Virtual Screening Of Novel Inhibitors Research Articles

Structure-Based Virtual Screening for Novel Inhibitors Targeting KRAS G12C.

KRAS is a protein that is critical to cell activation, but when it becomes mutated, it can contribute to the development of cancer. There is an urgent need for reliable and effective drugs to treat cancer, and KRAS G12C has been a major focus of research in this area. In this study, we used structure-based virtual screening to search for novel inhibitors that can target KRAS G12C. Specifically, we conducted a search for inhibitors that bind to the protein's P2 pocket, which can trap the oncoprotein in an inactive GDP-bound state. Using quantitative analysis and virtual screening, we identified a set of eight potential inhibitors that have the potential to become the next generation of drugs to treat cancer. These findings offer new insights into the mechanisms underlying KRAS G12C inhibition and provide a promising avenue for future drug development efforts.

Virtual screening for novel inhibitors of human Histone Deacetylase 6: Promising new leads for Oral Squamous Cell Carcinoma

Over 90% of Oral Cancers are Oral Squamous Cell Carcinomas (OSCCs). Despite having advanced treatment modalities, there is no significant improvement in the survival rate of Oral Cancer patients over the years. Thus, there arises a need for the identification of new drug targets besides development of new and effective drugs for this disease. Since Histone Deacetylase 6 (HDAC6), a class IIB member of HDAC family, is known to be upregulated in this disease in addition to being associated with tumor growth, it can be considered as a promising drug target for this disease. In this study, a structure-based virtual screening strategy was used to screen a library of 1,539 natural compounds from Naturally Occurring Plant-based Anti-cancerous Compound– Activity–Target (NPACT) database. Upon filtering and docking, top 30 hits were identified and two of them, namely Camptothecin and Diosgenin, were tested experimentally on OSCCs cell lines for anti-proliferative effects. Both of these compounds exhibited inhibitory activity against Oral Cancer cells, therefore suggesting that they can be potential HDAC6 inhibitors, which can further serve as promising leads for OSCCs.

In silico study of 3-hydroxypyrimidine-2,4-diones as inhibitors of HIV RT-associated RNase H using molecular docking, molecular dynamics, 3D-QSAR, and pharmacophore models

Rational design and virtual screening of novel inhibitors of HIV reverse transcriptase associated ribonuclease H based on a combined molecular modeling study.

Molecular Docking and Pharmacophore-Based Virtual Screening of Novel Inhibitors for HCV NS5B RNA-Dependent RNA Polymerase Enzyme from Crude Sesame Essential Oil.

Concern has been expressed worldwide about the rising prevalence of HCV induced acute hepatitis and chronic liver diseases with associated cirrhosis and liver cancers. However, the available synthetic drugs are ineffective for all the HCV genotypes especially in genotype-1 patients with about 40% viral response rates and numerous side effects. Besides, the availability of veritable bioinformatics tools which includes molecular docking and virtual screening studies have shown that computational generated models nowadays assists in modern drug design and development of novel and more potent inhibitors through the understanding of protein (receptors) -ligand (drugs) interaction mechanisms. Non-structural proteins especially the 5B (NS5B) is an RNA-dependent RNA polymerase implicated in the synthesis and replication of the HCV RNA; and has been a potential target for its inhibitory activities. Due to the paucity of knowledge, we aimed to determine the differential inhibitory activity of essential oils present in the crude Sesame leaves extracts on HCV-NS5B RNA dependent RNA polymerase. Using in-silico studies- a Microsoft pharmacophore-based virtual screening and molecular docking tools on the iGEMDOCK vs 2.0 software was used to dock the essential oil ligands on the generated HCV NS5B (PDB ID: 4EO6) RNA-dependent RNA polymerase protein. GC-MS of the leaves confirmed carboxylic acids and phenolic groups in the essential oils especially some potent antioxidants like alpha-linolenic acid, linoleic acid, oleic acid, etc. Moreover, Alpha-Linolenic acid/ALA (-102.2/-103.4 kcal/mol) and Linoleic acid/LA (-94.8/-109.8 kcal/mol) showed higher inhibitory impacts among the six top different docked ligands, selected based on their high differential binding affinity and pharmacological interaction energy profiles against HCV NS5B RNA polymerase activities, by forming more H-bond interactions than the NS5B co-crystallized ligand. ADMET showed that ALA is well tolerated without any apparent toxicity in the body. Hence, ALA having the highest inhibitory impacts against the HCV NS5B goes to confirm the beneficial impacts of carboxylic acids from Sesame plant in maintaining liver cellular integrity and as a natural inhibitor of HCV NS5B RNA dependent RNA Polymerase enzyme activities.

Pharmacophore-Based Virtual Screening of Novel Inhibitors and Docking Analysis for CYP51A from Penicillium italicum.

Sterol 14α-demethylases from Cytochrome P450 family (CYP51s) are essential enzymes in sterol biosynthesis and well-known as the target of antifungal drugs. The 3D structure of CYP51A from Penicillium italicum (PiCYP51A) was constructed through homology modeling based on the crystal structure of human CYP51A (PDB: 3LD6). Molecular dynamics (MD) simulation was operated to relax the initial model and followed by quality assessment using PROCHECK program. On the basis of the docking information on the currently available CYP51s with the patent demethylase inhibitors (DMIs), pharmacophore-based virtual screening combined with docking analysis was performed to pick out twelve new compounds from ZINC database. Six hits revealed in the ligand database suggested potential ability to inhibit PiCYP51A. Compared to patent fungicide triazolone, the top three lead compounds had similar or higher affinity with the target enzyme, and accordingly, exhibited comparable or lower EC50 values to P. italicum isolates. The results could provide references for de novo antifungal drug design.

Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening.

Botulinum neurotoxin serotype A (BoNT/A) is the most lethal toxin among the Tier 1 Select Agents. Development of potent and selective small molecule inhibitors against BoNT/A zinc metalloprotease remains a challenging problem due to its exceptionally large substrate binding surface and conformational plasticity. The exosites of the catalytic domain of BoNT/A are intriguing alternative sites for small molecule intervention, but their suitability for inhibitor design remains largely unexplored. In this study, we employed two recently identified exosite inhibitors, D-chicoric acid and lomofungin, to probe the structural features of the exosites and molecular mechanisms of synergistic inhibition. The results showed that D-chicoric acid favors binding at the α-exosite, whereas lomofungin preferentially binds at the β-exosite by mimicking the substrate β-sheet binding interaction. Molecular dynamics simulations and binding interaction analysis of the exosite inhibitors with BoNT/A revealed key elements and hotspots that likely contribute to the inhibitor binding and synergistic inhibition. Finally, we performed database virtual screening for novel inhibitors of BoNT/A targeting the exosites. Hits C1 and C2 showed non-competitive inhibition and likely target the α- and β-exosites, respectively. The identified exosite inhibitors may provide novel candidates for structure-based development of therapeutics against BoNT/A intoxication.

Construction of a Full-Atomic Mechanistic Model of Human Apurinic/Apyrimidinic Endonuclease APE1 for Virtual Screening of Novel Inhibitors

A full-atomic molecular model of human apurinic/apyrimidinic endonuclease APE1, an important enzyme in the DNA repair system, has been constructed. The research consisted of hybrid quantum mechanics/molecular mechanics modeling of the enzyme-substrate interactions, as well as calculations of the ionization states of the amino acid residues of the active site of the enzyme. The choice of the APE1 mechanism with an Asp210 residue as a proton acceptor was validated by means of a generalization of modeling and experimental data. Interactions were revealed in the active site that are of greatest significance for binding the substrate and potential APE1 inhibitors (potential co-drugs of interest in the chemo- and radiotherapy of oncological diseases).

Construction of a Full-Atomic Mechanistic Model of Human Apurinic/Apyrimidinic Endonuclease APE1 for Virtual Screening of Novel Inhibitors

A full-atomic molecular model of human apurinic/apyrimidinic endonuclease APE1, an important enzyme in the DNA repair system, has been constructed. The research consisted of hybrid quantum mechanics/ molecular mechanics modeling of the enzyme-substrate interactions, as well as calculations of the ionization states of the amino acid residues of the active site of the enzyme. The choice of the APE1 mechanism with an Asp210 residue as a proton acceptor was validated by means of a generalization of modeling and experimental data. Interactions were revealed in the active site that are of greatest significance for binding the substrate and potential APE1 inhibitors (potential co-drugs of interest in the chemo- and radiotherapy of oncological diseases).

Structure based virtual screening of novel inhibitors against multidrug resistant superbugs.

Pathogenic microorganisms are persistently expressing resistance towards present generation antibiotics and are on the verge of joining the superbug family. Recent studies revealed that, notorious pathogens such as Salmonella typhi, Shigella dysenteriae and Vibrio cholerae have acquired multiple drug resistance and the treatment became a serious concern. This necessitates an alternative therapeutic solution. Present study investigates the utility of computer aided method to study the mechanism of receptor-ligand interactions and thereby inhibition of virulence factors (shiga toxin of Shigella dysenteriae, cholera toxin of Vibrio cholerae and hemolysin-E of Salmonella typhi) by novel phytoligands. The rational designs of improved therapeutics require the crystal structure for the drug targets. The structures of the virulent toxins were identified as probable drug targets. However, out of the three virulent factors, the structure for hemolysin-E is not yet available in its native form. Thus, we tried to model the structure by homology modeling using Modeller 9v9. After extensive literature survey, we selected 50 phytoligands based on their medicinal significance and drug likenesses. The receptor-ligands interactions between selected leads and toxins were studied by molecular docking using Auto Dock 4.0. We have identified two novel sesquiterpenes, Cadinane [(1S, 4S, 4aS, 6S, 8aS)- 4- Isopropyl- 1, 6- dimethyldecahydronaphthalene] and Cedrol [(8α)-Cedran-8-ol] against Shiga (binding energy -5.56 kcal/mol) and cholera toxins (binding energy -5.33 kcal/mol) respectively which have good inhibitory properties. Similarly, a natural Xanthophyll, Violaxanthin [3S, 3'S, 5R, 5'R, 6S, 6'S)-5, 5', 6, 6'-Tetrahydro-5, 6:5', 6'-diepoxy-β, β-carotene-3, 3'-diol] was identified as novel therapeutic lead for hemolysin-E (binding energy of –5.99 kcal/mol). This data provide an insight for populating the pool of novel inhibitors against various drug targets of superbugs when all current generation drugs seem to have failed.

Structure-based virtual screening of novel inhibitors of the uridyltransferase activity of Xanthomonas oryzae pv. oryzae GlmU

N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU) catalyzes the formation of UDP-GlcNAc, a fundamental precursor in cell wall biosynthesis. GlmU represents an attractive target for new antibacterial agents. In this study, a theoretical three-dimensional (3D) structure of GlmU from Xanthomonas oryzae pv. oryzae (Xo-GlmU) was generated, and the ligand–receptor interaction was investigated by molecular docking. Then a structure-based virtual screening was performed, three hit compounds were identified as specific inhibitors of the uridyltransferase activity of Xo-GlmU, with IC50 values in the 0.81–23.21μM range. Subsequently, the mode-of-inhibition and Ki values of the three inhibitors were confirmed. The minimum inhibitory concentrations (MICs) of the candidate compounds for X. oryzae pv. oryzae (Xoo) were also determined. The research provided novel chemical scaffolds for antimicrobial drug discovery.

Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase

DNA methyltransferase 1 (DNMT1) is an emerging epigenetic target for the treatment of cancer and other diseases. To date, several inhibitors from different structural classes have been published. In this work, we report a comprehensive molecular modeling study of 14 established DNTM1 inhibitors with a herein developed homology model of the catalytic domain of human DNTM1. The geometry of the homology model was in agreement with the proposed mechanism of DNA methylation. Docking results revealed that all inhibitors studied in this work have hydrogen bond interactions with a glutamic acid and arginine residues that play a central role in the mechanism of cytosine DNA methylation. The binding models of compounds such as curcumin and parthenolide suggest that these natural products are covalent blockers of the catalytic site. A pharmacophore model was also developed for all DNMT1 inhibitors considered in this work using the most favorable binding conformations and energetic terms of the docked poses. To the best of our knowledge, this is the first pharmacophore model proposed for compounds with inhibitory activity of DNMT1. The results presented in this work represent a conceptual advance for understanding the protein-ligand interactions and mechanism of action of DNMT1 inhibitors. The insights obtained in this work can be used for the structure-based design and virtual screening for novel inhibitors targeting DNMT1.

Docking and virtual screening of novel inhibitors for mono-ADP-ribosylating toxins

ADP-ribosyltransferases (ADP-RTs) are a family of enzymes secreted by pathogenic bacteria. They catalyse the hydrolysis of NAD+ and the transfer of the ADP-ribosyl group onto specific target proteins [1,2]. Figure ​Figure11 Figure 1 Although ADP-RTs are important drug targets, only few inhibitors are known so far. The high selectivity of these inhibitors suggest different mechanism of binding to the ADP-RTs active sites. To explain the structural differences, we started a systematic program towards the development of new ADP-RT inhibitors. This is based on multiple virtual screening experiments (e.g. docking, pharmacophore searching and binding free-energy calculations) and the development of an in vitro assay for ADP-RTs. Active compounds identified in the first screening round are the basis for further in silico studies and optimisation steps. The aim of the current work is the discovery of novel drug-leads and the formulation of structure-function relationships which can explain the selectivity of ligand binding to the NAD+ pocket. This is interesting from a drug discovery perspective, as many enzymes utilizing NAD+ are valid or potential drug targets.

A three-dimensional pharmacophore modelling of ITK inhibitors and virtual screening for novel inhibitors

Interleukin-2-inducible T-cell kinase (ITK) is a key member of the Tec family of non-receptor tyrosine kinases, and has been found to be a novel target for a number of inflammatory and autoimmune diseases. A three-dimensional pharmacophore model has been generated for protein ITK from its known inhibitors. The best HypoGen model consisted of four pharmacophore features: one hydrogen bond acceptor, one hydrogen bond donor and two hydrophobic rings. This model showed a correlation coefficient of 0.947, a root mean square deviation of 0.914 and a configuration cost of 16.866. The model was validated using test set prediction and Fischer's test. A test set containing 204 compounds showed an r 2 of 0.745 between estimated activity and activity measured experimentally. Fisher's test gave a confidence level of 95%. The best pharmacophore model (Hypo1) was then employed for virtual screening (3D database searching), including Lipinsiki's filter, to obtain a pool of more drug-like molecules. The molecular pool thus retrieved was subjected to docking analysis with a study protein to remove any molecules showing false positive activity for ITK.

Structure-based virtual screening for novel inhibitors of Japanese encephalitis virus NS3 helicase/nucleoside triphosphatase

Japanese encephalitis (JE) is a significant cause of human morbidity and mortality throughout Asia and Africa. Vaccines have reduced the incidence of JE in some countries, but no specific antiviral therapy is currently available. The NS3 protein of Japanese encephalitis virus (JEV) is a multifunctional protein combining protease, helicase and nucleoside 5′‐triphosphatase (NTPase) activities. The crystal structure of the catalytic domain of this protein has recently been solved using a roentgenographic method. This enabled structure‐based virtual screening for novel inhibitors of JEV NS3 helicase/NTPase. The aim of the present research was to identify novel potent medicinal substances for the treatment of JE. In the first step of studies, the natural ligand ATP and two known JEV NS3 helicase/NTPase inhibitors were docked to their molecular target. The refined structure of the enzyme was used to construct a pharmacophore model for JEV NS3 helicase/NTPase inhibitors. The freely available ZINC database of lead‐like compounds was then screened for novel inhibitors. About 1 161 000 compounds have been screened and 15 derivatives of the highest scores have been selected. These compounds were docked to the JEV NS3 helicase/NTPase to examine their binding mode and verify screening results by consensus scoring procedure.

Structure-based virtual screening for novel inhibitors of the sarco/endoplasmic reticulum calcium ATPase and their experimental evaluation

A public compound library with 260,000 compounds was screened virtually by computational docking for novel inhibitors of the transmembrane enzyme sarco/endoplasmic reticulum calcium ATPase (SERCA). Docking was performed with the program GOLD in conjunction with a high resolution X-ray crystal structure of SERCA. Compounds that were predicted to be active were tested in bioassays. Nineteen novel compounds were discovered that were capable of inhibiting the ATP hydrolysis activity of SERCA at concentrations below 50 μM. Crucial enzyme/inhibitor interactions were identified by analyzing the docking-predicted binding poses of active compounds. Like other SERCA inhibitors, the newly discovered compounds are of considerable medicinal interest because of their potential for cancer chemotherapy.

Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors

Pyruvate phosphate dikinase (PPDK) is the key enzyme essential for the glycolytic pathway in most common and perilous parasite Entamoeba histolytica. Inhibiting the function of this enzyme could control the wide spread of intestinal infections caused by Entamoeba histolytica in humans. With this objective, we modeled the three dimensional structure of the PPDK protein. We used templates with 51% identity and 67% similarity to employ homology-modeling approach. Stereo chemical quality of protein structure was validated by protein structure validation program PROCHECK and VERIFY3D. Experimental proof available in literature along with the in silico studies indicated Lys21, Arg91, Asp323, Glu325 and Gln337 to be the probable active sites in the target protein. Virtual screening was carried out using the genetic docking algorithm GOLD and a consensus scoring function X-Score to substantiate the prediction. The small molecule libraries (ChemDivision database, Diversity dataset, Kinase inhibitor database) were used for screening process. Along with the high scoring results, the interaction studies provided promising ligands for future experimental screening to inhibit the function of PPDK in Entamoeba histolytica. Further, the phylogeny study was carried out to assess the possibility of using the proposed ligands as inhibitors in related pathogens.

Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation.

Virtual screening of compound libraries is an alternative and complementary approach to high-throughput screening in the lead discovery process. A new strategy is described to search for possible leads of human carbonic anhydrase II, applying a protocol of several consecutive hierarchical filters involving a preselection based on functional group requirements and fast pharmacophore matching. A suitable pharmacophore is derived by a sophisticated "hot spot" analysis of the binding site to detect regions favorable for protein-ligand interactions. In subsequent steps, molecular similarity with known reference ligands is used to rerank the hits from the pharmacophore matching. Finally the best scored candidates are docked flexibly into the protein binding pocket. After examination of the affinity predictions, 13 compounds were selected for experimental testing. Of these 13, three could be shown to be subnanomolar, one is nanomolar, while a further seven are micromolar inhibitors. The binding mode of two hits could be confirmed by crystal structure analysis. The novelty of the discovered leads is best supported by the fact that a search in the patent literature showed the newly discovered subnanomolar compounds to comprise scaffolds not yet covered by existing patents.