused and have low toxicity is of great importance.

OBJECTIVE

This study aimed to investigate the effects of vic-dioxime derivatives carrying hydrazone group and its Zn(II) complex on cancer using molecular docking, bioactivity and quantum chemical calculations.

METHODS

Molecular docking studies were performed on epidermal growth factor receptor and vascular endothelial growth factor receptor 2 target proteins. Furthermore, molecular geometry was performed, and the frontier molecular orbitals, Mulliken charges and molecular electron density distribution were evaluated using density functional theory. Also, the bioactivity parameters of the compounds were evaluated, and ADME analysis was performed using web-based tools.

RESULTS

Higher binding affinity was observed for Zn(II) complex with target proteins vascular endothelial growth factor receptor 2 and against epidermal growth factor receptor when compared with LH2. Only the Zn(II) complex against the epidermal growth factor receptor had ligand efficiency and fit quality in the valid range. Furthermore, LH2 has the most potent electrophilic ability (acceptor) among other compounds. Moreover, both LH2 and Zn(II) complexes strongly satisfy Lipinski's rule of five.

CONCLUSION

In conclusion, these novel compounds, especially Zn(II) complex, can be new candidates for anticancer drug development studies which are target-focused and have low toxicity.

ADMET profiling and molecular docking of potential antimicrobial peptides previously isolated from African catfish, Clarias gariepinus

Amidst rising cases of antimicrobial resistance, antimicrobial peptides (AMPs) are regarded as a promising alternative to traditional antibiotics. Even so, poor pharmacokinetic profiles of certain AMPs impede their utility necessitating, a careful assessment of potential AMPs' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties during novel lead exploration. Accordingly, the present study utilized ADMET scores to profile seven previously isolated African catfish antimicrobial peptides (ACAPs). After profiling, the peptides were docked against approved bacterial protein targets to gain insight into their possible mode of action. Promising ACAPs were then chemically synthesized, and their antibacterial activity was validated in vitro utilizing the broth dilution method. All seven examined antimicrobial peptides passed the ADMET screening, with two (ACAP-IV and ACAP-V) exhibiting the best ADMET profile scores. The ACAP-V had a higher average binding energy (-8.47 kcal/mol) and average global energy (-70.78 kcal/mol) compared to ACAP-IV (-7.60 kcal/mol and -57.53 kcal/mol), with the potential to penetrate and disrupt bacterial cell membrane (PDB Id: 2w6d). Conversely, ACAP-IV peptide had higher antibacterial activity against E. coli and S. aureus (Minimum Inhibitory Concentration, 520.7 ± 104.3 μg/ml and 1666.7 ± 416.7 μg/ml, respectively) compared to ACAP-V. Collectively, the two antimicrobial peptides (ACAP-IV and ACAP-V) are potential novel leads for the food, cosmetic and pharmaceutical industries. Future research is recommended to optimize the expression of such peptides in biological systems for extended evaluation.

Chemoinformatic Design and Profiling of Derivatives of Dasabuvir, Efavirenz, and Tipranavir as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase and Methyltransferase

Zika virus (ZIKV) infection is one of the mosquito-borne flaviviruses of human importance with more than 2 million suspected cases and more than 1 million people infected in about 30 countries. There are reported inhibitors of the zika virus replication machinery, but no approved effective antiviral therapy including vaccines directed against the virus for treatment or prevention is currently available. The study investigated the chemoinformatic design and profiling of derivatives of dasabuvir, efavirenz, and tipranavir as potential inhibitors of the zika virus RNA-dependent RNA polymerase (RdRP) and/or methyltransferase (MTase). The three-dimensional (3D) coordinates of dasabuvir, efavirenz, and tipranavir were obtained from the PubChem database, and their respective derivatives were designed with DataWarrior-5.2.1 using an evolutionary algorithm. Derivatives that were not mutagenic, tumorigenic, or irritant were selected; docked into RdRP and MTase; and further subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) evaluation with Swiss-ADME and pkCSM web tools. Some of the designed compounds are Lipinski's rule-of-five compliant, with good synthetic accessibilities. Compounds 20d, 21d, 22d, and 1e are nontoxic with the only limitation of CYP1A2, CYP2C19, and/or CYP2C9 inhibition. Replacements of -CH₃ and -NH- in the methanesulfonamide moiety of dasabuvir with -OH and -CH₂- or -CH₂CH₂-, respectively, improved the safety/toxicity profile. Hepatotoxicity in 5d, 4d, and 18d is likely due to -NH- in their methanesulfonamide/sulfamic acid moieties. These compounds are potent inhibitors of N-7 and 2'-methylation activities of ZIKV methyltransferase and/or RNA synthesis through interactions with amino acid residues in the priming loop/"N-pocket" in the virus RdRP. Synthesis of these compounds and wet laboratory validation against ZIKV are recommended.

Recurrent Ebola outbreaks in the eastern Democratic Republic of the Congo: A wake-up call to scale up the integrated disease surveillance and response strategy

Ebola virus disease (EVD) is a dangerous viral zoonotic hemorrhagic fever caused by a deadly pathogenic filovirus. Frugivorous bats are recognized as being the natural reservoir, playing a pivotal role in the epidemiological dynamics. Since its discovery in 1976, the disease has been shown to be endemic in the Democratic Republic of the Congo (DRC). So far, thirteen outbreaks have occurred, and EVD has been prioritized in the national surveillance system. Additionally, EVD is targeted by the Integrated Disease Surveillance and Response (IDSR) strategy in DRC. The IDSR strategy is a collaborative, comprehensive and innovative surveillance approach developed and adopted by WHO's African region member states (WHO/Afro) to strengthen their surveillance capacity at all levels for early detection, response and recovery from priority diseases and public health events. We provide an overview of the IDSR strategy and the issues that can prevent its expected outcome (early detection for timely response) in eastern DRC where there are still delays in EVD outbreaks detection and weaknesses in response capacity and health crisis recovery. Therefore, this paper highlights the advantages linked to the implementation of the IDSR and calls for an urgent need to scale up its materialization against the recurrent Ebola outbreaks in eastern DRC. Consequently, the paper advocates for rapidly addressing the obstacles hindering its operationalization and adapting the approach to the local context using implementation science.

Antibreast cancer activities of phytochemicals from Anonna muricata using computer-aided drug design (CADD) approach

Antibreast cancer activities of 131 phytochemicals from Annona muricata (Soursop) were investigated against human placental aromatase (PDB ID: 3S7S), a prominent target receptor in breast cancer therapy using computer aided-drug design approach. An antibreast cancer drug (tamoxifen) was used for comparison. The result of this work flourishes caffeoquinic acid (−8.4 kcal/mol), roseoside (−8.3 kcal/mol), chlorogenic acid (−8.2 kcal/mol), feruloylglycoside (−8.1 kcal/mol), citroside A (−8.0 kcal/mol), and coreximine (−7.8 kcal/mol), as probable inhibitors of human placental aromatase. This is due to their excellent binding affinities (ΔG), coupled with outstanding druglike, absorption, distribution, metabolism, excretion, and toxicity profiles, bioavailability and oral-bioavailability properties, and the interactions of important residues with the active pocket of human placental aromatase. All the results obtained were similar to that of the standards tamoxifen (−8.0 kcal/mol) but could be better when optimized. Thus, lead optimization, molecular dynamics, and in vivo investigations are thereby recommended on the identified potent compounds in the quest of developing new therapeutic agents against breast cancer.

Target-based drug discovery, ADMET profiling and bioactivity studies of antibiotics as potential inhibitors of SARS-CoV-2 main protease (Mpro)

A recent outbreak of a new strain of Coronavirus (SARS-CoV-2) has become a global health burden, which has resulted in deaths. No proven drug has been found to effectively cure this fast-spreading infection, hence the need to explore old drugs with the known profile in tackling this pandemic. A computer-aided drug design approach involving virtual screening was used to obtain the binding scores and inhibiting efficiencies of previously known antibiotics against SARS-CoV-2 main protease (Mpro). The drug-likeness analysis of the repurposed drugs were done using the Molinspiration chemoinformatics tool, while the Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis was carried out using ADMET SAR-2 webserver. Other analyses performed include bioactivities of the repurposed drug as a probable anti-SARS-CoV-2 agent and oral bioavailability analyses among others. The results were compared with those of drugs currently involved in clinical trials in the ongoing pandemic. Although antibiotics have been speculated to be of no use in the treatment of viral infections, literature has emerged lately to reveal the antiviral potential and immune-boosting ability of antibiotics. This study identified Tarivid and Ciprofloxacin with binding affinities of - 8.3 kcal/mol and - 8.1 kcal/mol, respectively as significant inhibitors of SARS-CoV-2 (Mpro) with better pharmacokinetics, drug-likeness and oral bioavailability, bioactivity properties, ADMET properties and inhibitory strength compared to Remdesivir (- 7.6 kcal/mol) and Azithromycin (- 6.3 kcal/mol). These observations will provide insight for further research (clinical trial) in the cure and management of COVID-19.

Computational Study on Potential Novel Anti-Ebola Virus Protein VP35 Natural Compounds

Ebola virus (EBOV) is one of the most lethal pathogens that can infect humans. The Ebola viral protein VP35 (EBOV VP35) inhibits host IFN-α/β production by interfering with host immune responses to viral invasion and is thus considered as a plausible drug target. The aim of this study was to identify potential novel lead compounds against EBOV VP35 using computational techniques in drug discovery. The 3D structure of the EBOV VP35 with PDB ID: 3FKE was used for molecular docking studies. An integrated library of 7675 African natural product was pre-filtered using ADMET risk, with a threshold of 7 and, as a result, 1470 ligands were obtained for the downstream molecular docking using AutoDock Vina, after an energy minimization of the protein via GROMACS. Five known inhibitors, namely, amodiaquine, chloroquine, gossypetin, taxifolin and EGCG were used as standard control compounds for this study. The area under the curve (AUC) value, evaluating the docking protocol obtained from the receiver operating characteristic (ROC) curve, generated was 0.72, which was considered to be acceptable. The four identified potential lead compounds of NANPDB4048, NANPDB2412, ZINC000095486250 and NANPDB2476 had binding affinities of −8.2, −8.2, −8.1 and −8.0 kcal/mol, respectively, and were predicted to possess desirable antiviral activity including the inhibition of RNA synthesis and membrane permeability, with the probable activity (Pa) being greater than the probable inactivity (Pi) values. The predicted anti-EBOV inhibition efficiency values (IC₅₀), found using a random forest classifier, ranged from 3.35 to 11.99 μM, while the Ki values ranged from 0.97 to 1.37 μM. The compounds NANPDB4048 and NANPDB2412 had the lowest binding energy of −8.2 kcal/mol, implying a higher binding affinity to EBOV VP35 which was greater than those of the known inhibitors. The compounds were predicted to possess a low toxicity risk and to possess reasonably good pharmacological profiles. Molecular dynamics (MD) simulations of the protein–ligand complexes, lasting 50 ns, and molecular mechanisms Poisson-Boltzmann surface area (MM-PBSA) calculations corroborated the binding affinities of the identified compounds and identified novel critical interacting residues. The antiviral potential of the molecules could be confirmed experimentally, while the scaffolds could be optimized for the design of future novel anti-EBOV chemotherapeutics.

Virtual screening, ADMET profiling, PASS prediction, and bioactivity studies of potential inhibitory roles of alkaloids, phytosterols, and flavonoids against COVID-19 main protease (Mpro)

The current research used a virtual screening method to study 57 isolated phytochemicals (alkaloids, phytosterols, and flavonoids) against the SARS-CoV-2 main protease (M^pro). The absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the selected compounds were analysed using admetSAR tool while SwissADME and Molinspiration chemoinformatics tools were used to examine the oral bioavailability and drug-likeness properties. Parameters such as physicochemical properties, activity spectra for substances (PASS) prediction, bioactivity, binding mode, and molecular interactions were also analysed. Our results favoured Lupeol (-8.6 kcal/mol), Lupenone (-7.7 kcal/mol), Hesperetin (-7.4 kcal/mol), Apigenin (-7.3 kcal/mol) and Castasterone (-7.3 kcal/mol) as probable inhibitors of SARS-CoV-2. This is because of their good binding affinities, bioactivities, drug-likeness, ADMET properties, PASS properties, oral bioavailability, binding mode and their interactions with the active site of the target receptor compared to Remdesivir and Azithromycin. Therefore, these compounds could be explored towards the development of new therapeutic agents against SARS-CoV-2.

Computational Screening of Potential Inhibitors of Desulfobacter postgatei for Pyrite Scale Prevention in Oil and Gas Wells

Sulfate-reducing bacteria (SRB), such as Desulfobacter postgatei are found in oil wells. However, they lead to the release of hydrogen sulfide. This in turn leads to the iron sulfide scale formation (pyrite). ATP sulfurylase is an enzyme present in SRB, which catalyzes the formation of adenylyl sulfate (APS) and inorganic pyrophosphatase (PPi) from ATP and sulfate. This reaction is the first among many in hydrogen sulfide production by D. postgatei . Consensus scoring using molecular docking and machine learning was used to identify three potential inhibitors of ATP sulfurylase from a database of about 40 million compounds. These selected hits ((S,E)-1-(4-methoxyphenyl)-3-(9-((m-tolylimino)methyl)-9,10-dihydroanthracen-9-yl)pyrrolidine-2,5-dione; methyl 2-[[(1S)-5-cyano-2-imino-1-(4-phenylthiazol-2-yl)-3-azaspiro[5.5]undec-4-en-4-yl]sulfanyl]acetate; and (4S)-4-(3-chloro-4-hydroxy-phenyl)-1-(6-hydroxypyridazin-3-yl)-3-methyl-4,5-dihydropyrazolo[3,4-b]pyridin-6-ol), known as A, B, and C, respectively) all had good binding affinities with ATP sulfurylase and were further analyzed for their toxicological properties. Compound A had the highest docking score. However, based on the physicochemical and toxicological properties, only compound C was predicted to be both safe and effective as a potential inhibitor of ATP sulfurylase, hence the preferred choice. The molecular interactions of compound C revealed favorable interactions with the following residues: LEU213, ASP308, ARG307, TRP347, LEU224, GLN212, MET211, and HIS309.

Repurposing of approved drug molecules for viral infectious diseases: a molecular modelling approach

The identification of new viral drugs has become a task of paramount significance due to the frequent occurrence of viral infections and especially during the current pandemic. Despite the recent advancements, the development of antiviral drugs has not made parallel progress. Reduction of time frame and cost of the drug development process is the major advantage of drug repurposing. Therefore, in this study, a drug repurposing strategy using molecular modelling techniques, i.e. biological activity prediction, virtual screening, and molecular dynamics simulation was employed to find promising repurposing candidates for viral infectious diseases. The biological activities of non-redundant (4171) drug molecules were predicted using PASS analysis, and 1401 drug molecules were selected which showed antiviral activities in the analysis. These drug molecules were subjected to virtual screening against the selected non-structural viral proteins. A series of filters, i.e. top 10 drug molecules based on binding affinity, mean value of binding affinity, visual inspection of protein-drug complexes, and number of H-bond between protein and drug molecules were used to narrow down the drug molecules. Molecular dynamics simulation analysis was carried out to validate the intrinsic atomic interactions and binding conformations of protein-drug complexes. The binding free energies of drug molecules were assessed by employing MMPBSA analysis. Finally, nine drug molecules were prioritized, as promising repurposing candidates with the potential to inhibit the selected non-structural viral proteins.Communicated by Ramaswamy H. Sarma.

Molecular Design of Novel Chemicals for Iron Sulfide Scale Removal

Scale deposition is a pertinent challenge in the oil and gas industry. Scales formed from iron sulfide are one of the troublous scales, particularly pyrite. Moreover, the use of biodegradable environmentally friendly chemicals reduces the cost compared to the conventional removal process. In this work, the chelating abilities of four novel chemicals, designed using the in silico technique of density functional theory (DFT), are studied as potential iron sulfide scale removers. Only one of the chemicals containing a hydroxamate functional group had a good chelating ability with Fe2+. The chelating strength and ecotoxicological properties of this chemical were compared to diethylenetriaminepentaacetic acid (DTPA), an already established iron sulfide scale remover. The new promising chemical surpassed DTPA in being a safer chemical and having a greater binding affinity to Fe2+ upon optimization, hence, a better choice. The presence of oxime (-NHOH) and carbonyl (C=O) moieties in the new chemical showed that the bidentate form of chelation is favored. Moreover, the presence of an intramolecular hydrogen bond enhanced its chelating ability.

COVID-19: CADD to the rescue

The recent outbreak of the deadly COVID-19 disease, being caused by the novel coronavirus (SARS-CoV-2), has put the world on red alert as it keeps spreading and recording more fatalities. Research efforts are being carried out to curtail the disease from spreading as it has been declared as of global health emergency. Hence, there is an exigent need to identify and design drugs that are capable of curing the infection and hinder its continual spread across the globe. Herein, a computer-aided drug design tool known as the virtual screening method was used to screen a database of 44 million compounds to find compounds that have the potential to inhibit the surface glycoprotein responsible for virus entry and binding. The consensus scoring approach selected three compounds with promising physicochemical properties and favorable molecular interactions with the target protein. These selected compounds can undergo lead optimization to be further developed as drugs that can be used in treating the COVID-19 disease.

In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach

Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+. Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+. The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes.

Identification of promising anti-DNA gyrase antibacterial compounds using de novo design, molecular docking and molecular dynamics studies

The rapidly increasing rate of antibiotic resistance is of great concern. Approximately two million deaths result annually from bacterial infections worldwide. Therefore, there is a paramount requirement to develop innovative and novel antibacterial agents with new mechanisms of action and activity against resistant bacterial strains. For this purpose, a set of benzothiazole and N-phenylpyrrolamides derivatives reported as DNA Gyrase B (GyrB) inhibitors were collected from the literature and docked inside the receptor cavity of DNA Gyrase B (PDB ID: 5L3J). The best 10 docked complexes were used to identify novel antibacterial chemical agents through a de novo design approach. Out of initial 300 chemical analogues, the best six analogues were identified using screening with a set of criteria followed by pharmacokinetic analysis. The binding interactions of the best six analogues revealed that all molecules formed a number of critical interactions with catalytic amino residues of DNA Gyrase B with high binding energy. The predicted inhibitory constant biological activity based on binding energy supported the potential of the molecules as DNA Gyrase B ligands. The RMSD, RMSF, and radius of gyration parameters obtained from the 100 ns molecular dynamics simulation study clearly demonstrated that all six analogues were efficient enough to form stable complexes with DNA Gyrase B. High negative binding energy of all ligands obtained from MM-GBSA approach undoubtedly explained the strong affinity toward the DNA Gyrase B. Therefore, the proposed de novo designed molecules can be considered as promising antibacterial chemical agents subject to experimental validation, in vitro.Communicated by Ramaswamy H. Sarma.

Molecular modelling studies on adamantane-based Ebola virus GP-1 inhibitors using docking, pharmacophore and 3D-QSAR

The pathogenic Ebola virus (EBOV) causes a potential health risk and global spread. To date, few drugs are available for the treatment of Ebola virus disease (EVD) that allow researchers to use computational methods for designing potential drugs. The developed PHASE-based common six-point pharmacophore hypothesis (AADHPR_1) showed the necessity of two hydrogen bond acceptor features, one hydrogen bond donor feature, one hydrophobic group feature, one positively ionizable and one aromatic ring feature for further designing. We developed best 3D-QSAR models with high regression coefficients for the training (r²>0.82) and test (Q²>0.5) sets for both atoms-based and field-based 3D-QSAR models. The molecule 1A-4 (docking score = -4.711 kcal/mol) was obtained as best docked (SP mode) on Ebola virus envelope glycoprotein (PDB ID-3CSY) as compared with the standards oseltamivir (docking score = -4.39 kcal/mol) and zanamivir (docking score = -3.392 kcal/mol). The obtained ZINC hit ZINC58935541 showed a good docking score of -4.892 kcal/mol. The ZINC58935541 molecule also showed a strong binding affinity towards the receptor cavity of Ebola virus envelope glycoprotein when simulated for 1.2 ns. The good QikProp parameters reflect the fact that this molecule, upon optimization into a lead, might become a good candidate for the treatment of EVD.