Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii

Identification of novel chemical scaffolds against kinase domain of cancer causing human epidermal growth factor receptor 2: a systemic chemoinformatic approach

The Human epidermal growth factor receptor 2 (HER2) is expressed in high magnitude in several cancers. Designing new drug molecules that target kinase domain of the HER2 enzyme might provide an appealing platform. Considering this, herein, a multi-phase bioinformatic approach is applied to screen diverse natural and chemical scaffolds to identify compounds that fit best at the kinase domain of HER2. By doing so, three compounds; LAS_51187157, LAC_51217113, LAC_51390233 were pointed with docking score of -11.4 kcal/mol, -11.3 kcal/mol and -11.2 kcal/mol, respectively. In molecular dynamic simulation, the complexes behaved in a stable dynamic with no major local/global structural variations. The intermolecular binding free energies were further estimated that concluded LAC_51390233 complex was the most stable and has less entropy energy. The good docked affinity of LAC_51390233 with HER2 was confirmed by WaterSwap absolute binding free energy. The entropy energy demonstrated that LAC_51390233 has less freedom energy compared to others. Similarly, all three compounds revealed very favorable druglike properties and pharmacokinetics. All the selected three compounds were also non-carcinogenic, non-immunotoxicity, non-mutagenicity, and non-cytotoxic. In a nutshell, the compounds are interesting scaffolds and might be subjected to extensive experimental testing to reveal their real biological potency.Communicated by Ramaswamy H. Sarma.

Efficacy assessment of novel methanimine derivatives in chronic constriction injury-induced neuropathic model: An in-vivo, ex-vivo and In-Silico approach

The multicomponent etiology, complex clinical implications, dose-based side effect and degree of pain mitigation associated with the current pharmacological therapy is incapable in complete resolution of chronic neuropathic pain patients which necessitates the perpetual requirement of novel medication therapy. Therefore, this study explored the ameliorative aptitude of two novel methanimine imitative like (E)-N-(4-nitrobenzylidene)-4‑chloro-2-iodobenzamine (KB 09) and (E)-N-(4-methylbenzylidene)-4‑chloro-2-iodobenzamine (KB 10) in chronic constriction injury (CCI) of sciatic nerve induced neuropathic pain in rat model. Standard behavioral tests like dynamic and static allodynia, cold, thermal and mechanical hyperalgesia along with rotarod activity were performed at various experimental days like 0, 3, 7, 14 and 21. Enzyme linked immunosorbent assay (ELISA) on spinal tissue and antioxidant assays on sciatic nerve were executed accompanied by molecular docking and simulation studies. Prolonged ligation of sciatic nerve expressively induced hyperalgesia as well as allodynia in rats. KB 09 and KB 10 substantially attenuated the CCI elicited hyperalgesia and allodynia. They significantly reduced the biomarkers of pain and inflammation like Interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) in ELISA and while enhanced the GSH, SOD and CAT and diminished the MDA levels during antioxidant assays. KB 09 displayed -9.62 kcal/mol with TNF-α and -7.68 kcal/mol binding energy with IL-6 whereas KB 10 exhibited binding energy of -8.20 kcal/mol with IL-6 while -11.68 kcal/mol with TNF-α and hence both trial compounds ensured stable interaction with IL-6 and TNF-α during computational analysis. The results advocated that both methanimine derivatives might be novel candidates for attenuation of CCI-induced neuropathic pain prospects via anti-nociceptive, anti-inflammatory and antioxidant mechanisms.

Targeting XGHPRT enzyme to manage Helicobacter pylori induced gastric cancer: A multi-pronged machine learning, artificial intelligence and biophysics-based study

Helicobacter pylori infects the stomach mucosa of over half of the global population and can lead to gastric cancer. This pathogen has demonstrated resistance to many frequently prescribed antibiotics, thereby underscoring the pressing need to identify novel therapeutic targets. The inhibition or disruption of nucleic acid biosynthesis constitutes a promising avenue for either restraining or eradicating bacterial proliferation. The synthesis of RNA and DNA precursors (6-oxopurine nucleoside monophosphates) is catalyzed by the XGHPRT enzyme. In this study, using machine learning, artificial intelligence and biophysics-based software, CHEMBRIDGE-10000196, CHEMBRIDGE-10000295, and CHEMBRIDGE-10000955 were predicted as promising binders to the XGHPRT with a binding score of -14.20, -13.64, and -12.08 kcal/mol, respectively, compared to a control guanosine-5'-monophosphate exhibiting a docking score of -10.52 kcal/mol. These agents formed strong interactions with Met33, Arg34, Ala57, Asp92, Ser93, and Gly94 at short distance. The docked complexes of the lead compounds exhibited stable dynamics during the simulation time with no global changes noticed. The docked complexes demonstrate a significantly stable MM-GBSA and MM-PBSA net binding energy of -60.1 and -61.18 kcal/mol for the CHEMBRIDGE-10000196 complex. The MM-GBSA net energy value of the CHEMBRIDGE-10000295 complex and the CHEMBRIDGE-10000955 complex is -71.17 and -65.29 kcal/mol, respectively. The CHEMBRIDGE-10000295 and CHEMBRIDGE-10000955 complexes displayed a net value of -71.91 and -63.49 kcal/mol, respectively, as per the MM-PBSA. The major driving intermolecular interactions for the docked complexes were found to be the electrostatic and van der Waals. The three filtered molecules hold potential for experimental evaluation of their potency against the XGHPRT enzyme.

Unveiling MurE ligase potential inhibitors for treating multi-drug resistant Acinetobacter baumannii

Acinetobacter baumannii is an opportunistic pathogen with ability to cause serious infection such as bacteremia, ventilator associated pneumonia, and wound infections. As strains of A. baumannii are resistant to almost all clinically used antibiotics and with the emergence of carbapenems resistant phenotypes warrants the search for novel antibiotics. Considering this, herein, a series of computer aided drug designing approach was utilized to search novel chemical scaffolds that bind stronger to MurE ligase enzyme of A. baumannii, which is involved peptidoglycan synthesis. The work identified LAS_22461675, LAS_34000090 and LAS_51177972 compounds as promising binding molecules with MurE enzyme having binding energy score of -10.5 kcal/mol, -9.3 kcal/mol and -8.6 kcal/mol, respectively. The compounds were found to achieve docked inside the MurE substrate binding pocket and established close distance chemical interactions. The interaction energies were dominated by van der Waals and less contributions were seen from hydrogen bonding energy. The dynamic simulation assay predicted the complexes stable with no major global and local changes noticed. The docked stability was also validated by MM/PBSA and MM/GBSA binding free energy methods. The net MM/GBSA binding free energy of LAS_22461675 complex, LAS_34000090 complex and LAS_51177972 complex is -26.25 kcal/mol, -27.23 kcal/mol and -29.64 kcal/mol, respectively. Similarly in case of MM-PBSA, the net energy value was in following order; LAS_22461675 complex (-27.67 kcal/mol), LAS_34000090 complex (-29.94 kcal/mol) and LAS_51177972 complex (-27.32 kcal/mol). The AMBER entropy and WaterSwap methods also confirmed stable complexes formation. Further, molecular features of the compounds were determined that predicted compounds to have good druglike properties and pharmacokinetic favorable. The study concluded the compounds to good candidates to be tested by in vivo and in vitro experimental assays.Communicated by Ramaswamy H. Sarma.

A hierarchical approach towards identification of novel inhibitors against L, D-transpeptidase YcbB as an anti-bacterial therapeutic target

The bacterial cell wall, being a vital component for cell viability, is regarded as a promising drug target. The L, D-Transpeptidase YcbB enzyme has been implicated for a significant role in cell wall polymers cross linking during typhoid toxin release, β-lactam resistance and outer membrane defect rescue. These observations have been recorded in different bacterial pathogens such as Salmonella Typhimurium, Citrobacter rodentium, and Salmonella typhi. In this work, we have shown structure based virtual screening of diverse natural and synthetic drug libraries against the enzyme and revealed three compounds as LAS_32135590, LAS_34036730 and LAS-51380924. These compounds showed highly stable energies and the findings are very competitive with the control molecule ((1RG or (4 R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid or ertapenem)) used. Compared to control (which has binding energy score of -11.63 kcal/mol), the compounds showed better binding energy. The binding energy score of LAS_32135590, LAS_34036730 and LAS-51380924 is -12.63 kcal/mol, -12.22 kcal/mol and -12.10 kcal/mol, respectively. Further, the docked snapshot of the lead compounds and control were investigated for stability under time dependent dynamics environment. All the three leads complex and control system showed significant equilibrium (mean RMSD < 3 Å) both in term of intermolecular docked conformation and binding interactions network. Further validation on the complex's stability was acquired from the end-state MMPB/GBSA analysis that observed greater contribution from van der Waals forces and electrostatic energy while less contribution was noticed from solvation part. The compounds were also showed good drug-likeness and are non-toxic and non-mutagenic. In short, the compounds can be used in experimental testing's and might be subjected to structure modification to get better results.Communicated by Ramaswamy H. Sarma.

In silico and in vitro prediction of new synthesized N-heterocyclic compounds as anti-SARS-CoV-2

Computer-aided drug design has been employed to get the medicinal effects against Corona virus from different pyridine derivatives after synthesizing the new compounds. Additionally, various computational studies are also employed between the newly prepared pyridine derivatives and three controls against three proteins (6Y2E, 6M71 and 6M3M). Different methods were employed to synthesize new pyridine derivatives according to the literature using different reaction mediums. MTT was performed for cytotoxicity study and IC50 for inhibitory concentration. Additionally, in-silico studies including DFT, molecular docking, molecular dynamics, MMPBSA, ADME, pharmacokinetics and Lipinski rules were evaluated. The chemical structures of all new compounds were elucidated based on spectroscopic investigation. A molecular docking study demonstrated that compounds 5, 11, and 12 have the best binders of the SARS-CoV-2 main protease enzyme, with energy scores of - 7.5 kcal/mol, - 7.2 kcal/mol, and - 7.9 kcal/mol, respectively. The net binding energy values of the 11-Mpro, 12-Mpro, and 5-Mpro complexes revealed their highly stable nature in terms of both intermolecular interactions and docked conformation across the simulation time. ADME properties, besides the pharmacokinetics and Lipinski rules, showed that all seven newly synthesized compounds follow Lipinski rules with high GI absorption. The In Vitro antiviral study against SARS-CoV-2 using MTT methods confirms that compound 5 has more potential and is safer than other tested compounds. The study shows that the newly synthesized pyridine derivatives have medicinal properties against SARS-CoV-2 without violating Lipinski rules. Compounds 5, 11, and 12, particularly compound 5, may serve as promising potential candidate for COVID-19.

Synthesis, Cytotoxic, and Computational Screening of Some Novel Indole-1,2,4-Triazole-Based S-Alkylated N-Aryl Acetamides

Molecular hybridization has emerged as the prime and most significant approach for the development of novel anticancer chemotherapeutic agents for combating cancer. In this pursuit, a novel series of indole-1,2,4-triazol-based N-phenyl acetamide structural motifs 8a-f were synthesized and screened against the in vitro hepatocellular cancer Hep-G2 cell line. The MTT assay was applied to determine the anti-proliferative potential of novel indole-triazole compounds 8a-f, which displayed cytotoxicity potential as cell viabilities at 100 µg/mL concentration, by using ellipticine and doxorubicin as standard reference drugs. The remarkable prominent bioactive structural hybrids 8a, 8c, and 8f demonstrated good-to-excellent anti-Hep-G2 cancer chemotherapeutic potential, with a cell viability of (11.72 ± 0.53), (18.92 ± 1.48), and (12.93 ± 0.55), respectively. The excellent cytotoxicity efficacy against the liver cancer cell line Hep-G2 was displayed by the 3,4-dichloro moiety containing indole-triazole scaffold 8b, which had the lowest cell viability (10.99 ± 0.59) compared with the standard drug ellipticine (cell viability = 11.5 ± 0.55) but displayed comparable potency in comparison with the standard drug doxorubicin (cell viability = 10.8 ± 0.41). The structure-activity relationship (SAR) of indole-triazoles 8a-f revealed that the 3,4-dichlorophenyl-based indole-triazole structural hybrid 8b displayed excellent anti-Hep-G2 cancer chemotherapeutic efficacy. The in silico approaches such as molecular docking scores, molecular dynamic simulation stability data, DFT, ADMET studies, and in vitro pharmacological profile clearly indicated that indole-triazole scaffold 8b could be the lead anti-Hep-G2 liver cancer therapeutic agent and a promising anti-Hep-G2 drug candidate for further clinical evaluations.

'Synthesis, antiviral activity, molecular docking, and molecular dynamics studies of ethoxy phthalimide pyrazole derivatives against Cytomegalovirus and Varicella-Zoster virus: potential consequences and strategies for developing new antiviral treatments'

Substituted ethoxy phthalimide pyrazole derivatives (6a-e) have been produced using a one-pot synthesis technique. Spectral analysis was used to establish the molecular structure of the synthesized compounds, and they were examined in silico and in vitro for their ability to bind to and inhibit replication of the AD-169 strain, the Davis strain of CMV, the OKA strain and the 07/1 strain of Varicella-Zoster virus (VZV). Molecular Docking was used to estimate the binding mechanism and energy of compounds 4, 6a-e to their respective target proteins, thymidine kinase (TK), Varicella-Zoster protease (VZP) of VZV and tegument protein pp71 (TPpp71) of Cytomegalovirus (CMV). The MIC50 and EC50 were utilized to evaluate the antiviral and cytotoxic activities of test compounds in human embryonic lung (HEL) cells against the two reference medicines, Ganciclovir and Acyclovir. The chemicals studied showed a high affinity for binding sites and near binding sites of target proteins by generating H-bonds, carbon-hydrogen bonds, π-anion, π-sulfur, π-sigma, alkyl and π-alkyl interactions. All of the test compounds (6a-e) had higher binding energy than the standard medications. The ADME/T data suggests that these potential inhibitors are less toxic. Drug-protein complexes are structurally compact and demonstrate minimal conformational change in molecular dynamics (MDs) simulations, indicating stability and stiffness. MM-PBSA and post-simulation analysis can predict lead compound active cavity binding stability. By inhibiting multitargeted proteins, these synthetic compounds may improve antiviral therapy. Our research suggests that these unique synthesized chemicals may be useful and accessible adjuvant antiviral therapy for Varicella Zoster and CMV. HighlightsTwo components synthesis of substituted ethoxy phthalimide pyrazole derivatives (6a-e).Tested compounds (6a-e) have antiviral and cytotoxicity activity against CMV and Varicella-Zoster virus (VZV) in HEL cells.Compounds bind to TK, Varicella-Zoster protease (VZP) of VZV, and modeled TPpp71 of Cytomegalovirus (CMV).In comparison to reference drugs, compounds have strong binding free energy and interactions with VZV and CMV protein complexes.The RMSD, RMSF, Rg, residual correlative motion (RCM), No. of hydrogen bonds, protein secondary structure content, per-residue protein secondary structure and MM/PBSA energy calculated for the selected compound with thymidine kinase (TK), VZP of VZV, and modeled tegument protein pp71 (TPpp71) of CMV through MD simulation studies for 50 ns.In comparison to the two reference drugs, ligands/compounds were found to meet the Lipinski rule of five and to have strong biological activity.Communicated by Ramaswamy H. Sarma.

Macromolecules: Synthesis, antimicrobial, POM analysis and computational approaches of some glucoside derivatives bearing acyl moieties

Macromolecules i.e., carbohydrate derivatives are crucial to biochemical and medical research. Herein, we designed and synthesized eight methyl α-D-glucopyranoside (MGP) derivatives (2-8) in good yields following the regioselective direct acylation method. The structural configurations of the synthesized MGP derivatives were analyzed and verified using multiple physicochemical and spectroscopic techniques. Antimicrobial experiments revealed that almost all derivatives demonstrated noticeable antifungal and antibacterial efficacy. The synthesized derivatives showed minimum inhibitory concentration (MIC) values ranging from 0.75 µg/mL to 1.50 µg/mL and minimum bactericidal concentrations (MBCs) ranging from 8.00 µg/mL to 16.00 µg/mL. Compound 6 inhibited Ehrlich ascites carcinoma (EAC) cell proliferation by 10.36% with an IC50 of 2602.23 μg/mL in the MTT colorimetric assay. The obtained results were further rationalized by docking analysis of the synthesized derivatives against 4URO and 4XE3 receptors to explore the binding affinities and nonbonding interactions of MGP derivatives with target proteins. Compound 6 demonstrated the potential to bind with the target with the highest binding energy. In a stimulating environment, a molecular dynamics study showed that MGP derivatives have a stable conformation and binding pattern. The MGP derivatives were examined using POM (Petra/Osiris/Molinspiration) bioinformatics, and as a result, these derivatives showed good toxicity, bioavailability, and pharmacokinetics. Various antifungal/antiviral pharmacophore (Oδ-, O'δ-) sites were identified by using POM investigations, and compound 6 was further tested against other pathogenic fungi and viruses, such as Micron and Delta mutants of SARS-CoV-2.

Screening of marine natural products for potential inhibitors targeting biotin biosynthesis pathway in Mycobacterium tuberculosis

Tuberculosis (TB) remains as one of the major public health concerns worldwide. A successful TB control and treatment is very challenging, due to continuing emergence of Mycobacterium tuberculosis strains resistant to known drugs. Therefore, the development of new drugs with different chemical and biological approaches is necessary to obtain more efficient anti-tubercular therapeutics. Biotin is an essential cofactor for lipid biosynthesis and gluconeogenesis in M. tuberculosis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. In this study, comprehensive in silico methods including structure-based virtual screening, molecular docking, and molecular dynamic simulation analysis for ∼8000 marine natural products were performed against two essential enzymes involved in biotin synthesis and ligation of M. tuberculosis namely, pyridoxal 5'-phosphate-dependent transaminase (BioA) and mycobacterial biotin protein ligase (MtBPL). Two compounds; CMNPD10112 and CMNPD10113 are unveiled to bind the enzymes consistently and with high affinities. The binding pattern of compounds is further noticed in very stable binding modes as analyzed by molecular dynamics simulation and the mean RMSD of the complexes is within 4 Å. The intermolecular binding free energies validated complexes are less than -40 kcal/mol, which demonstrates strong and stable complexes formation. The identified hit compounds could be seeds for design of effective anti-mycobacterium therapeutics by inhibition of bacterial growth through blocking the biotin biosynthesis.Communicated by Ramaswamy H. Sarma.

Cheminformatics and biomolecular dynamics studies towards the discovery of anti-staphylococcal nuclease domain-containing 1 (SND1) inhibitors to treat metastatic breast cancer

Metastatic breast cancer is a prime health concern and leading health burden across the globe. Previous efforts have shown that protein-protein interaction between Metadherin and Staphylococcal nuclease domaincontaining 1 (SND1) promotes initiation of breast cancer, progression, therapy resistance and metastasis. Therefore, small drug molecules that can interrupt the Metadherin and SND1 interaction may be ideal to suppress tumor growth, metastasis and increases chemotherapy sensitivity of triple negative breast cancer. Here, in this study, structure based virtual screening was conducted against the reported active site of SND1 enzyme, which revealed three promising lead molecules from Asinex library. These compounds were; BAS_00381028, BAS_00327287, and BAS_01293454 with binding energy score -10.25 kcal/mol, -9.65 kcal/mol and -9.32 kcal/mol, respectively. Compared to control (5-chloro-2-methoxy-N-([1,2,4]triazolo[1,5-a]pyridin-8-yl)benzene-1-sulfonamide) the lead molecules showed robust hydrophilic and hydrophobic interactions with the enzyme and revealed stable docked conformation in molecular dynamics simulation. During the simulation time, the compounds reported stable dynamics with no obvious fluctuation in binding mode and interactions noticed. The mean root mean square deviation (RMSD) of BAS_00381028, BAS_00327287, and BAS_01293454 complexes were 1.87 Å, 1.75 Å, 1.34 Å, respectively. Furthermore, the MM/GBSA analysis was conduction on the simulation trajectories of complexes that unveiled binding energy score of -19.25 kcal/mol, -27.03 kcal/mol, -34.6 kcal/mol and -29.61 kcal/mol for control, BAS_00381028, BAS_00327287, and BAS_01293454, respectively. In MM/PBSA, the binding energy value of for control, BAS_00381028, BAS_00327287, and BAS_01293454 was -20.45 kcal/mol, -27.89 kcal/mol, -36.41 kcal/mol and -32.01 kcal/mol, respectively. Additionally, the compounds were classified as druglike and have favorable pharmacokinetic properties. The compounds were predicted as promising leads and might be used in experimental investigation to study their anti-SND1 activity.

Identification and dynamics of novel scaffolds against Enterococcus faecium serine hydroxymethyltransferase enzyme: a potential target for antibiotics development

Serine hydroxymethyltransferase enzyme is a significant player in purine, thymidylate, and L-serine biosynthesis and has been tagged as a potential target for cancer, viruses, and parasites. However, this enzyme as an anti-bacterial druggable target has not been explored much. Herein, in this work, different computational chemistry and biophysics techniques were applied to identify potential computational predicted inhibitory molecules against Enterococcus faecium serine hydroxymethyltransferase enzyme. By structure based virtual screening process of ASINEX antibacterial library against the enzyme two main compounds: Top-1_BDC_21204033 and Top-2_BDC_20700155 were reported as best binding molecules. The Top-1_BDC_21204033 and Top-2_BDC_20700155 binding energy value is -9.3 and -8.9 kcal/mol, respectively. The control molecule binding energy score is -6.55 kcal/mol. The mean RMSD of Top-1-BDC_21204033, Top-2-BDC_20700155 and control is 3.7 Å (maximum 5.03 Å), 1.7 Å (maximum 3.05 Å), and 3.84 Å (maximum of 6.7 Å), respectively. During the simulation time, the intermolecular docked conformation and interactions were seen stable despite of few small jumps by the compounds/control, responsible for high RMSD in some frames. The MM/GBSA and MM/PBSA binding free energy of lead Top-2-BDC_20700155 complex is -79.52 and -82.63 kcal/mol, respectively. This complex was seen as the most stable compared to the control. Furthermore, the lead molecules and control showed good druglikeness and pharmacokinetics profile. The lead molecules were non-toxic and non-mutagenic. In short, the compounds are promising in terms of binding to the serine hydroxymethyltransferase enzyme and need to be subjected to experimental studies.Communicated by Ramaswamy H. Sarma.

A cheminformatics-biophysics correlate to identify promising lead molecules against matrix metalloproteinase-2 (MMP-2) enzyme: A promising anti-cancer target

Matrix metalloproteinase-2 (MMP-2) is an endopeptidase enzyme that is devoted to extracellular matrix proteins degradation. The enzyme is warranted as promising drugs target for different light threating diseases such as arthritis, cancer and fibrosis. Herein, in this study, three drug molecules: CMNPD8322, CMNPD8320, and CMNPD8318 were filtered as high affinity binding compounds with binding energy score of -9.75 kcal/mol, -9.11 kcal/mol, -9.05 kcal/mol, respectively. The control binding energy score was -9.01 kcal/mol. The compounds docked deeply inside the pocket interacting with S1 pocket residues. The docked complexes dynamics in real time at cellular environment was then done to decipher the stable binding conformation and intermolecular interactions network. The compounds complexes achieved very stable dynamics with root mean square deviation (RMSD) with mean value of around 2-3 Å compared to control complex that showed higher fluctuations of 5 Å. The simulation trajectories frames based binding free energy demonstrated all the compounds-MMP-2 complexes reported highly stable energy, particularly the van der Waals energy dominate the overall net energy. Similarly, the complexes revalidation of WaterSwap based energies also disclosed the complexes highly stable in term docked conformation. Also, the compounds illustrated the compounds favorable pharmacokinetics and were non-toxic and non-mutagenic. Thus, the compounds might be used thorough experimental assays to confirm compounds selective biological potency against MMP-2 enzyme.

Uridine Derivatives: Synthesis, Biological Evaluation, and In Silico Studies as Antimicrobial and Anticancer Agents

Nucleoside analogs are frequently used in the control of viral infections and neoplastic diseases. However, relatively few studies have shown that nucleoside analogs have antibacterial and antifungal activities. In this study, a fused pyrimidine molecule, uridine, was modified with various aliphatic chains and aromatic groups to produce new derivatives as antimicrobial agents. All newly synthesized uridine derivatives were analyzed by spectral (NMR, FTIR, mass spectrometry), elemental, and physicochemical analyses. Prediction of activity spectra for substances (PASS) and in vitro biological evaluation against bacteria and fungi indicated promising antimicrobial capability of these uridine derivatives. The tested compounds were more effective against fungal phytopathogens than bacterial strains, as determined by their in vitro antimicrobial activity. Cytotoxicity testing indicated that the compounds were less toxic. In addition, antiproliferative activity against Ehrlich ascites carcinoma (EAC) cells was investigated, and compound 6 (2',3'-di-O-cinnamoyl-5'-O-palmitoyluridine) demonstrated promising anticancer activity. Their molecular docking against Escherichia coli (1RXF) and Salmonella typhi (3000) revealed notable binding affinities and nonbonding interactions in support of this finding. Stable conformation and binding patterns/energy were found in a stimulating 400 ns molecular dynamics (MD) simulation. Structure-activity relationship (SAR) investigation indicated that acyl chains, CH₃(CH₂)₁₀CO-, (C₆H₅)₃C-, and C₂H₅C₆H₄CO-, combined with deoxyribose, were most effective against the tested bacterial and fungal pathogens. Pharmacokinetic predictions were examined to determine their ADMET characteristics, and the results in silico were intriguing. Finally, the synthesized uridine derivatives demonstrated increased medicinal activity and high potential for future antimicrobial/anticancer agent(s).

An integrated computational approach towards novel drugs discovery against polyketide synthase 13 thioesterase domain of Mycobacterium tuberculosis

The acquired drug resistance by Mycobacterium tuberculosis (M. tuberculosis) to antibiotics urges the need for developing novel anti-M. tuberculosis drugs that possess novel mechanism of action. Since traditional drug discovery is a labor-intensive and costly process, computer aided drug design is highly appreciated tool as it speeds up and lower the cost of drug development process. Herein, Asinex antibacterial compounds were virtually screened against thioesterase domain of Polyketide synthase 13, a unique enzyme that forms α-alkyl β-ketoesters as a direct precursor of mycolic acids which are essential components of the lipid-rich cell wall of M. tuberculosis. The study identified three drug-like compounds as the most promising leads; BBB_26582140, BBD_30878599 and BBC_29956160 with binding energy value of - 11.25 kcal/mol, - 9.87 kcal/mol and - 9.33 kcal/mol, respectively. The control molecule binding energy score is -9.25 kcal/mol. Also, the docked complexes were dynamically stable with maximum root mean square deviation (RMSD) value of 3 Å. Similarly, the MM-GB\PBSA method revealed highly stable complexes with mean energy values < - 75 kcal/mol for all three systems. The net binding energy scores are validated by WaterSwap and entropy energy analysis. Furthermore, The in silico druglike and pharmacokinetic investigation revealed that the compounds could be suitable candidates for additional experimentations. In summary, the study findings are significant, and the compounds may be used in experimental validation pipeline to develop potential drugs against drug-resistant tuberculosis.

Targeting Toxoplasma gondii ME49 TgAPN2: A Bioinformatics Approach for Antiparasitic Drug Discovery

As fewer therapeutic options are available for treating toxoplasmosis, newer antiparasitic drugs that can block TgAPN2 M1 aminopeptidase are of significant value. Herein, we employed several computer-aided drug-design approaches with the objective of identifying drug molecules from the Asinex library with stable conformation and binding energy scores. By a structure-based virtual screening process, three molecules—LAS_52160953, LAS_51177972, and LAS_52506311—were identified as promising candidates, with binding affinity scores of −8.6 kcal/mol, −8.5 kcal/mol, and −8.3 kcal/mol, respectively. The compounds produced balanced interacting networks of hydrophilic and hydrophobic interactions, vital for holding the compounds at the docked cavity and stable binding conformation. The docked compound complexes with TgAPN2 were further subjected to molecular dynamic simulations that revealed mean RMSD for the LAS_52160953 complex of 1.45 Å), LAS_51177972 complex 1.02 Å, and LAS_52506311 complex 1.087 Å. Another round of binding free energy validation by MM-GBSA/MM-PBSA was done to confirm docking and simulation findings. The analysis predicted average MM-GBSA value of <−36 kcal/mol and <−35 kcal/mol by MM-PBSA. The compounds were further classified as appropriate candidates to be used as drug-like molecules and showed favorable pharmacokinetics. The shortlisted compounds showed promising biological potency against the TgAPN2 enzyme and may be used in experimental validation. They may also serve as parent structures to design novel derivatives with enhanced biological potency.

Proteome-Wide Screening of Potential Vaccine Targets against Brucella melitensis

The ongoing antibiotic-resistance crisis is becoming a global problem affecting public health. Urgent efforts are required to design novel therapeutics against pathogenic bacterial species. Brucella melitensis is an etiological agent of brucellosis, which mostly affects sheep and goats but several cases have also been reported in cattle, water buffalo, yaks and dogs. Infected animals also represent the major source of infection for humans. Development of safer and effective vaccines for brucellosis remains a priority to support disease control and eradication in animals and to prevent infection to humans. In this research study, we designed an in-silico multi-epitopes vaccine for B. melitensis using computational approaches. The pathogen core proteome was screened for good vaccine candidates using subtractive proteomics, reverse vaccinology and immunoinformatic tools. In total, 10 proteins: catalase; siderophore ABC transporter substrate-binding protein; pyridoxamine 5'-phosphate oxidase; superoxide dismutase; peptidylprolyl isomerase; superoxide dismutase family protein; septation protein A; hypothetical protein; binding-protein-dependent transport systems inner membrane component; and 4-hydroxy-2-oxoheptanedioate aldolase were selected for epitopes prediction. To induce cellular and antibody base immune responses, the vaccine must comprise both B and T-cells epitopes. The epitopes were next screened for antigenicity, allergic nature and water solubility and the probable antigenic, non-allergic, water-soluble and non-toxic nine epitopes were shortlisted for multi-epitopes vaccine construction. The designed vaccine construct comprises 274 amino acid long sequences having a molecular weight of 28.14 kDa and instability index of 27.62. The vaccine construct was further assessed for binding efficacy with immune cell receptors. Docking results revealed that the designed vaccine had good binding potency with selected immune cell receptors. Furthermore, vaccine-MHC-I, vaccine-MHC-II and vaccine-TLR-4 complexes were opted based on a least-binding energy score of -5.48 kcal/mol, 0.64 kcal/mol and -2.69 kcal/mol. Those selected were then energy refined and subjected to simulation studies to understand dynamic movements of the docked complexes. The docking results were further validated through MMPBSA and MMGBSA analyses. The MMPBSA calculated -235.18 kcal/mol, -206.79 kcal/mol, and -215.73 kcal/mol net binding free energy, while MMGBSA estimated -259.48 kcal/mol, -206.79 kcal/mol and -215.73 kcal/mol for TLR-4, MHC-I and MHC-II complexes, respectively. These findings were validated by water-swap and entropy calculations. Overall, the designed vaccine construct can evoke proper immune responses and the construct could be helpful for experimental researchers in formulation of a protective vaccine against the targeted pathogen for both animal and human use.

Unlocking SGK1 inhibitor potential of bis-[1-N,7-N, pyrazolo tetraethoxyphthalimido{-4-(3,5-Dimethyl-4-(spiro-3-methylpyazolo)-1,7-dihydro-1H-dipyrazolo[3,4-b;4',3'-e]pyridin-8-yl)}]p-disubstituted phenyl compounds: a computational study

SGK1 (Serum and Glucocorticoid Regulated Kinase 1), a serine/threonine kinase that is activated by various stimuli, including serum and glucocorticoids. It controls inflammation, apoptosis, hormone release, neuro-excitability and cell proliferation, all of which play an important role in cancer progression and metastasis. SGK1 was recently proposed as a potential drug target for cancer, diabetes, and neurodegenerative diseases. In this study, molecular docking, physiochemical, toxicological properties and molecular dynamic simulation of the Bis-[1-N,7-N, Pyrazolo tetraethoxyphthalimido{-4-(3,5-Dimethyl-4-(spiro-3-methylpyazolo)-1,7-dihydro-1H-dipyrazolo[3,4-b;4',3'-e]pyridin-8-yl)}]p-disubstituted phenyl compoundsand reference EMD638683 against new SGK1 target protein. Compared to the reference inhibitor EMD638683, we choose the best compounds (series 2-6) based on the binding energy (in the range from -11.0 to -10.6 kcal/mol). With the exception of compounds 2 and 6, none of the compounds posed a risk for AMES toxicity or carcinogenicity due to their toxicological properties. 100 ns MD simulation accompanied by MM/PBSA energy calculations and PCA. According to MD simulation results, the binding of compounds 3, 4 and 5 stabilizes the SGK1 structure and causes febrile conformational changes compared to EMD638683. As a result of this research, the final selected compounds 3, 4 and 5 can be used as scaffolds to develop promising SGK1 inhibitors for the treatment of related diseases such as cancer.Communicated by Ramaswamy H. Sarma.

Molecular docking and simulation studies of flavonoid compounds against PBP-2a of methicillin-resistant Staphylococcus aureus

Methicillin-Resistant Staphylococcus aureus (MRSA), a pathogenic bacterium that causes life-threatening outbreaks such as community-onset and nosocomial infections as emerging 'superbug'. Time and motion study of its virulent property developed resistance against most of the antibiotics such as Vancomycin. Thereby, to curb this problem entails the development of new therapeutic agents. Plant-derived antimicrobial agents have recently piqued people's interest, so in this research, 186 flavonoids compound selected to unmask the best candidates that can act as potent inhibitors against the Penicillin Binding Protein-2a (PBP-2a) of MRSA. Molecular docking performed using PyRx and GOLD suite to determine the binding affinities and interactions between the phytochemicals and the PBP-2a. The selected candidates strongly interact with the different amino acid residues. The 30 ns molecular dynamics (MD) simulations with five top-ranked compounds such as Naringin, Hesperidin, Neohesperidin, Didymin and Icariin validated the docking interactions. These findings are also strongly supported by root-mean-square deviation, root-mean-square fluctuation and the radius of gyration. ADME/T analysis demonstrates that these candidates appear to be safer inhibitors. Our findings point to natural flavonoids as a promising and readily available source of adjuvant antimicrobial therapy against resistant strains in the future.Communicated by Ramaswamy H. Sarma.

Virtual Screening of Artemisia annua Phytochemicals as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human coronaviruses that emerged in China at Wuhan city, Hubei province during December 2019. Subsequently, SARS-CoV-2 has spread worldwide and caused millions of deaths around the globe. Several compounds and vaccines have been proposed to tackle this crisis. Novel recommended in silico approaches have been commonly used to screen for specific SARS-CoV-2 inhibitors of different types. Herein, the phytochemicals of Pakistani medicinal plants (especially Artemisia annua) were virtually screened to identify potential inhibitors of the SARS-CoV-2 main protease enzyme. The X-ray crystal structure of the main protease of SARS-CoV-2 with an N3 inhibitor was obtained from the protein data bank while A. annua phytochemicals were retrieved from different drug databases. The docking technique was carried out to assess the binding efficacy of the retrieved phytochemicals; the docking results revealed that several phytochemicals have potential to inhibit the SARS-CoV-2 main protease enzyme. Among the total docked compounds, the top-10 docked complexes were considered for further study and evaluated for their physiochemical and pharmacokinetic properties. The top-3 docked complexes with the best binding energies were as follows: the top-1 docked complex with a -7 kcal/mol binding energy score, the top-2 docked complex with a -6.9 kcal/mol binding energy score, and the top-3 docked complex with a -6.8 kcal/mol binding energy score. These complexes were subjected to a molecular dynamic simulation analysis for further validation to check the dynamic behavior of the selected top-complexes. During the whole simulation time, no major changes were observed in the docked complexes, which indicated complex stability. Additionally, the free binding energies for the selected docked complexes were also estimated via the MM-GB/PBSA approach, and the results revealed that the total delta energies of MMGBSA were -24.23 kcal/mol, -26.38 kcal/mol, and -25 kcal/mol for top-1, top-2, and top-3, respectively. MMPBSA calculated the delta total energy as -17.23 kcal/mol (top-1 complex), -24.75 kcal/mol (top-2 complex), and -24.86 kcal/mol (top-3 complex). This study explored in silico screened phytochemicals against the main protease of the SARS-CoV-2 virus; however, the findings require an experimentally based study to further validate the obtained results.

A New Zn(II) Metal Hybrid Material of 5-Nitrobenzimidazolium Organic Cation (C7H6N3O2)2[ZnCl4]: Elaboration, Structure, Hirshfeld Surface, Spectroscopic, Molecular Docking Analysis, Electric and Dielectric Properties

The slow solvent evaporation approach was used to create a single crystal of (C₇H₆N₃O₂)₂[ZnCl₄] at room temperature. Our compound has been investigated by single-crystal XRD which declares that the complex crystallizes in the monoclinic crystallographic system with the P2₁/c as a space group. The molecular arrangement of the compound can be described by slightly distorted tetrahedral ZnCl₄^2- anionic entities and 5-nitrobenzimidazolium as cations, linked together by different non-covalent interaction types (H-bonds, Cl…Cl, π…π and C-H…π). Hirshfeld's surface study allows us to identify that the dominant contacts in the crystal building are H…Cl/Cl…H contacts (37.3%). FT-IR method was used to identify the different groups in (C₇H₆N₃O₂)₂[ZnCl₄]. Furthermore, impedance spectroscopy analysis in 393 ≤ T ≤ 438 K shows that the temperature dependence of DC conductivity follows Arrhenius' law. The frequency-temperature dependence of AC conductivity for the studied sample shows one region (E_a = 2.75 eV). In order to determine modes of interactions of compound with double stranded DNA, molecular docking simulations were performed at molecular level.

Structure Based in Silico Screening Revealed a Potent Acinetobacter Baumannii Ftsz Inhibitor From Asinex Antibacterial Library

The superbug Acinetobacter baumannii is an increasingly prevalent pathogen of the intensive care units where its treatment is challenging. The identification of newer drug targets and the development of propitious therapeutics against this pathogen is of utmost importance. A drug target, cell division enzyme (FtsZ), involved in A. baumannii cytokinesis is a promising avenue for antibacterial therapy. Structure based virtual screening illustrated a lead-like molecule from Asinex antibacterial library to have the best binding affinity for the FtsZ active pocket. Computational pharmacokinetics predicted the compound to have the safest pharmacokinetics profile, thus maximizing the chances of the molecule reaching the market with enhanced efficacy and lesser toxicity. Molecular dynamics simulations in an aqueous environment revealed the flexibility of protein loop regions, and upward extension followed by the backward movement of the inhibitor N, N-dimethylpyridazin-3-amine ring on its axis. The active pocket residue Thr310 demonstrated to play significant role in inhibitor binding. The binding free energy predicted by MM/GBSA and MM/PBSA reflected system stability with a total value of -62.15 kcal/mol and -10.60 kcal/mol, respectively. The absolute binding free energy estimated by WaterSwap was -16 kcal/mol that validates and affirms complex stability. The inhibitor represents a promising scaffold as a lead optimization for the FtsZ enzyme.

Novel Chimeric Vaccine Candidate Development against Leptotrichia buccalis

The misuse of antibiotics in our daily lives has led to the emergence of antimicrobial resistance. As a result, many antibiotics are becoming ineffective. This phenomenon is linked with high rates of mortality and morbidity. Therefore, new approaches are required to address this major health issue. Leptotrichia buccalis is a Gram-negative, rod-shaped bacterium which normally resides in the oral and vaginal cavities. It is an emerging bacterial pathogen which is developing new antibiotic-resistance mechanisms. No approved vaccine is available against this pathogen, which is a cause for growing concern. In this study, an in silico-based, multi-epitopes vaccine against this pathogen was designed by applying reverse vaccinology and immunoinformatic approaches. Of a total of 2193 predicted proteins, 294 were found to be redundant while 1899 were non-redundant. Among the non-redundant proteins, 6 were predicted to be present in the extracellular region, 12 in the periplasmic region and 23 in the outer-membrane region. Three proteins (trypsin-like peptidase domain-containing protein, sel1 repeat family protein and TrbI/VirB10 family protein) were predicted to be virulent and potential subunit vaccine targets. In the epitopes prediction phase, the three proteins were subjected to B- and T-cell epitope mapping; 19 epitopes were used for vaccine design. The vaccine construct was docked with MHC-I, MHC-II and TLR-4 immune receptors and only the top-ranked complex (based on global energy value) was selected in each case. The selected docked complexes were examined in a molecular dynamic simulation and binding free energies analysis in order to assess their intermolecular stability. It was observed that the vaccine binding mode with receptors was stable and that the system presented stable dynamics. The net binding free energy of complexes was in the range of -300 to -500 kcal/mol, indicating the formation of stable complexes. In conclusion, the data reported herein might help vaccinologists to formulate a chimeric vaccine against the aforementioned target pathogen.

Immunoinformatics- and Bioinformatics-Assisted Computational Designing of a Novel Multiepitopes Vaccine Against Cancer-Causing Merkel Cell Polyomavirus

Merkel cell polyomavirus (MCV) contains double-stranded DNA as its genome and is the fifth polyomavirus that infects humans. The virus causes Merkel cell carcinoma (aggressive skin cancer). Till present, no proper drug or vaccines are available to treat/prevent the virus infection and stop the emergence of Merkel cell carcinoma. In this study, computational vaccine design strategies were applied to design a chimeric-epitopes vaccine against the virus. The complete proteome comprised of four proteins was filtered through various vaccine candidacy parameters and as such two proteins, namely, capsid protein VP1 and capsid protein VP2, were considered as good vaccine targets. Furthermore, they harbor safe and potential B and T cell epitopes, which can be used in a chimeric multiepitopes-based vaccine design. The epitopes of the vaccine have maximum world population coverage of 95.04%. The designed vaccine structure was modeled in 3D that reported maximum residues in favored regions (95.7%) of the Ramachandran plot. The interactions analysis with different human immune receptors like TLR3, MHC-I, and MHC-II illustrated vaccine's good binding affinity and stable dynamics. The structural deviations of the vaccine receptor(s) complexes are within 5 Å, where majority of the receptors residues remain in good equilibrium in the simulation time. Also, the vaccine was found to form between 60 and 100 hydrogen bonds to receptors. The vaccine stimulated strong immune responses in addition to interferon and cytokines. The strength of vaccine-receptor(s) binding was further affirmed by binding energies estimation that concluded &lt;-150.32 kcal/mol of net binding energy. All these findings suggest the vaccine as a promising candidate that needs further experimental testing to disclose its real immune protective efficacy. Furthermore, the designed vaccine might accelerate vaccine development against the MCV and could save time and expenses.

Computational Exploration of Maternal Embryonic Leucine Zipper Kinase (MELK) As a Cancer Drug Target

Maternal embryonic leucine zipper kinase (MELK) is of vital importance due to its significant role in cancer development and its association with poor prognosis in different cancers. Here, we employed several computer aided drug design approaches to shortlist potential binding molecules of MELK. For virtual screening, asinex oncology library (containing 6334 drugs) and comprehensive marine natural products database (containing approximately 32,000 drugs) were used. The study identified two drug molecules: Top-2 and Top-3 as high affinity binding MELK molecules compared to the control co-crystalized Top-1 inhibitor. Both the shortlisted compounds and the control showed high stable binding free energy and high GOLD score. The compounds and control also reported stable dynamics with root mean square deviations (RMSD) value ∼ 2 Å in 500 ns. Similarly, the MELK active site residues were observed in good stability with the compounds. Further, it was noticed the compounds/control formed multiple hydrogen bonds with the MELK active pocket residues which is the main reason of high intermolecular stability. Atomic level binding free energies determined van der Waals and electrostatic energies to play vital role in stable complex formation. From drug likeness and pharmacokinetics perspective, the compounds are ideal molecules for further investigation. Overall, the results are promising and might be tested in in vivo and in vitro studies against MELK.

"In silico identification of ethoxy phthalimide pyrazole derivatives as IL-17A and IL-18 targeted gouty arthritis agents"

Two proinflammatory cytokines, IL17A and IL18, are observed to be elevated in the serum of gout patients and they play a crucial role in the development and worsening of inflammation, which has severe effects. In present study, we have combined molecular docking, molecular dynamics studies and MM-PBSA analysis to study the effectiveness of ethoxy phthalimide pyrazole derivatives (series 3a to 3e) as potential inhibitors against cytokines IL17A and IL18 as a druggable targets. The binding energy of the docked series ranges from -13.5 to -10.0 kcal/mol and extensively interacts with the amino acids in the active pocket of IL17A and IL18. Compound 3e had the lowest binding energy with IL17A at -12.6 kcal/mol compared to control allopurinol (3.32 kcal/mol). With IL18, compound 3a seems to have the lowest binding energy of -9.6 kcal/mol compared to control allopurinol (3.18 kcal/mol). In MD simulation studies, compound 3a forms a stable and energetically stabilized complex with the target protein. Depending on properties of the bound IL17A-3a and IL18-3a complexes was compared by means of MM-PBSA analysis. These derivatives can be used as a scaffold to develop promising IL17A and IL18 inhibitors to assess their potential for gouty arthritis and other related diseases.

Identification of 1, 2, 4-Triazine and Its Derivatives Against Lanosterol 14-Demethylase (CYP51) Property of Candida albicans: Influence on the Development of New Antifungal Therapeutic Strategies

This research aims to find out whether the 1, 2, 4-triazine and its derivatives have antifungal effects and can protect humans from infection with Candida albicans. Molecular docking and molecular dynamic simulation are widely used in modern drug design to target a particular protein with a ligand. We are interested in using molecular docking and molecular dynamics modeling to investigate the interaction between the derivatives of 1, 2, 4-triazine with enzyme Lanosterol 14-demethylase (CYP51) of Candida albicans. The inhibition of Candida albicans CYP51 is the main goal of our research. The 1, 2, 4-triazine and its derivatives have been docked to the CYP51 enzyme, which is involved in Candida albicans Multidrug Drug Resistance (MDR). Autodock tools were used to identify the binding affinities of molecules against the target proteins. Compared to conventional fluconazole, the molecular docking results indicated that each drug has a high binding affinity for CYP51 proteins and forms unbound interactions and hydrogen bonds with their active residues and surrounding allosteric residues. The docking contacts were made using a 10 ns MD simulation with nine molecules. RMSD, RMSF, hydrogen bonds, and the Rg all confirm these conclusions. In addition, these compounds were expected to have a favorable pharmacological profile and low toxicity. The compounds are being offered as scaffolds for the development of new antifungal drugs and as candidates for future in vitro testing.

An in silico study to unveil potential drugs and vaccine chimera for HBV capsid assembly protein: combined molecular docking and dynamics simulation approach

Humans are a major reservoir of the hepatitis B virus (HBV), therefore promising treatment and control vaccination strategies are needed to eradicate the virus. Though promising drugs and vaccines are available against HBV, still efforts are required to enrich the therapy options. Herein, the HBV assembly protein was explored to identify novel targets for future use against HBV. Computer-aided drug designing and immune-informatics techniques were employed for the identification of putative inhibitors and vaccine ensemble against HBV using capsid assembly protein. The identified drug molecule binds with high affinity to the active pocket of the protein, and several epitopes are scanned in the protein sequence. The drug molecule, besides being a good putative inhibitor, has acceptable drug-like properties. A multi-epitope vaccine is also constructed to overcome the limitations of weakly immunogenic epitopes. In contrast to the MHC II level, the set of predicted epitopes has been recognized to interact with significant numbers of HLA alleles of MHC I. Selected epitopes are extremely virulent, antigenic, nontoxic, nonallergic, have suitable affinity to bind with the prevailing DRB*0101 allele, and also spectacle 86% mediocre population coverage. A multi-epitope peptide-based vaccine chimera having 73 amino acids was designed. It emerged as substantially immunogenic, thermally stable, robust in producing cellular as well as humoral immune responses, and had competent physicochemical properties to analyze in vitro and in vivo studies. The capsid assembly protein is a in more stable nature in the presence of the drug molecule compared to the TLR3 receptor in the vaccine presence. These particulars were confirmed by exposing the docked molecules to absolute and relative binding free energy approaches of MMGBSA/PBSA. The purpose to investigate the interactions between the vaccine and a representative TLR3 immune receptor can reveal the intermolecular affinity and possible presentation mechanism of the vaccine by TLR3 to the host immune system. It was revealed that the vaccine is showing a very good affinity of binding for the TLR3 and forming a network of hydrophobic and hydrophilic interactions. Overall, the findings of this study are promising and might be useful for further experimental validations.

Molecular Insights into Binding Mode and Interactions of Structure-Based Virtually Screened Inhibitors for Pseudomonas aeruginosa Multiple Virulence Factor Regulator (MvfR)

Multi-drug resistance (MDR) bacterial pathogens pose a threat to global health and warrant the discovery of new therapeutic molecules, particularly those that can neutralize their virulence and stop the evolution of new resistant mechanisms. The superbug nosocomial pathogen, Pseudomonas aeruginosa, uses a multiple virulence factor regulator (MvfR) to regulate the expression of multiple virulence proteins during acute and persistent infections. The present study targeted MvfR with the intention of designing novel anti-virulent compounds, which will function in two ways: first, they will block the virulence and pathogenesis P. aeruginosa by disrupting the quorum-sensing network of the bacteria, and second, they will stop the evolution of new resistant mechanisms. A structure-based virtual screening (SBVS) method was used to screen druglike compounds from the Asinex antibacterial library (~5968 molecules) and the comprehensive marine natural products database (CMNPD) (~32 thousand compounds), against the ligand-binding domain (LBD) of MvfR, to identify molecules that show high binding potential for the relevant pocket. In this way, two compounds were identified: Top-1 (4-((carbamoyloxy)methyl)-10,10-dihydroxy-2,6-diiminiodecahydropyrrolo[1,2-c]purin-9-yl sulfate) and Top-2 (10,10-dihydroxy-2,6-diiminio-4-(((sulfonatocarbamoyl)oxy)methyl)decahydropyrrolo[1,2-c]purin-9-yl sulfate), in contrast to the co-crystallized M64 control. Both of the screened leads were found to show deep pocket binding and interactions with several key residues through a network of hydrophobic and hydrophilic interactions. The docking results were validated by a long run of 200 ns of molecular dynamics simulation and MM-PB/GBSA binding free energies. All of these analyses confirmed the presence of strong complex formation and rigorous intermolecular interactions. An additional analysis of normal mode entropy and a WaterSwap assay were also performed to complement the aforementioned studies. Lastly, the compounds were found to show an acceptable range of pharmacokinetic properties, making both compounds potential candidates for further experimental studies to decipher their real biological potency.

Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii

Morganella morganii is one of the main etiological agents of hospital-acquired infections and no licensed vaccine is available against the pathogen. Herein, we designed a multi-epitope-based vaccine against M. morganii. Predicted proteins from fully sequenced genomes of the pathogen were subjected to a core sequences analysis, followed by the prioritization of non-redundant, host non-homologous and extracellular, outer membrane and periplasmic membrane virulent proteins as vaccine targets. Five proteins (TonB-dependent siderophore receptor, serralysin family metalloprotease, type 1 fimbrial protein, flagellar hook protein (FlgE), and pilus periplasmic chaperone) were shortlisted for the epitope prediction. The predicted epitopes were checked for antigenicity, toxicity, solubility, and binding affinity with the DRB*0101 allele. The selected epitopes were linked with each other through GPGPG linkers and were joined with the cholera toxin B subunit (CTBS) to boost immune responses. The tertiary structure of the vaccine was modeled and blindly docked with MHC-I, MHC-II, and Toll-like receptors 4 (TLR4). Molecular dynamic simulations of 250 nanoseconds affirmed that the designed vaccine showed stable conformation with the receptors. Further, intermolecular binding free energies demonstrated the domination of both the van der Waals and electrostatic energies. Overall, the results of the current study might help experimentalists to develop a novel vaccine against M. morganii.

A Comprehensive Computer Aided Vaccine Design Approach to Propose a Multi-Epitopes Subunit Vaccine against Genus Klebsiella Using Pan-Genomics, Reverse Vaccinology, and Biophysical Techniques

Klebsiella is a genus of nosocomial bacterial pathogens and is placed in the most critical list of World Health Organization (WHO) for development of novel therapeutics. The pathogens of the genus are associated with high mortality and morbidity. Owing to their strong resistance profile against different classes of antibiotics and nonavailability of a licensed vaccine, urgent efforts are required to develop a novel vaccine candidate that can tackle all pathogenic species of the Klebsiella genus. The present study aims to design a broad-spectrum vaccine against all species of the Klebsiella genus with objectives to identify the core proteome of pathogen species, prioritize potential core vaccine proteins, analyze immunoinformatics of the vaccine proteins, construct a multi-epitopes vaccine, and provide its biophysical analysis. Herein, we investigated all reference species of the genus to reveal their core proteome. The core proteins were then subjected to multiple reverse vaccinology checks that are mandatory for the prioritization of potential vaccine candidates. Two proteins (TonB-dependent siderophore receptor and siderophore enterobactin receptor FepA) were found to fulfill all vaccine parameters. Both these proteins harbor several potent B-cell-derived T-cell epitopes that are antigenic, nonallergic, nontoxic, virulent, water soluble, IFN-γ producer, and efficient binder of DRB*0101 allele. The selected epitopes were modeled into a multi-epitope peptide comprising linkers and Cholera Toxin B adjuvant. For docking with innate immune and MHC receptors and afterward molecular dynamics simulations and binding free energy analysis, the vaccine structure was modeled for tertiary structure and refined for structural errors. To assess the binding affinity and presentation of the designed vaccine construct, binding mode and interactions analysis were performed using molecular docking and molecular dynamics simulation techniques. These biophysical approaches illustrated the vaccine as a good binder to the immune receptors and revealed robust interactions energies. The vaccine sequence was further translated to nucleotide sequence and cloned into an appropriate vector for expressing it at high rate in Escherichia coli K12 strain. In addition, the vaccine was illustrated to generate a good level of primary, secondary, and tertiary immune responses, proving good immunogenicity of the vaccine. Based on the reported results, the vaccine can be a good candidate to be evaluated for effectiveness in wet laboratory validation studies.

Interpretations on the Interaction between Protein Tyrosine Phosphatase and E7 Oncoproteins of High and Low-Risk HPV: A Computational Perception

The most prevalent and common sexually transmitted infection is caused by human papillomavirus (HPV) among sexually active women. Numerous genotypes of HPV are available, among which the major oncoproteins E6 and E7 lead to the progression of cervical cancer. The E7 oncoprotein interacts with cytoplasmic tumor suppressor protein PTPN14, which is the key regulator of cellular growth control pathways effecting the reduction of steady-state level. Disrupting the interaction between the tumor suppressor and the oncoprotein is vital to cease the development of cancer. Hence, the mechanism of interaction between E7 and tumor suppressor is explored through protein-protein and protein-ligand binding along with the conformational stability studies. The obtained results state that the LXCXE domain of HPV E7 of high and low risks binds with the tumor suppressor protein. Also, the small molecules bind in the interface of E7-PTPN14 that disrupts the interaction between the tumor suppressor and oncoprotein. These results were further supported by the dynamics simulation stating the stability over the bounded complex and the energy maintained during postdocking as well as postdynamics calculations. These observations possess an avenue in the drug discovery that leads to further validation and also proposes a potent drug candidate to treat cervical cancer caused by HPV.

Antifungal activity of amino-alcohols based cationic surfactants and in silico, homology modeling, docking and molecular dynamics studies against lanosterol 14-α-demethylase enzyme

Fungi are being responsible for causing serious infections in humans and animals. The opportunistic microorganisms provoke environmental contaminations in health and storage facilities to represent a serious concern to health security. The present work investigates the antifungal activity of two amino-alcohols based cationic surfactants such as C_nEtOH, C_nPrOH (with n = 14 and 16 are the carbon numbers of alkyl chain and EtOH = Ethanol and PrOH = Propanol) against a collection of different Candida species (Candida tropicalis, Candida albicans, Candida auris, Cyberlindnera jadinii, Candida parapsilosis, Candida glabrata and Candida rugosa) respectively. The amino-alcohols based cationic surfactants exhibited good antifungal activity against all Candida strains tested with minimum inhibitory concentrations (MIC) ranging from 0.002 to 0.30 mM. The MIC evaluation shows an increase as a function of the hydrophobicity of all inhibitors against the majority of the Candida strains tested. The different location of the alcoholic OH function in the polar head shows the influence on the availability of N⁺ responsible for electrostatic interactions with the candidate's cell walls, which remains a very important step in the mode of action of quaternary ammonium cationic surfactants. Hence, a 3D structure of lanosterol 14-α-demethylase enzyme from C. auris was constructed by homology modeling using an online SWISS-MODEL server. The predicted model was analyzed by serval servers. Furthermore, a molecular docking study was carried out to better understand the binding mechanism of lanosterol homologous protein with surfactant ligands. Then, the docked complexes lanosterol-surfactants were refined by the molecular dynamic simulation to analyze their interaction behavior during the simulation.Communicated by Ramaswamy H. Sarma.

Synthesis and Identification of Novel Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

The novel coronavirus disease that arises in the end of 2019 (COVID-19) in Wuhan, China, has rapidly spread over the globe and was considered as a world pandemic. Currently, various antiviral therapies or vaccines are available, and many researches are ongoing for further treatments. Targeting the coronavirus' main protease (key enzyme: 3CLpro) is growing in importance in anti-SARS-CoV-2 drug discovery process. The present study aims at predicting the antiviral activity of two novel compounds using in silico approaches that might become potential leads against SARS-CoV-2. The 3D structures of the new compounds are elucidated by single-crystal X-ray techniques. The interactions between different units of 4 and 5 were emphasized by analyzing their corresponding Hirshfeld surfaces and ESP plots. NBO and FMO analyses were investigated as well. Molecular docking combined with molecular dynamics simulations (MDs) was performed to investigate the binding modes and molecular interactions of 4 and 5 with the amino acids of coronavirus main protease (6LU7) protein. The best docking scores were obtained for both ligands through the major binding interactions via hydrogen/hydrophobic bonds with the key amino acids in the active site: HIS41, CYS145, MET49, MET165, HIS172, and GLU166 amino acids. A MD simulation study was also performed for 100 ns to validate the stability behavior of the main protease 3CLpro-ligand complexes. The MD simulation study successfully confirmed the stability of the ligands in the binding site as potent anti-SARS-CoV-2 (COVID-19) inhibitors. Additionally, MMPBSA energy of both docked complexes was determined as a validation assay of docking and MD simulations to validate compound conformation and interaction stability with 3CLpro. The synthesized compounds might be helpful in the fight against COVID-19 prior to biological activity confirmation in vitro and in vivo.

Rational Drug Design for Pseudomonas aeruginosa PqsA Enzyme: An in silico Guided Study to Block Biofilm Formation

Pseudomonas aeruginosa is an opportunistic gram-negative bacterium implicated in acute and chronic nosocomial infections and a leading cause of patient mortality. Such infections occur owing to biofilm formation that confers multidrug resistance and enhanced pathogenesis to the bacterium. In this study, we used a rational drug design strategy to inhibit the quorum signaling system of P. aeruginosa by designing potent inhibitory lead molecules against anthranilate-CoA ligase enzyme encoded by the pqsA gene. This enzyme produces autoinducers for cell-to-cell communication, which result in biofilm formation, and thus plays a pivotal role in the virulence of P. aeruginosa. A library of potential drug molecules was prepared by performing ligand-based screening using an available set of enzyme inhibitors. Subsequently, structure-based virtual screening was performed to identify compounds showing the best binding conformation with the target enzyme and forming a stable complex. The two hit compounds interact with the binding site of the enzyme through multiple short-range hydrophilic and hydrophobic interactions. Molecular dynamic simulation and MM-PBSA/GBSA results to calculate the affinity and stability of the hit compounds with the PqsA enzyme further confirmed their strong interactions. The hit compounds might be useful in tackling the resistant phenotypes of this pathogen.

Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking, molecular dynamics simulation and binding free energy calculation

Abstract

The pandemic outbreak of the Corona viral infection has become a critical global health issue. Biophysical and structural evidence shows that spike protein possesses a high binding affinity towards host angiotensin-converting enzyme 2 and viral hemagglutinin-acetylesterase (HE) glycoprotein receptor. We selected HE as a target in this study to identify potential inhibitors using a combination of various computational approaches such as molecular docking, ADMET analysis, dynamics simulations and binding free energy calculations. Virtual screening of NPACT compounds identified 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]benzo[7]annulen-6-one, Silymarin, Withanolide D, Spirosolane and Oridonin as potential HE inhibitors with better binding energy. Furthermore, molecular dynamics simulations for 100 ns time scale revealed that most of the key HE contacts were retained throughout the simulations trajectories. Binding free energy calculations using MM/PBSA approach ranked the top-five potential NPACT compounds which can act as effective HE inhibitors.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s11030-020-10135-w) contains supplementary material, which is available to authorized users.

Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine

The COVID-19 pandemic caused by SARS-CoV-2 is a public health emergency of international concern and thus calling for the development of effective and safe therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for a vaccine, antibodies, and inhibitors development because of the many roles it plays in attachment, fusion and entry into the host cell. In the present investigation, we characterized the SARS-CoV-2 spike glycoprotein by immunoinformatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in aqueous milieu aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel axial frequency distribution (AFD) analytical tool. Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus could be considered in experimental studies.

Screening Pipeline for Flavivirus Based Inhibitors for Zika Virus NS1

In-silico pipeline is applied for identifying and designing novel inhibitors against ZIKV NS1 protein. Comparative molecular docking studies are performed to explore the binding of structurally diverse compounds to ZIKV NS1 by AutoDock/Vina and GOLD. The Zika virus (ZIKV) is a flavivirus, responsible for life-threatening infections and transmitted by Aedes mosquitoes in other organisms. It is associated with Guillain Barre Syndrome (GBS) and microcephaly. This epidemic increase in GBS and microcephaly convoyed the World Health Organization to affirm ZIKV a public health crisis. To combat the ZIKV infections, non-structural protein 1 (NS1), a major host-interaction molecule contributing towards replication, pathogenesis and immune evasion is targeted in the current study. For this purpose, a comprehensive study is required to develop potential novel antiviral inhibitors. Three compounds were identified through docking programs exhibiting properties which are non-toxic to human host and could inhibit the elusive ZIKV. Significant interaction with active site residues and H-bond interactions with the key residues were analyzed for these compounds using molecular dynamics simulation. Free energy calculation predicted higher affinity of Deoxycalyxin-A for ZIKV NS1. This study contributes towards fighting ZIKV infections and can help researchers in designing drug for the treatment of ZIKV.

Deciphering the Inhibition Mechanism of under Trial Hsp90 Inhibitors and Their Analogues: A Comparative Molecular Dynamics Simulation

Heat shock protein 90 (Hsp90) performs functions in cellular activities together with other signaling pathways. Hsp90 is evolutionarily conserved and universally articulated as a human cancer-causing agent involved in lung cancer and breast cancer followed by colon and rectum cancers. It has emerged as an effective drug candidate, and inhibition may affect several signaling pathways associated with cancer spread. Therefore, in-silico approaches, molecular docking, molecular dynamics simulation, and binding free energy calculations were applied to create insights into the inhibition mechanism against Hsp90 to identify new cancer therapeutic drugs. Top-docked Hsp90-inhibitor complexes with their analogues were selected as the best complexes based on the GOLD fitness score and orientation. The significant interaction of Hsp90 inhibitors and their analogues were observed to be bound with active site residues as well as residing within the same cavity region. System stability factors RMSD, RMSF, beta-factor, and radius of gyration were analyzed for top-docked complexes and ensure strong binding interaction between inhibitors and the Hsp90 cavity. Cavity bound inhibitors were found to retain consistent hydrogen bonding during the simulation. The radial distribution function (RDF) illustrated that interacting active site residues drive the binding and stability of the inhibitors. Similarly, the axial frequency distribution, which is an indigenously developed analytical tool, produced noteworthy knowledge of the hydrogen-bonding pattern. Results yielded new insights into the design of cancer therapeutic drugs against Hsp90. This finding suggests that under trial Hsp90 inhibitors MPC-3100 could be a potential starting point into the development of potential anticancer agents with the possibility of future directions for the improvement of early existing Hsp90 inhibitors CNF-2024 and SNX-5422 as an anticancer agent.

Vaccine candidate designed against carcinoembryonic antigen-related cell adhesion molecules using immunoinformatics tools

Carcinoembryonic antigen-related cell adhesion (CEACAM) molecules belong to a family of membrane glycoproteins that mediate intercellular interactions influencing cellular growth, immune cell activation, apoptosis, and tumor suppression. Several family members (CEACAM1, CEACAM5, and CEACAM6) are highly expressed in cancers, and they share a conserved N-terminal domain that serves as an attractive target for cancer immunotherapy. A multi-epitope vaccine candidate against this conserved domain has been developed using immunoinformatics tools. Specifically, several epitopes predicted to interact with MHC class I and II molecules were linked together with appropriate linkers. The tertiary structure of the vaccine is generated by homology and ab initio modeling. Molecular docking of epitopes to MHC structures have revealed that the lowest energy conformations are the epitopes bound to the antigen-binding groove of the MHC molecules. Subsequent molecular dynamics simulation has confirmed the stability of the binding conformations in solution. The predicted vaccine has relatively high antigenicity and low allergenicity, suggesting that it is an ideal candidate for further refinement and development.Communicated by Ramaswamy H. Sarma.

Identification of inhibitor binding hotspots in Acinetobacter baumannii β-ketoacyl acyl carrier protein synthase III using molecular dynamics simulation

Acinetobacter baumannii is a gram-negative bacterium that is rapidly developing drug resistance due to the abuse of antibiotics. The emergence of multidrug-resistant A. baumannii has greatly contributed to the urgency of developing new antibiotics. Previously, we had discovered two potent inhibitors of A. baumannii β-ketoacyl acyl carrier protein synthase III (abKAS III), YKab-4 and YKab-6, which showed potent activity against A. baumannii. In addition, we have reported the crystal structure of abKAS III. In the present study, we investigated the binding between abKAS III and its inhibitors by docking simulation. Molecular dynamics (MD) simulations were performed using docked inhibitor models to identify the hotspot residues related to inhibitor binding. The binding free energies estimated using the MD simulations suggest that residues I198 and F260 of abKAS III serve as the inhibitor binding hotspots. I198, found to be responsible for mediating hydrophobic interactions with inhibitors, had the strongest residual binding energy among all abKAS III residues. We modeled glutamine substitutions of residues I198 and F260 and estimated the relative binding energies of the I198Q and F260Q variants. The results confirmed that I198 and F260 are the key inhibitor binding residues. The roles of the key residues in inhibitor binding, i.e. F260 in the α9 helix and the I198 in the β6β7 loop region, were investigated using principal component analysis (PCA). PCA revealed the structural changes resulting from the abKAS III I198Q and F260Q mutations and described the essential dynamics of the α9 helix. In addition, the results suggest that the β6β7 loop region may act as a gate keeper for ligand binding. Hydrophobic interactions involving I198 and F260 in abKAS III appear to be essential for the binding of the inhibitors YKab-4 and YKab-6. In conclusion, this study provides valuable information for the rational design of antibiotics via the inhibition of abKAS III.